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Conserved domains on  [gi|1537972313|ref|XP_027252290|]
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histone-lysine N-methyltransferase 2D isoform X9 [Cricetulus griseus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SET_KMT2D cd19209
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2D (KMT2D) ...
 5366-5520 1.50e-109

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2D (KMT2D) and similar proteins; KMT2D (EC2.1.1.43; also termed lysine N-methyltransferase 2D, ALL1-related protein (ALR), or myeloid/lymphoid or mixed-lineage leukemia protein 2 (MLL2)), acts as histone methyltransferase that methylates 'Lys-4' of histone H3 (H3K4me). It is a coactivator for estrogen receptor by being recruited by ESR1, thereby activating transcription. KMT2D is a subunit of MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation.


:

Pssm-ID: 380986 [Multi-domain]  Cd Length: 155  Bit Score: 346.30  E-value: 1.50e-109
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5366 HSKSSQYRRLRTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVI 5445
Cdd:cd19209      1 HSKSSQYRRLKTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVI 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1537972313 5446 DATLTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWM 5520
Cdd:cd19209     81 DATLTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWM 155
ePHD2_KMT2D cd15698
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 5000-5106 9.70e-77

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2D. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions.


:

Pssm-ID: 277168  Cd Length: 107  Bit Score: 250.35  E-value: 9.70e-77
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5000 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQRTGATSSCNRMRCPN 5079
Cdd:cd15698      1 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQKTGATNSCNRLRCPN 80

                           90       100
                   ....*....|....*....|....*..
gi 1537972313 5080 VYHFACAIRAKCMFFKDKTMLCPMHKI 5106
Cdd:cd15698     81 VYHFACAIRAKCMFFKDKTMLCPMHKL 107
HMG-box_KMT2D cd22027
high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2D (KMT2D) and ...
 1987-2070 7.43e-60

high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2D (KMT2D) and similar proteins; KMT2D, also called ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis.


:

Pssm-ID: 438836  Cd Length: 84  Bit Score: 201.08  E-value: 7.43e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 1987 GLSYNQRSLQRWEKDEELGQLSTISPVLYANINFPNLKQDYPDWSSRCKQIMKLWRKVPAADKAPYLQKAKDNRAAHRIN 2066
Cdd:cd22027      1 GLSYNQRSLQRWEKDEELGELSTISPVLYANINFPNLKQDYPDWSSRCKQIMKLWRKVPAADKAPYLQKAKDNRAAHRIN 80


                   ....
gi 1537972313 2067 KVQK 2070
Cdd:cd22027     81 KVQK 84
ePHD1_KMT2D cd15695
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 134-217 8.05e-52

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMT2D. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 at Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions.


:

Pssm-ID: 277165  Cd Length: 90  Bit Score: 178.57  E-value: 8.05e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  134 GHCWAHHWCAVWSAGVWGQEGPELCGVDKAIFSGISQRCSHCTRFGASIPCRSPGCPRLYHFPCATASGSFLSMKTLQLL 213
Cdd:cd15695      7 GECWVHHWCAAWSAGVKQHEGDGLIGVDKAVFSGISQKCEHCKRLGATIQCHAEGCPRFYHFPCAAASGSFQSMKTLLLL 86


                   ....
gi 1537972313  214 CPDH 217
Cdd:cd15695     87 CPEH 90
PHD5_KMT2D cd15601
PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 1501-1551 3.65e-33

PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such asHOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is downregulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger.


:

Pssm-ID: 277074  Cd Length: 51  Bit Score: 123.86  E-value: 3.65e-33
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1537972313 1501 TCPVCHAPYVEEDLLIQCRHCERWMHAGCESLFTEDEVEQAADEGFDCVSC 1551
Cdd:cd15601      1 TCPVCRAKYVEEDLLIQCRHCDRWVHAVCESLFTEDEVEQAADEGFDCSSC 51
PHD3_KMT2D cd15597
PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 1373-1423 8.23e-33

PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the third PHD finger.


:

Pssm-ID: 277072  Cd Length: 51  Bit Score: 122.84  E-value: 8.23e-33
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1537972313 1373 DMCVVCGSFGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVECI 1423
Cdd:cd15597      1 DMCVVCGSFGRGSEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVECI 51
FYRC smart00542
FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region ...
 5208-5295 2.17e-32

FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region (FYRN), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.


:

Pssm-ID: 197781  Cd Length: 86  Bit Score: 122.79  E-value: 2.17e-32
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  5208 EFVIKVIEQGleDLVFTDASPQAVWNRIIEPVAAMRKEADMLRLFPEYLKGEELFGLTVHAVLRIAESLPGVESCQNYLF 5287
Cdd:smart00542    1 LFRVEIESDP--GEVFKGESPEKCWEMVLERVQEARIAADLLQLLPEGVSGEEMFGLSSPAVVKLIEALPGVHQCTNYWF 78


                    ....*...
gi 1537972313  5288 RYGRHPLM 5295
Cdd:smart00542   79 RYHRSPLL 86
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
 1424-1470 5.81e-29

PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger of KMT2C and the fourth PHD finger of KMT2D.


:

Pssm-ID: 276988  Cd Length: 47  Bit Score: 111.80  E-value: 5.81e-29
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1537972313 1424 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWCV 1470
Cdd:cd15513      1 VCEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 47
PHD_SF super family cl22851
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 276-320 7.43e-26

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


The actual alignment was detected with superfamily member cd15595:

Pssm-ID: 473978  Cd Length: 46  Bit Score: 102.77  E-value: 7.43e-26
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15595      2 CQTCRKPGEDSKMLVCEACDKGYHTFCLKPAMESLPTDSWKCKAC 46
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 228-273 1.23e-21

PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the first PHD finger.


:

Pssm-ID: 276984  Cd Length: 48  Bit Score: 90.83  E-value: 1.23e-21
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1537972313  228 HCAVCEGPGELCDLFFCTSCGHHYHGACLDTAL--TARKRAGWQCPEC 273
Cdd:cd15509      1 NCAVCDSPGDLSDLLFCTSCGQHYHGSCLDPAVrpTPLVRAGWQCPEC 48
FYRN pfam05964
F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 5149-5200 3.62e-18

F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00541.


:

Pssm-ID: 461787  Cd Length: 51  Bit Score: 81.01  E-value: 3.62e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1537972313 5149 GGLVFHAIGQLLPHQMAdFHSATALYPVGYEATRIYWSLRTNNRRCCYRCSI 5200
Cdd:pfam05964    1 GSLTVLSLGEIVPDRPA-FHTERYIYPVGYKSTRLYWSTKDPRKRCRYTCEI 51
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 2102-2668 3.92e-14

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 80.37  E-value: 3.92e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2102 PGALGSPPPAA-------APTIFIGSPT---TPAGLSTSADGFLKPPAGTVPGPDSPgelflkLPPQVPAQVPSQD-Pfg 2170
Cdd:PHA03247  2498 PGGGGPPDPDAppapsrlAPAILPDEPVgepVHPRMLTWIRGLEELASDDAGDPPPP------LPPAAPPAAPDRSvP-- 2569

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2171 lAPAYAPEPrfsaAPPTYPPYPTPSGAPAQPpilgttTRPGTgqPGEFHTTPPGTPRHQPSTPDPFlKPRCPSLDNLAVP 2250
Cdd:PHA03247  2570 -PPRPAPRP----SEPAVTSRARRPDAPPQS------ARPRA--PVDDRGDPRGPAPPSPLPPDTH-APDPPPPSPSPAA 2635

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2251 ESPGVAGGKASEPLLSP-----PPFGESRKTLEVKKEELGASSPGYGPPNLGCvdSPSSGSHLGGLELKAPDVFKAPLTP 2325
Cdd:PHA03247  2636 NEPDPHPPPTVPPPERPrddpaPGRVSRPRRARRLGRAAQASSPPQRPRRRAA--RPTVGSLTSLADPPPPPPTPEPAPH 2713

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2326 RASQVEPQSPGLGLRAQEPPAAQALAPSPPSHSDVFRSASYPDPYAQPPLTPRPQPPPPESCCALPPRSLPSDPFSRVPA 2405
Cdd:PHA03247  2714 ALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSE 2793

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2406 SPQSQSSSQSpltPRPLSAEAFCPSPVTPRFQSPDPYSRPPSRPQSRDPFAPLHKPPRPQPPEVAFK-AGPLAH--TPLG 2482
Cdd:PHA03247  2794 SRESLPSPWD---PADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVApGGDVRRrpPSRS 2870

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2483 AGGFPAALPSGPAGELHAKVPSGQPPNFARSPgtgafvgtPSPMRFTFPQGVGEPSLKPPVPQPGLPPPhginshfgPGP 2562
Cdd:PHA03247  2871 PAAKPAAPARPPVRRLARPAVSRSTESFALPP--------DQPERPPQPQAPPPPQPQPQPPPPPQPQP--------PPP 2934

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2563 TLGKPQS--TNYTVATGNFHPSGSPLGPNTGPTGEGYGLSPLRPAsvmPPPTPEGSLPylshgasqrAGITSPVEKREDA 2640
Cdd:PHA03247  2935 PPPRPQPplAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRV---PQPAPSREAP---------ASSTPPLTGHSLS 3002

                          570       580
                   ....*....|....*....|....*...
gi 1537972313 2641 GATMSSSSLAtpeLSSAQDAGMPSLSQT 2668
Cdd:PHA03247  3003 RVSSWASSLA---LHEETDPPPVSLKQT 3027
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 374-921 1.72e-10

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 68.43  E-value: 1.72e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  374 PPEPGDIPTDEPDALYVA--CQGQPKGGHVTSMQPKEPGPLQcEAKPLGRAGTQLEAQLEAPLNEEMPLLPPPP--PPEE 449
Cdd:PHA03247  2553 PPLPPAAPPAAPDRSVPPprPAPRPSEPAVTSRARRPDAPPQ-SARPRAPVDDRGDPRGPAPPSPLPPDTHAPDppPPSP 2631

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  450 SPLSPPPEESPTSPPPEASRLSPPPEESPESMPPEASRLSPPPEESPESM-----------PPEASRLSPPPEESPLSPP 518
Cdd:PHA03247  2632 SPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQrprrraarptvGSLTSLADPPPPPPTPEPA 2711

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  519 PEECPLSPPPESSPFSPLEESPSSPAleTPLSPPPEASPLSPPFEESPLSPPPEALPTSPPPEASRLSPPPEESPMSPPP 598
Cdd:PHA03247  2712 PHALVSATPLPPGPAAARQASPALPA--APAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVA 2789

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  599 EESPMSPPPEASRlfPPFEESPLSPPPEESPLSPPPEASRLSPPPEDSPMSPPPedsPMSPPPEvsrfsPLPVLSHLSPL 678
Cdd:PHA03247  2790 SLSESRESLPSPW--DPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPP---PPGPPPP-----SLPLGGSVAPG 2859

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  679 PEVSRLSPPPEESPlspppedSPTSPP-PEASRLSPPpedsPVSPPPEdslmSLPLEESPLSPLPEgPRLCPQPEEPYLS 757
Cdd:PHA03247  2860 GDVRRRPPSRSPAA-------KPAAPArPPVRRLARP----AVSRSTE----SFALPPDQPERPPQ-PQAPPPPQPQPQP 2923

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  758 PQPEEPRLCPQPEELPLSPRSEEPCLSPVLAEPCLSSQPEEPHLSP----VPQEQHLSPQPEEPHLSPQPKEPHLSPQSE 833
Cdd:PHA03247  2924 PPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPgrvaVPRFRVPQPAPSREAPASSTPPLTGHSLSR 3003

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  834 EPCLSPML---EEPclSPKPEELYQS------PRPEEPPEELSQCPAPKELSLFPPTGEPPLSPMLGEPAVSEPGEPPL- 903
Cdd:PHA03247  3004 VSSWASSLalhEET--DPPPVSLKQTlwppddTEDSDADSLFDSDSERSDLEALDPLPPEPHDPFAHEPDPATPEAGARe 3081

                          570
                   ....*....|....*...
gi 1537972313  904 SPLPEELPLSLSEEPALS 921
Cdd:PHA03247  3082 SPSSQFGPPPLSANAALS 3099
Med15 super family cl26621
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 3970-4359 7.89e-06

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


The actual alignment was detected with superfamily member pfam09606:

Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 52.70  E-value: 7.89e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 3970 LGPGMPAKPLQHFSSPGALGPTLLLTGKEQ-NITEASLPSE---VTEGPSTHQGGPLAVGTTPESMSVEPGEVKPSvSGD 4045
Cdd:pfam09606  102 MGPGPGGPMGQQMGGPGTASNLLASLGRPQmPMGGAGFPSQmsrVGRMQPGGQAGGMMQPSSGQPGSGTPNQMGPN-GGP 180

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4046 SQLLLVQSQAQAQpIPVQLQPPLRL-------PGQPQQQQVNLLHTTGGGNHGQQLGSSSEVP--SVPHLLNQPSVSLGE 4116
Cdd:pfam09606  181 GQGQAGGMNGGQQ-GPMGGQMPPQMgvpgmpgPADAGAQMGQQAQANGGMNPQQMGGAPNQVAmqQQQPQQQGQQSQLGM 259

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4117 QPGPMTQNLLGSQQPLGLDRPIQNntgpqppktGPVPQSGQGLPGVGVMPTVGQLRAQLQGvlaKNPQLRhlspqqqqQL 4196
Cdd:pfam09606  260 GINQMQQMPQGVGGGAGQGGPGQP---------MGPPGQQPGAMPNVMSIGDQNNYQQQQT---RQQQQQ--------QG 319

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4197 QALLMQRQLQQSQAVrqtppiqEPGSQPSPLQGLLGCQPQ-SGGFSGSQTGPLQELGAGPRPQGPPrLPVPQGALSTGPV 4275
Cdd:pfam09606  320 GNHPAAHQQQMNQSV-------GQGGQVVALGGLNHLETWnPGNFGGLGANPMQRGQPGMMSSPSP-VPGQQVRQVTPNQ 391

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4276 LGPVHPTPPPSSPQEP-KRPSQLPSPSAQPTPTHPGTPKPQ---GPTLELPPGRVSPAAAqLADTFFGKGLGPWDPSDNL 4351
Cdd:pfam09606  392 FMRQSPQPSVPSPQGPgSQPPQSHPGGMIPSPALIPSPSPQmsqQPAQQRTIGQDSPGGS-LNTPGQSAVNSPLNPQEEQ 470


                   ....*...
gi 1537972313 4352 TEAQKPEQ 4359
Cdd:pfam09606  471 LYREKYRQ 478
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 2390-2995 9.84e-04

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 46.08  E-value: 9.84e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2390 LPPRSLPSDPFSRVPASPQSQSSSQSPLTPRPLSAEAfCPSPVTPRfqSPDPYSRPPSRPQSRDPFAPLHKPPRPQPPev 2469
Cdd:PHA03247  2555 LPPAAPPAAPDRSVPPPRPAPRPSEPAVTSRARRPDA-PPQSARPR--APVDDRGDPRGPAPPSPLPPDTHAPDPPPP-- 2629

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2470 afkaGPLAHTPLGAGGFPAALPSGPAGELHAKVPSGQPPNFARSPGTGAFVGTPspmrftfPQGVGEPSLKPPvpqpglp 2549
Cdd:PHA03247  2630 ----SPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSP-------PQRPRRRAARPT------- 2691

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2550 pphginshFGPGPTLGKPQSTNYTVATGNfhPSGSPLGPNTGPTGEGYGLSPLRPASVMPPPTPEGslpylshgASQRAG 2629
Cdd:PHA03247  2692 --------VGSLTSLADPPPPPPTPEPAP--HALVSATPLPPGPAAARQASPALPAAPAPPAVPAG--------PATPGG 2753

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2630 ITSPVEKREDAGATmSSSSLATPELSSAQDAGMPSLSqtelekqrqrqrlrellirqqiqrnNLRQEKETAAAAASAVGP 2709
Cdd:PHA03247  2754 PARPARPPTTAGPP-APAPPAAPAAGPPRRLTRPAVA-------------------------SLSESRESLPSPWDPADP 2807

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2710 PGnwgaePSSPAFEQLSRGQTPFTGSQDKSSIVGLPSSKLGGPI-----LGPGAFSSDDRLSRPLPPATPSSMDMNSRQL 2784
Cdd:PHA03247  2808 PA-----AVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPppslpLGGSVAPGGDVRRRPPSRSPAAKPAAPARPP 2882

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2785 VggsqafyQRTPYPgsLPLQQQQQQQQQPLWQQQQQQATVATsmrlamsarfPSTPGPELGRQALGSPLAGIPTRLPGPA 2864
Cdd:PHA03247  2883 V-------RRLARP--AVSRSTESFALPPDQPERPPQPQAPP----------PPQPQPQPPPPPQPQPPPPPPPRPQPPL 2943

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2865 EPVPGPAGPAQfielrhnVQKGLGPGGPPFPGQGPPQRPRFYPVSEEPHRLAPeglrgvAISGLPPQKPSAPPVPELNNS 2944
Cdd:PHA03247  2944 APTTDPAGAGE-------PSGAVPQPWLGALVPGRVAVPRFRVPQPAPSREAP------ASSTPPLTGHSLSRVSSWASS 3010

                          570       580       590       600       610
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1537972313 2945 LhqTSHTKSPALPTGLELVSRPPSSTELSRP-------PLALEAGKLPCEDPELDDDF 2995
Cdd:PHA03247  3011 L--ALHEETDPPPVSLKQTLWPPDDTEDSDAdslfdsdSERSDLEALDPLPPEPHDPF 3066
 
Name Accession Description Interval E-value
SET_KMT2D cd19209
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2D (KMT2D) ...
 5366-5520 1.50e-109

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2D (KMT2D) and similar proteins; KMT2D (EC2.1.1.43; also termed lysine N-methyltransferase 2D, ALL1-related protein (ALR), or myeloid/lymphoid or mixed-lineage leukemia protein 2 (MLL2)), acts as histone methyltransferase that methylates 'Lys-4' of histone H3 (H3K4me). It is a coactivator for estrogen receptor by being recruited by ESR1, thereby activating transcription. KMT2D is a subunit of MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation.


Pssm-ID: 380986 [Multi-domain]  Cd Length: 155  Bit Score: 346.30  E-value: 1.50e-109
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5366 HSKSSQYRRLRTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVI 5445
Cdd:cd19209      1 HSKSSQYRRLKTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVI 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1537972313 5446 DATLTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWM 5520
Cdd:cd19209     81 DATLTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWM 155
ePHD2_KMT2D cd15698
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 5000-5106 9.70e-77

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2D. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions.


Pssm-ID: 277168  Cd Length: 107  Bit Score: 250.35  E-value: 9.70e-77
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5000 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQRTGATSSCNRMRCPN 5079
Cdd:cd15698      1 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQKTGATNSCNRLRCPN 80

                           90       100
                   ....*....|....*....|....*..
gi 1537972313 5080 VYHFACAIRAKCMFFKDKTMLCPMHKI 5106
Cdd:cd15698     81 VYHFACAIRAKCMFFKDKTMLCPMHKL 107
HMG-box_KMT2D cd22027
high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2D (KMT2D) and ...
 1987-2070 7.43e-60

high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2D (KMT2D) and similar proteins; KMT2D, also called ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis.


Pssm-ID: 438836  Cd Length: 84  Bit Score: 201.08  E-value: 7.43e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 1987 GLSYNQRSLQRWEKDEELGQLSTISPVLYANINFPNLKQDYPDWSSRCKQIMKLWRKVPAADKAPYLQKAKDNRAAHRIN 2066
Cdd:cd22027      1 GLSYNQRSLQRWEKDEELGELSTISPVLYANINFPNLKQDYPDWSSRCKQIMKLWRKVPAADKAPYLQKAKDNRAAHRIN 80


                   ....
gi 1537972313 2067 KVQK 2070
Cdd:cd22027     81 KVQK 84
ePHD1_KMT2D cd15695
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 134-217 8.05e-52

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMT2D. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 at Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions.


Pssm-ID: 277165  Cd Length: 90  Bit Score: 178.57  E-value: 8.05e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  134 GHCWAHHWCAVWSAGVWGQEGPELCGVDKAIFSGISQRCSHCTRFGASIPCRSPGCPRLYHFPCATASGSFLSMKTLQLL 213
Cdd:cd15695      7 GECWVHHWCAAWSAGVKQHEGDGLIGVDKAVFSGISQKCEHCKRLGATIQCHAEGCPRFYHFPCAAASGSFQSMKTLLLL 86


                   ....
gi 1537972313  214 CPDH 217
Cdd:cd15695     87 CPEH 90
PHD5_KMT2D cd15601
PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 1501-1551 3.65e-33

PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such asHOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is downregulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger.


Pssm-ID: 277074  Cd Length: 51  Bit Score: 123.86  E-value: 3.65e-33
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1537972313 1501 TCPVCHAPYVEEDLLIQCRHCERWMHAGCESLFTEDEVEQAADEGFDCVSC 1551
Cdd:cd15601      1 TCPVCRAKYVEEDLLIQCRHCDRWVHAVCESLFTEDEVEQAADEGFDCSSC 51
PHD3_KMT2D cd15597
PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 1373-1423 8.23e-33

PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the third PHD finger.


Pssm-ID: 277072  Cd Length: 51  Bit Score: 122.84  E-value: 8.23e-33
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1537972313 1373 DMCVVCGSFGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVECI 1423
Cdd:cd15597      1 DMCVVCGSFGRGSEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVECI 51
FYRC smart00542
FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region ...
 5208-5295 2.17e-32

FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region (FYRN), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.


Pssm-ID: 197781  Cd Length: 86  Bit Score: 122.79  E-value: 2.17e-32
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  5208 EFVIKVIEQGleDLVFTDASPQAVWNRIIEPVAAMRKEADMLRLFPEYLKGEELFGLTVHAVLRIAESLPGVESCQNYLF 5287
Cdd:smart00542    1 LFRVEIESDP--GEVFKGESPEKCWEMVLERVQEARIAADLLQLLPEGVSGEEMFGLSSPAVVKLIEALPGVHQCTNYWF 78


                    ....*...
gi 1537972313  5288 RYGRHPLM 5295
Cdd:smart00542   79 RYHRSPLL 86
SET COG2940
SET domain-containing protein (function unknown) [General function prediction only];
5382-5519 9.42e-32

SET domain-containing protein (function unknown) [General function prediction only];


Pssm-ID: 442183 [Multi-domain]  Cd Length: 134  Bit Score: 122.76  E-value: 9.42e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5382 NVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRgiYMFRINNEHVIDATLTGGPARYINHSC 5461
Cdd:COG2940      7 RIEVRPSPIHGRGVFATRDIPKGTLIGEYPGEVITWAEAERREPHKEPLHT--YLFELDDDGVIDGALGGNPARFINHSC 84

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1537972313 5462 APNCVAEVVTFD-----KEDkiiiissrrIPKGEELTYDYQFDFEDDQHkiPCHCGawNCRKW 5519
Cdd:COG2940     85 DPNCEADEEDGRifivaLRD---------IAAGEELTYDYGLDYDEEEY--PCRCP--NCRGT 134
SET smart00317
SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Putative methyl transferase, based on ...
 5381-5503 4.16e-31

SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Putative methyl transferase, based on outlier plant homologues


Pssm-ID: 214614 [Multi-domain]  Cd Length: 124  Bit Score: 120.52  E-value: 4.16e-31
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  5381 NNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYE-EQNRGIYMFRINNEHVIDATLTGGPARYINH 5459
Cdd:smart00317    1 NKLEVFKSPGKGWGVRATEDIPKGEFIGEYVGEIITSEEAEERPKAYDtDGAKAFYLFDIDSDLCIDARRKGNLARFINH 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....
gi 1537972313  5460 SCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDD 5503
Cdd:smart00317   81 SCEPNCELLFVEVNGDDRIVIFALRDIKPGEELTIDYGSDYANE 124
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
 1424-1470 5.81e-29

PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger of KMT2C and the fourth PHD finger of KMT2D.


Pssm-ID: 276988  Cd Length: 47  Bit Score: 111.80  E-value: 5.81e-29
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1537972313 1424 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWCV 1470
Cdd:cd15513      1 VCEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 47
FYRC pfam05965
F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 5206-5290 2.67e-26

F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00542.


Pssm-ID: 461788  Cd Length: 83  Bit Score: 105.38  E-value: 2.67e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5206 RPEFVIKVIEQglEDLVFTDASPQAVWNRIIEPVAAMRKEADMLRLFPEYLKGEELFGLTVHAVLRIAESLPGVESCQNY 5285
Cdd:pfam05965    1 GPLFRVTVEED--PDESFEGSSPTKCWSMVLERVQELRREAGLKLKLPESISGEDMFGLTHPAVVRLIESLPGAEKCTNY 78


                   ....*
gi 1537972313 5286 LFRYG 5290
Cdd:pfam05965   79 KFRYG 83
PHD2_KMT2D cd15595
PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 276-320 7.43e-26

PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such asHOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 277070  Cd Length: 46  Bit Score: 102.77  E-value: 7.43e-26
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15595      2 CQTCRKPGEDSKMLVCEACDKGYHTFCLKPAMESLPTDSWKCKAC 46
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 228-273 1.23e-21

PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the first PHD finger.


Pssm-ID: 276984  Cd Length: 48  Bit Score: 90.83  E-value: 1.23e-21
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1537972313  228 HCAVCEGPGELCDLFFCTSCGHHYHGACLDTAL--TARKRAGWQCPEC 273
Cdd:cd15509      1 NCAVCDSPGDLSDLLFCTSCGQHYHGSCLDPAVrpTPLVRAGWQCPEC 48
SET pfam00856
SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be ...
 5392-5496 5.83e-21

SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure.


Pssm-ID: 459965 [Multi-domain]  Cd Length: 115  Bit Score: 91.43  E-value: 5.83e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5392 GLGLYAAKDLEKHTMVIEYIGT-IIRNEVANRREKIYEEQNR----GIYMFRIN--NEHVIDATLT--GGPARYINHSCA 5462
Cdd:pfam00856    1 GRGLFATEDIPKGEFIGEYVEVlLITKEEADKRELLYYDKLElrlwGPYLFTLDedSEYCIDARALyyGNWARFINHSCD 80

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1537972313 5463 PNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDY 5496
Cdd:pfam00856   81 PNCEVRVVYVNGGPRIVIFALRDIKPGEELTIDY 114
FYRN pfam05964
F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 5149-5200 3.62e-18

F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00541.


Pssm-ID: 461787  Cd Length: 51  Bit Score: 81.01  E-value: 3.62e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1537972313 5149 GGLVFHAIGQLLPHQMAdFHSATALYPVGYEATRIYWSLRTNNRRCCYRCSI 5200
Cdd:pfam05964    1 GSLTVLSLGEIVPDRPA-FHTERYIYPVGYKSTRLYWSTKDPRKRCRYTCEI 51
FYRN smart00541
FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region ...
 5159-5202 2.34e-16

FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region (FYRC), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.


Pssm-ID: 128814  Cd Length: 44  Bit Score: 75.78  E-value: 2.34e-16
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....
gi 1537972313  5159 LLPHQMADFHSATALYPVGYEATRIYWSLRTNNRRCCYRCSISE 5202
Cdd:smart00541    1 LLPIQGKLFHSESAIFPVGYKSTRKYWSVKDPNRRCLYSCVIDE 44
PHA03247 PHA03247
large tegument protein UL36; Provisional
 2102-2668 3.92e-14

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 80.37  E-value: 3.92e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2102 PGALGSPPPAA-------APTIFIGSPT---TPAGLSTSADGFLKPPAGTVPGPDSPgelflkLPPQVPAQVPSQD-Pfg 2170
Cdd:PHA03247  2498 PGGGGPPDPDAppapsrlAPAILPDEPVgepVHPRMLTWIRGLEELASDDAGDPPPP------LPPAAPPAAPDRSvP-- 2569

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2171 lAPAYAPEPrfsaAPPTYPPYPTPSGAPAQPpilgttTRPGTgqPGEFHTTPPGTPRHQPSTPDPFlKPRCPSLDNLAVP 2250
Cdd:PHA03247  2570 -PPRPAPRP----SEPAVTSRARRPDAPPQS------ARPRA--PVDDRGDPRGPAPPSPLPPDTH-APDPPPPSPSPAA 2635

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2251 ESPGVAGGKASEPLLSP-----PPFGESRKTLEVKKEELGASSPGYGPPNLGCvdSPSSGSHLGGLELKAPDVFKAPLTP 2325
Cdd:PHA03247  2636 NEPDPHPPPTVPPPERPrddpaPGRVSRPRRARRLGRAAQASSPPQRPRRRAA--RPTVGSLTSLADPPPPPPTPEPAPH 2713

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2326 RASQVEPQSPGLGLRAQEPPAAQALAPSPPSHSDVFRSASYPDPYAQPPLTPRPQPPPPESCCALPPRSLPSDPFSRVPA 2405
Cdd:PHA03247  2714 ALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSE 2793

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2406 SPQSQSSSQSpltPRPLSAEAFCPSPVTPRFQSPDPYSRPPSRPQSRDPFAPLHKPPRPQPPEVAFK-AGPLAH--TPLG 2482
Cdd:PHA03247  2794 SRESLPSPWD---PADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVApGGDVRRrpPSRS 2870

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2483 AGGFPAALPSGPAGELHAKVPSGQPPNFARSPgtgafvgtPSPMRFTFPQGVGEPSLKPPVPQPGLPPPhginshfgPGP 2562
Cdd:PHA03247  2871 PAAKPAAPARPPVRRLARPAVSRSTESFALPP--------DQPERPPQPQAPPPPQPQPQPPPPPQPQP--------PPP 2934

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2563 TLGKPQS--TNYTVATGNFHPSGSPLGPNTGPTGEGYGLSPLRPAsvmPPPTPEGSLPylshgasqrAGITSPVEKREDA 2640
Cdd:PHA03247  2935 PPPRPQPplAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRV---PQPAPSREAP---------ASSTPPLTGHSLS 3002

                          570       580
                   ....*....|....*....|....*...
gi 1537972313 2641 GATMSSSSLAtpeLSSAQDAGMPSLSQT 2668
Cdd:PHA03247  3003 RVSSWASSLA---LHEETDPPPVSLKQT 3027
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1424-1472 2.73e-13

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 67.13  E-value: 2.73e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1537972313 1424 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPL--LTVPKGGWKCKWCVSC 1472
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPPLdpAEIPSGEWLCPECKPK 51
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 276-323 3.62e-13

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 66.75  E-value: 3.62e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1537972313  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEELPAHS--WKCMTCRVC 323
Cdd:pfam00628    2 CAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPAEIPSgeWLCPECKPK 51
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 5027-5104 3.83e-13

PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH.


Pssm-ID: 463977 [Multi-domain]  Cd Length: 88  Bit Score: 68.12  E-value: 3.83e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5027 HLNCALWSTEVY----ETQGGALMNVEVALHRGLLTKCSLC-QRTGATSSCNRMRCPNVYHFACAIRAKCMF-FKDKT-- 5098
Cdd:pfam13771    1 HVVCALWSPELVqrgnDSMGFPIEDIEKIPKRRWKLKCYLCkKKGGACIQCSKKNCRRAFHVTCALEAGLLMqFDEDNgt 80


                   ....*...
gi 1537972313 5099 --MLCPMH 5104
Cdd:pfam13771   81 fkSYCKKH 88
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1424-1469 2.51e-12

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 64.16  E-value: 2.51e-12
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 1537972313  1424 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLT-VPKGGWKCKWC 1469
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 139-217 9.85e-12

PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH.


Pssm-ID: 463977 [Multi-domain]  Cd Length: 88  Bit Score: 63.89  E-value: 9.85e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  139 HHWCAVWSAGVWgQEGPE-----LCGVDKAIFSGISQRCSHC-TRFGASIPCRSPGCPRLYHFPCATASGSFLSMK---- 208
Cdd:pfam13771    1 HVVCALWSPELV-QRGNDsmgfpIEDIEKIPKRRWKLKCYLCkKKGGACIQCSKKNCRRAFHVTCALEAGLLMQFDedng 79


                   ....*....
gi 1537972313  209 TLQLLCPDH 217
Cdd:pfam13771   80 TFKSYCKKH 88
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 276-320 7.61e-11

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 60.30  E-value: 7.61e-11
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*.
gi 1537972313   276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEE-LPAHSWKCMTC 320
Cdd:smart00249    2 CSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 229-276 8.78e-11

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 60.20  E-value: 8.78e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1537972313  229 CAVCEGPGELCDLFFCTSCGHHYHGACLDTALTARKRA--GWQCPECKEC 276
Cdd:pfam00628    2 CAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPAEIPsgEWLCPECKPK 51
PHA03247 PHA03247
large tegument protein UL36; Provisional
 374-921 1.72e-10

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 68.43  E-value: 1.72e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  374 PPEPGDIPTDEPDALYVA--CQGQPKGGHVTSMQPKEPGPLQcEAKPLGRAGTQLEAQLEAPLNEEMPLLPPPP--PPEE 449
Cdd:PHA03247  2553 PPLPPAAPPAAPDRSVPPprPAPRPSEPAVTSRARRPDAPPQ-SARPRAPVDDRGDPRGPAPPSPLPPDTHAPDppPPSP 2631

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  450 SPLSPPPEESPTSPPPEASRLSPPPEESPESMPPEASRLSPPPEESPESM-----------PPEASRLSPPPEESPLSPP 518
Cdd:PHA03247  2632 SPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQrprrraarptvGSLTSLADPPPPPPTPEPA 2711

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  519 PEECPLSPPPESSPFSPLEESPSSPAleTPLSPPPEASPLSPPFEESPLSPPPEALPTSPPPEASRLSPPPEESPMSPPP 598
Cdd:PHA03247  2712 PHALVSATPLPPGPAAARQASPALPA--APAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVA 2789

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  599 EESPMSPPPEASRlfPPFEESPLSPPPEESPLSPPPEASRLSPPPEDSPMSPPPedsPMSPPPEvsrfsPLPVLSHLSPL 678
Cdd:PHA03247  2790 SLSESRESLPSPW--DPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPP---PPGPPPP-----SLPLGGSVAPG 2859

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  679 PEVSRLSPPPEESPlspppedSPTSPP-PEASRLSPPpedsPVSPPPEdslmSLPLEESPLSPLPEgPRLCPQPEEPYLS 757
Cdd:PHA03247  2860 GDVRRRPPSRSPAA-------KPAAPArPPVRRLARP----AVSRSTE----SFALPPDQPERPPQ-PQAPPPPQPQPQP 2923

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  758 PQPEEPRLCPQPEELPLSPRSEEPCLSPVLAEPCLSSQPEEPHLSP----VPQEQHLSPQPEEPHLSPQPKEPHLSPQSE 833
Cdd:PHA03247  2924 PPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPgrvaVPRFRVPQPAPSREAPASSTPPLTGHSLSR 3003

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  834 EPCLSPML---EEPclSPKPEELYQS------PRPEEPPEELSQCPAPKELSLFPPTGEPPLSPMLGEPAVSEPGEPPL- 903
Cdd:PHA03247  3004 VSSWASSLalhEET--DPPPVSLKQTlwppddTEDSDADSLFDSDSERSDLEALDPLPPEPHDPFAHEPDPATPEAGARe 3081

                          570
                   ....*....|....*...
gi 1537972313  904 SPLPEELPLSLSEEPALS 921
Cdd:PHA03247  3082 SPSSQFGPPPLSANAALS 3099
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1375-1425 4.68e-10

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 57.89  E-value: 4.68e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1537972313 1375 CVVCGsfGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKG-WRCVECIVC 1425
Cdd:pfam00628    2 CAVCG--KSDDGGELVQCDGCDDWFHLACLGPPLDPAEIPSGeWLCPECKPK 51
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1374-1422 9.96e-10

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 56.84  E-value: 9.96e-10
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*....
gi 1537972313  1374 MCVVCGsfGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVEC 1422
Cdd:smart00249    1 YCSVCG--KPDDGGELLQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 229-273 1.44e-08

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 53.75  E-value: 1.44e-08
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*.
gi 1537972313   229 CAVCEGPGELCDLFFCTSCGHHYHGACLDTALT-ARKRAGWQCPEC 273
Cdd:smart00249    2 CSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLeEEPDGKWYCPKC 47
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 539-848 1.53e-08

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 61.71  E-value: 1.53e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  539 SPSSPALETPLSPPPEASPLSPPFEESPLSPPPEALPTSPPPEASRLSPPPEESPMSPPPEESPMSPPPEASRLFPPFEE 618
Cdd:pfam03154  182 SPPSPPPPGTTQAATAGPTPSAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQTPTLHPQRLPSPHPPLQPMTQPPPPSQV 261

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  619 SPLSPPPEESPLSPPPEASRLSPPPEDSPMSPPPEDSPMSPPPEVSRFSPLPVLSHLSPLPEVSRLSPPPEESPLSPPPE 698
Cdd:pfam03154  262 SPQPLPQPSLHGQMPPMPHSLQTGPSHMQHPVPPQPFPLTPQSSQSQVPPGPSPAAPGQSQQRIHTPPSQSQLQSQQPPR 341

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  699 DSPTSPPPEASRLSPPPEDSPVSPPPEDSLMSLPLEESPLSPLPEGPRLCPQPEEPYLSPQPEEPRLCPQPEELPLSPRS 778
Cdd:pfam03154  342 EQPLPPAPLSMPHIKPPPTTPIPQLPNPQSHKHPPHLSGPSPFQMNSNLPPPPALKPLSSLSTHHPPSAHPPPLQLMPQS 421

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1537972313  779 EE----PCLSPVLAE-----PCLSSQPEEPHLSPVPQEQHLSPQPEEPHLSPqPKEPHLSPQSEEPCLSPMLEEPCLSP 848
Cdd:pfam03154  422 QQlpppPAQPPVLTQsqslpPPAASHPPTSGLHQVPSQSPFPQHPFVPGGPP-PITPPSGPPTSTSSAMPGIQPPSSAS 499
HMG smart00398
high mobility group;
2013-2064 5.29e-07

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 50.01  E-value: 5.29e-07
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....
gi 1537972313  2013 VLYANINFPNLKQDYPDWSS--RCKQIMKLWRKVPAADKAPYLQKAKDNRAAHR 2064
Cdd:smart00398   10 MLFSQENRAKIKAENPDLSNaeISKKLGERWKLLSEEEKAPYEEKAKKDKERYE 63
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1501-1551 6.84e-07

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 48.75  E-value: 6.84e-07
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|.
gi 1537972313  1501 TCPVCHAPYvEEDLLIQCRHCERWMHAGCESLFTEDEVEqaaDEGFDCVSC 1551
Cdd:smart00249    1 YCSVCGKPD-DGGELLQCDGCDRWYHQTCLGPPLLEEEP---DGKWYCPKC 47
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 3970-4359 7.89e-06

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 52.70  E-value: 7.89e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 3970 LGPGMPAKPLQHFSSPGALGPTLLLTGKEQ-NITEASLPSE---VTEGPSTHQGGPLAVGTTPESMSVEPGEVKPSvSGD 4045
Cdd:pfam09606  102 MGPGPGGPMGQQMGGPGTASNLLASLGRPQmPMGGAGFPSQmsrVGRMQPGGQAGGMMQPSSGQPGSGTPNQMGPN-GGP 180

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4046 SQLLLVQSQAQAQpIPVQLQPPLRL-------PGQPQQQQVNLLHTTGGGNHGQQLGSSSEVP--SVPHLLNQPSVSLGE 4116
Cdd:pfam09606  181 GQGQAGGMNGGQQ-GPMGGQMPPQMgvpgmpgPADAGAQMGQQAQANGGMNPQQMGGAPNQVAmqQQQPQQQGQQSQLGM 259

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4117 QPGPMTQNLLGSQQPLGLDRPIQNntgpqppktGPVPQSGQGLPGVGVMPTVGQLRAQLQGvlaKNPQLRhlspqqqqQL 4196
Cdd:pfam09606  260 GINQMQQMPQGVGGGAGQGGPGQP---------MGPPGQQPGAMPNVMSIGDQNNYQQQQT---RQQQQQ--------QG 319

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4197 QALLMQRQLQQSQAVrqtppiqEPGSQPSPLQGLLGCQPQ-SGGFSGSQTGPLQELGAGPRPQGPPrLPVPQGALSTGPV 4275
Cdd:pfam09606  320 GNHPAAHQQQMNQSV-------GQGGQVVALGGLNHLETWnPGNFGGLGANPMQRGQPGMMSSPSP-VPGQQVRQVTPNQ 391

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4276 LGPVHPTPPPSSPQEP-KRPSQLPSPSAQPTPTHPGTPKPQ---GPTLELPPGRVSPAAAqLADTFFGKGLGPWDPSDNL 4351
Cdd:pfam09606  392 FMRQSPQPSVPSPQGPgSQPPQSHPGGMIPSPALIPSPSPQmsqQPAQQRTIGQDSPGGS-LNTPGQSAVNSPLNPQEEQ 470


                   ....*...
gi 1537972313 4352 TEAQKPEQ 4359
Cdd:pfam09606  471 LYREKYRQ 478
PspC_subgroup_2 NF033839
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 538-851 1.08e-05

pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, as described in Streptococcus pneumoniae, is a repetitive and highly variable protein, recognized by a conserved N-terminal domain and also by genomic location. This form, subgroup 2, is anchored covalently after cleavage by sortase at a C-terminal LPXTG site. The other form, subgroup 1, has variable numbers of a choline-binding repeat in the C-terminal region, and is also known as choline-binding protein A.


Pssm-ID: 468202 [Multi-domain]  Cd Length: 557  Bit Score: 52.08  E-value: 1.08e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  538 ESPSSPALETPLSPPPEASPLSPPFEESPLSPPPEALPtSPPPEASRLSPPPEESPMSPPPEESPMSPPPEASRLFPPFE 617
Cdd:NF033839   144 EKDSSSSSSSGSSTKPETPQPENPEHQKPTTPAPDTKP-SPQPEGKKPSVPDINQEKEKAKLAVATYMSKILDDIQKHHL 222

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  618 ESPLSPPPEESPLSPPPEASRLSPPPEDSPMSPPPEDSPMSPPPEVSRFsplpvlshlsplpeVSRLSPPPEESPLSPPP 697
Cdd:NF033839   223 QKEKHRQIVALIKELDELKKQALSEIDNVNTKVEIENTVHKIFADMDAV--------------VTKFKKGLTQDTPKEPG 288

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  698 EDSPTSPPPEAsRLSPPPEDSPVSPPPE----DSLMSLPLEESPLSPLPEGPR--LCPQPE--EPYLSPQPEEPR--LCP 767
Cdd:NF033839   289 NKKPSAPKPGM-QPSPQPEKKEVKPEPEtpkpEVKPQLEKPKPEVKPQPEKPKpeVKPQLEtpKPEVKPQPEKPKpeVKP 367

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  768 QPE----ELPLSPRSEEPCLSPVLAEPCLSSQPEEPHLSPVPQEQHLSPQPEEPHlSPQPKEPHLSPQSEEPclspmleE 843
Cdd:NF033839   368 QPEkpkpEVKPQPETPKPEVKPQPEKPKPEVKPQPEKPKPEVKPQPEKPKPEVKP-QPEKPKPEVKPQPEKP-------K 439


                   ....*...
gi 1537972313  844 PCLSPKPE 851
Cdd:NF033839   440 PEVKPQPE 447
PHA03247 PHA03247
large tegument protein UL36; Provisional
 4057-4347 1.19e-05

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 52.25  E-value: 1.19e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4057 AQPIPVQLQPPLRLPGQPQqqqvnllhTTGGGNHGQQLGSSSEVPSVPHLLNQPSVSLGEQPGPMTQNLLGSQQPLGLDR 4136
Cdd:PHA03247  2703 PPPPTPEPAPHALVSATPL--------PPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAA 2774

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4137 PIQNntgpqPPKTGPVPQSGQGLPGVGVMPTVGQLRAQLQGVLAKNPQLrhlspqqqqqLQALLMQRQLQQSQAVRQTPP 4216
Cdd:PHA03247  2775 PAAG-----PPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAAL----------PPAASPAGPLPPPTSAQPTAP 2839

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4217 IQEPGSQPSPLQGLLGCQPqsgGFSGSQTGPLQELGAGP-RPQGPP--RLPVPQGALSTGPVLGPVHPTPPPSSPQEPKR 4293
Cdd:PHA03247  2840 PPPPGPPPPSLPLGGSVAP---GGDVRRRPPSRSPAAKPaAPARPPvrRLARPAVSRSTESFALPPDQPERPPQPQAPPP 2916

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1537972313 4294 PSQLPSPSAQPTPTHPGTPKPQgPTLELPPGRVSPAAAQLADTFFGKGLGPWDP 4347
Cdd:PHA03247  2917 PQPQPQPPPPPQPQPPPPPPPR-PQPPLAPTTDPAGAGEPSGAVPQPWLGALVP 2969
HMG_box pfam00505
HMG (high mobility group) box;
2013-2064 1.49e-05

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 45.68  E-value: 1.49e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1537972313 2013 VLYANINFPNLKQDYPDWSSR--CKQIMKLWRKVPAADKAPYLQKAKDNRAAHR 2064
Cdd:pfam00505    9 FLFSKEQRAKLKAENPGLKNAeiSKILGEKWKALSEEEKKPYEEKAEKEKARYE 62
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 2212-2723 9.03e-05

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 49.38  E-value: 9.03e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2212 TGQPGEFHTTPPGTPRHQPSTPDPFLKPRCPSLDNLAVPESPGVAGGKASEPLLSPPPfgeSRKTLEVKKEELGASSPGY 2291
Cdd:pfam03154  161 SAQQQILQTQPPVLQAQSGAASPPSPPPPGTTQAATAGPTPSAPSVPPQGSPATSQPP---NQTQSTAAPHTLIQQTPTL 237

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2292 GPPNLGCVDSPSSGshlgglelkapdvfkAPLTPRASQVEPQS-PGLGLRAQEPPAAQALAPSPPSHSDVFRSASYPDPy 2370
Cdd:pfam03154  238 HPQRLPSPHPPLQP---------------MTQPPPPSQVSPQPlPQPSLHGQMPPMPHSLQTGPSHMQHPVPPQPFPLT- 301

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2371 aqPPLTPRPQPPPPESCCALPPRSLPSDPFSRvPASPQSQSSSQSPLTPRPLSAEAFCPSPVTPRFQSPDPYS-RPPSRP 2449
Cdd:pfam03154  302 --PQSSQSQVPPGPSPAAPGQSQQRIHTPPSQ-SQLQSQQPPREQPLPPAPLSMPHIKPPPTTPIPQLPNPQShKHPPHL 378

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2450 QSRDPF---APLHKPPRPQP-PEVAFKAGPLAH-TPLGAGGFPAALPSGPAGELHAKVPSGQPPNFARSPGTGAFvgTPS 2524
Cdd:pfam03154  379 SGPSPFqmnSNLPPPPALKPlSSLSTHHPPSAHpPPLQLMPQSQQLPPPPAQPPVLTQSQSLPPPAASHPPTSGL--HQV 456

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2525 PMRFTFPQGVGEPSLKPPVPQPGLPPPHGINSHFGPGPTLGKPQSTNYTVAtGNFHPSGSPLGPNTGPTGEgyglsPLRP 2604
Cdd:pfam03154  457 PSQSPFPQHPFVPGGPPPITPPSGPPTSTSSAMPGIQPPSSASVSSSGPVP-AAVSCPLPPVQIKEEALDE-----AEEP 530

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2605 ASVMPP---PTPEGSLPYLSHGASQRAGITSPVEKREDAGA-------TMSSSSLATPELSSAQDAGMPSLSQTELEKQR 2674
Cdd:pfam03154  531 ESPPPPprsPSPEPTVVNTPSHASQSARFYKHLDRGYNSCArtdlyfmPLAGSKLAKKREEALEKAKREAEQKAREEKER 610

                          490       500       510       520
                   ....*....|....*....|....*....|....*....|....*....
gi 1537972313 2675 QRQRLRELLIRQQIQRNNLRQEKETAAAAASAVGPPGNWGAEPSSPAFE 2723
Cdd:pfam03154  611 EKEKEKEREREREREREAERAAKASSSSHEGRMGDPQLAGPAHMRPSFE 659
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1502-1553 1.02e-04

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 42.86  E-value: 1.02e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1537972313 1502 CPVCHAPyVEEDLLIQCRHCERWMHAGCESLftEDEVEQAADEGFDCVSCQP 1553
Cdd:pfam00628    2 CAVCGKS-DDGGELVQCDGCDDWFHLACLGP--PLDPAEIPSGEWLCPECKP 50
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 5060-5104 4.55e-04

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 41.04  E-value: 4.55e-04
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 1537972313  5060 CSLCQRTGATS---SCNRmrCPNVYHFACAIRAKCMFFKDKTMLCPMH 5104
Cdd:smart00249    2 CSVCGKPDDGGellQCDG--CDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
PHA03247 PHA03247
large tegument protein UL36; Provisional
 2390-2995 9.84e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 46.08  E-value: 9.84e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2390 LPPRSLPSDPFSRVPASPQSQSSSQSPLTPRPLSAEAfCPSPVTPRfqSPDPYSRPPSRPQSRDPFAPLHKPPRPQPPev 2469
Cdd:PHA03247  2555 LPPAAPPAAPDRSVPPPRPAPRPSEPAVTSRARRPDA-PPQSARPR--APVDDRGDPRGPAPPSPLPPDTHAPDPPPP-- 2629

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2470 afkaGPLAHTPLGAGGFPAALPSGPAGELHAKVPSGQPPNFARSPGTGAFVGTPspmrftfPQGVGEPSLKPPvpqpglp 2549
Cdd:PHA03247  2630 ----SPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSP-------PQRPRRRAARPT------- 2691

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2550 pphginshFGPGPTLGKPQSTNYTVATGNfhPSGSPLGPNTGPTGEGYGLSPLRPASVMPPPTPEGslpylshgASQRAG 2629
Cdd:PHA03247  2692 --------VGSLTSLADPPPPPPTPEPAP--HALVSATPLPPGPAAARQASPALPAAPAPPAVPAG--------PATPGG 2753

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2630 ITSPVEKREDAGATmSSSSLATPELSSAQDAGMPSLSqtelekqrqrqrlrellirqqiqrnNLRQEKETAAAAASAVGP 2709
Cdd:PHA03247  2754 PARPARPPTTAGPP-APAPPAAPAAGPPRRLTRPAVA-------------------------SLSESRESLPSPWDPADP 2807

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2710 PGnwgaePSSPAFEQLSRGQTPFTGSQDKSSIVGLPSSKLGGPI-----LGPGAFSSDDRLSRPLPPATPSSMDMNSRQL 2784
Cdd:PHA03247  2808 PA-----AVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPppslpLGGSVAPGGDVRRRPPSRSPAAKPAAPARPP 2882

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2785 VggsqafyQRTPYPgsLPLQQQQQQQQQPLWQQQQQQATVATsmrlamsarfPSTPGPELGRQALGSPLAGIPTRLPGPA 2864
Cdd:PHA03247  2883 V-------RRLARP--AVSRSTESFALPPDQPERPPQPQAPP----------PPQPQPQPPPPPQPQPPPPPPPRPQPPL 2943

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2865 EPVPGPAGPAQfielrhnVQKGLGPGGPPFPGQGPPQRPRFYPVSEEPHRLAPeglrgvAISGLPPQKPSAPPVPELNNS 2944
Cdd:PHA03247  2944 APTTDPAGAGE-------PSGAVPQPWLGALVPGRVAVPRFRVPQPAPSREAP------ASSTPPLTGHSLSRVSSWASS 3010

                          570       580       590       600       610
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1537972313 2945 LhqTSHTKSPALPTGLELVSRPPSSTELSRP-------PLALEAGKLPCEDPELDDDF 2995
Cdd:PHA03247  3011 L--ALHEETDPPPVSLKQTLWPPDDTEDSDAdslfdsdSERSDLEALDPLPPEPHDPF 3066
half-pint TIGR01645
poly-U binding splicing factor, half-pint family; The proteins represented by this model ...
 4243-4436 1.43e-03

poly-U binding splicing factor, half-pint family; The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.


Pssm-ID: 130706 [Multi-domain]  Cd Length: 612  Bit Score: 45.06  E-value: 1.43e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4243 SQTGPLQELGAGPRPQGPPrlPVPQGALSTGPVLGPVHPTPPPSSPQEpkrPSQLPSPSAQPTPTHPGTPKPQG---PTl 4319
Cdd:TIGR01645  327 RAQSPATPSSSLPTDIGNK--AVVSSAKKEAEEVPPLPQAAPAVVKPG---PMEIPTPVPPPGLAIPSLVAPPGlvaPT- 400

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4320 ELPPGRVSPAAAQLADTFFGKGLGPWDPSDNLTEAQKPEQSSlVSGHLEQVNGQVVQESPQLSIKQEPREEscalGAQAV 4399
Cdd:TIGR01645  401 EINPSFLASPRKKMKREKLPVTFGALDDTLAWKEPSKEDQTS-EDGKMLAIMGEAAAALALEPKKKKKEKE----GEELQ 475

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 1537972313 4400 KREADGEPGGTPGTSNHLLLAGsrSEAGHLLLQKLLR 4436
Cdd:TIGR01645  476 PKLVMNSEDASLASQEGMSIRG--NSARHLVMQKLMR 510
SP2_N cd22540
N-terminal domain of transcription factor Specificity Protein (SP) 2; Specificity Proteins ...
 4040-4336 2.33e-03

N-terminal domain of transcription factor Specificity Protein (SP) 2; Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. SP2 contains the least conserved DNA-binding domain within the SP subfamily of proteins, and its DNA sequence specificity differs from the other SP proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate, or in some cases, repress expression from different promoters. The transcription factor SP2 serves as a paradigm for indirect genomic binding. It does not require its DNA-binding domain for genomic DNA binding and occupies target promoters independently of whether they contain a cognate DNA-binding motif. SP2 belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. SP1-4 have similar N-terminal transactivation domains characterized by glutamine-rich regions, which, in most cases, have adjacent serine/threonine-rich regions. This model represents the N-terminal domain of SP2.


Pssm-ID: 411776 [Multi-domain]  Cd Length: 511  Bit Score: 44.15  E-value: 2.33e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4040 PSVSGDSQLLLVQSQAQAQPIPVQLQPPLRlpGQPQQQQVNLLHTTGGGNHGQQLGSSsevpsvphLLNQPSVSLGEQPG 4119
Cdd:cd22540    138 INNSGQIQIIPGTNQAIITPVQVLQQPQQA--HKPVPIKPAPLQTSNTNSASLQVPGN--------VIKLQSGGNVALTL 207

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4120 PMtQNLLGSQqplglDRPIQNNTGPQPPKTGPVpQSGQGLPGVGVMPTVGQlraQLQGVLAKNPQLRHLSPQQQQQLQAL 4199
Cdd:cd22540    208 PV-NNLVGTQ-----DGATQLQLAAAPSKPSKK-IRKKSAQAAQPAVTVAE---QVETVLIETTADNIIQAGNNLLIVQS 277

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4200 LMQRQLQQSQAVRQTPPIQEPGSQPSPLQGLLGCQPQSGGFSGSQTGPLQ--ELGAGPRPQGPPRLPVPQGALSTgpVLG 4277
Cdd:cd22540    278 PGTGQPAVLQQVQVLQPKQEQQVVQIPQQALRVVQAASATLPTVPQKPLQniQIQNSEPTPTQVYIKTPSGEVQT--VLL 355

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1537972313 4278 PVHPTPPPSSPQEPKRPSQLPSPSAQPTPTHPGTPKPQGPTLELPP---GRVSPAAAQLADT 4336
Cdd:cd22540    356 QEAPAATATPSSSTSTVQQQVTANNGTGTSKPNYNVRKERTLPKIApagGIISLNAAQLAAA 417
 
Name Accession Description Interval E-value
SET_KMT2D cd19209
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2D (KMT2D) ...
 5366-5520 1.50e-109

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2D (KMT2D) and similar proteins; KMT2D (EC2.1.1.43; also termed lysine N-methyltransferase 2D, ALL1-related protein (ALR), or myeloid/lymphoid or mixed-lineage leukemia protein 2 (MLL2)), acts as histone methyltransferase that methylates 'Lys-4' of histone H3 (H3K4me). It is a coactivator for estrogen receptor by being recruited by ESR1, thereby activating transcription. KMT2D is a subunit of MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation.


Pssm-ID: 380986 [Multi-domain]  Cd Length: 155  Bit Score: 346.30  E-value: 1.50e-109
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5366 HSKSSQYRRLRTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVI 5445
Cdd:cd19209      1 HSKSSQYRRLKTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVI 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1537972313 5446 DATLTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWM 5520
Cdd:cd19209     81 DATLTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWM 155
SET_KMT2C_2D cd19171
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C), ...
 5368-5520 2.11e-109

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C), 2D (KMT2D) and similar proteins; This family includes KMT2C and KMT2D. Both, KMT2C (also termed HALR or MLL3) and KMT2D (also termed ALR or MLL2), act as histone methyltransferases that methylate 'Lys-4' of histone H3 (H3K4me). They are subunits of MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation.


Pssm-ID: 380948 [Multi-domain]  Cd Length: 153  Bit Score: 345.95  E-value: 2.11e-109
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5368 KSSQYRRLRTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVIDA 5447
Cdd:cd19171      1 KSSQYRKLKTEWRSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGEIIRNEVANRREKIYESQNRGIYMFRIDNDWVIDA 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1537972313 5448 TLTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWM 5520
Cdd:cd19171     81 TMTGGPARYINHSCNPNCVAEVVTFDKEKKIIIISNRRIAKGEELTYDYKFDFEDDQHKIPCLCGAPNCRKWM 153
SET_KMT2C cd19208
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C) ...
 5367-5520 5.77e-90

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C) and similar proteins; KMT2C (EC2.1.1.43; also termed lysine N-methyltransferase 2C, homologous to ALR protein (HALR) myeloid/lymphoid, or mixed-lineage leukemia protein 3 (MLL3)), acts as a histone methyltransferase that methylates 'Lys-4' of histone H3 (H3K4me) and may be involved in leukemogenesis and developmental disorder. KMT2C is a catalytic subunit of MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation. Overexpression of KMT2C is associated with estrogen receptor-positive breast cancer; KMT2C mediates the estrogen dependence of breast cancer through regulation of estrogen receptor alpha (ERalpha) enhancer function. KMT2C is frequently mutated in certain populations with diffuse-type gastric adenocarcinomas (DGA); its loss promotes epithelial-to-mesenchymal transition (EMT) and is associated with worse overall survival.


Pssm-ID: 380985 [Multi-domain]  Cd Length: 154  Bit Score: 290.37  E-value: 5.77e-90
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5367 SKSSQYRRLRTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVID 5446
Cdd:cd19208      1 SKSSQYRKMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGVYMFRIDNDHVID 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1537972313 5447 ATLTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWM 5520
Cdd:cd19208     81 ATLTGGPARYINHSCAPNCVAEVVTFEKGHKIIISSSRRIQKGEELCYDYKFDFEDDQHKIPCHCGAVNCRKWM 154
ePHD2_KMT2D cd15698
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 5000-5106 9.70e-77

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2D. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions.


Pssm-ID: 277168  Cd Length: 107  Bit Score: 250.35  E-value: 9.70e-77
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5000 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQRTGATSSCNRMRCPN 5079
Cdd:cd15698      1 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQKTGATNSCNRLRCPN 80

                           90       100
                   ....*....|....*....|....*..
gi 1537972313 5080 VYHFACAIRAKCMFFKDKTMLCPMHKI 5106
Cdd:cd15698     81 VYHFACAIRAKCMFFKDKTMLCPMHKL 107
ePHD2_KMT2C_like cd15666
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
 5000-5104 6.35e-71

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2C, and KMT2D. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions.


Pssm-ID: 277136  Cd Length: 105  Bit Score: 233.73  E-value: 6.35e-71
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5000 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQRTGATSSCNRMRCPN 5079
Cdd:cd15666      1 CVLCGGEGDGDTDGPGRLLNLDVDKWVHLNCALWSYEVYETQNGALMNVEEALRRALTTTCSHCGRTGATVPCFKPRCAN 80

                           90       100
                   ....*....|....*....|....*
gi 1537972313 5080 VYHFACAIRAKCMFFKDKTMLCPMH 5104
Cdd:cd15666     81 VYHLPCAIKDGCMFFKDKTMLCPSH 105
SET_SETD1-like cd10518
SET domain (including post-SET domain) found in SET domain-containing proteins (SETD1A/SETD1B), ...
 5369-5517 5.36e-70

SET domain (including post-SET domain) found in SET domain-containing proteins (SETD1A/SETD1B), histone-lysine N-methyltransferases (KMT2A/KMT2B/KMT2C/KMT2D) and similar proteins; This family includes SET domain-containing protein 1A (SETD1A), 1B (SETD1B), as well as histone-lysine N-methyltransferase 2A (KMT2A), 2B (KMT2B), 2C (KMT2C), 2D (KMT2D). These proteins are histone-lysine N-methyltransferases (EC 2.1.1.43) that specifically methylate 'Lys-4' of histone H3 (H3K4me).


Pssm-ID: 380916  Cd Length: 150  Bit Score: 232.87  E-value: 5.36e-70
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5369 SSQYRRLRTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQN-RGIYMFRINNEHVIDA 5447
Cdd:cd10518      2 SKRFRQLRSRLKERLRVGKSGIHGWGLFAKRPIAAGEMVIEYVGEVIRPIVADKREKRYDEEGgGGTYMFRIDEDLVIDA 81

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5448 TLTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQhKIPCHCGAWNCR 5517
Cdd:cd10518     82 TKKGNIARFINHSCDPNCYAKIITVDGEKHIVIFAKRDIAPGEELTYDYKFPIEDEE-KIPCLCGAPNCR 150
ePHD2_KMT2C cd15697
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 5000-5104 2.31e-62

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2C. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains PHD fingers, two ePHD fingers, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains.


Pssm-ID: 277167  Cd Length: 105  Bit Score: 209.13  E-value: 2.31e-62
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5000 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQRTGATSSCNRMRCPN 5079
Cdd:cd15697      1 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRLRCTN 80

                           90       100
                   ....*....|....*....|....*
gi 1537972313 5080 VYHFACAIRAKCMFFKDKTMLCPMH 5104
Cdd:cd15697     81 VYHFTCAIKAQCMFFKDKTMLCPMH 105
HMG-box_KMT2D cd22027
high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2D (KMT2D) and ...
 1987-2070 7.43e-60

high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2D (KMT2D) and similar proteins; KMT2D, also called ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis.


Pssm-ID: 438836  Cd Length: 84  Bit Score: 201.08  E-value: 7.43e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 1987 GLSYNQRSLQRWEKDEELGQLSTISPVLYANINFPNLKQDYPDWSSRCKQIMKLWRKVPAADKAPYLQKAKDNRAAHRIN 2066
Cdd:cd22027      1 GLSYNQRSLQRWEKDEELGELSTISPVLYANINFPNLKQDYPDWSSRCKQIMKLWRKVPAADKAPYLQKAKDNRAAHRIN 80


                   ....
gi 1537972313 2067 KVQK 2070
Cdd:cd22027     81 KVQK 84
ePHD1_KMT2D cd15695
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 134-217 8.05e-52

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMT2D. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 at Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions.


Pssm-ID: 277165  Cd Length: 90  Bit Score: 178.57  E-value: 8.05e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  134 GHCWAHHWCAVWSAGVWGQEGPELCGVDKAIFSGISQRCSHCTRFGASIPCRSPGCPRLYHFPCATASGSFLSMKTLQLL 213
Cdd:cd15695      7 GECWVHHWCAAWSAGVKQHEGDGLIGVDKAVFSGISQKCEHCKRLGATIQCHAEGCPRFYHFPCAAASGSFQSMKTLLLL 86


                   ....
gi 1537972313  214 CPDH 217
Cdd:cd15695     87 CPEH 90
SET_KMT2A_2B cd19170
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A), ...
 5369-5521 1.49e-51

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A), 2B (KMT2B) and similar proteins; This family includes KMT2A and KMT2B. Both KMT2A (also termed ALL-1 or CXXC7 or MLL or MLL1 or TRX1 or HRX) and KMT2B (also termed MLL4 or TRX2) act as histone methyltransferases that methylate 'Lys-4' of histone H3 (H3K4me).


Pssm-ID: 380947 [Multi-domain]  Cd Length: 152  Bit Score: 180.28  E-value: 1.49e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5369 SSQYRRLRTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVIDAT 5448
Cdd:cd19170      2 AMRFRHLRKTAKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGEVIRSVLTDKREKYYESKGIGCYMFRIDDDEVVDAT 81

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1537972313 5449 LTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDqhKIPCHCGAWNCRKWMN 5521
Cdd:cd19170     82 MHGNAARFINHSCEPNCYSRVVNIDGKKHIVIFALRRILRGEELTYDYKFPIEDV--KIPCTCGSKKCRKYLN 152
SET_SETD1 cd19169
SET domain (including post-SET domain) found in SET domain-containing protein 1 (SETD1) and ...
 5380-5517 1.19e-47

SET domain (including post-SET domain) found in SET domain-containing protein 1 (SETD1) and similar proteins; This family includes SET domain-containing protein 1A (SETD1A) and SET domain-containing protein 1B (SETD1B). These proteins are histone-lysine N-methyltransferases that specifically methylate 'Lys-4' of histone H3 (H3K4me) when part of the SET1 histone methyltransferase (HMT) complex, but not if the neighboring 'Lys-9' residue is already methylated.


Pssm-ID: 380946  Cd Length: 148  Bit Score: 168.67  E-value: 1.19e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5380 KNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEqnRGI---YMFRINNEHVIDATLTGGPARY 5456
Cdd:cd19169     12 KKQLKFAKSRIHDWGLFALEPIAADEMVIEYVGQVIRQSVADEREKRYEA--IGIgssYLFRVDDDTIIDATKCGNLARF 89

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1537972313 5457 INHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDqhKIPCHCGAWNCR 5517
Cdd:cd19169     90 INHSCNPNCYAKIITVESQKKIVIYSKRPIAVNEEITYDYKFPIEDE--KIPCLCGAPQCR 148
ePHD1_KMT2C_like cd15665
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
 134-217 1.32e-45

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMTC2C and KMTC2D. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five plant PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions.


Pssm-ID: 277135  Cd Length: 90  Bit Score: 160.56  E-value: 1.32e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  134 GHCWAHHWCAVWSAGVWGQEGPELCGVDKAIFSGISQRCSHCTRFGASIPCRSPGCPRLYHFPCATASGSFLSMKTLQLL 213
Cdd:cd15665      7 GEVYAHHCCAAWSEGVCQTEDGALENVDKAVAKALSQKCSFCLRYGASISCRMPSCSKSFHFPCAAAAGCFQDIKTLTLF 86


                   ....
gi 1537972313  214 CPDH 217
Cdd:cd15665     87 CPEH 90
SET_KMT2A cd19206
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A) ...
 5371-5521 1.24e-42

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A) and similar proteins; KMT2A (EC2.1.1.43; also termed lysine N-methyltransferase 2A, ALL-1, CXXC-type zinc finger protein 7 (CXXC7), myeloid/lymphoid or mixed-lineage leukemia (MLL), myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), trithorax-like protein (TRX1), or zinc finger protein HRX) acts as a histone methyltransferase that plays an essential role in early development and hematopoiesis. It is a catalytic subunit of the MLL1/MLL complex, a multiprotein complex that mediates both methylation of 'Lys-4' of histone H3 (H3K4me) complex and acetylation of 'Lys-16' of histone H4 (H4K16ac).


Pssm-ID: 380983 [Multi-domain]  Cd Length: 154  Bit Score: 154.79  E-value: 1.24e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5371 QYRRLRTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVIDATLT 5450
Cdd:cd19206      4 RFRHLKKTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYSGNVIRSILTDKREKYYDSKGIGCYMFRIDDSEVVDATMH 83

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1537972313 5451 GGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWMN 5521
Cdd:cd19206     84 GNAARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDASNKLPCNCGAKKCRKFLN 154
SET_SET1 cd20072
SET domain (including post-SET domain) found in catalytic component of the Saccharomyces ...
 5380-5517 1.61e-42

SET domain (including post-SET domain) found in catalytic component of the Saccharomyces cerevisiae COMPASS complex and similar proteins; The family contains mostly fungal SET domains, including SET1 found in the catalytic component of the Saccharomyces cerevisiae COMPASS (complex of proteins associated with Set1). SET1 is a histone-lysine N-methyltransferase that specifically methylates 'Lys-4' of histone H3 (H3K4me), when part of the SET1 histone methyltransferase (HMT) complex. The activity of this catalytic domain is established through forming a complex with a set of core proteins; it is extensively contacted by Cps60 (Bre2), Cps50 (Swd1), and Cps30 (Swd3).


Pssm-ID: 380998  Cd Length: 148  Bit Score: 154.12  E-value: 1.61e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5380 KNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRG-IYMFRINNEHVIDATLTGGPARYIN 5458
Cdd:cd20072     12 KKQLKFARSAIHNWGLYAMENISAKDMVIEYVGEVIRQQVADEREKRYLRQGIGsSYLFRIDDDTVVDATKKGNIARFIN 91

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1537972313 5459 HSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDqhKIPCHCGAWNCR 5517
Cdd:cd20072     92 HCCDPNCTAKIIKVEGEKRIVIYAKRDIAAGEELTYDYKFPREED--KIPCLCGAPNCR 148
HMG_KMT2C-like cd21997
high mobility group (HMG)-box found in histone-lysine N-methyltransferases KMT2C, KMT2D and ...
 1997-2063 6.83e-42

high mobility group (HMG)-box found in histone-lysine N-methyltransferases KMT2C, KMT2D and similar proteins; This subfamily includes KMT2C and KMT2D. KMT2C, also called myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, and farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also called ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. All subfamily members contain one HMG-box domain.


Pssm-ID: 438813  Cd Length: 67  Bit Score: 149.04  E-value: 6.83e-42
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1537972313 1997 RWEKDEELGQLSTISPVLYANINFPNLKQDYPDWSSRCKQIMKLWRKVPAADKAPYLQKAKDNRAAH 2063
Cdd:cd21997      1 KWEKDEPLGDMATISPVLYANINHPNLKQEYPDWTDRAKQIAKLWRKLSAEERAPYLQKARENRAAL 67
HMG-box_KMT2C cd22026
high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2C (KMT2C) and ...
 1992-2069 6.92e-38

high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2C (KMT2C) and similar proteins; KMT2C, also called myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis.


Pssm-ID: 438835  Cd Length: 81  Bit Score: 138.38  E-value: 6.92e-38
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1537972313 1992 QRSLQRWEKDEELGQLSTISPVLYANINFPNLKQDYPDWSSRCKQIMKLWRKVPAADKAPYLQKAKDNRAAHRINKVQ 2069
Cdd:cd22026      1 QRSTLKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIAKLWRKASSQERAPYVQKARDNRAALRINKVQ 78
SET_KMT2B cd19207
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2B (KMT2B) ...
 5371-5521 1.83e-37

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2B (KMT2B) and similar proteins; KMT2B (EC2.1.1.43; also termed lysine N-methyltransferase 2B, myeloid/lymphoid or mixed-lineage leukemia protein 4 (MLL2/MLL4), trithorax homolog 2 (TRX2), or WW domain-binding protein 7 (WBP-7)), acts as a histone methyltransferase that methylates 'Lys-4' of histone H3 (H3K4me). It is required during the transcriptionally active period of oocyte growth for the establishment and/or maintenance of bulk H3K4 trimethylation (H3K4me3), global transcriptional silencing that precedes resumption of meiosis, oocyte survival and normal zygotic genome activation.


Pssm-ID: 380984 [Multi-domain]  Cd Length: 154  Bit Score: 140.16  E-value: 1.83e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5371 QYRRLRTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVIDATLT 5450
Cdd:cd19207      4 RFRHLKKTSKEAVGVYRSAIHGRGLFCKRNIDAGEMVIEYSGIVIRSVLTDKREKFYDSKGIGCYMFRIDDFDVVDATMH 83

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1537972313 5451 GGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWMN 5521
Cdd:cd19207     84 GNAARFINHSCEPNCYSRVIHVEGQKHIVIFALRKIYRGEELTYDYKFPIEDASNKLPCNCGAKRCRRFLN 154
ePHD_KMT2A_like cd15664
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); The ...
 5000-5104 4.02e-35

Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A/MLL1 and KMT2B/MLL2. KMT2A and KMT2B comprise the mammalian Trx branch of COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation by mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three PHD fingers, this extended PHD (ePHD) finger, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain.


Pssm-ID: 277134  Cd Length: 105  Bit Score: 131.37  E-value: 4.02e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5000 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQRTGATSSCNRMRCPN 5079
Cdd:cd15664      1 CALCGVYGDDEPNDAGRLLYCGQDEWVHINCALWSAEVFEEDDGSLQNVHSAVSRGRMMKCELCGKPGATVGCCLKSCPA 80

                           90       100
                   ....*....|....*....|....*
gi 1537972313 5080 VYHFACAIRAKCMFFKDKTMLCPMH 5104
Cdd:cd15664     81 NYHFMCARKAECVFQDDKKVFCPAH 105
SET_SETD1A cd19204
SET domain (including post-SET domain) found in SET domain-containing protein 1A (SETD1A) and ...
 5380-5521 1.25e-34

SET domain (including post-SET domain) found in SET domain-containing protein 1A (SETD1A) and similar proteins; SETD1A (EC2.1.1.43), also termed lysine N-methyltransferase 2F, or Set1/Ash2 histone methyltransferase complex subunit SET1, is a histone-lysine N-methyltransferase that specifically methylates 'Lys-4' of histone H3 (H3K4me), when part of the SET1 histone methyltransferase (HMT) complex, but not if the neighboring 'Lys-9' residue is already methylated. Human SET domain containing protein 1A (hSETD1A) expression occurs at a high rate in hepatocellular carcinoma patients and controls tumor metastasis in breast cancer by activating MMP expression.


Pssm-ID: 380981 [Multi-domain]  Cd Length: 153  Bit Score: 131.69  E-value: 1.25e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5380 KNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGI-YMFRINNEHVIDATLTGGPARYIN 5458
Cdd:cd19204     13 KKKLRFGRSRIHEWGLFAMEPIAADEMVIEYVGQNIRQVVADMREKRYVQEGIGSsYLFRVDHDTIIDATKCGNLARFIN 92

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1537972313 5459 HSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDqhKIPCHCGAWNCRKWMN 5521
Cdd:cd19204     93 HCCTPNCYAKVITIESQKKIVIYSKQPIGVNEEITYDYKFPIEDN--KIPCLCGTENCRGTLN 153
SET_SETD1B cd19205
SET domain (including post-SET domain) found in SET domain-containing protein 1B (SETD1B) and ...
 5380-5521 5.17e-34

SET domain (including post-SET domain) found in SET domain-containing protein 1B (SETD1B) and similar proteins; SETD1B (EC2.1.1.43), also termed lysine N-methyltransferase 2G, is a histone-lysine N-methyltransferase that specifically methylates 'Lys-4' of histone H3 (H3K4me) when part of the SET1 histone methyltransferase (HMT) complex, but not if the neighboring 'Lys-9' residue is already methylated. Loss of SETD1B occurs in up to half the gastric and colorectal cancers, most commonly via SETD1B mutations, while de novo variants in SETD1B are associated with intellectual disability, epilepsy and autism.


Pssm-ID: 380982 [Multi-domain]  Cd Length: 153  Bit Score: 130.18  E-value: 5.17e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5380 KNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGI-YMFRINNEHVIDATLTGGPARYIN 5458
Cdd:cd19205     13 KKKLKFCKSHIHDWGLFAMEPIAADEMVIEYVGQNIRQVIADMREKRYEDEGIGSsYMFRVDHDTIIDATKCGNFARFIN 92

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1537972313 5459 HSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDqhKIPCHCGAWNCRKWMN 5521
Cdd:cd19205     93 HSCNPNCYAKVITVESQKKIVIYSKQHINVNEEITYDYKFPIEDV--KIPCLCGSENCRGTLN 153
PHD5_KMT2D cd15601
PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 1501-1551 3.65e-33

PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such asHOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is downregulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger.


Pssm-ID: 277074  Cd Length: 51  Bit Score: 123.86  E-value: 3.65e-33
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1537972313 1501 TCPVCHAPYVEEDLLIQCRHCERWMHAGCESLFTEDEVEQAADEGFDCVSC 1551
Cdd:cd15601      1 TCPVCRAKYVEEDLLIQCRHCDRWVHAVCESLFTEDEVEQAADEGFDCSSC 51
PHD3_KMT2D cd15597
PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 1373-1423 8.23e-33

PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the third PHD finger.


Pssm-ID: 277072  Cd Length: 51  Bit Score: 122.84  E-value: 8.23e-33
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1537972313 1373 DMCVVCGSFGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVECI 1423
Cdd:cd15597      1 DMCVVCGSFGRGSEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVECI 51
FYRC smart00542
FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region ...
 5208-5295 2.17e-32

FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region (FYRN), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.


Pssm-ID: 197781  Cd Length: 86  Bit Score: 122.79  E-value: 2.17e-32
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  5208 EFVIKVIEQGleDLVFTDASPQAVWNRIIEPVAAMRKEADMLRLFPEYLKGEELFGLTVHAVLRIAESLPGVESCQNYLF 5287
Cdd:smart00542    1 LFRVEIESDP--GEVFKGESPEKCWEMVLERVQEARIAADLLQLLPEGVSGEEMFGLSSPAVVKLIEALPGVHQCTNYWF 78


                    ....*...
gi 1537972313  5288 RYGRHPLM 5295
Cdd:smart00542   79 RYHRSPLL 86
SET_SETD2 cd19172
SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2) and ...
 5376-5520 5.11e-32

SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2) and similar proteins; SETD2 (also termed HIF-1, huntingtin yeast partner B, huntingtin-interacting protein 1 (HIP-1), huntingtin-interacting protein B, lysine N-methyltransferase 3A or protein-lysine N-methyltransferase SETD2) acts as histone-lysine N-methyltransferase that specifically trimethylates 'Lys-36' of histone H3 (H3K36me3) using demethylated 'Lys-36' (H3K36me2) as substrate. It has been shown that methylation is a posttranslational modification of dynamic microtubules and that SETD2 methylates alpha-tubulin at lysine 40, the same lysine that is marked by acetylation on microtubules. Methylation of microtubules occurs during mitosis and cytokinesis and can be ablated by SETD2 deletion, which causes mitotic spindle and cytokinesis defects, micronuclei, and polyploidy.


Pssm-ID: 380949 [Multi-domain]  Cd Length: 142  Bit Score: 123.85  E-value: 5.11e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5376 RTEWKnnvylarsriqGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYE-EQNRGIYMFRINNEHVIDATLTGGPA 5454
Cdd:cd19172      8 RTEKK-----------GWGLRAAEDLPKGTFVIEYVGEVLDEKEFKRRMKEYArEGNRHYYFMALKSDEIIDATKKGNLS 76

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1537972313 5455 RYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFD--FEDDQhkiPCHCGAWNCRKWM 5520
Cdd:cd19172     77 RFINHSCEPNCETQKWTVNGELRVGFFAKRDIPAGEELTFDYQFEryGKEAQ---KCYCGSPNCRGYI 141
SET COG2940
SET domain-containing protein (function unknown) [General function prediction only];
5382-5519 9.42e-32

SET domain-containing protein (function unknown) [General function prediction only];


Pssm-ID: 442183 [Multi-domain]  Cd Length: 134  Bit Score: 122.76  E-value: 9.42e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5382 NVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRgiYMFRINNEHVIDATLTGGPARYINHSC 5461
Cdd:COG2940      7 RIEVRPSPIHGRGVFATRDIPKGTLIGEYPGEVITWAEAERREPHKEPLHT--YLFELDDDGVIDGALGGNPARFINHSC 84

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1537972313 5462 APNCVAEVVTFD-----KEDkiiiissrrIPKGEELTYDYQFDFEDDQHkiPCHCGawNCRKW 5519
Cdd:COG2940     85 DPNCEADEEDGRifivaLRD---------IAAGEELTYDYGLDYDEEEY--PCRCP--NCRGT 134
SET smart00317
SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Putative methyl transferase, based on ...
 5381-5503 4.16e-31

SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Putative methyl transferase, based on outlier plant homologues


Pssm-ID: 214614 [Multi-domain]  Cd Length: 124  Bit Score: 120.52  E-value: 4.16e-31
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  5381 NNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYE-EQNRGIYMFRINNEHVIDATLTGGPARYINH 5459
Cdd:smart00317    1 NKLEVFKSPGKGWGVRATEDIPKGEFIGEYVGEIITSEEAEERPKAYDtDGAKAFYLFDIDSDLCIDARRKGNLARFINH 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....
gi 1537972313  5460 SCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDD 5503
Cdd:smart00317   81 SCEPNCELLFVEVNGDDRIVIFALRDIKPGEELTIDYGSDYANE 124
ePHD_KMT2A cd15693
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A); The extended plant ...
 4998-5108 1.95e-30

Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of KMT2A. KMT2A also termed ALL-1, or CXXC-type zinc finger protein 7, or myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), or trithorax-like protein (Htrx), or zinc finger protein HRX, is a histone methyltransferase that belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2). It regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex, which also contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL1 complex is highly active and specific for H3K4methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three PHD fingers, a Bromodomain domain, this extended PHD finger, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain.


Pssm-ID: 277163  Cd Length: 113  Bit Score: 118.18  E-value: 1.95e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4998 RRCCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQRTGATSSCNRMRC 5077
Cdd:cd15693      1 RQCALCLKYGDDSANDAGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSC 80

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1537972313 5078 PNVYHFACAIRAKCMFFKDKTMLCPMHK--IKG 5108
Cdd:cd15693     81 TSNYHFMCSRAKNCVFLEDKKVYCQRHKdlIKG 113
PHD4_KMT2C cd15596
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 1367-1422 2.21e-30

PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the fourth PHD finger.


Pssm-ID: 277071  Cd Length: 57  Bit Score: 115.88  E-value: 2.21e-30
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1537972313 1367 KFVLMQDMCVVCGSFGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVEC 1422
Cdd:cd15596      1 KFTLNQDMCVVCGSFGQGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLEC 56
SET_SETD2-like cd10531
SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2), ...
 5382-5517 2.27e-30

SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2), nuclear SETD2 (NSD2), ASH1-like protein (ASH1L) and similar proteins; This family includes SET domain-containing protein 2 (SETD2), nuclear SETD2 (NSD2) and ASH1-like protein (ASH1L), which function as histone-lysine N-methyltransferases. SETD2 specifically trimethylates 'Lys-36' of histone H3 (H3K36me3) using demethylated 'Lys-36' (H3K36me2) as substrate. NSD2 shows histone H3 'Lys-27' (H3K27me) methyltransferase activity. ASH1L specifically methylates 'Lys-36' of histone H3 (H3K36me). The family also includes Arabidopsis thaliana ASH1-related protein 3 (ASHR3) and similar proteins.


Pssm-ID: 380929  Cd Length: 136  Bit Score: 118.90  E-value: 2.27e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5382 NVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRR-EKIYEEQNRGIYMFRINNEHVIDATLTGGPARYINHS 5460
Cdd:cd10531      1 KLELFRTEKKGWGVKAKEDIQKGEFIIEYVGEVIDKKEFKERlDEYEELGKSNFYILSLSDDVVIDATRKGNLSRFINHS 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1537972313 5461 CAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQhKIPCHCGAWNCR 5517
Cdd:cd10531     81 CEPNCETQKWIVNGEYRIGIFALRDIPAGEELTFDYNFVNYNEA-KQVCLCGAQNCR 136
SET_ASHR3-like cd19175
SET domain (including post-SET domain) found in Arabidopsis thaliana ASH1-related protein 3 ...
 5392-5520 4.72e-29

SET domain (including post-SET domain) found in Arabidopsis thaliana ASH1-related protein 3 (ASHR3) and similar proteins; This family includes Arabidopsis thaliana ASH1-related protein 3 (ASHR3, also termed protein SET DOMAIN GROUP 4 or protein stamen loss), ASH1 homolog 3 (ASHH3, also termed protein SET DOMAIN GROUP 7) and homolog 4 (ASHH4, also termed protein SET DOMAIN GROUP 24). They all function as histone-lysine N-methyltransferases (EC 2.1.1.43).


Pssm-ID: 380952 [Multi-domain]  Cd Length: 139  Bit Score: 115.21  E-value: 4.72e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5392 GLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQ-NRGIYMFRINNEHVIDATLTGGPARYINHSCAPNCVAEVV 5470
Cdd:cd19175     11 GWGLVADEDINAGEFIIEYVGEVIDDKTCEERLWDMKHKgEKNFYMCEIDKDMVIDATFKGNLSRFINHSCDPNCELQKW 90

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1537972313 5471 TFDKEDKIIIISSRRIPKGEELTYDYQF-DFEDDQHkipCHCGAWNCRKWM 5520
Cdd:cd19175     91 QVDGETRIGVFAIRDIKKGEELTYDYQFvQFGADQD---CHCGSKNCRGKL 138
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
 1424-1470 5.81e-29

PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger of KMT2C and the fourth PHD finger of KMT2D.


Pssm-ID: 276988  Cd Length: 47  Bit Score: 111.80  E-value: 5.81e-29
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1537972313 1424 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWCV 1470
Cdd:cd15513      1 VCEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 47
ePHD cd15571
Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is ...
 5000-5104 8.79e-29

Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. The extended PHD finger is characterized as Cys2HisCys5HisCys2His, which has been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors.


Pssm-ID: 277046 [Multi-domain]  Cd Length: 112  Bit Score: 113.45  E-value: 8.79e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5000 CCFCHEEGdGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALM--NVEVALHRGLLTKCSLCQRT-GATSSCNRMR 5076
Cdd:cd15571      1 CALCPRSG-GALKGGGALKTTSDGLWVHVVCALWSPEVYFDDGTLLEveGVSKIPKRRKKLKCSICGKRgGACIQCSYPG 79

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1537972313 5077 CPNVYHFACAIRAKCMF-----FKDKTMLCPMH 5104
Cdd:cd15571     80 CPRSFHVSCAIRAGCLFefedgPGNFVVYCPKH 112
ePHD1_KMT2C cd15696
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 134-217 9.00e-29

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMT2C. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several PHD fingers, two ePHD fingers, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains.


Pssm-ID: 277166  Cd Length: 90  Bit Score: 112.73  E-value: 9.00e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  134 GHCWAHHWCAVWSAGVWGQEGPELCGVDKAIFSGISQRCSHCTRFGASIPCRSPGCPRLYHFPCATASGSFLSMKTLQLL 213
Cdd:cd15696      7 GECWAHLRCAEWSLGVCQGEEQLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQDFSRRLLL 86


                   ....
gi 1537972313  214 CPDH 217
Cdd:cd15696     87 CPTH 90
PHD4_KMT2C_like cd15512
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD domain 3 found in ...
 1374-1422 3.34e-28

PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD domain 3 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, two extended PHD (ePHD) fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fourth PHD finger of KMT2C and the third domain of KMT2D.


Pssm-ID: 276987  Cd Length: 49  Bit Score: 109.47  E-value: 3.34e-28
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1537972313 1374 MCVVCGSFGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVEC 1422
Cdd:cd15512      1 MCVSCGSFGRGAEGRLIACSQCGQCYHPYCVNVKVTKVILSKGWRCLDC 49
SET_EZH cd10519
SET domain found in enhancer of zeste homolog 1 (EZH1), zeste homolog 2 (EZH2) and similar ...
 5383-5498 8.38e-28

SET domain found in enhancer of zeste homolog 1 (EZH1), zeste homolog 2 (EZH2) and similar proteins; The family includes EZH1 and EZH2. EZH1 (EC 2.1.1.43; also termed ENX-2, or histone-lysine N-methyltransferase EZH1) is a catalytic subunit of the PRC2/EED-EZH1 complex, which methylates 'Lys-27' of histone H3, leading to transcriptional repression of the affected target gene. EZH2 (EC 2.1.1.43; also termed lysine N-methyltransferase 6, ENX-1, or histone-lysine N-methyltransferase EZH2) is a catalytic subunit of the PRC2/EED-EZH2 complex, which methylates 'Lys-9' (H3K9me) and 'Lys-27' (H3K27me) of histone H3, leading to transcriptional repression of the affected target gene. Both, EZH1 and EZH2, can mono-, di- and trimethylate 'Lys-27' of histone H3 to form H3K27me1, H3K27me2 and H3K27me3, respectively.


Pssm-ID: 380917  Cd Length: 117  Bit Score: 110.80  E-value: 8.38e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5383 VYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGiYMFRINNEHVIDATLTGGPARYINHSCA 5462
Cdd:cd10519      3 LLLGKSDVAGWGLFLKEPIKKDEFIGEYTGELISQDEADRRGKIYDKYNSS-YLFNLNDQFVVDATRKGNKIRFANHSSN 81

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1537972313 5463 PNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQF 5498
Cdd:cd10519     82 PNCYAKVMMVNGDHRIGIFAKRDIEAGEELFFDYGY 117
PHD6_KMT2C_like cd15514
PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 5 found in ...
 1501-1551 7.58e-27

PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 5 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the sixth PHD finger of KMT2C and the fifth PHD finger of KMT2D.


Pssm-ID: 276989  Cd Length: 51  Bit Score: 105.83  E-value: 7.58e-27
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1537972313 1501 TCPVCHAPYVEEDLLIQCRHCERWMHAGCESLFTEDEVEQAADEGFDCVSC 1551
Cdd:cd15514      1 KCPVCSRSYNEGELIIQCSQCERWLHGACDSLRTEEEAERAADNGYRCLLC 51
SET_NSD cd19173
SET domain (including post-SET domain) found in nuclear SET domain-containing proteins, NSD1, ...
 5392-5516 8.32e-27

SET domain (including post-SET domain) found in nuclear SET domain-containing proteins, NSD1, NSD2, NSD3 and similar proteins; The nuclear receptor-binding SET Domain (NSD) family of histone H3 lysine 36 methyltransferases is comprised of NSD1, NSD2, and NSD3, which are primarily known to be involved in chromatin integrity and gene expression through mono-, di-, or tri-methylating lysine 36 of histone H3 (H3K36), respectively. NSD1 (EC 2.1.1.43; also termed histone-lysine N-methyltransferase H3 lysine-36 and H4 lysine-20 specific, androgen receptor coactivator 267 kDa protein (ARA267), androgen receptor-associated protein of 267 kDa, H3-K36-HMTase, H4-K20-HMTase, lysine N-methyltransferase 3B (KMT3B) or NR-binding SET domain-containing protein 1) functions as a histone-lysine N-methyltransferase that preferentially methylates 'Lys-36' of histone H3 and 'Lys-20' of histone H4. NSD2 (EC 2.1.1.43; also termed multiple myeloma SET domain-containing protein (MMSET), protein trithorax-5 (TRX5), or wolf-Hirschhorn syndrome candidate 1 protein (WHSC1)) acts as histone-lysine N-methyltransferase with histone H3 'Lys-27' (H3K27me) methyltransferase activity. NSD3 (EC 2.1.1.43; also termed protein whistle, WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1L1), or WHSC1-like protein 1) functions as a histone-lysine N-methyltransferase that preferentially methylates 'Lys-4' and 'Lys-27' of histone H3.


Pssm-ID: 380950 [Multi-domain]  Cd Length: 142  Bit Score: 108.94  E-value: 8.32e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5392 GLGLYAAKDLEKHTMVIEYIGTIIRNEVANRR-EKIYEEQNRGIYMFRINNEHVIDATLTGGPARYINHSCAPNCVAEVV 5470
Cdd:cd19173     13 GWGLRTKRDIKKGDFVIEYVGELIDEEECRRRlKKAHENNITNFYMLTLDKDRIIDAGPKGNLSRFMNHSCQPNCETQKW 92

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1537972313 5471 TFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQhKIPCHCGAWNC 5516
Cdd:cd19173     93 TVNGDTRVGLFAVRDIPAGEELTFNYNLDCLGNE-KKVCRCGAPNC 137
FYRC pfam05965
F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 5206-5290 2.67e-26

F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00542.


Pssm-ID: 461788  Cd Length: 83  Bit Score: 105.38  E-value: 2.67e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5206 RPEFVIKVIEQglEDLVFTDASPQAVWNRIIEPVAAMRKEADMLRLFPEYLKGEELFGLTVHAVLRIAESLPGVESCQNY 5285
Cdd:pfam05965    1 GPLFRVTVEED--PDESFEGSSPTKCWSMVLERVQELRREAGLKLKLPESISGEDMFGLTHPAVVRLIESLPGAEKCTNY 78


                   ....*
gi 1537972313 5286 LFRYG 5290
Cdd:pfam05965   79 KFRYG 83
ePHD_KMT2B cd15694
Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B); The extended plant ...
 5000-5104 4.28e-26

Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of KMT2B. KMT2B is also called trithorax homolog 2 or WW domain-binding protein 7 (WBP-7). KMT2B is encoded by the gene that was first named myeloid/lymphoid or mixed-lineage leukemia 2 (MLL2), a second human homolog of Drosophila trithorax, located on chromosome 19. It belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2) and is vital for normal mammalian embryonic development. KMT2B functions as the catalytic subunit in the MLL2 complex, which contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL2 complex is highly active and specific for histone 3 lysine 4 (H3K4) methylation, which stimulates chromatin transcription in a SAM- and H3K4-dependent manner. Moreover, KMT2B plays a critical role in memory formation by mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. KMT2B contains a CxxC (x for any residue) zinc finger domain, three PHD fingers, this ePHD finger, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain.


Pssm-ID: 277164  Cd Length: 105  Bit Score: 105.51  E-value: 4.28e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5000 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQRTGATSSCNRMRCPN 5079
Cdd:cd15694      1 CALCLKYGDADSKDAGRLLYIGQNEWTHVNCAIWSAEVFEENDGSLKNVHAAVARGRQMRCEHCQKIGATVGCCLSACLS 80

                           90       100
                   ....*....|....*....|....*
gi 1537972313 5080 VYHFACAIRAKCMFFKDKTMLCPMH 5104
Cdd:cd15694     81 NFHFMCARASRCCFQDDKKVFCQKH 105
PHD2_KMT2D cd15595
PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 276-320 7.43e-26

PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such asHOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 277070  Cd Length: 46  Bit Score: 102.77  E-value: 7.43e-26
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15595      2 CQTCRKPGEDSKMLVCEACDKGYHTFCLKPAMESLPTDSWKCKAC 46
PHD2_KMT2C_like cd15510
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 276-320 5.76e-24

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 276985  Cd Length: 46  Bit Score: 97.50  E-value: 5.76e-24
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15510      2 CQACRQPGDDTKMLVCETCDKGYHTSCLRPVMSSIPKYGWKCKNC 46
SET_SUV39H cd10542
SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 ...
 5392-5520 8.71e-24

SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homologs, SUV39H1, SUV39H2 and similar proteins; This family includes SUV39H1 (also termed histone H3-K9 methyltransferase 1, H3-K9-HMTase 1, lysine N-methyltransferase 1A, KMT1A, position-effect variegation 3-9 homolog, SUV39H, or Su(var)3-9 homolog 1) and SUV39H2 (also termed histone H3-K9 methyltransferase 2, H3-K9-HMTase 2, lysine N-methyltransferase 1B, KMT1B, or Su(var)3-9 homolog 2), both act as histone-lysine N-methyltransferases that specifically trimethylate 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. They mainly function in heterochromatin regions, thereby playing central roles in the establishment of constitutive heterochromatin at pericentric and telomere regions. Also included are Schizosaccharomyces pombe H3K9 methyltransferase Clr4 (SUV39H homolog) and Neurospora crassa DIM-5, both of which also methylate 'Lys-9' of histone H3.


Pssm-ID: 380940 [Multi-domain]  Cd Length: 245  Bit Score: 103.91  E-value: 8.71e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5392 GLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRgIYMFRIN-----NEHVIDATLTGGPARYINHSCAPN-- 5464
Cdd:cd10542     99 GWGVKTLEDIKKGTFVMEYVGEIITSEEAERRGKIYDANGR-TYLFDLDyndddCEYTVDAAYYGNISHFINHSCDPNla 177

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1537972313 5465 ---CVAE--------VVTFDKEDkiiiissrrIPKGEELTYDYQFDFEDDQH----------KIPCHCGAWNCRKWM 5520
Cdd:cd10542    178 vyaVWINhldprlprIAFFAKRD---------IKAGEELTFDYLMTGTGGSSestipkpkdvRVPCLCGSKNCRKYL 245
SET_ASH1L cd19174
SET domain (including post-SET domain) found in ASH1-like protein (ASH1L) and similar proteins; ...
 5392-5521 4.48e-22

SET domain (including post-SET domain) found in ASH1-like protein (ASH1L) and similar proteins; ASH1L (EC 2.1.1.43; also termed absent small and homeotic disks protein 1 homolog, KMT2H, or lysine N-methyltransferase 2H) acts as histone-lysine N-methyltransferase that specifically methylates 'Lys-36' of histone H3 (H3K36me). It plays important roles in development; heterozygous mutation of ASH1L is associated with severe intellectual disability (ID) and multiple congenital anomaly (MCA).


Pssm-ID: 380951 [Multi-domain]  Cd Length: 141  Bit Score: 95.44  E-value: 4.48e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5392 GLGLYAAKDLEKHTMVIEYIGTII-RNEVANRREKIYEeQNRGIYMFRINNEHVIDATLTGGPARYINHSCAPNC----- 5465
Cdd:cd19174     11 GWGVRTKEPIKAGQFIIEYVGEVVsEQEFRRRMIEQYH-NHSHHYCLNLDSGMVIDGYRMGNEARFVNHSCDPNCemqkw 89

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5466 ----VAEVVTFDKEDkiiiissrrIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWMN 5521
Cdd:cd19174     90 svngVYRIGLFALKD---------IPAGEELTYDYNFHSFNVEKQQPCKCGSPNCRGVIG 140
PHD6_KMT2C cd15600
PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 1501-1551 4.74e-22

PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the sixth PHD finger.


Pssm-ID: 277073  Cd Length: 51  Bit Score: 91.91  E-value: 4.74e-22
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1537972313 1501 TCPVCHAPYVEEDLLIQCRHCERWMHAGCESLFTEDEVEQAADEGFDCVSC 1551
Cdd:cd15600      1 TCPICYRNYREEELILQCRQCDRWMHASCQNLNTEEEVENAADNGFDCTMC 51
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 228-273 1.23e-21

PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the first PHD finger.


Pssm-ID: 276984  Cd Length: 48  Bit Score: 90.83  E-value: 1.23e-21
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1537972313  228 HCAVCEGPGELCDLFFCTSCGHHYHGACLDTAL--TARKRAGWQCPEC 273
Cdd:cd15509      1 NCAVCDSPGDLSDLLFCTSCGQHYHGSCLDPAVrpTPLVRAGWQCPEC 48
PHD2_KMT2C cd15594
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 276-320 4.75e-21

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the second PHD finger.


Pssm-ID: 277069  Cd Length: 46  Bit Score: 89.23  E-value: 4.75e-21
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15594      2 CQTCRQPGDDNKMLVCDTCDKGYHTFCLQPVMTTIPKNGWKCKNC 46
SET pfam00856
SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be ...
 5392-5496 5.83e-21

SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure.


Pssm-ID: 459965 [Multi-domain]  Cd Length: 115  Bit Score: 91.43  E-value: 5.83e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5392 GLGLYAAKDLEKHTMVIEYIGT-IIRNEVANRREKIYEEQNR----GIYMFRIN--NEHVIDATLT--GGPARYINHSCA 5462
Cdd:pfam00856    1 GRGLFATEDIPKGEFIGEYVEVlLITKEEADKRELLYYDKLElrlwGPYLFTLDedSEYCIDARALyyGNWARFINHSCD 80

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1537972313 5463 PNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDY 5496
Cdd:pfam00856   81 PNCEVRVVYVNGGPRIVIFALRDIKPGEELTIDY 114
ePHD cd15571
Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is ...
 136-217 9.32e-21

Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. The extended PHD finger is characterized as Cys2HisCys5HisCys2His, which has been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors.


Pssm-ID: 277046 [Multi-domain]  Cd Length: 112  Bit Score: 90.72  E-value: 9.32e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  136 CWAHHWCAVWSAGVWGQEG--PELCGVDKAIFSGISQRCSHC-TRFGASIPCRSPGCPRLYHFPCATASGSFLSMKT--- 209
Cdd:cd15571     24 LWVHVVCALWSPEVYFDDGtlLEVEGVSKIPKRRKKLKCSICgKRGGACIQCSYPGCPRSFHVSCAIRAGCLFEFEDgpg 103


                   ....*....
gi 1537972313  210 -LQLLCPDH 217
Cdd:cd15571    104 nFVVYCPKH 112
ePHD1_KMT2C_like cd15665
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
 5000-5104 7.08e-20

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMTC2C and KMTC2D. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five plant PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions.


Pssm-ID: 277135  Cd Length: 90  Bit Score: 87.38  E-value: 7.08e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5000 CCFCheegdgatdgparllNLDlDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQRTGATSSCNRMRCPN 5079
Cdd:cd15665      1 CALC---------------NLG-EVYAHHCCAAWSEGVCQTEDGALENVDKAVAKALSQKCSFCLRYGASISCRMPSCSK 64

                           90       100
                   ....*....|....*....|....*..
gi 1537972313 5080 VYHFACAIRAKCmF--FKDKTMLCPMH 5104
Cdd:cd15665     65 SFHFPCAAAAGC-FqdIKTLTLFCPEH 90
ePHD2_KMT2C_like cd15666
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
 137-217 3.74e-19

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2C, and KMT2D. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions.


Pssm-ID: 277136  Cd Length: 105  Bit Score: 85.82  E-value: 3.74e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  137 WAHHWCAVWSAGVWGQEGPELCGVDKAIFSGISQRCSHCTRFGASIPCRSPGCPRLYHFPCATASG-SFLSMKTlqLLCP 215
Cdd:cd15666     26 WVHLNCALWSYEVYETQNGALMNVEEALRRALTTTCSHCGRTGATVPCFKPRCANVYHLPCAIKDGcMFFKDKT--MLCP 103


                   ..
gi 1537972313  216 DH 217
Cdd:cd15666    104 SH 105
SET_NSD2 cd19211
SET domain (including post-SET domain) found in nuclear SET domain-containing protein 2 (NSD2) ...
 5385-5516 4.05e-19

SET domain (including post-SET domain) found in nuclear SET domain-containing protein 2 (NSD2) and similar proteins; NSD2 (EC 2.1.1.43; also termed multiple myeloma SET domain-containing protein (MMSET), protein trithorax-5 (TRX5), or wolf-Hirschhorn syndrome candidate 1 protein (WHSC1)) acts as histone-lysine N-methyltransferase with histone H3 'Lys-36' (H3K36me) methyltransferase activity. NSD2 has been shown to mediate di- and trimethylation of H3K36 and dimethylation of H4K20 in different systems, and has been characterized as a transcriptional repressor interacting with histone deacetylase HDAC1 and histone demethylase LSD1. NSD2 mediates constitutive NF-kappaB signaling for cancer cell proliferation, survival and tumor growth. It is highly overexpressed in several types of human cancers, including small-cell lung cancers, neuroblastoma, carcinomas of stomach and colon, and bladder cancers, and its overexpression tends to be associated with tumor aggressiveness. WHSC1 is frequently deleted in Wolf-Hirschhorn syndrome (WHS).


Pssm-ID: 380988 [Multi-domain]  Cd Length: 142  Bit Score: 86.97  E-value: 4.05e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5385 LARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQN-RGIYMFRINNEHVIDATLTGGPARYINHSCAP 5463
Cdd:cd19211      6 IIKTEGKGWGLIAKRDIKKGEFVNEYVGELIDEEECMARIKHAHENDiTHFYMLTIDKDRIIDAGPKGNYSRFMNHSCQP 85

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1537972313 5464 NCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIpCHCGAWNC 5516
Cdd:cd19211     86 NCETQKWTVNGDTRVGLFAVCDIPAGTELTFNYNLDCLGNEKTV-CRCGAPNC 137
SET_EZH2 cd19218
SET domain found in enhancer of zeste homolog 2 (EZH2) and similar proteins; EZH2 (EC 2.1.1.43) ...
 5379-5498 8.10e-19

SET domain found in enhancer of zeste homolog 2 (EZH2) and similar proteins; EZH2 (EC 2.1.1.43), also termed lysine N-methyltransferase 6, or ENX-1, or histone-lysine N-methyltransferase EZH2, is a catalytic subunit of the polycomb repressive complex 2 (PRC2)/EED-EZH2 complex, which methylates 'Lys-9' (H3K9me) and 'Lys-27' (H3K27me) of histone H3, leading to transcriptional repression of the affected target gene. It can mono-, di- and trimethylate 'Lys-27' of histone H3 to form H3K27me1, H3K27me2 and H3K27me3, respectively. PRC2 is involved in several cancers; EZH2 is overexpressed in breast, liver and prostate cancer, while point mutations in EZH2 alter the substrate preference and product specificity of PRC2 in Non-Hodgkin lymphomas (NHLs). Thus, PRC2 is a popular target for cancer therapeutics.


Pssm-ID: 380995  Cd Length: 120  Bit Score: 85.35  E-value: 8.10e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5379 WKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEqnrgiYM----FRINNEHVIDATLTGGPA 5454
Cdd:cd19218      2 SKKHLLLAPSDVAGWGIFIKDPVQKNEFISEYCGEIISQDEADRRGKVYDK-----YMcsflFNLNNDFVVDATRKGNKI 76

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 1537972313 5455 RYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQF 5498
Cdd:cd19218     77 RFANHSVNPNCYAKVMMVNGDHRIGIFAKRAIQTGEELFFDYRY 120
FYRN pfam05964
F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 5149-5200 3.62e-18

F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00541.


Pssm-ID: 461787  Cd Length: 51  Bit Score: 81.01  E-value: 3.62e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1537972313 5149 GGLVFHAIGQLLPHQMAdFHSATALYPVGYEATRIYWSLRTNNRRCCYRCSI 5200
Cdd:pfam05964    1 GSLTVLSLGEIVPDRPA-FHTERYIYPVGYKSTRLYWSTKDPRKRCRYTCEI 51
SET_EZH1 cd19217
SET domain found in enhancer of zeste homolog 1 (EZH1) and similar proteins; EZH1 (EC 2.1.1.43) ...
 5380-5502 7.34e-18

SET domain found in enhancer of zeste homolog 1 (EZH1) and similar proteins; EZH1 (EC 2.1.1.43), also termed ENX-2, or histone-lysine N-methyltransferase EZH1, is a catalytic subunit of the PRC2/EED-EZH1 complex, which methylates 'Lys-27' of histone H3, leading to transcriptional repression of the affected target gene. It can mono-, di- and trimethylate 'Lys-27' of histone H3 to form H3K27me1, H3K27me2 and H3K27me3, respectively.


Pssm-ID: 380994  Cd Length: 136  Bit Score: 83.19  E-value: 7.34e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5380 KNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGiYMFRINNEHVIDATLTGGPARYINH 5459
Cdd:cd19217      5 KKHLLLAPSDVAGWGTFIKESVQKNEFISEYCGELISQDEADRRGKVYDKYMSS-FLFNLNNDFVVDATRKGNKIRFANH 83

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1537972313 5460 SCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFED 5502
Cdd:cd19217     84 SVNPNCYAKVVMVNGDHRIGIFAKRAIQQGEELFFDYRYSQAD 126
ePHD_RAI1_like cd15668
Extended PHD finger found in retinoic acid-induced protein 1 (RAI1), transcription factor 20 ...
 5000-5104 1.00e-17

Extended PHD finger found in retinoic acid-induced protein 1 (RAI1), transcription factor 20 (TCF-20) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of RAI1 and TCF-20. RAI1, a homolog of stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPBP, also termed TCF-20), is a chromatin-binding protein implicated in the regulation of gene expression. TCF-20 is involved in transcriptional activation of the MMP3 (matrix metalloprotease 3) promoter. It also functions as a transcriptional co-regulator that enhances or represses the transcriptional activity of certain transcription factors/cofactors, such as specificity protein 1 (Sp1), E twenty-six 1 (Ets1), paired box protein 6 (Pax6), small nuclear RING-finger (SNURF)/RNF4, c-Jun, androgen receptor (AR) and estrogen receptor alpha (ERalpha). Both RAI1 and TCF-20 are strongly enriched in chromatin in interphase HeLa cells, and display low nuclear mobility, and have been implicated in Smith-Magenis syndrome and Potocki-Lupski syndrome.


Pssm-ID: 277138  Cd Length: 103  Bit Score: 81.58  E-value: 1.00e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5000 CCFC----HEEGDGATDGPArllnldLDLWVHLNCALWSTEVYETqGGALMNVEVALHRGLLTKCSLCQRTGATSSCNRM 5075
Cdd:cd15668      1 CVFCkrgpHYKGLGDLFGPY------YEVWVHEDCAVWAPGVYLV-GGKLYGLEEAVWVAKQSVCSSCQQTGATIGCLHK 73

                           90       100       110
                   ....*....|....*....|....*....|
gi 1537972313 5076 RCPNVYHFACAIRAKCMFFKDK-TMLCPMH 5104
Cdd:cd15668     74 GCKAKYHYPCAVESGCQLDEENfSLLCPKH 103
SET_NSD3 cd19212
SET domain (including post-SET domain) found in nuclear receptor-binding SET domain-containing ...
 5391-5516 2.75e-17

SET domain (including post-SET domain) found in nuclear receptor-binding SET domain-containing protein 3 (NSD3) and similar proteins; NSD3 (EC 2.1.1.43; also termed protein whistle, WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1L1), or WHSC1-like protein 1) functions as a histone-lysine N-methyltransferase that preferentially methylates 'Lys-4' and 'Lys-27' of histone H3. NSD3 is amplified and overexpressed in multiple cancer types, including acute myeloid leukemia (AML), breast, lung, pancreatic and bladder cancers, as well as squamous cell carcinoma of the head and neck (SCCHN). NSD3 contributes to tumorigenesis by interacting with bromodomain-containing protein 4 (BRD4), the bromodomain and extraterminal (BET) protein, which is a potential therapeutic target in acute myeloid leukemia (AML). NSD3 is amplified in primary tumors and cell lines from breast carcinoma, and can promote the cell viability of small-cell lung cancer and pancreatic ductal adenocarcinoma. High NSD3 expression is implicated in poor grade and heavy smoking history in SCCHN. Thus, NSD3 may serve as a potential druggable target for selective cancer therapy.


Pssm-ID: 380989 [Multi-domain]  Cd Length: 142  Bit Score: 81.90  E-value: 2.75e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5391 QGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQN-RGIYMFRINNEHVIDATLTGGPARYINHSCAPNCVAEV 5469
Cdd:cd19212     12 RGWGLRTKRSIKKGEFVNEYVGELIDEEECRLRIKRAHENSvTNFYMLTVTKDRIIDAGPKGNYSRFMNHSCNPNCETQK 91

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1537972313 5470 VTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIpCHCGAWNC 5516
Cdd:cd19212     92 WTVNGDVRVGLFALCDIPAGMELTFNYNLDCLGNGRTE-CHCGADNC 137
SET_SETDB-like cd10538
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) ...
 5387-5497 4.75e-17

SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and 2 (SETDB2), suppressor of variegation 3-9 homologs, SUV39H1 and SUV39H2, euchromatic histone-lysine N-methyltransferase EHMT1 and EHMT2, and similar proteins; The family includes SET domain bifurcated 1 (SETDB1) and 2 (SETDB2), suppressor of variegation 3-9 homologs, SUV39H1 and SUV39H2, euchromatic histone-lysine N-methyltransferase EHMT1 and EHMT2. SETDB1 (EC 2.1.1.43; also termed ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. SETDB2 (EC 2.1.1.43; also termed chronic lymphocytic leukemia deletion region gene 8 protein (CLLD8), or lysine N-methyltransferase 1F (KMT1F)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It is involved in left-right axis specification in early development and mitosis. SUV39H1 (also termed histone H3-K9 methyltransferase 1, H3-K9-HMTase 1, lysine N-methyltransferase 1A, KMT1A, position-effect variegation 3-9 homolog, SUV39H, or Su(var)3-9 homolog 1) and SUV39H2 (also termed histone H3-K9 methyltransferase 2, H3-K9-HMTase 2, lysine N-methyltransferase 1B, KMT1B, or Su(var)3-9 homolog 2), both act as histone-lysine N-methyltransferases that specifically trimethylate 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. They mainly function in heterochromatin regions, thereby playing central roles in the establishment of constitutive heterochromatin at pericentric and telomere regions. EHMT1 (also termed Eu-HMTase1, G9a-like protein 1, GLP, GLP1, histone H3-K9 methyltransferase 5, H3-K9-HMTase 5, lysine N-methyltransferase 1D, or KMT1D) and EHMT2 (also termed Eu-HMTase2, HLA-B-associated transcript 8, histone H3-K9 methyltransferase 3, H3-K9-HMTase 3, lysine N-methyltransferase 1C, KMT1C, or protein G9a), both act as histone-lysine N-methyltransferases that specifically mono- and dimethylate 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin. This family also includes the pre-SET domain, which is found in a number of histone methyltransferases (HMTase), N-terminal to the SET domain. Pre-SET domain is a zinc binding motif which contains 9 conserved cysteines that coordinate three zinc ions. It is thought that this region plays a structural role in stabilizing SET domains. Most family members, except for Arabidopsis thaliana SUVH9, contain a post-SET domain which harbors a zinc-binding site.


Pssm-ID: 380936 [Multi-domain]  Cd Length: 217  Bit Score: 83.57  E-value: 4.75e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5387 RSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEeQNRGIYMFRINN---------EHVIDATLTGGPARYI 5457
Cdd:cd10538     95 RTSKKGWGVRSLEFIPKGSFVCEYVGEVITTSEADRRGKIYD-KSGGSYLFDLDEfsdsdgdgeELCVDATFCGNVSRFI 173

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 1537972313 5458 NHSCAPNCVAEVVTFDKEDKIIII----SSRRIPKGEELTYDYQ 5497
Cdd:cd10538    174 NHSCDPNLFPFNVVIDHDDLRYPRialfATRDILPGEELTFDYG 217
FYRN smart00541
FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region ...
 5159-5202 2.34e-16

FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region (FYRC), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.


Pssm-ID: 128814  Cd Length: 44  Bit Score: 75.78  E-value: 2.34e-16
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....
gi 1537972313  5159 LLPHQMADFHSATALYPVGYEATRIYWSLRTNNRRCCYRCSISE 5202
Cdd:smart00541    1 LLPIQGKLFHSESAIFPVGYKSTRKYWSVKDPNRRCLYSCVIDE 44
SET_NSD1 cd19210
SET domain (including post-SET domain) found in nuclear receptor-binding SET domain-containing ...
 5383-5516 2.83e-16

SET domain (including post-SET domain) found in nuclear receptor-binding SET domain-containing protein 1 (NSD1) and similar proteins; NSD1 (EC 2.1.1.43; also termed Histone-lysine N-methyltransferase H3 lysine-36 and H4 lysine-20 specific, androgen receptor coactivator 267 kDa protein (ARA267), androgen receptor-associated protein of 267 kDa, H3-K36-HMTase, H4-K20-HMTase, lysine N-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein 1) functions as a histone-lysine N-methyltransferase that preferentially methylates 'Lys-36' of histone H3 and 'Lys-20' of histone H4. NSD1 is altered in approximately 10% of head and neck cancer patients with 55% decrease in risk of death in NSD1-mutated versus non-mutated patients; its disruption promotes favorable chemotherapeutic responses linked to hypomethylation.


Pssm-ID: 380987 [Multi-domain]  Cd Length: 142  Bit Score: 78.82  E-value: 2.83e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5383 VYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQN-RGIYMFRINNEHVIDATLTGGPARYINHSC 5461
Cdd:cd19210      4 VEIFRTLGRGWGLRCKTDIKKGEFVNEYVGELIDEEECRARIRYAQEHDiTNFYMLTLDKDRIIDAGPKGNYARFMNHCC 83

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1537972313 5462 APNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQhKIPCHCGAWNC 5516
Cdd:cd19210     84 QPNCETQKWTVNGDTRVGLFALCDIKAGTELTFNYNLECLGNG-KTVCKCGAPNC 137
ePHD_RAI1_like cd15668
Extended PHD finger found in retinoic acid-induced protein 1 (RAI1), transcription factor 20 ...
 137-217 3.78e-16

Extended PHD finger found in retinoic acid-induced protein 1 (RAI1), transcription factor 20 (TCF-20) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of RAI1 and TCF-20. RAI1, a homolog of stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPBP, also termed TCF-20), is a chromatin-binding protein implicated in the regulation of gene expression. TCF-20 is involved in transcriptional activation of the MMP3 (matrix metalloprotease 3) promoter. It also functions as a transcriptional co-regulator that enhances or represses the transcriptional activity of certain transcription factors/cofactors, such as specificity protein 1 (Sp1), E twenty-six 1 (Ets1), paired box protein 6 (Pax6), small nuclear RING-finger (SNURF)/RNF4, c-Jun, androgen receptor (AR) and estrogen receptor alpha (ERalpha). Both RAI1 and TCF-20 are strongly enriched in chromatin in interphase HeLa cells, and display low nuclear mobility, and have been implicated in Smith-Magenis syndrome and Potocki-Lupski syndrome.


Pssm-ID: 277138  Cd Length: 103  Bit Score: 76.96  E-value: 3.78e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  137 WAHHWCAVWSAGVWgQEGPELCGVDKAIFSGISQRCSHCTRFGASIPCRSPGCPRLYHFPCATASGSFLSMKTLQLLCPD 216
Cdd:cd15668     24 WVHEDCAVWAPGVY-LVGGKLYGLEEAVWVAKQSVCSSCQQTGATIGCLHKGCKAKYHYPCAVESGCQLDEENFSLLCPK 102


                   .
gi 1537972313  217 H 217
Cdd:cd15668    103 H 103
ePHD_RAI1 cd15700
Extended PHD finger (ePHD) found in retinoic acid-induced protein 1 (RAI1); The extended plant ...
 126-217 1.51e-15

Extended PHD finger (ePHD) found in retinoic acid-induced protein 1 (RAI1); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of RAI1. RAI1, a homolog of stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPBP, also termed TCF-20), is a chromatin-binding protein implicated in the regulation of gene expression. It is strongly enriched on chromatin in interphase HeLa cells, and displays low nuclear mobility, and has been implicated in Smith-Magenis syndrome, Potocki-Lupski syndrome, and non-syndromic autism. RAI1 contains a region with homology to the novel nucleosome-binding region SPBP and an ePHD/ADD domain with ability to bind nucleosomes.


Pssm-ID: 277170  Cd Length: 104  Bit Score: 75.30  E-value: 1.51e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  126 PAHLGEPGGHC-------WAHHWCAVWSAGVWGQEGpELCGVDKAIFSGISQRCSHCTRFGASIPCRSPGCPRLYHFPCA 198
Cdd:cd15700      7 PANYKDLGDLCgpyypehWVHEACAVWTTGVYLVAG-KLFGLQEAVQKAADAKCSSCQGAGATVGCCHKGCTQSYHYICA 85

                           90
                   ....*....|....*....
gi 1537972313  199 TASGSFLSMKTLQLLCPDH 217
Cdd:cd15700     86 VEAGCLFEEENFSLRCPKH 104
PHD2_KMT2C cd15594
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 1424-1469 2.08e-15

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the second PHD finger.


Pssm-ID: 277069  Cd Length: 46  Bit Score: 73.05  E-value: 2.08e-15
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1537972313 1424 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1469
Cdd:cd15594      1 VCQTCRQPGDDNKMLVCDTCDKGYHTFCLQPVMTTIPKNGWKCKNC 46
PHD_BAZ1A cd15627
PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also ...
 276-320 3.49e-15

PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1A contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277097 [Multi-domain]  Cd Length: 46  Bit Score: 72.43  E-value: 3.49e-15
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15627      2 CRICRRKGDAEKMLLCDGCDRGHHMYCLRPPLKKVPEGDWFCPDC 46
SET_SUV39H_Clr4-like cd20073
SET domain (including pre-SET and post-SET domains) found in of Schizosaccharomyces pombe H3K9 ...
 5391-5520 6.88e-15

SET domain (including pre-SET and post-SET domains) found in of Schizosaccharomyces pombe H3K9 methyltransferase Clr4, and similar proteins; This subfamily contains fission yeast Schizosaccharomyces pombe H3K9 methyltransferase Clr4 (also known as Suv39h), the sole homolog of the mammalian SUV39H1 and SUV39H2 enzymes, that has a critical role in preventing aberrant heterochromatin formation. It is known to di- and tri-methylate Lys-9 of histone H3, a central heterochromatic histone modification, with its specificity profile most similar to that of the human SUV39H2 homolog.


Pssm-ID: 380999 [Multi-domain]  Cd Length: 259  Bit Score: 78.00  E-value: 6.88e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5391 QGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEeqNRGI-YMF-------RINNEHVIDATLTGGPARYINHSCA 5462
Cdd:cd20073    103 KGWGLRCPRFIKAGTFIGVYLGEVITQSEAEIRGKKYD--NVGVtYLFdldlfedQVDEYYTVDAQYCGDVTRFINHSCD 180

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1537972313 5463 PNCVAEVVTFDKEDKIIIISS----RRIPKGEELTYDYQFDFEDDQ----------------HKIPCHCGAWNCRKWM 5520
Cdd:cd20073    181 PNLAIYSVLRDKSDSKIYDLAffaiKDIPALEELTFDYSGRNNFDQlgfignrsnskyinlkNKRPCYCGSANCRGWL 258
SET_SETD8 cd10528
SET domain found in SET domain-containing protein 8 (SETD8) and similar proteins; SETD8 (EC 2. ...
 5389-5496 7.22e-15

SET domain found in SET domain-containing protein 8 (SETD8) and similar proteins; SETD8 (EC 2.1.1.43; also termed N-lysine methyltransferase KMT5A, H4-K20-HMTase KMT5A, lysine N-methyltransferase 5A, lysine-specific methylase 5A, PR/SET domain-containing protein 07, PR-Set7 or PR/SET07) is a nucleosomal histone-lysine N-methyltransferase that specifically monomethylates 'Lys-20' of histone H4 (H4K20me1). It plays a central role in the silencing of euchromatic genes.


Pssm-ID: 380926 [Multi-domain]  Cd Length: 141  Bit Score: 74.92  E-value: 7.22e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5389 RIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEE-QNRGIYM--FRINNE-HVIDATL-TGGPARYINHSC-A 5462
Cdd:cd10528     25 DGKGRGVIATRPFEKGDFVVEYHGDLITITEAKKREALYAKdPSTGCYMyyFQYKGKtYCVDATKeSGRLGRLINHSKkK 104

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1537972313 5463 PNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDY 5496
Cdd:cd10528    105 PNLKTKLLVIDGVPHLILVAKRDIKPGEELLYDY 138
PHD1_KDM5B cd15603
PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
 1424-1469 1.73e-14

PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis antigen 31 (CT31), Histone demethylase JARID1B, Jumonji/ARID domain-containing protein 1B (JARID1B), PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A)) is a member of the JARID subfamily within the JmjC proteins. It has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of pregnant females and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well as TIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277076  Cd Length: 46  Bit Score: 70.37  E-value: 1.73e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1537972313 1424 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1469
Cdd:cd15603      1 VCLVCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 46
PHD2_KMT2C_like cd15510
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 1424-1469 2.10e-14

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 276985  Cd Length: 46  Bit Score: 70.16  E-value: 2.10e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1537972313 1424 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1469
Cdd:cd15510      1 VCQACRQPGDDTKMLVCETCDKGYHTSCLRPVMSSIPKYGWKCKNC 46
PHD_BAZ2A_like cd15545
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B ...
 276-320 2.38e-14

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B (BAZ2B); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A. Both BAZ2A and BAZ2B contain a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain. BAZ2B also harbors an extra Apolipophorin-III like domain in its N-terminal region.


Pssm-ID: 277020 [Multi-domain]  Cd Length: 46  Bit Score: 70.03  E-value: 2.38e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15545      2 CQICRSGDNEDQLLLCDGCDRGYHTYCFKPKMTNVPEGDWFCPEC 46
PHD_RSF1 cd15543
PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV ...
 1425-1469 2.48e-14

PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV pX-associated protein 8, or Hepatitis B virus X-associated protein alpha (HBxAPalpha), or p325 subunit of RSF chromatin-remodeling complex, is a novel nuclear protein with histone chaperon function. It is a subunit of an ISWI chromatin remodeling complex, remodeling and spacing factor (RSF), and plays a role in mediating ATPase-dependent chromatin remodeling and conferring tumor aggressiveness in common carcinomas. As an ataxia-telangiectasia mutated (ATM)-dependent chromatin remodeler, Rsf-1 facilitates DNA damage checkpoints and homologous recombination repair. It regulates the mitotic spindle checkpoint and chromosome instability through the association with serine/threonine kinase BubR1 (BubR1) and Hepatitis B virus (HBV) X protein (HBx) in the chromatin fraction during mitosis. It also interacts with cyclin E1 and promotes tumor development. Rsf-1 contains a plant homeodomain (PHD) finger.


Pssm-ID: 277018 [Multi-domain]  Cd Length: 46  Bit Score: 69.99  E-value: 2.48e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313 1425 CEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1469
Cdd:cd15543      2 CRKCGLSDHPEWILLCDRCDAGYHTACLRPPLMIIPDGNWFCPPC 46
SET_SETMAR cd10544
SET domain (including pre-SET and post-SET domains) found in SET domain and mariner ...
 5392-5520 2.80e-14

SET domain (including pre-SET and post-SET domains) found in SET domain and mariner transposase fusion protein (SETMAR) and similar proteins; SETMAR (also termed metnase) is a DNA-binding protein that is indirectly recruited to sites of DNA damage through protein-protein interactions. It has a sequence-specific DNA-binding activity recognizing the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element and displays a DNA nicking and end joining activity. SETMAR also acts as a histone-lysine N-methyltransferase that methylates 'Lys-4' and 'Lys-36' of histone H3. It specifically mediates dimethylation of H3 'Lys-36' at sites of DNA double-strand break and may recruit proteins required for efficient DSB repair through non-homologous end-joining.


Pssm-ID: 380942 [Multi-domain]  Cd Length: 254  Bit Score: 76.18  E-value: 2.80e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5392 GLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKiyeEQNRGI--YMFRINnEHV---------IDATLTGGPARYINHS 5460
Cdd:cd10544    101 GWGLRTLEFIPKGRFVCEYAGEVIGFEEARRRTK---SQTKGDmnYIIVLR-EHLssgkvletfVDPTYIGNIGRFLNHS 176

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5461 CAPNC----------VAEVVTFDKEDkiiiissrrIPKGEELTYDY------------QFDFEDDQHKIPCHCGAWNCRK 5518
Cdd:cd10544    177 CEPNLfmvpvrvdsmVPKLALFAARD---------IVAGEELSFDYsgefsnsvesvtLARQDESKSRKPCLCGAENCRG 247


                   ..
gi 1537972313 5519 WM 5520
Cdd:cd10544    248 FL 249
PHA03247 PHA03247
large tegument protein UL36; Provisional
 2102-2668 3.92e-14

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 80.37  E-value: 3.92e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2102 PGALGSPPPAA-------APTIFIGSPT---TPAGLSTSADGFLKPPAGTVPGPDSPgelflkLPPQVPAQVPSQD-Pfg 2170
Cdd:PHA03247  2498 PGGGGPPDPDAppapsrlAPAILPDEPVgepVHPRMLTWIRGLEELASDDAGDPPPP------LPPAAPPAAPDRSvP-- 2569

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2171 lAPAYAPEPrfsaAPPTYPPYPTPSGAPAQPpilgttTRPGTgqPGEFHTTPPGTPRHQPSTPDPFlKPRCPSLDNLAVP 2250
Cdd:PHA03247  2570 -PPRPAPRP----SEPAVTSRARRPDAPPQS------ARPRA--PVDDRGDPRGPAPPSPLPPDTH-APDPPPPSPSPAA 2635

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2251 ESPGVAGGKASEPLLSP-----PPFGESRKTLEVKKEELGASSPGYGPPNLGCvdSPSSGSHLGGLELKAPDVFKAPLTP 2325
Cdd:PHA03247  2636 NEPDPHPPPTVPPPERPrddpaPGRVSRPRRARRLGRAAQASSPPQRPRRRAA--RPTVGSLTSLADPPPPPPTPEPAPH 2713

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2326 RASQVEPQSPGLGLRAQEPPAAQALAPSPPSHSDVFRSASYPDPYAQPPLTPRPQPPPPESCCALPPRSLPSDPFSRVPA 2405
Cdd:PHA03247  2714 ALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSE 2793

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2406 SPQSQSSSQSpltPRPLSAEAFCPSPVTPRFQSPDPYSRPPSRPQSRDPFAPLHKPPRPQPPEVAFK-AGPLAH--TPLG 2482
Cdd:PHA03247  2794 SRESLPSPWD---PADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVApGGDVRRrpPSRS 2870

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2483 AGGFPAALPSGPAGELHAKVPSGQPPNFARSPgtgafvgtPSPMRFTFPQGVGEPSLKPPVPQPGLPPPhginshfgPGP 2562
Cdd:PHA03247  2871 PAAKPAAPARPPVRRLARPAVSRSTESFALPP--------DQPERPPQPQAPPPPQPQPQPPPPPQPQP--------PPP 2934

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2563 TLGKPQS--TNYTVATGNFHPSGSPLGPNTGPTGEGYGLSPLRPAsvmPPPTPEGSLPylshgasqrAGITSPVEKREDA 2640
Cdd:PHA03247  2935 PPPRPQPplAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRV---PQPAPSREAP---------ASSTPPLTGHSLS 3002

                          570       580
                   ....*....|....*....|....*...
gi 1537972313 2641 GATMSSSSLAtpeLSSAQDAGMPSLSQT 2668
Cdd:PHA03247  3003 RVSSWASSLA---LHEETDPPPVSLKQT 3027
PHD1_KDM5A_like cd15515
PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar ...
 1424-1469 4.64e-14

PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar proteins; The JARID subfamily within the JmjC proteins includes Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and a Drosophila homolog, protein little imaginal discs (Lid). KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. KDM5C is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me2 and H3K4me3), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. This family also includes Drosophila melanogaster protein little imaginal discs (Lid) that functions as a JmjC-dependent H3K4me3 demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Members in this family contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two or three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 276990  Cd Length: 46  Bit Score: 69.34  E-value: 4.64e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1537972313 1424 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1469
Cdd:cd15515      1 ICQVCGRGDDEDKLLLCDGCDDSYHTFCLIPPLPDIPPGDWRCPKC 46
PHD1_Lid2p_like cd15519
PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
 1424-1469 6.02e-14

PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar proteins; Lid2p is a trimethyl H3K4 (H3K4me3) demethylase responsible for H3K4 hypomethylation in heterochromatin. It interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, and mediates H3K9 methylation and small RNA production. It also acts cooperatively with the histone modification enzymes Set1 and Lsd1 and plays an essential role in cross-talk between H3K4 and H3K9 methylation in euchromatin. Lid2p contains a JmjC domain, three PHD fingers and a JmjN domain. This model corresponds to the first PHD finger.


Pssm-ID: 276994 [Multi-domain]  Cd Length: 46  Bit Score: 69.03  E-value: 6.02e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1537972313 1424 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1469
Cdd:cd15519      1 GCEVCGLDDNEGEVLLCDGCDAEYHTSCLDPPLGEIPPGTWFCPSC 46
ePHD1_KMT2D cd15695
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 5023-5104 6.45e-14

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMT2D. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 at Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions.


Pssm-ID: 277165  Cd Length: 90  Bit Score: 70.33  E-value: 6.45e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5023 DLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQRTGATSSCNRMRCPNVYHFACAIrAKCMFFKDKT--ML 5100
Cdd:cd15695      8 ECWVHHWCAAWSAGVKQHEGDGLIGVDKAVFSGISQKCEHCKRLGATIQCHAEGCPRFYHFPCAA-ASGSFQSMKTllLL 86


                   ....
gi 1537972313 5101 CPMH 5104
Cdd:cd15695     87 CPEH 90
PHD_BAZ1A cd15627
PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also ...
 1425-1469 6.98e-14

PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1A contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277097 [Multi-domain]  Cd Length: 46  Bit Score: 68.57  E-value: 6.98e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313 1425 CEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1469
Cdd:cd15627      2 CRICRRKGDAEKMLLCDGCDRGHHMYCLRPPLKKVPEGDWFCPDC 46
SET_SUV39H_DIM5-like cd19473
SET domain (including pre-SET domain) found in Neurospora crassa (DIM-5) and similar proteins; ...
 5392-5520 8.34e-14

SET domain (including pre-SET domain) found in Neurospora crassa (DIM-5) and similar proteins; This subfamily contains Neurospora crassa DIM-5 (also termed H3-K9-HMTase dim-5, or HKMT) which functions as histone-lysine N-methyltransferase that specifically trimethylates histone H3 to form H3K9me3.


Pssm-ID: 380996 [Multi-domain]  Cd Length: 274  Bit Score: 75.43  E-value: 8.34e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5392 GLGLYAAKDLEKHTMVIEYIGTIIRNEVAN-RREKIYEEQNRGIYMF-------------RINNE-HVIDATLTGGPARY 5456
Cdd:cd19473    117 GWGVRSTVDIKRGQFVDCYVGEIITPEEAQrRRDAATIAQRKDVYLFaldkfsdpdsldpRLRGDpYEIDGEFMSGPTRF 196

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1537972313 5457 INHSCAPNC-VAEVVTfDKEDKIIII----SSRRIPKGEELTYDY----------QFDFEDDQHKIPCHCGAWNCRKWM 5520
Cdd:cd19473    197 INHSCDPNLrIFARVG-DHADKHIHDlaffAIKDIPRGTELTFDYvdgvtgldddAGDEEKEKEMTKCLCGSPKCRGYL 274
PHD_BAZ1A_like cd15544
PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, ...
 276-320 1.19e-13

PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. Both BAZ1A and BAZ1B contain a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277019  Cd Length: 46  Bit Score: 68.21  E-value: 1.19e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15544      2 CKVCRKKGDPDNMILCDGCDKAFHLYCLRPALREVPSGDWFCPAC 46
ePHD1_KMT2C cd15696
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 5023-5104 1.46e-13

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMT2C. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several PHD fingers, two ePHD fingers, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains.


Pssm-ID: 277166  Cd Length: 90  Bit Score: 69.20  E-value: 1.46e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5023 DLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQRTGATSSCNRMRCPNVYHFACAIRAKCMF-FKDKTMLC 5101
Cdd:cd15696      8 ECWAHLRCAEWSLGVCQGEEQLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQdFSRRLLLC 87


                   ...
gi 1537972313 5102 PMH 5104
Cdd:cd15696     88 PTH 90
ePHD_TCF20 cd15699
Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20); The extended plant ...
 128-217 2.12e-13

Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of TCF-20. TCF-20, also termed nuclear factor SPBP, or protein AR1, or stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPRE-binding protein), is involved in transcriptional activation of the MMP3 (matrix metalloprotease 3) promoter. It is strongly enriched on chromatin in interphase HeLa cells, and displays low nuclear mobility, and has been implicated in Smith-Magenis syndrome and Potocki-Lupski syndrome. As a chromatin-binding protein, TCF-20 plays a role in the regulation of gene expression. It also functions as a transcriptional co-regulator that enhances or represses the transcriptional activity of certain transcription factors/cofactors, such as specificity protein 1 (Sp1), E twenty-six 1 (Ets1), paired box protein 6 (Pax6), small nuclear RING-finger (SNURF)/RNF4, c-Jun, androgen receptor (AR) and estrogen receptor alpha (ERalpha). TCF-20 contains an N-terminal transactivation domain, a novel DNA-binding domain with an AT-hook motif, three nuclear localization signals (NLSs) and a C-terminal ePHD/ADD domain.


Pssm-ID: 277169  Cd Length: 103  Bit Score: 69.17  E-value: 2.12e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  128 HLGE---PGGHCWAHHWCAVWSAGVWGQEGpELCGVDKAIFSGISQRCSHCTRFGASIPCRSPGCPRLYHFPCATASGSF 204
Cdd:cd15699     12 NLGDlfgPFYEFWVHEGCILWANGIYLVCG-RLYGLQEALDIAREMKCSHCQEAGATLGCYNKGCSFRYHYPCAIDADCL 90

                           90
                   ....*....|...
gi 1537972313  205 LSMKTLQLLCPDH 217
Cdd:cd15699     91 LNEENFSVRCPKH 103
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1424-1472 2.73e-13

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 67.13  E-value: 2.73e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1537972313 1424 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPL--LTVPKGGWKCKWCVSC 1472
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPPLdpAEIPSGEWLCPECKPK 51
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 276-323 3.62e-13

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 66.75  E-value: 3.62e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1537972313  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEELPAHS--WKCMTCRVC 323
Cdd:pfam00628    2 CAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPAEIPSgeWLCPECKPK 51
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 5027-5104 3.83e-13

PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH.


Pssm-ID: 463977 [Multi-domain]  Cd Length: 88  Bit Score: 68.12  E-value: 3.83e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5027 HLNCALWSTEVY----ETQGGALMNVEVALHRGLLTKCSLC-QRTGATSSCNRMRCPNVYHFACAIRAKCMF-FKDKT-- 5098
Cdd:pfam13771    1 HVVCALWSPELVqrgnDSMGFPIEDIEKIPKRRWKLKCYLCkKKGGACIQCSKKNCRRAFHVTCALEAGLLMqFDEDNgt 80


                   ....*...
gi 1537972313 5099 --MLCPMH 5104
Cdd:pfam13771   81 fkSYCKKH 88
PHD1_KDM5A cd15602
PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone ...
 1424-1471 5.36e-13

PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone demethylase JARID1A, Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2)) was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5A functions as a trimethylated histone H3 lysine 4 (H3K4me3) demethylase that belongs to the JARID subfamily within the JmjC proteins. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5A contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277075  Cd Length: 49  Bit Score: 66.13  E-value: 5.36e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1537972313 1424 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWCVS 1471
Cdd:cd15602      1 VCLFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKCVA 48
PHD_BAZ1A_like cd15544
PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, ...
 1425-1469 5.57e-13

PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. Both BAZ1A and BAZ1B contain a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277019  Cd Length: 46  Bit Score: 66.28  E-value: 5.57e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313 1425 CEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1469
Cdd:cd15544      2 CKVCRKKGDPDNMILCDGCDKAFHLYCLRPALREVPSGDWFCPAC 46
SET_EHMT cd10543
SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine ...
 5385-5517 6.99e-13

SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine N-methyltransferase EHMT1, EHMT2 and similar proteins; This family includes EHMT1 (also termed Eu-HMTase1, G9a-like protein 1, GLP, GLP1, histone H3-K9 methyltransferase 5, H3-K9-HMTase 5, lysine N-methyltransferase 1D, or KMT1D) and EHMT2 (also termed Eu-HMTase2, HLA-B-associated transcript 8, histone H3-K9 methyltransferase 3, H3-K9-HMTase 3, lysine N-methyltransferase 1C, KMT1C, or protein G9a), both act as histone-lysine N-methyltransferases that specifically mono- and dimethylate 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin.


Pssm-ID: 380941 [Multi-domain]  Cd Length: 231  Bit Score: 71.60  E-value: 6.99e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5385 LARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKiyeeqnrGIYMFRINNE----HVIDATLTGGPARYINHS 5460
Cdd:cd10543     95 LFRTRGMGWGVRALQDIPKGTFVCEYIGELISDSEADSRED-------DSYLFDLDNKdgetYCIDARRYGNISRFINHL 167

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1537972313 5461 CAPNCVAEVVTFDKED----KIIIISSRRIPKGEELTYDYQFDFEDDQHK-IPCHCGAWNCR 5517
Cdd:cd10543    168 CEPNLIPVRVFVEHQDlrfpRIAFFASRDIKAGEELGFDYGEKFWRIKGKyFTCRCGSPKCK 229
ePHD_TCF20 cd15699
Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20); The extended plant ...
 5000-5104 7.50e-13

Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of TCF-20. TCF-20, also termed nuclear factor SPBP, or protein AR1, or stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPRE-binding protein), is involved in transcriptional activation of the MMP3 (matrix metalloprotease 3) promoter. It is strongly enriched on chromatin in interphase HeLa cells, and displays low nuclear mobility, and has been implicated in Smith-Magenis syndrome and Potocki-Lupski syndrome. As a chromatin-binding protein, TCF-20 plays a role in the regulation of gene expression. It also functions as a transcriptional co-regulator that enhances or represses the transcriptional activity of certain transcription factors/cofactors, such as specificity protein 1 (Sp1), E twenty-six 1 (Ets1), paired box protein 6 (Pax6), small nuclear RING-finger (SNURF)/RNF4, c-Jun, androgen receptor (AR) and estrogen receptor alpha (ERalpha). TCF-20 contains an N-terminal transactivation domain, a novel DNA-binding domain with an AT-hook motif, three nuclear localization signals (NLSs) and a C-terminal ePHD/ADD domain.


Pssm-ID: 277169  Cd Length: 103  Bit Score: 67.63  E-value: 7.50e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5000 CCFCHEEGD----GATDGPArllnldLDLWVHLNCALWSTEVYETQGgALMNVEVALHRGLLTKCSLCQRTGATSSCNRM 5075
Cdd:cd15699      1 CCLCGKWANyrnlGDLFGPF------YEFWVHEGCILWANGIYLVCG-RLYGLQEALDIAREMKCSHCQEAGATLGCYNK 73

                           90       100       110
                   ....*....|....*....|....*....|
gi 1537972313 5076 RCPNVYHFACAIRAKCMFFKDK-TMLCPMH 5104
Cdd:cd15699     74 GCSFRYHYPCAIDADCLLNEENfSVRCPKH 103
ePHD_KMT2A_like cd15664
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); The ...
 133-217 7.81e-13

Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A/MLL1 and KMT2B/MLL2. KMT2A and KMT2B comprise the mammalian Trx branch of COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation by mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three PHD fingers, this extended PHD (ePHD) finger, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain.


Pssm-ID: 277134  Cd Length: 105  Bit Score: 67.82  E-value: 7.81e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  133 GGHCWAHHWCAVWSAGVWGQEGPELCGVDKAIFSGISQRCSHCTRFGASIPCRSPGCPRLYHFPCA-TASGSFLSMKtlQ 211
Cdd:cd15664     22 GQDEWVHINCALWSAEVFEEDDGSLQNVHSAVSRGRMMKCELCGKPGATVGCCLKSCPANYHFMCArKAECVFQDDK--K 99


                   ....*.
gi 1537972313  212 LLCPDH 217
Cdd:cd15664    100 VFCPAH 105
PHD_UHRF1_2 cd15525
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and ...
 1425-1469 8.19e-13

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and UHRF2; UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277000  Cd Length: 47  Bit Score: 65.85  E-value: 8.19e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1537972313 1425 CEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGG-WKCKWC 1469
Cdd:cd15525      2 CHVCGGKQDPEKQLLCDECDMAYHLYCLDPPLTSLPDDDeWYCPDC 47
SET_SUV39H1 cd10525
SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 ...
 5391-5520 8.54e-13

SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homolog 1 (SUV39H1) and similar proteins; SUV39H1 (EC 2.1.1.43; also termed histone H3-K9 methyltransferase 1, H3-K9-HMTase 1, lysine N-methyltransferase 1A (KMT1A), position-effect variegation 3-9 homolog (SUV39H), or Su(var)3-9 homolog 1) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. It mainly functions in heterochromatin regions, thereby playing a central role in the establishment of constitutive heterochromatin at pericentric and telomere regions.


Pssm-ID: 380923 [Multi-domain]  Cd Length: 255  Bit Score: 71.85  E-value: 8.54e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5391 QGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNrGIYMFR---INNEHVIDATLTGGPARYINHSCAPNCVA 5467
Cdd:cd10525     97 RGWGVRTLEKIRKNSFVMEYVGEIITSEEAERRGQIYDRQG-ATYLFDldyVEDVYTVDAAYYGNISHFVNHSCDPNLQV 175

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1537972313 5468 EVVTFDKEDKIIIISSRRIPK----GEELTYDYQF-----DFEDDQH-----------------KIPCHCGAWNCRKWM 5520
Cdd:cd10525    176 YNVFIDNLDERLPRIALFATRtiraGEELTFDYNMqvdpvDAESTKMdsnfglaglpgspkkrvRIECKCGVRSCRKYL 254
SET_EZH-like cd19168
SET domain found in enhancer of zeste homolog 1 (EZH1) and zeste homolog 2 (EZH2) of polycomb ...
 5383-5500 9.75e-13

SET domain found in enhancer of zeste homolog 1 (EZH1) and zeste homolog 2 (EZH2) of polycomb repressive complex 2 (PRC2), and similar proteins; The family includes EZH1 and EZH2. EZH1 (EC 2.1.1.43; also termed ENX-2, or histone-lysine N-methyltransferase EZH1) is a catalytic subunit of the PRC2/EED-EZH1 complex, which methylates 'Lys-27' of histone H3, leading to transcriptional repression of the affected target gene. EZH2 (EC 2.1.1.43; also termed lysine N-methyltransferase 6, ENX-1, or histone-lysine N-methyltransferase EZH2) is a catalytic subunit of the PRC2/EED-EZH2 complex, which methylates 'Lys-9' (H3K9me) and 'Lys-27' (H3K27me) of histone H3, leading to transcriptional repression of the affected target gene. Both EZH1 and EZH2 can mono-, di- and trimethylate 'Lys-27' of histone H3 to form H3K27me1, H3K27me2 and H3K27me3, respectively. PRC2 is involved in several cancers; EZH2 is overexpressed in breast, liver and prostate cancer, while point mutations in EZH2 alter the substrate preference and product specificity of PRC2 in Non-Hodgkin lymphomas (NHLs). Thus, PRC2 is a popular target for cancer therapeutics.


Pssm-ID: 380945  Cd Length: 124  Bit Score: 67.98  E-value: 9.75e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5383 VYLARSRIQ-GLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRgIYMFRINNEHVIDATLTGGPARYINH-- 5459
Cdd:cd19168      3 VVLGKSQLEcGLGLFAAEDIKEGEFVIEYTGELISHDEGVRREHRRGDVSY-LYLFEEQEGIWVDAAIYGNLSRYINHat 81

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1537972313 5460 --SCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDF 5500
Cdd:cd19168     82 dkVKTGNCMPKIMYVNHEWRIKFTAIKDIKIGEELFFNYGDNF 124
ePHD2_KMT2D cd15698
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 137-217 1.00e-12

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2D. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions.


Pssm-ID: 277168  Cd Length: 107  Bit Score: 67.38  E-value: 1.00e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  137 WAHHWCAVWSAGVWGQEGPELCGVDKAIFSGISQRCSHCTRFGASIPCRSPGCPRLYHFPCAT-ASGSFLSMKTlqLLCP 215
Cdd:cd15698     26 WVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQKTGATNSCNRLRCPNVYHFACAIrAKCMFFKDKT--MLCP 103


                   ..
gi 1537972313  216 DH 217
Cdd:cd15698    104 MH 105
SET_SUV39H2 cd10532
SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 ...
 5391-5520 1.10e-12

SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homolog 2 (SUV39H2) and similar proteins; SUV39H2 (EC 2.1.1.43; also termed histone H3-K9 methyltransferase 2, H3-K9-HMTase 2, lysine N-methyltransferase 1B (KMT1B), or Su(var)3-9 homolog 2) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. It mainly functions in heterochromatin regions, thereby playing a central role in the establishment of constitutive heterochromatin at pericentric and telomere regions.


Pssm-ID: 380930 [Multi-domain]  Cd Length: 243  Bit Score: 71.46  E-value: 1.10e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5391 QGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEeqNRGI-YMFRIN---NEHVIDATLTGGPARYINHSCAPNCV 5466
Cdd:cd10532     95 RGWGVKTLQKIKKNSFVMEYVGEVITSEEAERRGQFYD--SKGItYLFDLDyesDEFTVDAARYGNVSHFVNHSCDPNLQ 172

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1537972313 5467 AEVVTFDKED----KIIIISSRRIPKGEELTYDYQFDFEDD-------------QHKIPCHCGAWNCRKWM 5520
Cdd:cd10532    173 VFNVFIDNLDtrlpRIALFSTRTIKAGEELTFDYQMKGSGDlssdsidnspakkRVRTVCKCGAVTCRGYL 243
PHD1_Lid_like cd15605
PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar ...
 1424-1469 1.11e-12

PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar proteins; Drosophila melanogaster Lid, also termed Retinoblastoma-binding protein 2 homolog, is identified genetically as a trithorax group (trxG) protein that is a Drosophila homolog of the human protein JARID1A/kdm5A, a member of the JARID subfamily within the JmjC proteins. Lid functions as a JmjC-dependent trimethyl histone H3K4 (H3K4me3) demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Lid contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger of Lid.


Pssm-ID: 277078  Cd Length: 46  Bit Score: 65.16  E-value: 1.11e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1537972313 1424 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1469
Cdd:cd15605      1 VCHTCGRGDGEESMLLCDGCDDSYHTFCLLPPLSEVPKGDWRCPKC 46
PHA03247 PHA03247
large tegument protein UL36; Provisional
 2099-2525 1.41e-12

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 75.36  E-value: 1.41e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2099 PSQPGALGSPPPAAAPTIFIGSPTTPAGLSTSADGFLKPPAGTVPGPDSPGELFLKLPPQVPAQVPSQDPFGLAPAYAPE 2178
Cdd:PHA03247  2570 PPRPAPRPSEPAVTSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPP 2649

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2179 PRFSAAPPTYPPYPTP-SGAPAQPPILGTTT---RPGTGQPGEFHTTPPGTPRHQPSTPDPFLKPRCPsldnlAVPESPG 2254
Cdd:PHA03247  2650 ERPRDDPAPGRVSRPRrARRLGRAAQASSPPqrpRRRAARPTVGSLTSLADPPPPPPTPEPAPHALVS-----ATPLPPG 2724

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2255 VAGGKASEPLLSP---PPFGESRKTLEVKKEELGASSPGYGPPNLGCVDSPSSGshlgglelkAPDVFKAPLTPRASQVE 2331
Cdd:PHA03247  2725 PAAARQASPALPAapaPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAG---------PPRRLTRPAVASLSESR 2795

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2332 PQSPGLglRAQEPPAAQALAPSPPSHSDVFRSASYPDPYAQPPLTPRPQPPPPESCCALPPRSLPSDPFSRVPASPQSQS 2411
Cdd:PHA03247  2796 ESLPSP--WDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAA 2873

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2412 SSQSPLTPRPLSAEAFCPSPVTPRF-QSPDPYSRP--PSRPQSRDPFAPLHKPPRPQPPE--VAFKAGPLAHTPlGAGGF 2486
Cdd:PHA03247  2874 KPAAPARPPVRRLARPAVSRSTESFaLPPDQPERPpqPQAPPPPQPQPQPPPPPQPQPPPppPPRPQPPLAPTT-DPAGA 2952

                          410       420       430
                   ....*....|....*....|....*....|....*....
gi 1537972313 2487 PAALPSGPAGELHAKVPSGQPPNFARSPGTGAFVGTPSP 2525
Cdd:PHA03247  2953 GEPSGAVPQPWLGALVPGRVAVPRFRVPQPAPSREAPAS 2991
ePHD_RAI1 cd15700
Extended PHD finger (ePHD) found in retinoic acid-induced protein 1 (RAI1); The extended plant ...
 5000-5104 1.64e-12

Extended PHD finger (ePHD) found in retinoic acid-induced protein 1 (RAI1); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of RAI1. RAI1, a homolog of stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPBP, also termed TCF-20), is a chromatin-binding protein implicated in the regulation of gene expression. It is strongly enriched on chromatin in interphase HeLa cells, and displays low nuclear mobility, and has been implicated in Smith-Magenis syndrome, Potocki-Lupski syndrome, and non-syndromic autism. RAI1 contains a region with homology to the novel nucleosome-binding region SPBP and an ePHD/ADD domain with ability to bind nucleosomes.


Pssm-ID: 277170  Cd Length: 104  Bit Score: 66.82  E-value: 1.64e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5000 CCFCHEegdgatdgPARLLNL-DL------DLWVHLNCALWSTEVYETqGGALMNVEVALHRGLLTKCSLCQRTGATSSC 5072
Cdd:cd15700      1 CCLCRN--------PANYKDLgDLcgpyypEHWVHEACAVWTTGVYLV-AGKLFGLQEAVQKAADAKCSSCQGAGATVGC 71

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1537972313 5073 NRMRCPNVYHFACAIRAKCMFFKDK-TMLCPMH 5104
Cdd:cd15700     72 CHKGCTQSYHYICAVEAGCLFEEENfSLRCPKH 104
PHD1_KDM5C_5D cd15604
PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family ...
 1424-1469 1.91e-12

PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family includes KDM5C and KDM5D, both of which belong to the JARID subfamily within the JmjC proteins. KDM5C (also termed Histone demethylase JARID1C, Jumonji/ARID domain-containing protein 1C, SmcX, or Xe169) is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D (also termed Histocompatibility Y antigen (H-Y), Histone demethylase JARID1D, Jumonji/ARID domain-containing protein 1D, or SmcY) is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me3 andH3K4me2), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. Both KDM5C and KDM5D contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277077  Cd Length: 46  Bit Score: 64.48  E-value: 1.91e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1537972313 1424 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1469
Cdd:cd15604      1 VCRMCSRGDEDDKLLLCDGCDDNYHTFCLLPPLPEPPKGIWRCPKC 46
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1424-1469 2.51e-12

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 64.16  E-value: 2.51e-12
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 1537972313  1424 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLT-VPKGGWKCKWC 1469
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
PHD_UHRF1 cd15616
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); ...
 1425-1469 3.70e-12

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); UHRF1 (also termed inverted CCAAT box-binding protein of 90 kDa, nuclear protein 95, nuclear zinc finger protein Np95 (Np95), RING finger protein 106, transcription factor ICBP90, or E3 ubiquitin-protein ligase UHRF1) is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF1 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET and RING finger associated (SRA) domain, and a C-terminal RING-finger domain. It specifically binds to hemimethylated DNA, double-stranded CpG dinucleotides, and recruits the maintenance methyltransferase DNMT1 to its hemimethylated DNA substrate through its SRA domain. UHRF1-dependent H3K23 ubiquitylation has an essential role in maintaining DNA methylation and replication. The tandem Tudor domain directs UHRF1 binding to the heterochromatin mark histone H3K9me3 and the PHD finger targets UHRF1 to unmodified histone H3 in euchromatic regions. The RING-finger domain exhibit both autocatalytic E3 ubiquitin (Ub) ligase activity and activity against histone H3 and DNMT1.


Pssm-ID: 277088  Cd Length: 47  Bit Score: 63.83  E-value: 3.70e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1537972313 1425 CEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVP-KGGWKCKWC 1469
Cdd:cd15616      2 CHVCGGKQDPDKQLMCDECDMAFHIYCLNPPLSSIPdDEDWYCPEC 47
ePHD2_KMT2C cd15697
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 120-217 6.27e-12

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2C. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains PHD fingers, two ePHD fingers, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains.


Pssm-ID: 277167  Cd Length: 105  Bit Score: 65.07  E-value: 6.27e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  120 FPEGLT--PAHLGEPGGHCWAHHWCAVWSAGVWGQEGPELCGVDKAIFSGISQRCSHCTRFGASIPCRSPGCPRLYHFPC 197
Cdd:cd15697      7 EGDGLTdgPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRLRCTNVYHFTC 86

                           90       100
                   ....*....|....*....|.
gi 1537972313  198 A-TASGSFLSMKTlqLLCPDH 217
Cdd:cd15697     87 AiKAQCMFFKDKT--MLCPMH 105
PHD_PHRF1 cd15536
PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also ...
 1425-1469 6.51e-12

PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also termed KIAA1542, or CTD-binding SR-like protein rA9, is a ubiquitin ligase that induces the ubiquitination of TGIF (TG-interacting factor) at lysine 130. It acts as a tumor suppressor that promotes the transforming growth factor (TGF)-beta cytostatic program through selective release of TGIF-driven promyelocytic leukemia protein (PML) inactivation. PHRF1 contains a plant homeodomain (PHD) finger and a RING finger.


Pssm-ID: 277011  Cd Length: 46  Bit Score: 63.20  E-value: 6.51e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313 1425 CEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1469
Cdd:cd15536      2 CEVCGRSDREDRLLLCDGCDAGYHMECLTPPLDEVPIEEWFCPEC 46
SET_LegAS4-like cd10522
SET domain found in Legionella pneumophila type IV secretion system effector LegAS4 and ...
 5392-5502 8.48e-12

SET domain found in Legionella pneumophila type IV secretion system effector LegAS4 and similar proteins; LegAS4 is a type IV secretion system effector of Legionella pneumophila. It contains a SET domain that is involved in the modification of Lys4 of histone H3 (H3K4) in the nucleolus of the host cell, thereby enhancing heterochromatic rDNA transcription. It also contains an ankyrin repeat domain of unknown function at its C-terminal region.


Pssm-ID: 380920 [Multi-domain]  Cd Length: 122  Bit Score: 65.44  E-value: 8.48e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5392 GLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNrgiYMFRINNEH-VIDATLTGGPARYINHSCAPNCVAEVV 5470
Cdd:cd10522     14 GLGLFAAETIAKGEFVGEYTGEVLDRWEEDRDSVYHYDPL---YPFDLNGDIlVIDAGKKGNLTRFINHSDQPNLELIVR 90

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1537972313 5471 TFDKEDKIIIISSRRIPKGEELTYDYQFDFED 5502
Cdd:cd10522     91 TLKGEQHIGFVAIRDIKPGEELFISYGPKYWK 122
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 139-217 9.85e-12

PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH.


Pssm-ID: 463977 [Multi-domain]  Cd Length: 88  Bit Score: 63.89  E-value: 9.85e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  139 HHWCAVWSAGVWgQEGPE-----LCGVDKAIFSGISQRCSHC-TRFGASIPCRSPGCPRLYHFPCATASGSFLSMK---- 208
Cdd:pfam13771    1 HVVCALWSPELV-QRGNDsmgfpIEDIEKIPKRRWKLKCYLCkKKGGACIQCSKKNCRRAFHVTCALEAGLLMQFDedng 79


                   ....*....
gi 1537972313  209 TLQLLCPDH 217
Cdd:pfam13771   80 TFKSYCKKH 88
PHD_BAZ2A_like cd15545
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B ...
 1425-1469 9.95e-12

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B (BAZ2B); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A. Both BAZ2A and BAZ2B contain a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain. BAZ2B also harbors an extra Apolipophorin-III like domain in its N-terminal region.


Pssm-ID: 277020 [Multi-domain]  Cd Length: 46  Bit Score: 62.71  E-value: 9.95e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313 1425 CEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1469
Cdd:cd15545      2 CQICRSGDNEDQLLLCDGCDRGYHTYCFKPKMTNVPEGDWFCPEC 46
SET_EHMT1 cd10535
SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine ...
 5368-5517 1.14e-11

SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine N-methyltransferase 1 (EHMT1) and similar proteins; EHMT1 (also termed Eu-HMTase1, G9a-like protein 1, GLP, GLP1, histone H3-K9 methyltransferase 5, H3-K9-HMTase 5, or lysine N-methyltransferase 1D (KMT1D)) acts as a histone-lysine N-methyltransferase that specifically mono- and dimethylates 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin.


Pssm-ID: 380933 [Multi-domain]  Cd Length: 231  Bit Score: 68.04  E-value: 1.14e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5368 KSSQYRRLRTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKiyeeqnrGIYMFRINNE----H 5443
Cdd:cd10535     78 RNCRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEYVGELISDSEADVREE-------DSYLFDLDNKdgevY 150

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1537972313 5444 VIDATLTGGPARYINHSCAPNCVAEVVTFDKED----KIIIISSRRIPKGEELTYDYQFDFEDDQHKI-PCHCGAWNCR 5517
Cdd:cd10535    151 CIDARFYGNVSRFINHHCEPNLVPVRVFMAHQDlrfpRIAFFSTRLIEAGEQLGFDYGERFWDIKGKLfSCRCGSPKCR 229
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
 1425-1469 1.29e-11

PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, also termed histone acetyltransferase KAT6A, YBF2/SAS3, SAS2 and TIP60 protein 3 (MYST-3), or runt-related transcription factor-binding protein 2, or zinc finger protein 220, is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ-related factor (MORF), also termed MOZ2, or histone acetyltransferase KAT6B, or MOZ, YBF2/SAS3, SAS2 and TIP60 protein 4 (MYST4), is a ubiquitously expressed transcriptional regulator with intrinsic HAT activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. Both MOZ and MORF are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are also implicated in human leukemias. MOZ is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphomagenesis and bone development, and its homologs. MOZ contains a linker histone 1 and histone 5 domains and two plant homeodomain (PHD) fingers. In contrast, MORF contains an N-terminal region containing two PHD fingers, a putative HAT domain, an acidic region, and a C-terminal Ser/Met-rich domain. The family corresponds to the first PHD finger.


Pssm-ID: 277002  Cd Length: 46  Bit Score: 62.40  E-value: 1.29e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313 1425 CEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1469
Cdd:cd15527      2 CSVCQDSGNADNLLFCDACDKGFHMECHDPPLTRMPKGKWVCQIC 46
PHD2_PHF10 cd15529
PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
 276-320 1.49e-11

PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed BRG1-associated factor 45a (BAF45a), or XAP135, is a ubiquitously expressed transcriptional regulator that is required for maintaining the undifferentiated status of neuroblasts. It contains a SAY (supporter of activation of yellow) domain and two adjacent plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger.


Pssm-ID: 277004  Cd Length: 44  Bit Score: 61.94  E-value: 1.49e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKppIEELPAHSWKCMTC 320
Cdd:cd15529      2 CTKCGDPHDEDKMMFCDQCDRGYHTFCVG--LRSIPDGRWICPLC 44
PHD_BAZ2A cd15629
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also ...
 276-320 1.99e-11

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. It contains a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277099  Cd Length: 47  Bit Score: 61.79  E-value: 1.99e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15629      2 CLVCRKGDNDEYLLLCDGCDRGCHMYCHRPKMLQVPEGDWFCPNC 46
PHD2_KMT2D cd15595
PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 1424-1469 2.03e-11

PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such asHOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 277070  Cd Length: 46  Bit Score: 61.55  E-value: 2.03e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1537972313 1424 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1469
Cdd:cd15595      1 VCQTCRKPGEDSKMLVCEACDKGYHTFCLKPAMESLPTDSWKCKAC 46
PHD_RSF1 cd15543
PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV ...
 276-320 2.75e-11

PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV pX-associated protein 8, or Hepatitis B virus X-associated protein alpha (HBxAPalpha), or p325 subunit of RSF chromatin-remodeling complex, is a novel nuclear protein with histone chaperon function. It is a subunit of an ISWI chromatin remodeling complex, remodeling and spacing factor (RSF), and plays a role in mediating ATPase-dependent chromatin remodeling and conferring tumor aggressiveness in common carcinomas. As an ataxia-telangiectasia mutated (ATM)-dependent chromatin remodeler, Rsf-1 facilitates DNA damage checkpoints and homologous recombination repair. It regulates the mitotic spindle checkpoint and chromosome instability through the association with serine/threonine kinase BubR1 (BubR1) and Hepatitis B virus (HBV) X protein (HBx) in the chromatin fraction during mitosis. It also interacts with cyclin E1 and promotes tumor development. Rsf-1 contains a plant homeodomain (PHD) finger.


Pssm-ID: 277018 [Multi-domain]  Cd Length: 46  Bit Score: 61.13  E-value: 2.75e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15543      2 CRKCGLSDHPEWILLCDRCDAGYHTACLRPPLMIIPDGNWFCPPC 46
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
 276-320 3.27e-11

PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger of KMT2C and the fourth PHD finger of KMT2D.


Pssm-ID: 276988  Cd Length: 47  Bit Score: 61.34  E-value: 3.27e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15513      2 CEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 46
PHD2_d4 cd15530
PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three ...
 1425-1469 5.08e-11

PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three members of the d4 gene family, DPF1 (neuro-d4), DPF2 (ubi-d4/Requiem), and DPF3 (cer-d4), which function as transcription factors and are involved in transcriptional regulation of genes by changing the condensed/decondensed state of chromatin in the nucleus. DPF2 is ubiquitously expressed and it acts as a transcription factor that may participate in developmentally programmed cell death. DPF1 and DPF3 are expressed predominantly in neural tissues, and they may be involved in the transcription regulation of neuro-specific gene clusters. The d4 family proteins show distinct domain organization with domain 2/3 in the N-terminal region, a Cys2His2 (C2H2) zinc finger or Kruppel-type zinc finger in the central part and two adjacent plant homeodomain (PHD) fingers (d4-domain) in the C-terminal part of the molecule. This model corresponds to the second PHD finger.


Pssm-ID: 277005  Cd Length: 46  Bit Score: 60.48  E-value: 5.08e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313 1425 CEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1469
Cdd:cd15530      2 CSLCGTSENDDQLLFCDDCDRGYHMYCLSPPMSEPPEGSWSCHLC 46
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
 276-320 5.96e-11

PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, also termed histone acetyltransferase KAT6A, YBF2/SAS3, SAS2 and TIP60 protein 3 (MYST-3), or runt-related transcription factor-binding protein 2, or zinc finger protein 220, is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ-related factor (MORF), also termed MOZ2, or histone acetyltransferase KAT6B, or MOZ, YBF2/SAS3, SAS2 and TIP60 protein 4 (MYST4), is a ubiquitously expressed transcriptional regulator with intrinsic HAT activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. Both MOZ and MORF are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are also implicated in human leukemias. MOZ is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphomagenesis and bone development, and its homologs. MOZ contains a linker histone 1 and histone 5 domains and two plant homeodomain (PHD) fingers. In contrast, MORF contains an N-terminal region containing two PHD fingers, a putative HAT domain, an acidic region, and a C-terminal Ser/Met-rich domain. The family corresponds to the first PHD finger.


Pssm-ID: 277002  Cd Length: 46  Bit Score: 60.47  E-value: 5.96e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15527      2 CSVCQDSGNADNLLFCDACDKGFHMECHDPPLTRMPKGKWVCQIC 46
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 276-320 7.61e-11

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 60.30  E-value: 7.61e-11
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*.
gi 1537972313   276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEE-LPAHSWKCMTC 320
Cdd:smart00249    2 CSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 229-276 8.78e-11

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 60.20  E-value: 8.78e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1537972313  229 CAVCEGPGELCDLFFCTSCGHHYHGACLDTALTARKRA--GWQCPECKEC 276
Cdd:pfam00628    2 CAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPAEIPsgEWLCPECKPK 51
SET_SETDB1 cd10517
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) ...
 5392-5518 9.96e-11

SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and similar proteins; SETDB1 (EC 2.1.1.43; also termed ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes.


Pssm-ID: 380915 [Multi-domain]  Cd Length: 288  Bit Score: 66.16  E-value: 9.96e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5392 GLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIY-------------EEQNRGIYMfRINNEH--VIDATLTGGPARY 5456
Cdd:cd10517    140 GWGIRCLDDIPKGSFVCIYAGQILTEDEANEEGLQYgdeyfaeldyievVEKLKEGYE-SDVEEHcyIIDAKSEGNLGRY 218

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1537972313 5457 INHSCAPNCVAEVVTFDKEDKIIII----SSRRIPKGEELTYDYQFDFEDDQHKI-PCHCGAWNCRK 5518
Cdd:cd10517    219 LNHSCSPNLFVQNVFVDTHDLRFPWvaffASRYIRAGTELTWDYNYEVGSVPGKVlYCYCGSSNCRG 285
zf-HC5HC2H_2 pfam13832
PHD-zinc-finger like domain;
4998-5093 1.09e-10

PHD-zinc-finger like domain;


Pssm-ID: 463991 [Multi-domain]  Cd Length: 109  Bit Score: 61.59  E-value: 1.09e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4998 RRCCFCHEEGdGAtdgparLLNLDLDLWVHLNCALWSTEV----YETQggALMNVEVALHRGLLTKCSLC-QRTGATSSC 5072
Cdd:pfam13832    1 VRCCLCPLRG-GA------LKQTSDGRWVHVLCAIFVPEVrfgnVATM--EPIDVSRIPPERWKLKCVFCkKRSGACIQC 71

                           90       100
                   ....*....|....*....|.
gi 1537972313 5073 NRMRCPNVYHFACAIRAKCMF 5093
Cdd:pfam13832   72 SKGRCTTAFHVTCAQAAGVYM 92
PHD_UHRF2 cd15617
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); ...
 1425-1469 1.22e-10

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); UHRF2 (also termed Np95/ICBP90-like RING finger protein (NIRF), Np95-like RING finger protein, nuclear protein 97, nuclear zinc finger protein Np97, RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2) was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs,p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277089  Cd Length: 47  Bit Score: 59.58  E-value: 1.22e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1537972313 1425 CEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKG-GWKCKWC 1469
Cdd:cd15617      2 CYVCGGKQDAHMQLLCDECNMAYHIYCLNPPLDKIPEDeDWYCPSC 47
PHA03247 PHA03247
large tegument protein UL36; Provisional
 374-921 1.72e-10

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 68.43  E-value: 1.72e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  374 PPEPGDIPTDEPDALYVA--CQGQPKGGHVTSMQPKEPGPLQcEAKPLGRAGTQLEAQLEAPLNEEMPLLPPPP--PPEE 449
Cdd:PHA03247  2553 PPLPPAAPPAAPDRSVPPprPAPRPSEPAVTSRARRPDAPPQ-SARPRAPVDDRGDPRGPAPPSPLPPDTHAPDppPPSP 2631

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  450 SPLSPPPEESPTSPPPEASRLSPPPEESPESMPPEASRLSPPPEESPESM-----------PPEASRLSPPPEESPLSPP 518
Cdd:PHA03247  2632 SPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQrprrraarptvGSLTSLADPPPPPPTPEPA 2711

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  519 PEECPLSPPPESSPFSPLEESPSSPAleTPLSPPPEASPLSPPFEESPLSPPPEALPTSPPPEASRLSPPPEESPMSPPP 598
Cdd:PHA03247  2712 PHALVSATPLPPGPAAARQASPALPA--APAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVA 2789

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  599 EESPMSPPPEASRlfPPFEESPLSPPPEESPLSPPPEASRLSPPPEDSPMSPPPedsPMSPPPEvsrfsPLPVLSHLSPL 678
Cdd:PHA03247  2790 SLSESRESLPSPW--DPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPP---PPGPPPP-----SLPLGGSVAPG 2859

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  679 PEVSRLSPPPEESPlspppedSPTSPP-PEASRLSPPpedsPVSPPPEdslmSLPLEESPLSPLPEgPRLCPQPEEPYLS 757
Cdd:PHA03247  2860 GDVRRRPPSRSPAA-------KPAAPArPPVRRLARP----AVSRSTE----SFALPPDQPERPPQ-PQAPPPPQPQPQP 2923

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  758 PQPEEPRLCPQPEELPLSPRSEEPCLSPVLAEPCLSSQPEEPHLSP----VPQEQHLSPQPEEPHLSPQPKEPHLSPQSE 833
Cdd:PHA03247  2924 PPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPgrvaVPRFRVPQPAPSREAPASSTPPLTGHSLSR 3003

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  834 EPCLSPML---EEPclSPKPEELYQS------PRPEEPPEELSQCPAPKELSLFPPTGEPPLSPMLGEPAVSEPGEPPL- 903
Cdd:PHA03247  3004 VSSWASSLalhEET--DPPPVSLKQTlwppddTEDSDADSLFDSDSERSDLEALDPLPPEPHDPFAHEPDPATPEAGARe 3081

                          570
                   ....*....|....*...
gi 1537972313  904 SPLPEELPLSLSEEPALS 921
Cdd:PHA03247  3082 SPSSQFGPPPLSANAALS 3099
SET_EHMT2 cd10533
SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine ...
 5368-5517 1.78e-10

SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine N-methyltransferase 2 (EHMT2) and similar proteins; EHMT2 (also termed Eu-HMTase2, HLA-B-associated transcript 8, histone H3-K9 methyltransferase 3, H3-K9-HMTase 3, lysine N-methyltransferase 1C (KMT1C), or protein G9a) acts as a histone-lysine N-methyltransferase that specifically mono- and dimethylates 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin.


Pssm-ID: 380931 [Multi-domain]  Cd Length: 239  Bit Score: 64.65  E-value: 1.78e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5368 KSSQYRRLRTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKiyeeqnrGIYMFRINNE----H 5443
Cdd:cd10533     78 RNCKNRVVQSGIKVRLQLYRTAKMGWGVRALQTIPQGTFICEYVGELISDAEADVRED-------DSYLFDLDNKdgevY 150

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1537972313 5444 VIDATLTGGPARYINHSCAPNCVAEVVTFDKED----KIIIISSRRIPKGEELTYDYQFDFEDDQHK-IPCHCGAWNCR 5517
Cdd:cd10533    151 CIDARYYGNISRFINHLCDPNIIPVRVFMLHQDlrfpRIAFFSSRDIRTGEELGFDYGDRFWDIKSKyFTCQCGSEKCK 229
PHD1_KDM5A_like cd15515
PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar ...
 276-320 2.44e-10

PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar proteins; The JARID subfamily within the JmjC proteins includes Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and a Drosophila homolog, protein little imaginal discs (Lid). KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. KDM5C is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me2 and H3K4me3), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. This family also includes Drosophila melanogaster protein little imaginal discs (Lid) that functions as a JmjC-dependent H3K4me3 demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Members in this family contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two or three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 276990  Cd Length: 46  Bit Score: 58.56  E-value: 2.44e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15515      2 CQVCGRGDDEDKLLLCDGCDDSYHTFCLIPPLPDIPPGDWRCPKC 46
PHD_BAZ1B cd15628
PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also ...
 276-320 2.53e-10

PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. BAZ1B contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277098  Cd Length: 46  Bit Score: 58.60  E-value: 2.53e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15628      2 CKVCRKKGEDDKLILCDECNQAFHLFCLRPALYEVPDGEWMCPAC 46
ePHD_PHF7_G2E3_like cd15669
Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ...
 138-217 2.88e-10

Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ubiquitin-protein ligase (G2E3); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of PHF7 and G2E3. PHF7, also termed testis development protein NYD-SP6, is a testis-specific PHD finger-containing protein that associates with chromatin and binds histone H3 N-terminal tails with a preference for dimethyl lysine 4 (H3K4me2). It may play an important role in stimulating transcription involved in testicular development and/or spermatogenesis. PHF7 contains a PHD finger and a non-canonical ePHD finger, both of which may be involved in activating transcriptional regulation. G2E3 is a dual function ubiquitin ligase (E3) that may play a possible role in cell cycle regulation and the cellular response to DNA damage. It is essential for prevention of apoptosis in early embryogenesis. It is also a nucleo-cytoplasmic shuttling protein with DNA damage responsive localization. G2E3 contains two distinct RING-like ubiquitin ligase domains that catalyze lysine 48-linked polyubiquitination, and a C-terminal catalytic HECT domain that plays an important role in ubiquitin ligase activity and in the dynamic subcellular localization of the protein. The RING-like ubiquitin ligase domains consist of a PHD finger and an ePHD finger.


Pssm-ID: 277139 [Multi-domain]  Cd Length: 112  Bit Score: 60.73  E-value: 2.88e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  138 AHHWCAVWSAGVWgQEGPELCGVDKAIFSGIS--------QRCSHCTRFGASIPCRSPGCPRLYHFPCATASGS-FLSMK 208
Cdd:cd15669     25 AHYFCLLFSSGLP-QRGEDNEGIYGFLPEDIRkevrrasrLRCFYCKKKGASIGCAVKGCRRSFHFPCGLENGCvTQFFG 103


                   ....*....
gi 1537972313  209 TLQLLCPDH 217
Cdd:cd15669    104 EYRSFCWEH 112
PHD2_d4 cd15530
PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three ...
 276-320 3.73e-10

PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three members of the d4 gene family, DPF1 (neuro-d4), DPF2 (ubi-d4/Requiem), and DPF3 (cer-d4), which function as transcription factors and are involved in transcriptional regulation of genes by changing the condensed/decondensed state of chromatin in the nucleus. DPF2 is ubiquitously expressed and it acts as a transcription factor that may participate in developmentally programmed cell death. DPF1 and DPF3 are expressed predominantly in neural tissues, and they may be involved in the transcription regulation of neuro-specific gene clusters. The d4 family proteins show distinct domain organization with domain 2/3 in the N-terminal region, a Cys2His2 (C2H2) zinc finger or Kruppel-type zinc finger in the central part and two adjacent plant homeodomain (PHD) fingers (d4-domain) in the C-terminal part of the molecule. This model corresponds to the second PHD finger.


Pssm-ID: 277005  Cd Length: 46  Bit Score: 58.16  E-value: 3.73e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15530      2 CSLCGTSENDDQLLFCDDCDRGYHMYCLSPPMSEPPEGSWSCHLC 46
PHD1_Lid2p_like cd15519
PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
 276-320 3.74e-10

PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar proteins; Lid2p is a trimethyl H3K4 (H3K4me3) demethylase responsible for H3K4 hypomethylation in heterochromatin. It interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, and mediates H3K9 methylation and small RNA production. It also acts cooperatively with the histone modification enzymes Set1 and Lsd1 and plays an essential role in cross-talk between H3K4 and H3K9 methylation in euchromatin. Lid2p contains a JmjC domain, three PHD fingers and a JmjN domain. This model corresponds to the first PHD finger.


Pssm-ID: 276994 [Multi-domain]  Cd Length: 46  Bit Score: 58.25  E-value: 3.74e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15519      2 CEVCGLDDNEGEVLLCDGCDAEYHTSCLDPPLGEIPPGTWFCPSC 46
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1375-1425 4.68e-10

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 57.89  E-value: 4.68e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1537972313 1375 CVVCGsfGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKG-WRCVECIVC 1425
Cdd:pfam00628    2 CAVCG--KSDDGGELVQCDGCDDWFHLACLGPPLDPAEIPSGeWLCPECKPK 51
ePHD_PHF7_G2E3_like cd15669
Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ...
 5000-5104 5.74e-10

Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ubiquitin-protein ligase (G2E3); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of PHF7 and G2E3. PHF7, also termed testis development protein NYD-SP6, is a testis-specific PHD finger-containing protein that associates with chromatin and binds histone H3 N-terminal tails with a preference for dimethyl lysine 4 (H3K4me2). It may play an important role in stimulating transcription involved in testicular development and/or spermatogenesis. PHF7 contains a PHD finger and a non-canonical ePHD finger, both of which may be involved in activating transcriptional regulation. G2E3 is a dual function ubiquitin ligase (E3) that may play a possible role in cell cycle regulation and the cellular response to DNA damage. It is essential for prevention of apoptosis in early embryogenesis. It is also a nucleo-cytoplasmic shuttling protein with DNA damage responsive localization. G2E3 contains two distinct RING-like ubiquitin ligase domains that catalyze lysine 48-linked polyubiquitination, and a C-terminal catalytic HECT domain that plays an important role in ubiquitin ligase activity and in the dynamic subcellular localization of the protein. The RING-like ubiquitin ligase domains consist of a PHD finger and an ePHD finger.


Pssm-ID: 277139 [Multi-domain]  Cd Length: 112  Bit Score: 59.96  E-value: 5.74e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5000 CCFCHEEgDGATDGPARLLNLDlDLWVHLNCALWSTEV----YETQG--GALMN-VEVALHRGLLTKCSLCQRTGATSSC 5072
Cdd:cd15669      1 CVLCGRS-DDDPDKYGEKLQKD-GICAHYFCLLFSSGLpqrgEDNEGiyGFLPEdIRKEVRRASRLRCFYCKKKGASIGC 78

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1537972313 5073 NRMRCPNVYHFACAIRAKC--MFFKDKTMLCPMH 5104
Cdd:cd15669     79 AVKGCRRSFHFPCGLENGCvtQFFGEYRSFCWEH 112
PHD2_PHF10 cd15529
PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
 1424-1469 5.83e-10

PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed BRG1-associated factor 45a (BAF45a), or XAP135, is a ubiquitously expressed transcriptional regulator that is required for maintaining the undifferentiated status of neuroblasts. It contains a SAY (supporter of activation of yellow) domain and two adjacent plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger.


Pssm-ID: 277004  Cd Length: 44  Bit Score: 57.32  E-value: 5.83e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1537972313 1424 VCEVCGQASDPSRLLLCDDCDISYHTYCLDppLLTVPKGGWKCKWC 1469
Cdd:cd15529      1 TCTKCGDPHDEDKMMFCDQCDRGYHTFCVG--LRSIPDGRWICPLC 44
PHD1_KDM5C_5D cd15604
PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family ...
 276-320 6.35e-10

PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family includes KDM5C and KDM5D, both of which belong to the JARID subfamily within the JmjC proteins. KDM5C (also termed Histone demethylase JARID1C, Jumonji/ARID domain-containing protein 1C, SmcX, or Xe169) is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D (also termed Histocompatibility Y antigen (H-Y), Histone demethylase JARID1D, Jumonji/ARID domain-containing protein 1D, or SmcY) is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me3 andH3K4me2), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. Both KDM5C and KDM5D contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277077  Cd Length: 46  Bit Score: 57.54  E-value: 6.35e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15604      2 CRMCSRGDEDDKLLLCDGCDDNYHTFCLLPPLPEPPKGIWRCPKC 46
PHD2_PHF14 cd15562
PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 1424-1469 6.75e-10

PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the second PHD finger.


Pssm-ID: 277037  Cd Length: 50  Bit Score: 57.42  E-value: 6.75e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1537972313 1424 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKG----GWKCKWC 1469
Cdd:cd15562      1 SCGICKKSNDQHLLALCDTCKLYYHLGCLDPPLTRMPKKtknsGWQCSEC 50
SET_SETDB2 cd10523
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 2 (SETDB2) ...
 5391-5520 8.62e-10

SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 2 (SETDB2) and similar proteins; SETDB2 (EC 2.1.1.43; also termed chronic lymphocytic leukemia deletion region gene 8 protein (CLLD8), or lysine N-methyltransferase 1F (KMT1F)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It is involved in left-right axis specification in early development and mitosis.


Pssm-ID: 380921 [Multi-domain]  Cd Length: 266  Bit Score: 63.31  E-value: 8.62e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5391 QGLGLYAAKDLEKHTMVIEYIGTIIRNEVA--------------NRREKIYEEQNRGIYMFRINNEHVIDATLTGGPARY 5456
Cdd:cd10523    118 KGWGVRCLDDIDKGTFVCIYAGRVLSRARSpteplppklelpseNEVEVVTSWLILSKKRKLRENVCFLDASKEGNVGRF 197

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5457 INHSCAPNCVAEVVTFDKEDKIIII----SSRRIPKGEELTYDYQFDF--EDDQhKIPCHCGAWNCRKWM 5520
Cdd:cd10523    198 LNHSCCPNLFVQNVFVDTHDKNFPWvaffTNRVVKAGTELTWDYSYDAgtSPEQ-EIPCLCGVNKCQKKI 266
SET_SETD5-like cd10529
SET domain found in SET domain-containing protein 5 (SETD5), inactive histone-lysine ...
 5394-5500 8.74e-10

SET domain found in SET domain-containing protein 5 (SETD5), inactive histone-lysine N-methyltransferase 2E (KMT2E) and similar proteins; SETD5 is a probable transcriptional regulator that acts via the formation of large multiprotein complexes that modify and/or remodel the chromatin. KMT2E (also termed inactive lysine N-methyltransferase 2E or myeloid/lymphoid or mixed-lineage leukemia protein 5 (MLL5)) associates with chromatin regions downstream of transcriptional start sites of active genes and thus regulates gene transcription. The family also includes Saccharomyces cerevisiae SET domain-containing proteins, SET3 and SET4, and Schizosaccharomyces pombe SET3. Most of these family members contain a post-SET domain which harbors a zinc-binding site.


Pssm-ID: 380927  Cd Length: 127  Bit Score: 59.60  E-value: 8.74e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5394 GLYAAKDLEKHTMVIEYIGTI-IRNEVanrrEKIYEEQNRGI-YMFRINNEH----VIDATLTGGPARYINHSCAPNCVA 5467
Cdd:cd10529     18 GLVATEDISPGEPILEYKGEVsLRSEF----KEDNGFFKRPSpFVFFYDGFEglplCVDARKYGNEARFIRRSCRPNAEL 93

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1537972313 5468 EVVTFDK-EDKIIIISSRRIPKGEELTYDYQFDF 5500
Cdd:cd10529     94 RHVVVSNgELRLFIFALKDIRKGTEITIPFDYDY 127
ePHD_KMT2B cd15694
Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B); The extended plant ...
 133-201 9.27e-10

Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of KMT2B. KMT2B is also called trithorax homolog 2 or WW domain-binding protein 7 (WBP-7). KMT2B is encoded by the gene that was first named myeloid/lymphoid or mixed-lineage leukemia 2 (MLL2), a second human homolog of Drosophila trithorax, located on chromosome 19. It belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2) and is vital for normal mammalian embryonic development. KMT2B functions as the catalytic subunit in the MLL2 complex, which contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL2 complex is highly active and specific for histone 3 lysine 4 (H3K4) methylation, which stimulates chromatin transcription in a SAM- and H3K4-dependent manner. Moreover, KMT2B plays a critical role in memory formation by mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. KMT2B contains a CxxC (x for any residue) zinc finger domain, three PHD fingers, this ePHD finger, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain.


Pssm-ID: 277164  Cd Length: 105  Bit Score: 58.90  E-value: 9.27e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1537972313  133 GGHCWAHHWCAVWSAGVWGQEGPELCGVDKAIFSGISQRCSHCTRFGASIPCRSPGCPRLYHFPCATAS 201
Cdd:cd15694     22 GQNEWTHVNCAIWSAEVFEENDGSLKNVHAAVARGRQMRCEHCQKIGATVGCCLSACLSNFHFMCARAS 90
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1374-1422 9.96e-10

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 56.84  E-value: 9.96e-10
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*....
gi 1537972313  1374 MCVVCGsfGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVEC 1422
Cdd:smart00249    1 YCSVCG--KPDDGGELLQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
PHD_BAZ1B cd15628
PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also ...
 1425-1469 1.06e-09

PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. BAZ1B contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277098  Cd Length: 46  Bit Score: 56.68  E-value: 1.06e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313 1425 CEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1469
Cdd:cd15628      2 CKVCRKKGEDDKLILCDECNQAFHLFCLRPALYEVPDGEWMCPAC 46
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 1424-1469 1.31e-09

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 56.56  E-value: 1.31e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1537972313 1424 VCEVCGQASD-PSRLLLCDDCDISYHTYCLDPPLLT-VPKGGWKCKWC 1469
Cdd:cd15489      1 SCIVCGKGGDlGGELLQCDGCGKWFHADCLGPPLSSfVPNGKWICPVC 48
PHA03247 PHA03247
large tegument protein UL36; Provisional
 2310-2677 1.39e-09

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 65.34  E-value: 1.39e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2310 GLELKAPDVFKAPLTPRASQVEPQSPGLGLraqePPAAQALAPSPPShsdVFRSASYPDPYAQPPLTPRPQPPPPESCCA 2389
Cdd:PHA03247  2539 GLEELASDDAGDPPPPLPPAAPPAAPDRSV----PPPRPAPRPSEPA---VTSRARRPDAPPQSARPRAPVDDRGDPRGP 2611

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2390 LPPRSLPSD-------PFSRVPASPQSQSSSQSPLTPRPLSAEAFCPSPVTP-----RFQSPDPYSRPPSRPQ---SRDP 2454
Cdd:PHA03247  2612 APPSPLPPDthapdppPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRprrarRLGRAAQASSPPQRPRrraARPT 2691

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2455 FAPLHKPPRPQPPEVAFKAGPLAHT-----PLGAGGFPAALPSGPAGELHAKVPSGQ--PPNFARSPGTGAFVGTPSPMR 2527
Cdd:PHA03247  2692 VGSLTSLADPPPPPPTPEPAPHALVsatplPPGPAAARQASPALPAAPAPPAVPAGPatPGGPARPARPPTTAGPPAPAP 2771

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2528 FTFPQGVGEPSLKPPVPQPGLPPPHGInshfgPGPTLGKPQSTNYTVATGNFHPSGSPLGPNTGPTGEGYGLSPLRPASV 2607
Cdd:PHA03247  2772 PAAPAAGPPRRLTRPAVASLSESRESL-----PSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPP 2846

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2608 MPPPTPEGSLpyLSHGASQRAGITSPVEKREDAGATMSSSSLATPELSSAQDagmpSLSQTELEKQRQRQ 2677
Cdd:PHA03247  2847 PPSLPLGGSV--APGGDVRRRPPSRSPAAKPAAPARPPVRRLARPAVSRSTE----SFALPPDQPERPPQ 2910
PHD2_CHD_II cd15532
PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 1424-1469 1.60e-09

PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the second PHD finger.


Pssm-ID: 277007 [Multi-domain]  Cd Length: 43  Bit Score: 56.13  E-value: 1.60e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1537972313 1424 VCEVCGQASDpsrLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1469
Cdd:cd15532      1 FCRVCKDGGE---LLCCDGCPSSYHLHCLNPPLAEIPDGDWFCPRC 43
PHD1_KDM5A cd15602
PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone ...
 276-320 1.72e-09

PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone demethylase JARID1A, Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2)) was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5A functions as a trimethylated histone H3 lysine 4 (H3K4me3) demethylase that belongs to the JARID subfamily within the JmjC proteins. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5A contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277075  Cd Length: 49  Bit Score: 56.50  E-value: 1.72e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15602      2 CLFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKC 46
PHA03247 PHA03247
large tegument protein UL36; Provisional
 551-981 1.75e-09

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 64.96  E-value: 1.75e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  551 PPPEASPLSPPFEESPLSPPPEALPTSPPP----EASRLSPPPEESPMSPPPEESPMSPPPEASRLFPPFEESPLSPPpe 626
Cdd:PHA03247  2551 PPPPLPPAAPPAAPDRSVPPPRPAPRPSEPavtsRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPP-- 2628

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  627 esplSPPPEASRLSPPPEDSPMSPPPEDSPMSPPPEVS---RFSPLPVLSHLSPLPEVSRLSPPPEESPLSPPPEDSPTS 703
Cdd:PHA03247  2629 ----PSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSrprRARRLGRAAQASSPPQRPRRRAARPTVGSLTSLADPPPP 2704

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  704 PPPEASRLSPPPEDSPVSPPPEDSLMSLP-LEESPLSP-------LPEGPRLCPQPEEPYLSPQPEEPRL--------CP 767
Cdd:PHA03247  2705 PPTPEPAPHALVSATPLPPGPAAARQASPaLPAAPAPPavpagpaTPGGPARPARPPTTAGPPAPAPPAApaagpprrLT 2784

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  768 QPEELPLSPRSEEPCLSPVLAEPCLSSQPEEPHLSPVPQEQHLSPQPEEPHLSPQPKEPHLSPQSEEPCLS-----PMLE 842
Cdd:PHA03247  2785 RPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSvapggDVRR 2864

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  843 EPCLSPKPEELYQSPRPEEPPEELSQCPAPKELSLFPPTGEPPLSPmlgePAVSEPGEPPLSPLPEELPLSLSEEPALSP 922
Cdd:PHA03247  2865 RPPSRSPAAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQ----PQAPPPPQPQPQPPPPPQPQPPPPPPPRPQ 2940

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1537972313  923 QLMPPDPLPPPLSPIIPAAAPPALSPLGELEYPFgakgdSDPESPLAAPILETPISPPP 981
Cdd:PHA03247  2941 PPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAV-----PRFRVPQPAPSREAPASSTP 2994
ePHD_PHF6_like cd15673
Extended PHD finger found in PHD finger protein 6 (PHF6) and PHD finger protein 11 (PHF11); ...
 5000-5104 2.27e-09

Extended PHD finger found in PHD finger protein 6 (PHF6) and PHD finger protein 11 (PHF11); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the two ePHD fingers of PFH6 and the single ePHD finger of PFH11. PHF6, also termed the X-linked mental retardation disorder Borjeson-Forssman-Lehmann syndrome-associated protein, is a nucleolus, ribosomal RNA promoter-associated protein that regulates cell cycle progression by suppressing ribosomal RNA synthesis. It has been implicated in cell cycle control, genomic maintenance, and tumor suppression. PHF6 shows transcriptional repression activity through directly interacting with the nucleosome remodeling and deacetylation complex component RBBP4. PHF6 contains two non-canonical ePHD fingers. PHF11, also termed BRCA1 C-terminus-associated protein, or renal carcinoma antigen NY-REN-34, is a transcriptional co-activator of the Th1 effector cytokine genes, interleukin-2 (IL2) and interferon-gamma (IFNG), co-operating with nuclear factor kappa B (NF-kappaB). It is involved in T-cell activation and viability. Polymorphisms within PHF11 are associated with total IgE, allergic asthma and eczema.


Pssm-ID: 277143  Cd Length: 116  Bit Score: 58.17  E-value: 2.27e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5000 CCFCHEEGDGATDGParLLNLDLDLWVHLNCALWSTEVYETQ-------GGALMN-VEVALHRGLLTKCSLCQRTGATSS 5071
Cdd:cd15673      1 CGFCKSGEENKETGG--KLASGEKIAAHHNCMLFSSGLVQYVspnendfGGFDIEdVKKEIKRGRKLKCNLCKKTGATIG 78

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1537972313 5072 CNRMRCPNVYHFACAIRAKCMFFKDK-----TMLCPMH 5104
Cdd:cd15673     79 CDVKQCKKTYHYHCAKKDDAKIIERNsqgiyRVYCKNH 116
PHD_PHRF1 cd15536
PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also ...
 276-320 2.44e-09

PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also termed KIAA1542, or CTD-binding SR-like protein rA9, is a ubiquitin ligase that induces the ubiquitination of TGIF (TG-interacting factor) at lysine 130. It acts as a tumor suppressor that promotes the transforming growth factor (TGF)-beta cytostatic program through selective release of TGIF-driven promyelocytic leukemia protein (PML) inactivation. PHRF1 contains a plant homeodomain (PHD) finger and a RING finger.


Pssm-ID: 277011  Cd Length: 46  Bit Score: 55.88  E-value: 2.44e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15536      2 CEVCGRSDREDRLLLCDGCDAGYHMECLTPPLDEVPIEEWFCPEC 46
PHD_BAZ2A cd15629
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also ...
 1425-1470 3.87e-09

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. It contains a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277099  Cd Length: 47  Bit Score: 55.24  E-value: 3.87e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1537972313 1425 CEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWCV 1470
Cdd:cd15629      2 CLVCRKGDNDEYLLLCDGCDRGCHMYCHRPKMLQVPEGDWFCPNCV 47
SET_SETDB cd10541
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1), ...
 5391-5518 3.98e-09

SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1), SET domain bifurcated 2 (SETDB2), and similar proteins; SETDB1 (EC 2.1.1.43; also termed ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. SETDB2 (EC 2.1.1.43; also termed chronic lymphocytic leukemia deletion region gene 8 protein (CLLD8), or lysine N-methyltransferase 1F (KMT1F)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It is involved in left-right axis specification in early development and mitosis.


Pssm-ID: 380939 [Multi-domain]  Cd Length: 236  Bit Score: 60.64  E-value: 3.98e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5391 QGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVIDATLTGGPARYINHSCAPNCVAEVV 5470
Cdd:cd10541    102 KGWGIRCLDDIAKGTFVCIYAGKILTDDFADKEGLEMGDEYFANLDHIEESCYIIDAKLEGNLGRYLNHSCSPNLFVQNV 181

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1537972313 5471 TFDKEDKIIIISSRRIPK----GEELTYDYQFDFED-DQHKIPCHCGAWNCRK 5518
Cdd:cd10541    182 FVDTHDLRFPWVAFFASKrikaGTELTWDYNYEVGSvEGKELLCCCGSNECRG 234
PHD1_Lid_like cd15605
PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar ...
 276-320 9.18e-09

PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar proteins; Drosophila melanogaster Lid, also termed Retinoblastoma-binding protein 2 homolog, is identified genetically as a trithorax group (trxG) protein that is a Drosophila homolog of the human protein JARID1A/kdm5A, a member of the JARID subfamily within the JmjC proteins. Lid functions as a JmjC-dependent trimethyl histone H3K4 (H3K4me3) demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Lid contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger of Lid.


Pssm-ID: 277078  Cd Length: 46  Bit Score: 53.99  E-value: 9.18e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15605      2 CHTCGRGDGEESMLLCDGCDDSYHTFCLLPPLSEVPKGDWRCPKC 46
PHD1_KDM5B cd15603
PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
 276-320 1.22e-08

PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis antigen 31 (CT31), Histone demethylase JARID1B, Jumonji/ARID domain-containing protein 1B (JARID1B), PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A)) is a member of the JARID subfamily within the JmjC proteins. It has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of pregnant females and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well as TIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277076  Cd Length: 46  Bit Score: 53.80  E-value: 1.22e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15603      2 CLVCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 46
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 229-273 1.44e-08

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 53.75  E-value: 1.44e-08
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*.
gi 1537972313   229 CAVCEGPGELCDLFFCTSCGHHYHGACLDTALT-ARKRAGWQCPEC 273
Cdd:smart00249    2 CSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLeEEPDGKWYCPKC 47
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 539-848 1.53e-08

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 61.71  E-value: 1.53e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  539 SPSSPALETPLSPPPEASPLSPPFEESPLSPPPEALPTSPPPEASRLSPPPEESPMSPPPEESPMSPPPEASRLFPPFEE 618
Cdd:pfam03154  182 SPPSPPPPGTTQAATAGPTPSAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQTPTLHPQRLPSPHPPLQPMTQPPPPSQV 261

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  619 SPLSPPPEESPLSPPPEASRLSPPPEDSPMSPPPEDSPMSPPPEVSRFSPLPVLSHLSPLPEVSRLSPPPEESPLSPPPE 698
Cdd:pfam03154  262 SPQPLPQPSLHGQMPPMPHSLQTGPSHMQHPVPPQPFPLTPQSSQSQVPPGPSPAAPGQSQQRIHTPPSQSQLQSQQPPR 341

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  699 DSPTSPPPEASRLSPPPEDSPVSPPPEDSLMSLPLEESPLSPLPEGPRLCPQPEEPYLSPQPEEPRLCPQPEELPLSPRS 778
Cdd:pfam03154  342 EQPLPPAPLSMPHIKPPPTTPIPQLPNPQSHKHPPHLSGPSPFQMNSNLPPPPALKPLSSLSTHHPPSAHPPPLQLMPQS 421

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1537972313  779 EE----PCLSPVLAE-----PCLSSQPEEPHLSPVPQEQHLSPQPEEPHLSPqPKEPHLSPQSEEPCLSPMLEEPCLSP 848
Cdd:pfam03154  422 QQlpppPAQPPVLTQsqslpPPAASHPPTSGLHQVPSQSPFPQHPFVPGGPP-PITPPSGPPTSTSSAMPGIQPPSSAS 499
PHD_BAZ2B cd15630
PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also ...
 276-320 1.56e-08

PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A, which is the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP-and histone H4 tail-dependent fashion. BAZ2B contains a TAM (TIP5/ARBP/MBD) domain, an Apolipophorin-III like domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277100  Cd Length: 49  Bit Score: 53.82  E-value: 1.56e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15630      3 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPEGDWFCPAC 47
ePHD_KMT2A cd15693
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A); The extended plant ...
 137-219 1.74e-08

Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of KMT2A. KMT2A also termed ALL-1, or CXXC-type zinc finger protein 7, or myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), or trithorax-like protein (Htrx), or zinc finger protein HRX, is a histone methyltransferase that belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2). It regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex, which also contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL1 complex is highly active and specific for H3K4methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three PHD fingers, a Bromodomain domain, this extended PHD finger, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain.


Pssm-ID: 277163  Cd Length: 113  Bit Score: 55.78  E-value: 1.74e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  137 WAHHWCAVWSAGVWGQEGPELCGVDKAIFSGISQRCSHCTRFGASIPCRSPGCPRLYHFPCATASG-SFLSMKtlQLLCP 215
Cdd:cd15693     28 WTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSCTSNYHFMCSRAKNcVFLEDK--KVYCQ 105


                   ....
gi 1537972313  216 DHSE 219
Cdd:cd15693    106 RHKD 109
PHD_PHF21A cd15523
PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC ...
 1424-1469 2.02e-08

PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC complex protein BHC80) along with HDAC1/2, CtBP1, CoREST, and BRAF35, is associated with LSD1, a lysine (K)-specific histone demethylase. It inhibits LSD1-mediated histone demethylation in vitro. PHF21A is predominantly present in the central nervous system and spermatogenic cells and is one of the six components of BRAF-HDAC complex (BHC) involved in REST-dependent transcriptional repression of neuron-specific genes in non-neuronal cells. It acts as a scaffold protein in BHC in neuronal as well as non-neuronal cells and also plays a role in spermatogenesis. PHF21A contains a C-terminal plant homeodomain (PHD) finger that is responsible for the binding directly to each of five other components of BHC, and of organizing BHC mediating transcriptional repression.


Pssm-ID: 276998 [Multi-domain]  Cd Length: 43  Bit Score: 53.17  E-value: 2.02e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1537972313 1424 VCEVCGQASDpsrLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1469
Cdd:cd15523      1 FCSVCRKSGE---LLMCDTCSLVYHLDCLDPPLKTIPKGMWICPKC 43
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 1501-1551 2.35e-08

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 53.09  E-value: 2.35e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1537972313 1501 TCPVCHAPYVEEDLLIQCRHCERWMHAGCESLFTEDEVEqaaDEGFDCVSC 1551
Cdd:cd15489      1 SCIVCGKGGDLGGELLQCDGCGKWFHADCLGPPLSSFVP---NGKWICPVC 48
SET cd08161
SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily; The Su(var)3-9, ...
 5382-5496 2.93e-08

SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily; The Su(var)3-9, Enhancer-of-zeste, Trithorax (SET) domain superfamily corresponds to SET domain-containing lysine methyltransferases, which catalyze site and state-specific methylation of lysine residues in histones that are fundamental in epigenetic regulation of gene activation and silencing in eukaryotic organisms. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains has been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as N-SET and C-SET. C-SET forms an unusual and conserved knot-like structure of probable functional importance. In addition to N-SET and C-SET, an insert region (I-SET) and flanking regions of high structural variability form part of the overall structure. Some family members contain a pre-SET domain, which is found in a number of histone methyltransferases (HMTase), and a post-SET domain, which harbors a zinc-binding site.


Pssm-ID: 380914 [Multi-domain]  Cd Length: 72  Bit Score: 53.41  E-value: 2.93e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5382 NVYLARSRIQGLGLYAAKDLEKhtmvieyiGTIIrnevanrrekiyeeqnrgiymfrinnehvidatltgGPARYINHSC 5461
Cdd:cd08161      1 EIRPSTIPGAGFGLFATRDIPK--------GEVI------------------------------------GLARFINHSC 36

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1537972313 5462 APNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDY 5496
Cdd:cd08161     37 EPNCEFEEVYVGGKPRVFIVALRDIKAGEELTVDY 71
PHD_BAZ2B cd15630
PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also ...
 1423-1471 3.07e-08

PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A, which is the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP-and histone H4 tail-dependent fashion. BAZ2B contains a TAM (TIP5/ARBP/MBD) domain, an Apolipophorin-III like domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277100  Cd Length: 49  Bit Score: 52.67  E-value: 3.07e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1537972313 1423 IVCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWCVS 1471
Cdd:cd15630      1 VYCQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPEGDWFCPACIA 49
PHD_UHRF1_2 cd15525
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and ...
 278-320 3.38e-08

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and UHRF2; UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277000  Cd Length: 47  Bit Score: 52.76  E-value: 3.38e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1537972313  278 ACRKPGN---DSKMLVCETCDKGYHTFCLKPPIEELPAHS-WKCMTC 320
Cdd:cd15525      1 ACHVCGGkqdPEKQLLCDECDMAYHLYCLDPPLTSLPDDDeWYCPDC 47
PHD3_PHF14 cd15563
PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 1424-1469 3.53e-08

PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the third PHD finger.


Pssm-ID: 277038  Cd Length: 49  Bit Score: 52.78  E-value: 3.53e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1537972313 1424 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKG---GWKCKWC 1469
Cdd:cd15563      1 ECCVCKQTGDNSQLVRCDECKLCYHFGCLDPPLKKSPKQrgyGWVCEEC 49
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
 1425-1469 3.60e-08

PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED) protein, functions as a regulator of gene transcription in the thymus. It is essential for prevention of autoimmunity. AIRE plays a critical role in the induction of central tolerance. It promotes self-tolerance through tissue-specific antigen (TSA) expression. It also acts as an active regulator of chondrocyte differentiation. AIRE contains a homogeneously-staining region (HSR) or caspase-recruitment domain (CARD), a nuclear localization signal (NLS), a SAND (for Sp100, AIRE, nuclear phosphoprotein 41/75 or NucP41/75, and deformed epidermal auto regulatory factor 1 or Deaf1) domain, two plant homeodomain (PHD) fingers, and four LXXLL (where L stands for leucine) motifs. This model corresponds to the first PHD finger that recognizes the unmethylated tail of histone H3 and targets AIRE-dependent genes.


Pssm-ID: 277014 [Multi-domain]  Cd Length: 43  Bit Score: 52.45  E-value: 3.60e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313 1425 CEVCGqasDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1469
Cdd:cd15539      2 CAVCG---DGGELLCCDGCPRAFHLACLVPPLTLIPSGTWRCSSC 43
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 276-320 3.80e-08

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 52.70  E-value: 3.80e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1537972313  276 CQACRKPGND-SKMLVCETCDKGYHTFCLKPPIEELPAH-SWKCMTC 320
Cdd:cd15489      2 CIVCGKGGDLgGELLQCDGCGKWFHADCLGPPLSSFVPNgKWICPVC 48
PHD2_CHD_II cd15532
PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 276-320 6.23e-08

PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the second PHD finger.


Pssm-ID: 277007 [Multi-domain]  Cd Length: 43  Bit Score: 51.90  E-value: 6.23e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGNdskMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15532      2 CRVCKDGGE---LLCCDGCPSSYHLHCLNPPLAEIPDGDWFCPRC 43
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 228-273 6.58e-08

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 51.93  E-value: 6.58e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1537972313  228 HCAVCEGPGELCD-LFFCTSCGHHYHGACLDTAL-TARKRAGWQCPEC 273
Cdd:cd15489      1 SCIVCGKGGDLGGeLLQCDGCGKWFHADCLGPPLsSFVPNGKWICPVC 48
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 1374-1422 1.53e-07

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 50.78  E-value: 1.53e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1537972313 1374 MCVVCGSfGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVEC 1422
Cdd:cd15489      1 SCIVCGK-GGDLGGELLQCDGCGKWFHADCLGPPLSSFVPNGKWICPVC 48
PHA03247 PHA03247
large tegument protein UL36; Provisional
 2086-2478 2.14e-07

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 58.03  E-value: 2.14e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2086 ARKTDRPALHLRIPSQPGALGSPPPAAAPTIFiGSPTTPAGLSTSADGFLKPPAGTVPGPDSPGELFlklPPQVPAQVPS 2165
Cdd:PHA03247  2667 ARRLGRAAQASSPPQRPRRRAARPTVGSLTSL-ADPPPPPPTPEPAPHALVSATPLPPGPAAARQAS---PALPAAPAPP 2742

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2166 QDPFGLAPAYAPEPRFSAAPPTYPPYPTPSGAPAQPPiLGTTTRPGTGQPGEFHTTPPGTPrhQPSTPDPFLKPRCPSLD 2245
Cdd:PHA03247  2743 AVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGP-PRRLTRPAVASLSESRESLPSPW--DPADPPAAVLAPAAALP 2819

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2246 NLAVPeSPGVAGGKASEPLLSPPPFGESRKTLEVKkeelGASSPG----YGPPNLGCVDSPSSGSHLGGLELKAPDVFKA 2321
Cdd:PHA03247  2820 PAASP-AGPLPPPTSAQPTAPPPPPGPPPPSLPLG----GSVAPGgdvrRRPPSRSPAAKPAAPARPPVRRLARPAVSRS 2894

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2322 PLT--------PRASQVEPQSPGLGLRAQEPPAAQALAPSPPSHSDvfrSASYPDPYAQPPLTPRPQPPPPESCCALP-- 2391
Cdd:PHA03247  2895 TESfalppdqpERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQ---PPLAPTTDPAGAGEPSGAVPQPWLGALVPgr 2971

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2392 ---PRSLPSDPFSRVPASPQSQSSSQSPLTPRPLS-------AEAFCPSPVT------------------PRFQSPDPYS 2443
Cdd:PHA03247  2972 vavPRFRVPQPAPSREAPASSTPPLTGHSLSRVSSwasslalHEETDPPPVSlkqtlwppddtedsdadsLFDSDSERSD 3051

                          410       420       430
                   ....*....|....*....|....*....|....*
gi 1537972313 2444 RPPSRPQSRDPFAPLHKPPRPQPPEVAFKAGPLAH 2478
Cdd:PHA03247  3052 LEALDPLPPEPHDPFAHEPDPATPEAGARESPSSQ 3086
HMG smart00398
high mobility group;
2013-2064 5.29e-07

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 50.01  E-value: 5.29e-07
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....
gi 1537972313  2013 VLYANINFPNLKQDYPDWSS--RCKQIMKLWRKVPAADKAPYLQKAKDNRAAHR 2064
Cdd:smart00398   10 MLFSQENRAKIKAENPDLSNaeISKKLGERWKLLSEEEKAPYEEKAKKDKERYE 63
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1501-1551 6.84e-07

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 48.75  E-value: 6.84e-07
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|.
gi 1537972313  1501 TCPVCHAPYvEEDLLIQCRHCERWMHAGCESLFTEDEVEqaaDEGFDCVSC 1551
Cdd:smart00249    1 YCSVCGKPD-DGGELLQCDGCDRWYHQTCLGPPLLEEEP---DGKWYCPKC 47
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
 699-918 6.88e-07

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 56.24  E-value: 6.88e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  699 DSPTSPPPEASRLSPPPEDSPVSPPPEDSLMSLPLEESPLSPLPEGPRLCPQPEEpylspqPEEPRlcpqpeeLPLSPRS 778
Cdd:PTZ00449   536 DSKESDEPKEGGKPGETKEGEVGKKPGPAKEHKPSKIPTLSKKPEFPKDPKHPKD------PEEPK-------KPKRPRS 602

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  779 EEPCLSPvlaepclsSQPEEPHLSPVPQEQHLSPQPEEPHLSPQPKEPhLSPQSEEPCLSPMLEEPCLSPKP-------E 851
Cdd:PTZ00449   603 AQRPTRP--------KSPKLPELLDIPKSPKRPESPKSPKRPPPPQRP-SSPERPEGPKIIKSPKPPKSPKPpfdpkfkE 673

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1537972313  852 ELYQSPRPEEPPEELSQCPAPKELSlFPPTGEPPLSPMLGEPAVSEPGEPPLSPLPEELPLSLSEEP 918
Cdd:PTZ00449   674 KFYDDYLDAAAKSKETKTTVVLDES-FESILKETLPETPGTPFTTPRPLPPKLPRDEEFPFEPIGDP 739
PHD1_BPTF cd15559
PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, ...
 276-320 7.10e-07

PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, also termed nucleosome-remodeling factor subunit BPTF, or fetal Alz-50 clone 1 protein (FAC1), or fetal Alzheimer antigen, functions as a transcriptional regulator that exhibits altered expression and subcellular localization during neuronal development and neurodegenerative diseases such as Alzheimer's disease. It interacts with the human orthologue of the Kelch-like Ech-associated protein (Keap1). Its function and subcellular localization can be regulated by Keap1. Moreover, BPTF is a novel DNA-binding protein that recognizes the DNA sequence CACAACAC and represses transcription through this site in a phosphorylation-dependent manner. Furthermore, BPTF interacts with the Myc-associated zinc finger protein (ZF87/MAZ) and alters its transcriptional activity, which has been implicated in gene regulation in neurodegeneration. Some family members contain two or three plant homeodomain (PHD) fingers, which may be involved in complex formation with histone H3 trimethylated at K4 (H3K4me3). This family corresponds to the first PHD finger.


Pssm-ID: 277034 [Multi-domain]  Cd Length: 43  Bit Score: 48.57  E-value: 7.10e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGNdskMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15559      2 CRVCHKLGD---LLCCETCSAVYHLECVDPPLEEVPEEDWQCEVC 43
PHD2_PHF12_Rco1 cd15534
PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, ...
 1424-1466 7.23e-07

PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, also termed PHD factor 1 (Pf1), is a plant homeodomain (PHD) zinc finger-containing protein that bridges the transducin-like enhancer of split (TLE) corepressor to the mSin3A-histone deacetylase (HDAC)-complex, and further represses transcription at targeted genes. PHF12 also interacts with MRG15 (mortality factor-related genes on chromosome 15), a member of the mortality factor (MORF) family of proteins implicated in regulating cellular senescence. PHF12 contains two plant homeodomain (PHD) zinc fingers followed by a polybasic region. The PHD fingers function downstream of phosphoinositide signaling triggered by the interaction between polybasic regions and phosphoinositides. This subfamily also includes yeast transcriptional regulatory protein Rco1 and similar proteins. Rco1 is a component of the Rpd3S histone deacetylase complex that plays an important role at actively transcribed genes. Rco1 contains two PHD fingers, which are required for the methylation of histone H3 lysine 36 (H3K36) nucleosome recognition by Rpd3S. This model corresponds to the second PHD finger.


Pssm-ID: 277009  Cd Length: 47  Bit Score: 48.88  E-value: 7.23e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1537972313 1424 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGG-WKC 1466
Cdd:cd15534      1 VCFKCNRSCRVAPLIQCDYCPLLFHLDCLDPPLTHPPATGrWMC 44
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 1425-1469 8.46e-07

PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the first PHD finger.


Pssm-ID: 277006 [Multi-domain]  Cd Length: 43  Bit Score: 48.37  E-value: 8.46e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313 1425 CEVCGQASDpsrLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1469
Cdd:cd15531      2 CEVCQQGGE---IILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 43
PHD1_Snt2p_like cd15497
PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and ...
 1425-1469 8.98e-07

PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and similar proteins; Snt2p is a yeast protein that may function in multiple stress pathways. It coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress through interaction with Ecm5 and the Rpd3 deacetylase. Snt2p contains a bromo adjacent homology (BAH) domain, two canonical Cys4HisCys3 plant homeodomain (PHD) fingers, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domain; this model corresponds to the first canonical Cys4HisCys3 PHD finger.


Pssm-ID: 276972  Cd Length: 48  Bit Score: 48.46  E-value: 8.98e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1537972313 1425 CEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGG--WKCKWC 1469
Cdd:cd15497      2 CKVCKEWCASDDSVRCDECKVSYHLLCVDPPLTKKPNRGfvWSCAPC 48
PHD1_PHF12 cd15533
PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is ...
 1424-1469 9.73e-07

PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is a plant homeodomain (PHD) zinc finger-containing protein that bridges the transducin-like enhancer of split (TLE) corepressor to the mSin3A-histone deacetylase (HDAC)-complex, and further represses transcription at targeted genes. PHF12 also interacts with MRG15 (mortality factor-related genes on chromosome 15), a member of the mortality factor (MORF) family of proteins implicated in regulating cellular senescence. PHF12 contains two plant-homeodomain (PHD) zinc fingers followed by a polybasic region. The PHD fingers function downstream of phosphoinositide signaling triggered by the interaction between polybasic regions and phosphoinositides. This model corresponds to the first PHD finger.


Pssm-ID: 277008 [Multi-domain]  Cd Length: 45  Bit Score: 48.51  E-value: 9.73e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1537972313 1424 VCEVCGQASDpsrLLLCDDCDISYHTYCLDPPL--LTVPKGGWKCKWC 1469
Cdd:cd15533      1 YCDSCGEGGD---LLCCDRCPASFHLQCCNPPLdeEDLPPGEWLCHRC 45
PHD_PRHA_like cd15504
PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and ...
 1424-1469 1.06e-06

PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and similar proteins; PRHA is a homeodomain protein encoded by a single-copy Arabidopsis thaliana homeobox gene, prha. It shows the capacity to bind to TAATTG core sequence elements but requires additional adjacent bases for high-affinity binding. PRHA contains a plant homeodomain (PHD) finger, a homeodomain, peptide repeats and a putative leucine zipper dimerization domain.


Pssm-ID: 276979  Cd Length: 53  Bit Score: 48.59  E-value: 1.06e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1537972313 1424 VCEVC--GQASDPSRLLLCD-DCDISYHTYCLDPPLLT--VPKG--GWKCKWC 1469
Cdd:cd15504      1 FCAKCqsGEASPDNDILLCDgGCNRAYHQKCLEPPLLTedIPPEdeGWLCPLC 53
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 1425-1469 1.15e-06

PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the first PHD finger.


Pssm-ID: 276984  Cd Length: 48  Bit Score: 48.46  E-value: 1.15e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1537972313 1425 CEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVP--KGGWKCKWC 1469
Cdd:cd15509      2 CAVCDSPGDLSDLLFCTSCGQHYHGSCLDPAVRPTPlvRAGWQCPEC 48
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 640-993 1.39e-06

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 55.16  E-value: 1.39e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  640 SPPPEDSPMSPPPEDSPMSPPPEVSRFSPLPVLSHLSPLPEVSrlspppeesplsPPPEDSPTSPPPEASRLSPPPEDSP 719
Cdd:pfam03154  196 TAGPTPSAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQTPTLH------------PQRLPSPHPPLQPMTQPPPPSQVSP 263

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  720 VSPPPedslmslPLEESPLSPLPE----GPRLCPQPeepyLSPQPeeprlcpqpeeLPLSPRSEEpCLSPVLAEPCLSSQ 795
Cdd:pfam03154  264 QPLPQ-------PSLHGQMPPMPHslqtGPSHMQHP----VPPQP-----------FPLTPQSSQ-SQVPPGPSPAAPGQ 320

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  796 PEEPHLSPVPQEQHLSPQP-EEPHLSPQPKE-PHLSPQSEEPClsPMLEEPCLSPKPEELyQSPRPEEPPEELSQCPAPK 873
Cdd:pfam03154  321 SQQRIHTPPSQSQLQSQQPpREQPLPPAPLSmPHIKPPPTTPI--PQLPNPQSHKHPPHL-SGPSPFQMNSNLPPPPALK 397

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  874 ELSLF----PPTGEPPLSPML--GEPAVSEPGEPPLSPLPEELPLSLSEEPALSPQLMPPDPLppplspiipaaappals 947
Cdd:pfam03154  398 PLSSLsthhPPSAHPPPLQLMpqSQQLPPPPAQPPVLTQSQSLPPPAASHPPTSGLHQVPSQS----------------- 460

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*.
gi 1537972313  948 plgeleyPFGakgdSDPESPLAAPILETPISPPPEANCTDPEPVPP 993
Cdd:pfam03154  461 -------PFP----QHPFVPGGPPPITPPSGPPTSTSSAMPGIQPP 495
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 538-831 1.43e-06

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 55.16  E-value: 1.43e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  538 ESPSSPALETPLSPPPEASPLSPPFEESPLSPPPEALPTS------PPPEASRLSPPPEESPMSPPPEESPMSPPPEASR 611
Cdd:pfam03154  264 QPLPQPSLHGQMPPMPHSLQTGPSHMQHPVPPQPFPLTPQssqsqvPPGPSPAAPGQSQQRIHTPPSQSQLQSQQPPREQ 343

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  612 LFPPfeesplspppeesplsPPPEASRLSPPPEdSPMSPPPEDSPMSPPPEVSRFSPLPVLSHLSPLPEVSrlspppEES 691
Cdd:pfam03154  344 PLPP----------------APLSMPHIKPPPT-TPIPQLPNPQSHKHPPHLSGPSPFQMNSNLPPPPALK------PLS 400

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  692 PLSPPPEDSPTSPPPEASRLSPPPEDSPVSPPPEDSLMSLPLEES---PLSPLPEGPRLCPQPEEPYL--SPQPEEPRLC 766
Cdd:pfam03154  401 SLSTHHPPSAHPPPLQLMPQSQQLPPPPAQPPVLTQSQSLPPPAAshpPTSGLHQVPSQSPFPQHPFVpgGPPPITPPSG 480

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1537972313  767 PQPEELPLSPRSEEPCLSPVLAEPCLSSQPEEPhLSPVPQEQHLSPQPEEPHlSPQPKEPHLSPQ 831
Cdd:pfam03154  481 PPTSTSSAMPGIQPPSSASVSSSGPVPAAVSCP-LPPVQIKEEALDEAEEPE-SPPPPPRSPSPE 543
PHD_TIF1_like cd15541
PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar ...
 1424-1469 1.97e-06

PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar proteins; The TIF1 family of transcriptional cofactors includes TIF1alpha (TRIM24), TIF1beta (TRIM28), TIF1gamma (TRIM33), and TIF1delta (TRIM66), which are characterized by an N-terminal RING-finger B-box coiled-coil (RBCC/TRIM) motif and plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region. TIF1 proteins couple chromatin modifications to transcriptional regulation, signaling, and tumor suppression. They exert a deacetylase-dependent silencing effect when tethered to a promoter region. TIF1alpha, TIF1beta, and TIF1delta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. TIF1alpha and TIF1beta bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. In contrast, TIF1delta appears to lack nuclear receptor- and KRAB-binding activity. Moreover, TIF1delta is specifically involved in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. TIF1gamma is structurally closely related to TIF1alpha and TIF1beta, but has very little functional features in common with them. It does not interact with the KRAB silencing domain of KOX1 or the heterochromatinic proteins HP1alpha, beta, and gamma. It cannot bind to nuclear receptors (NRs). This family also includes Sp100/Sp140 family proteins, the nuclear body SP100 and SP140. Sp110 is a leukocyte-specific component of the nuclear body. It may function as a nuclear hormone receptor transcriptional coactivator that may play a role in inducing differentiation of myeloid cells. It is also involved in resisting intracellular pathogens and functions as an important drug target for preventing intracellular pathogen diseases, such as tuberculosis, hepatic veno-occlusive disease, and intracellular cancers. SP140 is an interferon inducible nuclear leukocyte-specific protein involved in primary biliary cirrhosis and a risk factor in chronic lymphocytic leukemia. It is also implicated in innate immune response to human immunodeficiency virus type 1 (HIV-1) by binding to the virus viral infectivity factor (Vif) protein. Both Sp110 and Sp140 contain a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD).


Pssm-ID: 277016 [Multi-domain]  Cd Length: 43  Bit Score: 47.34  E-value: 1.97e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1537972313 1424 VCEVCGqasDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1469
Cdd:cd15541      1 WCAVCQ---NGGELLCCDKCPRVFHLDCHIPPIPEFPSGEWSCSLC 43
PHD_Phf1p_Phf2p_like cd15502
PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 ...
 1422-1469 2.06e-06

PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 (Phf1p) and Phf2 (Phf2p); Phf1p and Phf2p are components of the SWM histone demethylase complex that specifically demethylates histone H3 at lysine 9 (H3K9me2), a specific tag for epigenetic transcriptional activation. They function as corepressors and play roles in regulating heterochromatin propagation and euchromatic transcription. Both Phf1p and Phf2p contain a plant homeodomain (PHD) finger.


Pssm-ID: 276977  Cd Length: 52  Bit Score: 47.82  E-value: 2.06e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1537972313 1422 CIVCEvCGQASDPSRLLLCDDCDISYHTYCLDPP----LLTVPKGGWKCKWC 1469
Cdd:cd15502      2 CIVCQ-RGHSPKSNRIVFCDGCNTPYHQLCHDPSiddeVVEDPDAEWFCKKC 52
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 699-913 2.16e-06

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 54.71  E-value: 2.16e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  699 DSPTSPPPEASRLSPPPED-SPVSPPPEDSLMSLPLEESPLSPLPEGPRLCPQPEEPYLSPQPEEPRLCPQPEELPLSPr 777
Cdd:PRK10263   350 DVPPAQPTVAWQPVPGPQTgEPVIAPAPEGYPQQSQYAQPAVQYNEPLQQPVQPQQPYYAPAAEQPAQQPYYAPAPEQP- 428

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  778 SEEPCLSPVLAEPCLSSQPEEPhlspvPQEQHLSP----QPEEPHLSPQPKEP-HLSPQSEEPclsPMLEEPclSPKPEE 852
Cdd:PRK10263   429 AQQPYYAPAPEQPVAGNAWQAE-----EQQSTFAPqstyQTEQTYQQPAAQEPlYQQPQPVEQ---QPVVEP--EPVVEE 498

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1537972313  853 LYQSPRPEEPPEELSQCPAPKELSL---FPPTGEPPLSPMLGEPAVSEPGE---PPLSPLPEELPLS 913
Cdd:PRK10263   499 TKPARPPLYYFEEVEEKRAREREQLaawYQPIPEPVKEPEPIKSSLKAPSVaavPPVEAAAAVSPLA 565
SET_SpSET3-like cd19183
SET domain (including post-SET domain) found in Schizosaccharomyces pombe SET ...
 5393-5507 2.23e-06

SET domain (including post-SET domain) found in Schizosaccharomyces pombe SET domain-containing protein 3 (SETD3) and similar proteins; Schizosaccharomyces pombe SETD3 functions as a transcriptional regulator that acts via the formation of large multiprotein complexes that modify and/or remodel the chromatin. It is required for both, gene activation and repression.


Pssm-ID: 380960  Cd Length: 173  Bit Score: 51.25  E-value: 2.23e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5393 LGLYAAKDLEKHTMVIEYIGtiirnEVANRREKIYEEQNRgiY----------MFRINNEHVIDATLTGGPARYINHSCA 5462
Cdd:cd19183     14 FGLFADRPIPAGDPIQELLG-----EIGLQSEYIADPENQ--YqilgapkphvFFHPQSPLYIDTRRSGSVARFIRRSCR 86

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1537972313 5463 PNCVAEVVTFDK--EDKIIIISSRRIPKGEELTYDYQFDFEDDQHKI 5507
Cdd:cd19183     87 PNAELVTVASDSgsVLKFVLYASRDISPGEEITIGWDWDNPHPFRRF 133
SET_AtSUVH-like cd10545
SET domain found in Arabidopsis thaliana histone H3-K9 methyltransferases (SUVHs) and similar ...
 5407-5496 2.60e-06

SET domain found in Arabidopsis thaliana histone H3-K9 methyltransferases (SUVHs) and similar proteins; Arabidopsis thaliana SUVH protein (also termed suppressor of variegation 3-9 homolog protein) is a histone-lysine N-methyltransferase that methylates 'Lys-9' of histone H3. H3 'Lys-9' methylation represents a specific tag for epigenetic transcriptional repression. Some family members contain a post-SET domain which binds a Zn2+ ion. Most family members, except for Arabidopsis thaliana SUVH9, contain a post-SET domain which harbors a zinc-binding site.


Pssm-ID: 380943 [Multi-domain]  Cd Length: 232  Bit Score: 52.02  E-value: 2.60e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5407 VIEYIGTIIRNEVANRREKiyeeqnRGIYMFRINN-------------------------------EHVIDATLTGGPAR 5455
Cdd:cd10545    112 ICEYVGELLDTSEADTRSG------NDDYLFDIDNrqtnrgwdggqrldvgmsdgerssaedeessEFTIDAGSFGNVAR 185

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313 5456 YINHSCAPNCVAEVVTFDKEDKIIII----SSRRIPKGEELTYDY 5496
Cdd:cd10545    186 FINHSCSPNLFVQCVLYDHNDLRLPRvmlfAADNIPPLQELTYDY 230
PHD1_MTF2_PHF19_like cd15499
PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ...
 1424-1472 3.14e-06

PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) family proteins MTF2, PHF19, and similar proteins; The family includes two PCL family proteins, metal-response element-binding transcription factor 2 (MTF2/PCL2) and PHF19/PCL3, which are homologs of PHD finger protein1 (PHF1). PCL family proteins are accessory components of the polycomb repressive complex 2 (PRC2) core complex and all contain an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. They specifically recognize tri-methylated H3K36 (H3K36me3) through their N-terminal Tudor domains. The interaction between their Tudor domains and H3K36me3 is critical for both the targeting and spreading of PRC2 into active chromatin regions and for the maintenance of optimal repression of poised developmental genes where PCL proteins, H3K36me3, and H3K27me3 coexist. Moreover, unlike other PHD finger-containing proteins, the first PHD fingers of PCL proteins do not display histone H3K4 binding affinity and they do not affect the Tudor domain binding to histones. This model corresponds to the first PHD finger.


Pssm-ID: 276974  Cd Length: 53  Bit Score: 47.11  E-value: 3.14e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1537972313 1424 VCEVCG--QASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWCVSC 1472
Cdd:cd15499      1 TCSICGgaEARDGNEILICDKCDKGYHQLCHSPKVRTSPLEGDEKWFCSRC 51
ePHD_PHF6_like cd15673
Extended PHD finger found in PHD finger protein 6 (PHF6) and PHD finger protein 11 (PHF11); ...
 136-217 3.22e-06

Extended PHD finger found in PHD finger protein 6 (PHF6) and PHD finger protein 11 (PHF11); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the two ePHD fingers of PFH6 and the single ePHD finger of PFH11. PHF6, also termed the X-linked mental retardation disorder Borjeson-Forssman-Lehmann syndrome-associated protein, is a nucleolus, ribosomal RNA promoter-associated protein that regulates cell cycle progression by suppressing ribosomal RNA synthesis. It has been implicated in cell cycle control, genomic maintenance, and tumor suppression. PHF6 shows transcriptional repression activity through directly interacting with the nucleosome remodeling and deacetylation complex component RBBP4. PHF6 contains two non-canonical ePHD fingers. PHF11, also termed BRCA1 C-terminus-associated protein, or renal carcinoma antigen NY-REN-34, is a transcriptional co-activator of the Th1 effector cytokine genes, interleukin-2 (IL2) and interferon-gamma (IFNG), co-operating with nuclear factor kappa B (NF-kappaB). It is involved in T-cell activation and viability. Polymorphisms within PHF11 are associated with total IgE, allergic asthma and eczema.


Pssm-ID: 277143  Cd Length: 116  Bit Score: 49.31  E-value: 3.22e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  136 CWAHHWCAVWSAGVWGQEGP---ELCG-----VDKAIFSGISQRCSHCTRFGASIPCRSPGCPRLYHFPCATASGSFLSM 207
Cdd:cd15673     23 IAAHHNCMLFSSGLVQYVSPnenDFGGfdiedVKKEIKRGRKLKCNLCKKTGATIGCDVKQCKKTYHYHCAKKDDAKIIE 102

                           90
                   ....*....|....
gi 1537972313  208 KTLQ----LLCPDH 217
Cdd:cd15673    103 RNSQgiyrVYCKNH 116
ePHD1_PHF6 cd15710
Extended PHD finger 1 found in PHD finger protein 6 (PHF6); The extended plant homeodomain ...
 5027-5090 3.48e-06

Extended PHD finger 1 found in PHD finger protein 6 (PHF6); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. PHF6 contains two non-canonical ePHD fingers, this model corresponds to the first ePHD finger. PHF6, also termed the X-linked mental retardation disorder Borjeson-Forssman-Lehmann syndrome-associated protein, is a nucleolus, ribosomal RNA promoter-associated protein that regulates cell cycle progression by suppressing ribosomal RNA synthesis. It has been implicated in cell cycle control, genomic maintenance, and tumor suppression. PHF6 shows transcriptional repression activity through directly interacting with the nucleosome remodeling and deacetylation complex component RBBP4. .


Pssm-ID: 277180  Cd Length: 115  Bit Score: 49.19  E-value: 3.48e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1537972313 5027 HLNCALWSTEVYETQ-------GGALMNVEVALHRGLLTKCSLCQRTGATSSCNRMRCPNVYHFACAIRAK 5090
Cdd:cd15710     26 HHKCMLFSSALVSSHsdsenlgGFSIEDVQKEIKRGTKLMCSLCHCPGATIGCDVKTCHRTYHYYCALHDK 96
SET_SETD5 cd19181
SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and ...
 5395-5516 3.54e-06

SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins; SETD5 is a probable transcriptional regulator that acts via the formation of large multiprotein complexes that modify and/or remodel the chromatin. SETD5 loss-of-function mutations are a likely cause of a familial syndromic intellectual disability with variable phenotypic expression.


Pssm-ID: 380958  Cd Length: 150  Bit Score: 50.01  E-value: 3.54e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5395 LYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINN--EHVIDATLTGGPARYINHSCAPNCVAEVVTF 5472
Cdd:cd19181     21 LRAARDLALDTLIIEYRGKVMLRQQFEVNGHFFKRPYPFVLFYSKFNgvEMCVDARTFGNDARFIRRSCTPNAEVRHMIA 100

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1537972313 5473 DKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHC--GAWNC 5516
Cdd:cd19181    101 DGMIHLCIYAVAAIAKDAEVTIAFDYEYSNCNYKVDCAChkGNRNC 146
PHD2_PHF14 cd15562
PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 229-273 4.12e-06

PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the second PHD finger.


Pssm-ID: 277037  Cd Length: 50  Bit Score: 46.63  E-value: 4.12e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1537972313  229 CAVCEGPGELCDLFFCTSCGHHYHGACLDTALT----ARKRAGWQCPEC 273
Cdd:cd15562      2 CGICKKSNDQHLLALCDTCKLYYHLGCLDPPLTrmpkKTKNSGWQCSEC 50
PHA03247 PHA03247
large tegument protein UL36; Provisional
 451-913 5.90e-06

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 53.40  E-value: 5.90e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  451 PLSP-------PPEESPTSPPPEASRLSPPPEESPESMPPEASRLSPPPEESPESMPPEASRLSPPPEESPLSPPPEECP 523
Cdd:PHA03247  2489 PFAAgaapdpgGGGPPDPDAPPAPSRLAPAILPDEPVGEPVHPRMLTWIRGLEELASDDAGDPPPPLPPAAPPAAPDRSV 2568

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  524 LSPPPESspfspleeSPSSPALET----PLSPPPEASPL-------SPPFEESPLSPPPEALPTSPPPEASRLSPPPEES 592
Cdd:PHA03247  2569 PPPRPAP--------RPSEPAVTSrarrPDAPPQSARPRapvddrgDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDP 2640

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  593 PMSPPPEESPMSPPPEASRLFPPFEESPLSPPPEESPLSPPPEASRLSPPP----EDSPMSPPPEDSPMSPPPEVSRFSP 668
Cdd:PHA03247  2641 HPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQRPRRRAARPTvgslTSLADPPPPPPTPEPAPHALVSATP 2720

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  669 LPVLSH----LSPLPEVSRLSPPPEESPLSPPPEDSPTSPPPEASRLSPPPEDSPVSPPP-----------EDSLMSLPL 733
Cdd:PHA03247  2721 LPPGPAaarqASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPrrltrpavaslSESRESLPS 2800

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  734 EESPLSPL------------------PEGPRLCPQPEEPYLSPQPEEPRLCPQPEELPLSPRSEEPCLSPVLAEPCLSSQ 795
Cdd:PHA03247  2801 PWDPADPPaavlapaaalppaaspagPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAPAR 2880

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  796 PE-----EPHLSPVPQEQHLSPQPEEPHLSPQPKEPHLSPQSEEPCLSPMLEEPCLSPKPEELYQSPRPEEPPEELSQCP 870
Cdd:PHA03247  2881 PPvrrlaRPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVP 2960

                          490       500       510       520
                   ....*....|....*....|....*....|....*....|...
gi 1537972313  871 APKELSLFPPTGEPPlSPMLGEPAVSEPGEPPLSPLPEELPLS 913
Cdd:PHA03247  2961 QPWLGALVPGRVAVP-RFRVPQPAPSREAPASSTPPLTGHSLS 3002
PHD2_KMT2A_like cd15507
PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 1422-1472 6.39e-06

PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger.


Pssm-ID: 276982  Cd Length: 50  Bit Score: 46.31  E-value: 6.39e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1537972313 1422 CIVCEVCGQASDPsrLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWCVSC 1472
Cdd:cd15507      2 CHVCGRKGQAQKQ--LLECEKCQRGYHVDCLGPSYPTKPTRKKKTWICSKC 50
PHD1_Rco1 cd15535
PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and ...
 276-320 6.89e-06

PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and similar proteins; Rco1 is a component of the Rpd3S histone deacetylase complex that plays an important role at actively transcribed genes. Rco1 contains two plant homeodomain (PHD) fingers, which are required for the methylation of histone H3 lysine 36 (H3K36) nucleosome recognition by Rpd3S. This model corresponds to the first PHD finger.


Pssm-ID: 277010 [Multi-domain]  Cd Length: 45  Bit Score: 45.87  E-value: 6.89e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1537972313  276 CQACRKPGNdskMLVCETCDKGYHTFCLKPPIEE--LPAHSWKCMTC 320
Cdd:cd15535      2 CSACGGYGS---FLCCDGCPRSFHFSCLDPPLEEdnLPDDEWFCNEC 45
PHD3_PHF14 cd15563
PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 275-320 6.95e-06

PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the third PHD finger.


Pssm-ID: 277038  Cd Length: 49  Bit Score: 46.23  E-value: 6.95e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1537972313  275 ECQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEELP---AHSWKCMTC 320
Cdd:cd15563      1 ECCVCKQTGDNSQLVRCDECKLCYHFGCLDPPLKKSPkqrGYGWVCEEC 49
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 3970-4359 7.89e-06

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 52.70  E-value: 7.89e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 3970 LGPGMPAKPLQHFSSPGALGPTLLLTGKEQ-NITEASLPSE---VTEGPSTHQGGPLAVGTTPESMSVEPGEVKPSvSGD 4045
Cdd:pfam09606  102 MGPGPGGPMGQQMGGPGTASNLLASLGRPQmPMGGAGFPSQmsrVGRMQPGGQAGGMMQPSSGQPGSGTPNQMGPN-GGP 180

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4046 SQLLLVQSQAQAQpIPVQLQPPLRL-------PGQPQQQQVNLLHTTGGGNHGQQLGSSSEVP--SVPHLLNQPSVSLGE 4116
Cdd:pfam09606  181 GQGQAGGMNGGQQ-GPMGGQMPPQMgvpgmpgPADAGAQMGQQAQANGGMNPQQMGGAPNQVAmqQQQPQQQGQQSQLGM 259

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4117 QPGPMTQNLLGSQQPLGLDRPIQNntgpqppktGPVPQSGQGLPGVGVMPTVGQLRAQLQGvlaKNPQLRhlspqqqqQL 4196
Cdd:pfam09606  260 GINQMQQMPQGVGGGAGQGGPGQP---------MGPPGQQPGAMPNVMSIGDQNNYQQQQT---RQQQQQ--------QG 319

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4197 QALLMQRQLQQSQAVrqtppiqEPGSQPSPLQGLLGCQPQ-SGGFSGSQTGPLQELGAGPRPQGPPrLPVPQGALSTGPV 4275
Cdd:pfam09606  320 GNHPAAHQQQMNQSV-------GQGGQVVALGGLNHLETWnPGNFGGLGANPMQRGQPGMMSSPSP-VPGQQVRQVTPNQ 391

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4276 LGPVHPTPPPSSPQEP-KRPSQLPSPSAQPTPTHPGTPKPQ---GPTLELPPGRVSPAAAqLADTFFGKGLGPWDPSDNL 4351
Cdd:pfam09606  392 FMRQSPQPSVPSPQGPgSQPPQSHPGGMIPSPALIPSPSPQmsqQPAQQRTIGQDSPGGS-LNTPGQSAVNSPLNPQEEQ 470


                   ....*...
gi 1537972313 4352 TEAQKPEQ 4359
Cdd:pfam09606  471 LYREKYRQ 478
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
 229-273 8.09e-06

PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, also termed histone acetyltransferase KAT6A, YBF2/SAS3, SAS2 and TIP60 protein 3 (MYST-3), or runt-related transcription factor-binding protein 2, or zinc finger protein 220, is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ-related factor (MORF), also termed MOZ2, or histone acetyltransferase KAT6B, or MOZ, YBF2/SAS3, SAS2 and TIP60 protein 4 (MYST4), is a ubiquitously expressed transcriptional regulator with intrinsic HAT activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. Both MOZ and MORF are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are also implicated in human leukemias. MOZ is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphomagenesis and bone development, and its homologs. MOZ contains a linker histone 1 and histone 5 domains and two plant homeodomain (PHD) fingers. In contrast, MORF contains an N-terminal region containing two PHD fingers, a putative HAT domain, an acidic region, and a C-terminal Ser/Met-rich domain. The family corresponds to the first PHD finger.


Pssm-ID: 277002  Cd Length: 46  Bit Score: 45.83  E-value: 8.09e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  229 CAVCEGPGELCDLFFCTSCGHHYHGACLDTALTARKRAGWQCPEC 273
Cdd:cd15527      2 CSVCQDSGNADNLLFCDACDKGFHMECHDPPLTRMPKGKWVCQIC 46
PHD_TIF1_like cd15541
PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar ...
 275-320 8.17e-06

PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar proteins; The TIF1 family of transcriptional cofactors includes TIF1alpha (TRIM24), TIF1beta (TRIM28), TIF1gamma (TRIM33), and TIF1delta (TRIM66), which are characterized by an N-terminal RING-finger B-box coiled-coil (RBCC/TRIM) motif and plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region. TIF1 proteins couple chromatin modifications to transcriptional regulation, signaling, and tumor suppression. They exert a deacetylase-dependent silencing effect when tethered to a promoter region. TIF1alpha, TIF1beta, and TIF1delta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. TIF1alpha and TIF1beta bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. In contrast, TIF1delta appears to lack nuclear receptor- and KRAB-binding activity. Moreover, TIF1delta is specifically involved in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. TIF1gamma is structurally closely related to TIF1alpha and TIF1beta, but has very little functional features in common with them. It does not interact with the KRAB silencing domain of KOX1 or the heterochromatinic proteins HP1alpha, beta, and gamma. It cannot bind to nuclear receptors (NRs). This family also includes Sp100/Sp140 family proteins, the nuclear body SP100 and SP140. Sp110 is a leukocyte-specific component of the nuclear body. It may function as a nuclear hormone receptor transcriptional coactivator that may play a role in inducing differentiation of myeloid cells. It is also involved in resisting intracellular pathogens and functions as an important drug target for preventing intracellular pathogen diseases, such as tuberculosis, hepatic veno-occlusive disease, and intracellular cancers. SP140 is an interferon inducible nuclear leukocyte-specific protein involved in primary biliary cirrhosis and a risk factor in chronic lymphocytic leukemia. It is also implicated in innate immune response to human immunodeficiency virus type 1 (HIV-1) by binding to the virus viral infectivity factor (Vif) protein. Both Sp110 and Sp140 contain a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD).


Pssm-ID: 277016 [Multi-domain]  Cd Length: 43  Bit Score: 45.80  E-value: 8.17e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1537972313  275 ECQACRKPGNdskMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15541      1 WCAVCQNGGE---LLCCDKCPRVFHLDCHIPPIPEFPSGEWSCSLC 43
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 732-944 9.11e-06

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 52.78  E-value: 9.11e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  732 PLEESPLSPLPEGPRLCPQPE-EPYLSPQPEEPRLCPQPEELPLSPRSEEPclSPVLAEPCLSSQPEEPHLSPVPQEQHL 810
Cdd:PRK10263   339 PVTQTPPVASVDVPPAQPTVAwQPVPGPQTGEPVIAPAPEGYPQQSQYAQP--AVQYNEPLQQPVQPQQPYYAPAAEQPA 416

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  811 SPQPEEPHLSPQPKEPHLSPQSEEPclspMLEEPCLSPKPEELYQSPRPEEPPEELSQcPAPKELSLFPPTGEPPLSPML 890
Cdd:PRK10263   417 QQPYYAPAPEQPAQQPYYAPAPEQP----VAGNAWQAEEQQSTFAPQSTYQTEQTYQQ-PAAQEPLYQQPQPVEQQPVVE 491

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1537972313  891 GEPAVSE--PGEPPLSPLPEELPLSLSE------------EPALSPQLMPPDPLPPPLSPIIPAAAPP 944
Cdd:PRK10263   492 PEPVVEEtkPARPPLYYFEEVEEKRAREreqlaawyqpipEPVKEPEPIKSSLKAPSVAAVPPVEAAA 559
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
 643-920 1.02e-05

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 52.38  E-value: 1.02e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  643 PEDsPMSPPPEDSPMSPPPEVSRFSPlpvlshlsPLPEVSRLSPppeesplspppedSPTSPPPEASRLSPPPEDSPVSP 722
Cdd:PTZ00449   588 PKD-PEEPKKPKRPRSAQRPTRPKSP--------KLPELLDIPK-------------SPKRPESPKSPKRPPPPQRPSSP 645

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  723 PPedslmslpleesplsplPEGPRLCPQPEEPYLSPQPEEPRLCPQ--PEELPLSPRSEEPCLSPVLAEPCLSSQPEEph 800
Cdd:PTZ00449   646 ER-----------------PEGPKIIKSPKPPKSPKPPFDPKFKEKfyDDYLDAAAKSKETKTTVVLDESFESILKET-- 706

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  801 lspvpqeqhLSPQPEEPHLSPQPKEPHLsPQSEEPCLSPMLEEPCLSPKPEELYQSPRPEEPPEELSQCPAPKELSLFPP 880
Cdd:PTZ00449   707 ---------LPETPGTPFTTPRPLPPKL-PRDEEFPFEPIGDPDAEQPDDIEFFTPPEEERTFFHETPADTPLPDILAEE 776

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|
gi 1537972313  881 TGEPPLSPMLGEPavSEPGEPPLSPLPEElPLSLSEEPAL 920
Cdd:PTZ00449   777 FKEEDIHAETGEP--DEAMKRPDSPSEHE-DKPPGDHPSL 813
PspC_subgroup_2 NF033839
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 538-851 1.08e-05

pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, as described in Streptococcus pneumoniae, is a repetitive and highly variable protein, recognized by a conserved N-terminal domain and also by genomic location. This form, subgroup 2, is anchored covalently after cleavage by sortase at a C-terminal LPXTG site. The other form, subgroup 1, has variable numbers of a choline-binding repeat in the C-terminal region, and is also known as choline-binding protein A.


Pssm-ID: 468202 [Multi-domain]  Cd Length: 557  Bit Score: 52.08  E-value: 1.08e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  538 ESPSSPALETPLSPPPEASPLSPPFEESPLSPPPEALPtSPPPEASRLSPPPEESPMSPPPEESPMSPPPEASRLFPPFE 617
Cdd:NF033839   144 EKDSSSSSSSGSSTKPETPQPENPEHQKPTTPAPDTKP-SPQPEGKKPSVPDINQEKEKAKLAVATYMSKILDDIQKHHL 222

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  618 ESPLSPPPEESPLSPPPEASRLSPPPEDSPMSPPPEDSPMSPPPEVSRFsplpvlshlsplpeVSRLSPPPEESPLSPPP 697
Cdd:NF033839   223 QKEKHRQIVALIKELDELKKQALSEIDNVNTKVEIENTVHKIFADMDAV--------------VTKFKKGLTQDTPKEPG 288

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  698 EDSPTSPPPEAsRLSPPPEDSPVSPPPE----DSLMSLPLEESPLSPLPEGPR--LCPQPE--EPYLSPQPEEPR--LCP 767
Cdd:NF033839   289 NKKPSAPKPGM-QPSPQPEKKEVKPEPEtpkpEVKPQLEKPKPEVKPQPEKPKpeVKPQLEtpKPEVKPQPEKPKpeVKP 367

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  768 QPE----ELPLSPRSEEPCLSPVLAEPCLSSQPEEPHLSPVPQEQHLSPQPEEPHlSPQPKEPHLSPQSEEPclspmleE 843
Cdd:NF033839   368 QPEkpkpEVKPQPETPKPEVKPQPEKPKPEVKPQPEKPKPEVKPQPEKPKPEVKP-QPEKPKPEVKPQPEKP-------K 439


                   ....*...
gi 1537972313  844 PCLSPKPE 851
Cdd:NF033839   440 PEVKPQPE 447
PHA03247 PHA03247
large tegument protein UL36; Provisional
 4057-4347 1.19e-05

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 52.25  E-value: 1.19e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4057 AQPIPVQLQPPLRLPGQPQqqqvnllhTTGGGNHGQQLGSSSEVPSVPHLLNQPSVSLGEQPGPMTQNLLGSQQPLGLDR 4136
Cdd:PHA03247  2703 PPPPTPEPAPHALVSATPL--------PPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAA 2774

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4137 PIQNntgpqPPKTGPVPQSGQGLPGVGVMPTVGQLRAQLQGVLAKNPQLrhlspqqqqqLQALLMQRQLQQSQAVRQTPP 4216
Cdd:PHA03247  2775 PAAG-----PPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAAL----------PPAASPAGPLPPPTSAQPTAP 2839

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4217 IQEPGSQPSPLQGLLGCQPqsgGFSGSQTGPLQELGAGP-RPQGPP--RLPVPQGALSTGPVLGPVHPTPPPSSPQEPKR 4293
Cdd:PHA03247  2840 PPPPGPPPPSLPLGGSVAP---GGDVRRRPPSRSPAAKPaAPARPPvrRLARPAVSRSTESFALPPDQPERPPQPQAPPP 2916

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1537972313 4294 PSQLPSPSAQPTPTHPGTPKPQgPTLELPPGRVSPAAAQLADTFFGKGLGPWDP 4347
Cdd:PHA03247  2917 PQPQPQPPPPPQPQPPPPPPPR-PQPPLAPTTDPAGAGEPSGAVPQPWLGALVP 2969
PHD_TIF1beta cd15623
PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also ...
 276-320 1.26e-05

PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also termed Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), or KRAB-interacting protein 1 (KRIP-1), or nuclear co-repressor KAP-1, or RING finger protein 96, or tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, acts as a nuclear co-repressor that plays a role in transcription and in DNA damage response. Upon DNA damage, the phosphorylation of KAP-1 on serine 824 by the ataxia telangiectasia-mutated (ATM) kinase enhances cell survival and facilitates chromatin relaxation and heterochromatic DNA repair. It also regulates CHD3 nucleosome remodeling during DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. In addition, KAP-1 is a co-activator of the orphan nuclear receptor NGFI-B (or Nur77) and is involved in NGFI-B-dependent transcription. It is also a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase. TIF1-beta contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), which can interact with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and mediates homo- and heterodimerization, a plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region, which interact with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity.


Pssm-ID: 277093  Cd Length: 43  Bit Score: 45.18  E-value: 1.26e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGNdskMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15623      2 CRVCQKAGA---LVMCDQCEFCFHLDCHLPALQEVPGEDWKCLLC 43
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
 275-320 1.37e-05

PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED) protein, functions as a regulator of gene transcription in the thymus. It is essential for prevention of autoimmunity. AIRE plays a critical role in the induction of central tolerance. It promotes self-tolerance through tissue-specific antigen (TSA) expression. It also acts as an active regulator of chondrocyte differentiation. AIRE contains a homogeneously-staining region (HSR) or caspase-recruitment domain (CARD), a nuclear localization signal (NLS), a SAND (for Sp100, AIRE, nuclear phosphoprotein 41/75 or NucP41/75, and deformed epidermal auto regulatory factor 1 or Deaf1) domain, two plant homeodomain (PHD) fingers, and four LXXLL (where L stands for leucine) motifs. This model corresponds to the first PHD finger that recognizes the unmethylated tail of histone H3 and targets AIRE-dependent genes.


Pssm-ID: 277014 [Multi-domain]  Cd Length: 43  Bit Score: 45.13  E-value: 1.37e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1537972313  275 ECQACRKPGNdskMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15539      1 ECAVCGDGGE---LLCCDGCPRAFHLACLVPPLTLIPSGTWRCSSC 43
HMG_box pfam00505
HMG (high mobility group) box;
2013-2064 1.49e-05

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 45.68  E-value: 1.49e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1537972313 2013 VLYANINFPNLKQDYPDWSSR--CKQIMKLWRKVPAADKAPYLQKAKDNRAAHR 2064
Cdd:pfam00505    9 FLFSKEQRAKLKAENPGLKNAeiSKILGEKWKALSEEEKKPYEEKAEKEKARYE 62
PHD1_Rco1 cd15535
PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and ...
 1425-1469 1.57e-05

PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and similar proteins; Rco1 is a component of the Rpd3S histone deacetylase complex that plays an important role at actively transcribed genes. Rco1 contains two plant homeodomain (PHD) fingers, which are required for the methylation of histone H3 lysine 36 (H3K36) nucleosome recognition by Rpd3S. This model corresponds to the first PHD finger.


Pssm-ID: 277010 [Multi-domain]  Cd Length: 45  Bit Score: 45.10  E-value: 1.57e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1537972313 1425 CEVCGQasdPSRLLLCDDCDISYHTYCLDPPL--LTVPKGGWKCKWC 1469
Cdd:cd15535      2 CSACGG---YGSFLCCDGCPRSFHFSCLDPPLeeDNLPDDEWFCNEC 45
PHD2_PHF14 cd15562
PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 275-320 1.69e-05

PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the second PHD finger.


Pssm-ID: 277037  Cd Length: 50  Bit Score: 45.09  E-value: 1.69e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1537972313  275 ECQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEELPAHS----WKCMTC 320
Cdd:cd15562      1 SCGICKKSNDQHLLALCDTCKLYYHLGCLDPPLTRMPKKTknsgWQCSEC 50
PHD3_PHF14 cd15563
PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 228-273 1.84e-05

PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the third PHD finger.


Pssm-ID: 277038  Cd Length: 49  Bit Score: 45.08  E-value: 1.84e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1537972313  228 HCAVCEGPGELCDLFFCTSCGHHYHGACLDTAL--TARKRA-GWQCPEC 273
Cdd:cd15563      1 ECCVCKQTGDNSQLVRCDECKLCYHFGCLDPPLkkSPKQRGyGWVCEEC 49
PHD1_BPTF cd15559
PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, ...
 1425-1469 2.16e-05

PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, also termed nucleosome-remodeling factor subunit BPTF, or fetal Alz-50 clone 1 protein (FAC1), or fetal Alzheimer antigen, functions as a transcriptional regulator that exhibits altered expression and subcellular localization during neuronal development and neurodegenerative diseases such as Alzheimer's disease. It interacts with the human orthologue of the Kelch-like Ech-associated protein (Keap1). Its function and subcellular localization can be regulated by Keap1. Moreover, BPTF is a novel DNA-binding protein that recognizes the DNA sequence CACAACAC and represses transcription through this site in a phosphorylation-dependent manner. Furthermore, BPTF interacts with the Myc-associated zinc finger protein (ZF87/MAZ) and alters its transcriptional activity, which has been implicated in gene regulation in neurodegeneration. Some family members contain two or three plant homeodomain (PHD) fingers, which may be involved in complex formation with histone H3 trimethylated at K4 (H3K4me3). This family corresponds to the first PHD finger.


Pssm-ID: 277034 [Multi-domain]  Cd Length: 43  Bit Score: 44.71  E-value: 2.16e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313 1425 CEVCGQASDpsrLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1469
Cdd:cd15559      2 CRVCHKLGD---LLCCETCSAVYHLECVDPPLEEVPEEDWQCEVC 43
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 2014-2063 2.74e-05

high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenetically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4, and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.


Pssm-ID: 438789 [Multi-domain]  Cd Length: 59  Bit Score: 44.82  E-value: 2.74e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1537972313 2014 LYANINFPNLKQDYPDWSSrcKQIMKL----WRKVPAADKAPYLQKAKDNRAAH 2063
Cdd:cd00084      8 LFSKEKRPKLKKENPDLSF--TEISKLlgerWKELSEEEKQPYEEKAKEDKERY 59
PHD_PHF21A cd15523
PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC ...
 276-320 3.18e-05

PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC complex protein BHC80) along with HDAC1/2, CtBP1, CoREST, and BRAF35, is associated with LSD1, a lysine (K)-specific histone demethylase. It inhibits LSD1-mediated histone demethylation in vitro. PHF21A is predominantly present in the central nervous system and spermatogenic cells and is one of the six components of BRAF-HDAC complex (BHC) involved in REST-dependent transcriptional repression of neuron-specific genes in non-neuronal cells. It acts as a scaffold protein in BHC in neuronal as well as non-neuronal cells and also plays a role in spermatogenesis. PHF21A contains a C-terminal plant homeodomain (PHD) finger that is responsible for the binding directly to each of five other components of BHC, and of organizing BHC mediating transcriptional repression.


Pssm-ID: 276998 [Multi-domain]  Cd Length: 43  Bit Score: 43.92  E-value: 3.18e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGndsKMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15523      2 CSVCRKSG---ELLMCDTCSLVYHLDCLDPPLKTIPKGMWICPKC 43
ePHD_PHF11 cd15712
Extended PHD finger found in PHD finger protein 11 (PHF11); The extended plant homeodomain ...
 5023-5104 3.72e-05

Extended PHD finger found in PHD finger protein 11 (PHF11); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of PHF11. PHF11, also termed BRCA1 C-terminus-associated protein, or renal carcinoma antigen NY-REN-34, is a transcriptional co-activator of the Th1 effector cytokine genes, interleukin-2 (IL2) and interferon-gamma (IFNG), co-operating with nuclear factor kappa B (NF-kappaB). It is involved in T-cell activation and viability. Polymorphisms within PHF11 are associated with total IgE, allergic asthma and eczema.


Pssm-ID: 277182 [Multi-domain]  Cd Length: 115  Bit Score: 46.04  E-value: 3.72e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5023 DLWVHLNCALWSTEVYETQGGALMNVEVA---------LHRGLLTKCSLCQRTGATSSCNRMRCPNVYHFACAIRAKCMF 5093
Cdd:cd15712     20 NIAAHQNCLLYSSGFVESEEYNPLNLDRRfdvesvlneIKRGKRLKCNFCRKKGATVGCEERACRRSYHYFCALCDDAAI 99

                           90
                   ....*....|....*.
gi 1537972313 5094 FKDKT-----MLCPMH 5104
Cdd:cd15712    100 ETDEVrgiyrVFCQKH 115
PHD_UHRF1 cd15616
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); ...
 276-320 3.77e-05

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); UHRF1 (also termed inverted CCAAT box-binding protein of 90 kDa, nuclear protein 95, nuclear zinc finger protein Np95 (Np95), RING finger protein 106, transcription factor ICBP90, or E3 ubiquitin-protein ligase UHRF1) is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF1 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET and RING finger associated (SRA) domain, and a C-terminal RING-finger domain. It specifically binds to hemimethylated DNA, double-stranded CpG dinucleotides, and recruits the maintenance methyltransferase DNMT1 to its hemimethylated DNA substrate through its SRA domain. UHRF1-dependent H3K23 ubiquitylation has an essential role in maintaining DNA methylation and replication. The tandem Tudor domain directs UHRF1 binding to the heterochromatin mark histone H3K9me3 and the PHD finger targets UHRF1 to unmodified histone H3 in euchromatic regions. The RING-finger domain exhibit both autocatalytic E3 ubiquitin (Ub) ligase activity and activity against histone H3 and DNMT1.


Pssm-ID: 277088  Cd Length: 47  Bit Score: 44.19  E-value: 3.77e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1537972313  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEELPA-HSWKCMTC 320
Cdd:cd15616      2 CHVCGGKQDPDKQLMCDECDMAFHIYCLNPPLSSIPDdEDWYCPEC 47
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 276-320 3.85e-05

PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the first PHD finger.


Pssm-ID: 277006 [Multi-domain]  Cd Length: 43  Bit Score: 43.74  E-value: 3.85e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGndsKMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15531      2 CEVCQQGG---EIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 43
PHD_Phf1p_Phf2p_like cd15502
PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 ...
 273-320 4.06e-05

PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 (Phf1p) and Phf2 (Phf2p); Phf1p and Phf2p are components of the SWM histone demethylase complex that specifically demethylates histone H3 at lysine 9 (H3K9me2), a specific tag for epigenetic transcriptional activation. They function as corepressors and play roles in regulating heterochromatin propagation and euchromatic transcription. Both Phf1p and Phf2p contain a plant homeodomain (PHD) finger.


Pssm-ID: 276977  Cd Length: 52  Bit Score: 43.96  E-value: 4.06e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1537972313  273 CKECQACRKPGNDsKMLVCETCDKGYHTFCLKPPIE----ELPAHSWKCMTC 320
Cdd:cd15502      2 CIVCQRGHSPKSN-RIVFCDGCNTPYHQLCHDPSIDdevvEDPDAEWFCKKC 52
PHD1_MTF2_PHF19_like cd15499
PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ...
 270-320 4.81e-05

PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) family proteins MTF2, PHF19, and similar proteins; The family includes two PCL family proteins, metal-response element-binding transcription factor 2 (MTF2/PCL2) and PHF19/PCL3, which are homologs of PHD finger protein1 (PHF1). PCL family proteins are accessory components of the polycomb repressive complex 2 (PRC2) core complex and all contain an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. They specifically recognize tri-methylated H3K36 (H3K36me3) through their N-terminal Tudor domains. The interaction between their Tudor domains and H3K36me3 is critical for both the targeting and spreading of PRC2 into active chromatin regions and for the maintenance of optimal repression of poised developmental genes where PCL proteins, H3K36me3, and H3K27me3 coexist. Moreover, unlike other PHD finger-containing proteins, the first PHD fingers of PCL proteins do not display histone H3K4 binding affinity and they do not affect the Tudor domain binding to histones. This model corresponds to the first PHD finger.


Pssm-ID: 276974  Cd Length: 53  Bit Score: 44.03  E-value: 4.81e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1537972313  270 CPECKECQAcrKPGNDskMLVCETCDKGYHTFCLKPPIEELPAHS---WKCMTC 320
Cdd:cd15499      2 CSICGGAEA--RDGNE--ILICDKCDKGYHQLCHSPKVRTSPLEGdekWFCSRC 51
PHD_UHRF2 cd15617
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); ...
 276-320 6.52e-05

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); UHRF2 (also termed Np95/ICBP90-like RING finger protein (NIRF), Np95-like RING finger protein, nuclear protein 97, nuclear zinc finger protein Np97, RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2) was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs,p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277089  Cd Length: 47  Bit Score: 43.40  E-value: 6.52e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1537972313  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEELPA-HSWKCMTC 320
Cdd:cd15617      2 CYVCGGKQDAHMQLLCDECNMAYHIYCLNPPLDKIPEdEDWYCPSC 47
SET_SMYD cd20071
SET domain (including SET domain and post-SET domain) found in SET and MYND domain-containing ...
 5392-5496 7.59e-05

SET domain (including SET domain and post-SET domain) found in SET and MYND domain-containing protein, and similar proteins; The family includes SET and MYND domain-containing proteins, SMYD1-SYMD5. SMYD1 (EC 2.1.1.43; also termed BOP) is a heart and muscle specific SET-MYND domain containing protein, which functions as a histone methyltransferase and regulates downstream gene transcription. It methylates histone H3 at 'Lys-4' (H3K4me), seems able to perform both mono-, di-, and trimethylation. SMYD2 (also termed HSKM-B, or lysine N-methyltransferase 3C (KMT3C)) functions as a histone methyltransferase that methylates both histones and non-histone proteins, including p53/TP53 and RB1. It specifically methylates histone H3 'Lys-4' (H3K4me) and dimethylates histone H3 'Lys-36' (H3K36me2). SMYD3 (also termed zinc finger MYND domain-containing protein 1) functions as a histone methyltransferase that specifically methylates 'Lys-4' of histone H3, inducing di- and tri-methylation, but not monomethylation. It also methylates 'Lys-5' of histone H4. SMYD3 plays an important role in transcriptional activation as a member of an RNA polymerase complex. SMYD4 functions as a potential tumor suppressor that plays a critical role in breast carcinogenesis at least partly through inhibiting the expression of PDGFR-alpha. SMYD5 (also termed protein NN8-4AG, or retinoic acid-induced protein 15) functions as histone lysine methyltransferase that mediates H4K20me3 at heterochromatin regions.


Pssm-ID: 380997 [Multi-domain]  Cd Length: 122  Bit Score: 45.45  E-value: 7.59e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5392 GLGLYAAKDLEKhtmvieyiGTIIRNE------VANRREKIYEEQNRGIYMFRInnehvidatltggpARYINHSCAPNC 5465
Cdd:cd20071     10 GRGLVATRDIEP--------GELILVEkplvsvPSNSFSLTDGLNEIGVGLFPL--------------ASLLNHSCDPNA 67

                           90       100       110
                   ....*....|....*....|....*....|.
gi 1537972313 5466 VaevVTFDKEDKIIIISSRRIPKGEELTYDY 5496
Cdd:cd20071     68 V---VVFDGNGTLRVRALRDIKAGEELTISY 95
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 4007-4189 8.67e-05

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 49.26  E-value: 8.67e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4007 PSEVTEGPSTHQGGPLAVGTTPES---MSVEpgEVkpsvsgDSQLLLVQSQAQAQPIPVQLQPPLRLPGQPQQQQVNLLH 4083
Cdd:pfam09770  167 PKKAAAPAPAPQPAAQPASLPAPSrkmMSLE--EV------EAAMRAQAKKPAQQPAPAPAQPPAAPPAQQAQQQQQFPP 238

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4084 TTGGGNHGQQLGSSSEVPSV----PHLLNQPSVSLGEQPGPMTQN---LLGSQQPLGLDRPIQNNTGPQPPKTGPVPQSG 4156
Cdd:pfam09770  239 QIQQQQQPQQQPQQPQQHPGqghpVTILQRPQSPQPDPAQPSIQPqaqQFHQQPPPVPVQPTQILQNPNRLSAARVGYPQ 318

                          170       180       190
                   ....*....|....*....|....*....|....*...
gi 1537972313 4157 QGLPGVGVMPTVGQLRAQ-----LQGVLAKNPQLRHLS 4189
Cdd:pfam09770  319 NPQPGVQPAPAHQAHRQQgsfgrQAPIITHPQQLAQLS 356
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 2212-2723 9.03e-05

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 49.38  E-value: 9.03e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2212 TGQPGEFHTTPPGTPRHQPSTPDPFLKPRCPSLDNLAVPESPGVAGGKASEPLLSPPPfgeSRKTLEVKKEELGASSPGY 2291
Cdd:pfam03154  161 SAQQQILQTQPPVLQAQSGAASPPSPPPPGTTQAATAGPTPSAPSVPPQGSPATSQPP---NQTQSTAAPHTLIQQTPTL 237

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2292 GPPNLGCVDSPSSGshlgglelkapdvfkAPLTPRASQVEPQS-PGLGLRAQEPPAAQALAPSPPSHSDVFRSASYPDPy 2370
Cdd:pfam03154  238 HPQRLPSPHPPLQP---------------MTQPPPPSQVSPQPlPQPSLHGQMPPMPHSLQTGPSHMQHPVPPQPFPLT- 301

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2371 aqPPLTPRPQPPPPESCCALPPRSLPSDPFSRvPASPQSQSSSQSPLTPRPLSAEAFCPSPVTPRFQSPDPYS-RPPSRP 2449
Cdd:pfam03154  302 --PQSSQSQVPPGPSPAAPGQSQQRIHTPPSQ-SQLQSQQPPREQPLPPAPLSMPHIKPPPTTPIPQLPNPQShKHPPHL 378

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2450 QSRDPF---APLHKPPRPQP-PEVAFKAGPLAH-TPLGAGGFPAALPSGPAGELHAKVPSGQPPNFARSPGTGAFvgTPS 2524
Cdd:pfam03154  379 SGPSPFqmnSNLPPPPALKPlSSLSTHHPPSAHpPPLQLMPQSQQLPPPPAQPPVLTQSQSLPPPAASHPPTSGL--HQV 456

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2525 PMRFTFPQGVGEPSLKPPVPQPGLPPPHGINSHFGPGPTLGKPQSTNYTVAtGNFHPSGSPLGPNTGPTGEgyglsPLRP 2604
Cdd:pfam03154  457 PSQSPFPQHPFVPGGPPPITPPSGPPTSTSSAMPGIQPPSSASVSSSGPVP-AAVSCPLPPVQIKEEALDE-----AEEP 530

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2605 ASVMPP---PTPEGSLPYLSHGASQRAGITSPVEKREDAGA-------TMSSSSLATPELSSAQDAGMPSLSQTELEKQR 2674
Cdd:pfam03154  531 ESPPPPprsPSPEPTVVNTPSHASQSARFYKHLDRGYNSCArtdlyfmPLAGSKLAKKREEALEKAKREAEQKAREEKER 610

                          490       500       510       520
                   ....*....|....*....|....*....|....*....|....*....
gi 1537972313 2675 QRQRLRELLIRQQIQRNNLRQEKETAAAAASAVGPPGNWGAEPSSPAFE 2723
Cdd:pfam03154  611 EKEKEKEREREREREREAERAAKASSSSHEGRMGDPQLAGPAHMRPSFE 659
PHD2_KMT2C cd15594
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 229-273 1.00e-04

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the second PHD finger.


Pssm-ID: 277069  Cd Length: 46  Bit Score: 42.62  E-value: 1.00e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  229 CAVCEGPGELCDLFFCTSCGHHYHGACLDTALTARKRAGWQCPEC 273
Cdd:cd15594      2 CQTCRQPGDDNKMLVCDTCDKGYHTFCLQPVMTTIPKNGWKCKNC 46
PHD2_KMT2B cd15591
PHD domain 2 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed ...
 1375-1422 1.01e-04

PHD domain 2 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed trithorax homolog 2 or WW domain-binding protein 7 (WBP-7), is encoded by the gene that was first named myeloid/lymphoid or mixed-lineage leukemia 2 (MLL2), a second human homolog of Drosophila trithorax, located on chromosome 19. It belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2) and is vital for normal mammalian embryonic development. KMT2B functions as the catalytic subunit in the MLL2 complex, which contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL2 complex is highly active and specific for histone 3lysine 4 (H3K4) methylation, which stimulates chromatin transcription in a SAM- and H3K4-dependent manner. Moreover, KMT2B plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. KMT2B contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD), an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger.


Pssm-ID: 277066  Cd Length: 50  Bit Score: 43.00  E-value: 1.01e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1537972313 1375 CVVCGSFGRGAEgHLLACSQCSQCYHPYCVNSKITKVMLLK--GWRCVEC 1422
Cdd:cd15591      2 CHVCGRKNKESK-PLLECERCRNCYHPACLGPNYPKPANRKkrPWICSAC 50
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1502-1553 1.02e-04

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 42.86  E-value: 1.02e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1537972313 1502 CPVCHAPyVEEDLLIQCRHCERWMHAGCESLftEDEVEQAADEGFDCVSCQP 1553
Cdd:pfam00628    2 CAVCGKS-DDGGELVQCDGCDDWFHLACLGP--PLDPAEIPSGEWLCPECKP 50
PHD3_KMT2A_like cd15508
PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 1502-1551 1.19e-04

PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the third PHD finger.


Pssm-ID: 276983  Cd Length: 57  Bit Score: 42.82  E-value: 1.19e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1537972313 1502 CPVCHAPYVEEDL---LIQCRHCERWMHAGCESLfTEDEVEQAAD----EGFDCVSC 1551
Cdd:cd15508      2 CPLCEKCYDDDDYdskMMQCSQCDHWVHAKCEGL-SDEMYEILSYlpesIEYTCSLC 57
PHD_TCF19_like cd15517
PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and ...
 276-320 1.66e-04

PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and KDM5B, and other similar proteins; TCF-19 was identified as a putative trans-activating factor with expression beginning at the late G1-S boundary in dividing cells. It functions as a novel islet factor necessary for proliferation and survival in the INS-1 beta cell line. It plays an important role in susceptibility to both Type 1 Diabetes Mellitus (T1DM) and Type 2 Diabetes Mellitus (T2DM); it has been suggested that it may positively impact beta cell mass under conditions of beta cell stress and increased insulin demand. KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interaction with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK, and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. This family also includes Caenorhabditis elegans Lysine-specific demethylase 7 homolog (ceKDM7A). ceKDM7A (also termed JmjC domain-containing protein 1.2, PHD finger protein 8 homolog, or PHF8 homolog) is a plant homeodomain (PHD)- and JmjC domain-containing protein that functions as a histone demethylase specific for H3K9me2 and H3K27me2. The binding of the PHD finger to H3K4me3 guides H3K9me2- and H3K27me2-specific demethylation by its catalytic JmjC domain in a trans-histone regulation mechanism. In addition, this family includes plant protein OBERON 1 and OBERON 2, Alfin1-like (AL) proteins, histone acetyltransferases (HATs) HAC, and AT-rich interactive domain-containing protein 4 (ARID4).


Pssm-ID: 276992 [Multi-domain]  Cd Length: 49  Bit Score: 42.15  E-value: 1.66e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1537972313  276 CQACRKPGNDSKML--VCETCDKGYHTFCLKPPIEELPAHS-WKCMTC 320
Cdd:cd15517      2 CGICNLETAAVDELwvQCDGCDKWFHQFCLGLSNERYADEDkFKCPNC 49
ePHD2_PHF6 cd15711
Extended PHD finger 2 found in PHD finger protein 6 (PHF6); The extended plant homeodomain ...
 5000-5096 1.75e-04

Extended PHD finger 2 found in PHD finger protein 6 (PHF6); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. PHF6 contains two non-canonical ePHD fingers, this model corresponds to the second ePHD finger. PHF6, also termed the X-linked mental retardation disorder Borjeson-Forssman-Lehmann syndrome-associated protein, is a nucleolus, ribosomal RNA promoter-associated protein that regulates cell cycle progression by suppressing ribosomal RNA synthesis. It has been implicated in cell cycle control, genomic maintenance, and tumor suppression. PHF6 shows transcriptional repression activity through directly interacting with the nucleosome remodeling and deacetylation complex component RBBP4.


Pssm-ID: 277181  Cd Length: 118  Bit Score: 44.30  E-value: 1.75e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5000 CCFCHE-EGDGATDGPARLLNLDlDLWVHLNCALWST---EVYETQGGALMNVEVA-----LHRGLLTKCSLCQRTGATS 5070
Cdd:cd15711      1 CGFCHAgEEENETRGKLHIFNAK-KAAAHYKCMLFSSgtvQLTTTSRAEFGDFDIKtviqeIKRGKRMKCTLCSQLGATI 79

                           90       100
                   ....*....|....*....|....*.
gi 1537972313 5071 SCNRMRCPNVYHFACAIRAKCMFFKD 5096
Cdd:cd15711     80 GCEIKACVKTYHYHCGVQDKAKYIEN 105
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 2090-2508 1.79e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 48.24  E-value: 1.79e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2090 DRPALHLRIPSQPGALGSPPPAAAPTIFIGSPTTPAGLSTSadgflKPPAGTVPGPDSPGELFLKLPPQVPAQVPSQDPF 2169
Cdd:PHA03307    29 GDAADDLLSGSQGQLVSDSAELAAVTVVAGAAACDRFEPPT-----GPPPGPGTEAPANESRSTPTWSLSTLAPASPARE 103

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2170 GL---APAYAPEPRFSAAPPTYPPYPTPSGAPAQPPILGTTTRPGTGQPGEFHTTPPGTPRHQPSTPDPFLkprcpsLDN 2246
Cdd:PHA03307   104 GSptpPGPSSPDPPPPTPPPASPPPSPAPDLSEMLRPVGSPGPPPAASPPAAGASPAAVASDAASSRQAAL------PLS 177

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2247 LAVPESPGVAGGKASEPLLSPPPFGESRKTLEVKKEELGASSPGYGPP---NLGCVDSPSSGSHLGGLELKAPDVFKAPL 2323
Cdd:PHA03307   178 SPEETARAPSSPPAEPPPSTPPAAASPRPPRRSSPISASASSPAPAPGrsaADDAGASSSDSSSSESSGCGWGPENECPL 257

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2324 TPRASQVEPQSPGLGLRAQEPPAAQALAPSPPShsdvfRSASYPDPyaqppltprpqPPPPESCCALPPRSLPSDPFSRV 2403
Cdd:PHA03307   258 PRPAPITLPTRIWEASGWNGPSSRPGPASSSSS-----PRERSPSP-----------SPSSPGSGPAPSSPRASSSSSSS 321

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2404 PASPQSQSSSQSPlTPRPLSAEAFCPSPVTPRFQSPDPYSRPPSRPQ----SRDPFAPLHKPPRPQPPEVAFKAGPLAHT 2479
Cdd:PHA03307   322 RESSSSSTSSSSE-SSRGAAVSPGPSPSRSPSPSRPPPPADPSSPRKrprpSRAPSSPAASAGRPTRRRARAAVAGRARR 400

                          410       420
                   ....*....|....*....|....*....
gi 1537972313 2480 PLGAGGFPAALPsgPAGELHAKVPSGQPP 2508
Cdd:PHA03307   401 RDATGRFPAGRP--RPSPLDAGAASGAFY 427
PHD_BRPF_JADE_like cd15492
PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; ...
 1424-1469 2.20e-04

PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; The family includes BRPF proteins, Jade proteins, protein AF-10 and AF-17. BRPF proteins are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. Jade proteins are required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6, to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. AF-10, also termed ALL1 (acute lymphoblastic leukemia)-fused gene from chromosome 10 protein, is a transcription factor that has been implicated in the development of leukemia following chromosomal rearrangements between the AF10 gene and one of at least two other genes, MLL and CALM. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is a putative transcription factor that may play a role in multiple signaling pathways. All Jade proteins, AF-10, and AF-17 contain a canonical PHD finger followed by a non-canonical ePHD finger. This model corresponds to the canonical PHD finger.


Pssm-ID: 276967 [Multi-domain]  Cd Length: 46  Bit Score: 41.84  E-value: 2.20e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1537972313 1424 VCEVCGQAS--DPSRLLLCDDCDISYHTYCLDppLLTVPKGGWKCKWC 1469
Cdd:cd15492      1 VCDVCLDGEseDDNEIVFCDGCNVAVHQSCYG--IPLIPEGDWFCRKC 46
PHD1_Snt2p_like cd15497
PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and ...
 276-320 2.28e-04

PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and similar proteins; Snt2p is a yeast protein that may function in multiple stress pathways. It coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress through interaction with Ecm5 and the Rpd3 deacetylase. Snt2p contains a bromo adjacent homology (BAH) domain, two canonical Cys4HisCys3 plant homeodomain (PHD) fingers, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domain; this model corresponds to the first canonical Cys4HisCys3 PHD finger.


Pssm-ID: 276972  Cd Length: 48  Bit Score: 41.91  E-value: 2.28e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1537972313  276 CQACRK--PGNDSkmLVCETCDKGYHTFCLKPPIEELPAH--SWKCMTC 320
Cdd:cd15497      2 CKVCKEwcASDDS--VRCDECKVSYHLLCVDPPLTKKPNRgfVWSCAPC 48
PHD_JADE2 cd15680
PHD finger found in protein Jade-2 and similar proteins; Jade-2, also termed PHD finger ...
 1424-1469 2.53e-04

PHD finger found in protein Jade-2 and similar proteins; Jade-2, also termed PHD finger protein 15 (PHF15), is a plant homeodomain (PHD) zinc finger protein that is closely related to Jade-1, which functions as an essential regulator of multiple cell signaling pathways. Like Jade-1, Jade-2 is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and Eaf6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. Jade-2 contains a canonical Cys4HisCys3 PHD finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277150 [Multi-domain]  Cd Length: 46  Bit Score: 41.53  E-value: 2.53e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1537972313 1424 VCEVC--GQASDPSRLLLCDDCDISYHTYCLDppLLTVPKGGWKCKWC 1469
Cdd:cd15680      1 VCDVCrsPEGEDGNEMVFCDKCNVCVHQACYG--ILKVPTGSWLCRTC 46
ePHD_BRPF cd15670
Extended PHD finger found in BRPF proteins; The extended plant homeodomain (ePHD) zinc finger ...
 5000-5089 2.53e-04

Extended PHD finger found in BRPF proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the ePHD finger of the family of BRPF proteins, which includes BRPF1, BRD1/BRPF2, and BRPF3. These are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a plant homeodomain (PHD) zinc finger followed by a non-canonical ePHD finger, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. This PHD finger binds to lysine 4 of histone H3 (K4H3), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties.


Pssm-ID: 277140  Cd Length: 116  Bit Score: 43.86  E-value: 2.53e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5000 CCFCHEEGdGA----TDGParllnldldlWVHLNCALWSTEVY-------EtqggALMNVE-VALHRGLLTkCSLC-QRT 5066
Cdd:cd15670      1 CVLCPNKG-GAfkqtDDGR----------WAHVVCALWIPEVSfantvflE----PIDGIQnIPKARWKLT-CYICkKRM 64

                           90       100
                   ....*....|....*....|...
gi 1537972313 5067 GATSSCNRMRCPNVYHFACAIRA 5089
Cdd:cd15670     65 GACIQCHKKNCYTAFHVTCAQQA 87
PHD_PRKCBP1 cd15538
PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed ...
 1386-1422 3.20e-04

PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed cutaneous T-cell lymphoma-associated antigen se14-3 (CTCL-associated antigen se14-3), or Rack7, or zinc finger MYND domain-containing protein 8 (ZMYND8), is a novel receptor for activated C-kinase (RACK)-like protein that may play an important role in the activation and regulation of PKC-beta I, and the PKC signaling cascade. It also has been identified as a formin homology-2-domain containing protein 1 (FHOD1)-binding protein that may be involved in FHOD1-regulated actin polymerization and transcription. Moreover, PRKCBP1 may function as a REST co-repressor 2 (RCOR2) interacting factor; the RCOR2/ZMYND8 complex which might be involved in the regulation of neural differentiation. PRKCBP1 contains a plant homeodomain (PHD) finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain.


Pssm-ID: 277013  Cd Length: 41  Bit Score: 41.16  E-value: 3.20e-04
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 1537972313 1386 EGHLLACSQCSQCYHPYCVNSKItkvMLLKGWRCVEC 1422
Cdd:cd15538      8 EGQVLCCSLCPRVYHKKCLKLTS---EPDEDWVCPEC 41
PHD_JADE1 cd15679
PHD finger found in protein Jade-1 and similar proteins; Jade-1, also termed PHD finger ...
 1424-1469 3.61e-04

PHD finger found in protein Jade-1 and similar proteins; Jade-1, also termed PHD finger protein 17 (PHF17), is a novel binding partner of von Hippel-Lindau (VHL) tumor suppressor Pvhl, a key regulator of the cellular oxygen sensing pathway. It is highly expressed in renal proximal tubules. Jade-1 functions as an essential regulator of multiple cell signaling pathways. It may be involved in the serine/threonine kinase AKT/AKT1 pathway during renal cancer pathogenesis and normally prevents renal epithelial cell proliferation and transformation. It also acts as a pro-apoptotic and growth suppressive ubiquitin ligase to inhibit canonical Wnt downstream effector beta-catenin for proteasomal degradation, and as a transcription factor associated with histone acetyltransferase activity and with increased abundance of cyclin-dependent kinase inhibitor p21. Moreover, Jade-1 is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and Eaf6 to form a HBO1 complex, and plays a role in epithelial cell regeneration. It has also been identified as a novel component of the nephrocystin protein (NPHP) complex and interacts with the ciliary protein nephrocystin-4 (NPHP4). Jade-1 contains a canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277149 [Multi-domain]  Cd Length: 46  Bit Score: 41.21  E-value: 3.61e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1537972313 1424 VCEVCGQ--ASDPSRLLLCDDCDISYHTYCLDppLLTVPKGGWKCKWC 1469
Cdd:cd15679      1 VCDVCQSpdGEDGNEMVFCDKCNICVHQACYG--ILKVPEGSWLCRTC 46
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 5060-5104 4.55e-04

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 41.04  E-value: 4.55e-04
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 1537972313  5060 CSLCQRTGATS---SCNRmrCPNVYHFACAIRAKCMFFKDKTMLCPMH 5104
Cdd:smart00249    2 CSVCGKPDDGGellQCDG--CDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
PHD_TIF1beta cd15623
PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also ...
 1425-1469 4.68e-04

PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also termed Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), or KRAB-interacting protein 1 (KRIP-1), or nuclear co-repressor KAP-1, or RING finger protein 96, or tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, acts as a nuclear co-repressor that plays a role in transcription and in DNA damage response. Upon DNA damage, the phosphorylation of KAP-1 on serine 824 by the ataxia telangiectasia-mutated (ATM) kinase enhances cell survival and facilitates chromatin relaxation and heterochromatic DNA repair. It also regulates CHD3 nucleosome remodeling during DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. In addition, KAP-1 is a co-activator of the orphan nuclear receptor NGFI-B (or Nur77) and is involved in NGFI-B-dependent transcription. It is also a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase. TIF1-beta contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), which can interact with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and mediates homo- and heterodimerization, a plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region, which interact with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity.


Pssm-ID: 277093  Cd Length: 43  Bit Score: 40.94  E-value: 4.68e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313 1425 CEVCGQASDpsrLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1469
Cdd:cd15623      2 CRVCQKAGA---LVMCDQCEFCFHLDCHLPALQEVPGEDWKCLLC 43
RING-H2 cd16448
H2 subclass of RING (RING-H2) fingers and its variants; The RING finger is a specialized type ...
 229-274 5.06e-04

H2 subclass of RING (RING-H2) fingers and its variants; The RING finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc. It is defined by the "cross-brace" motif that chelates zinc atoms by eight amino acid residues, typically Cys or His, arranged in a characteristic spacing. Canonical RING motifs have been categorized into two major subclasses, RING-HC (C3HC4-type) and RING-H2 (C3H2C3-type), according to their Cys/His content. There are also many variants of RING fingers: some have different Cys/His patterns while some lack a single Cys or His residue at typical Zn ligand positions (the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can indeed chelate Zn in a RING finger as well). This family corresponds to the H2 subclass of RING (RING-H2) finger proteins that are characterized by containing C3H2C3-type canonical RING-H2 fingers or noncanonical RING-H2 finger variants, including C4HC3- (RING-CH alias RINGv), C3H3C2-, C3H2C2D-, C3DHC3-, and C4HC2H-type modified RING-H2 fingers. The canonical RING-H2 finger has been defined as C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-H-X2-C-X(4-48)-C-X2-C, X is any amino acid and the number of X residues varies in different fingers. It binds two Zn ions in a unique "cross-brace" arrangement, which distinguishes it from tandem zinc fingers and other similar motifs. RING-H2 finger can be found in a group of diverse proteins with a variety of cellular functions, including oncogenesis, development, viral replication, signal transduction, the cell cycle and apoptosis. Many of them are ubiquitin-protein ligases (E3s) that serves as a scaffold for binding to ubiquitin-conjugating enzymes (E2s, also referred to as ubiquitin carrier proteins or UBCs) in close proximity to substrate proteins, which enables efficient transfer of ubiquitin from E2 to the substrates.


Pssm-ID: 438112 [Multi-domain]  Cd Length: 43  Bit Score: 40.85  E-value: 5.06e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1537972313  229 CAVCEGPGELCDLFFCTSCGHHYHGACLDTALTARKRagwQCPECK 274
Cdd:cd16448      1 CVICLEEFEEGDVVRLLPCGHVFHLACILRWLESGNN---TCPLCR 43
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 2341-2661 5.18e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 46.70  E-value: 5.18e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2341 AQEPPAAQALAPSPPSHSDVFRSASYPDPYAQPPLTPRPQPPPPESCCALPPRSLPSDPFSRVPASPQSQSSSQSPLTPR 2420
Cdd:PHA03307    17 GGEFFPRPPATPGDAADDLLSGSQGQLVSDSAELAAVTVVAGAAACDRFEPPTGPPPGPGTEAPANESRSTPTWSLSTLA 96

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2421 PLSAEAfCPSPVTPRFQSPDPYSRPPSRPQSRDPFAPLHKPPRPQPPEVAF------KAGPLAHTPLGAGGFPAALPSGP 2494
Cdd:PHA03307    97 PASPAR-EGSPTPPGPSSPDPPPPTPPPASPPPSPAPDLSEMLRPVGSPGPppaaspPAAGASPAAVASDAASSRQAALP 175

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2495 AGELHAKVPSGQPPNFARSPGTGAFVGTPSPMRFTFPQGVGEPSLKPPVPQPGLPPPHGINSHFGPGPTLGKPQSTNYTV 2574
Cdd:PHA03307   176 LSSPEETARAPSSPPAEPPPSTPPAAASPRPPRRSSPISASASSPAPAPGRSAADDAGASSSDSSSSESSGCGWGPENEC 255

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2575 ATGNFHPSGSPLGPNTGPTGEGYGLSPLRPASVMPPPTPEGSLPYLSHGASQRAGITSPVEKREDAGATMSSSSLATPEL 2654
Cdd:PHA03307   256 PLPRPAPITLPTRIWEASGWNGPSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSSSSES 335


                   ....*..
gi 1537972313 2655 SSAQDAG 2661
Cdd:PHA03307   336 SRGAAVS 342
ePHD1_PHF6 cd15710
Extended PHD finger 1 found in PHD finger protein 6 (PHF6); The extended plant homeodomain ...
 138-198 5.48e-04

Extended PHD finger 1 found in PHD finger protein 6 (PHF6); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. PHF6 contains two non-canonical ePHD fingers, this model corresponds to the first ePHD finger. PHF6, also termed the X-linked mental retardation disorder Borjeson-Forssman-Lehmann syndrome-associated protein, is a nucleolus, ribosomal RNA promoter-associated protein that regulates cell cycle progression by suppressing ribosomal RNA synthesis. It has been implicated in cell cycle control, genomic maintenance, and tumor suppression. PHF6 shows transcriptional repression activity through directly interacting with the nucleosome remodeling and deacetylation complex component RBBP4. .


Pssm-ID: 277180  Cd Length: 115  Bit Score: 43.03  E-value: 5.48e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1537972313  138 AHHWCAVWSAG-VWGQEGPELCG------VDKAIFSGISQRCSHCTRFGASIPCRSPGCPRLYHFPCA 198
Cdd:cd15710     25 AHHKCMLFSSAlVSSHSDSENLGgfsiedVQKEIKRGTKLMCSLCHCPGATIGCDVKTCHRTYHYYCA 92
ePHD_JMJD2A cd15713
Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A); The ...
 5000-5096 5.78e-04

Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2A. JMJD2A, also termed lysine-specific demethylase 4A (KDM4A), or JmjC domain-containing histone demethylation protein 3A (JHDM3A), catalyzes the demethylation of di- and trimethylated H3K9 and H3K36. It is involved in carcinogenesis and functions as a transcription regulator that may either stimulate or repress gene transcription. It associates with nuclear receptor co-repressor complex or histone deacetylases. Moreover, JMJD2A forms complexes with both the androgen and estrogen receptor (ER) and plays an essential role in growth of both ER-positive and -negative breast tumors. It is also involved in prostate, colon, and lung cancer progression. JMJD2A contains jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD finger, this non-canonical ePHD finger, and a Tudor domain.


Pssm-ID: 277183  Cd Length: 110  Bit Score: 42.65  E-value: 5.78e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5000 CCFCHEEGdGAtdgparLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVA---LHRGLLtKCSLCQR-----TGATSS 5071
Cdd:cd15713      1 CCLCSLRG-GA------LQRANDDKWVHVMCAVAVLEARFVNIAERSPVDVSkipLQRFKL-KCIFCKKrrkrtAGCCVQ 72

                           90       100
                   ....*....|....*....|....*
gi 1537972313 5072 CNRMRCPNVYHFACAIRAKCMFFKD 5096
Cdd:cd15713     73 CSHGRCPTSFHASCAQAAGVMMQPD 97
SET_KMT2E cd19182
SET domain found in inactive histone-lysine N-methyltransferase 2E (KMT2E) and similar ...
 5395-5500 6.01e-04

SET domain found in inactive histone-lysine N-methyltransferase 2E (KMT2E) and similar proteins; KMT2E (also termed inactive lysine N-methyltransferase 2E, myeloid/lymphoid or mixed-lineage leukemia protein 5 (MLL5)) plays a key role in hematopoiesis, spermatogenesis and cell cycle progression. It associates with chromatin regions downstream of transcriptional start sites of active genes and thus regulates gene transcription. Lack of key residues in the SET domain as well as the presence of an unusually large loop in the SET-I subdomain preclude the interaction of MLL5 SET with its cofactor and substrate thus making MLL5 devoid of any in vitro methyltransferase activity on full-length histones and histone H3 peptide.


Pssm-ID: 380959  Cd Length: 129  Bit Score: 42.96  E-value: 6.01e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 5395 LYAAKDLEKHTMVIEYIGTIIRNEV--AN----RREK---IYEEQNRGIYMfrinnehVIDATLTGGPARYINHSCAPNC 5465
Cdd:cd19182     21 LKAAKDLPPDTLIIEYRGKFMLREQfeANgyffKRPYpfvLFYSKFHGLEM-------CVDARTFGNEARFIRRSCTPNA 93

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1537972313 5466 VAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDF 5500
Cdd:cd19182     94 EVRHVIEDGTIHLYIYSIRSIPKGTEITIAFDFDY 128
PHD_PHF21A cd15523
PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC ...
 229-273 6.37e-04

PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC complex protein BHC80) along with HDAC1/2, CtBP1, CoREST, and BRAF35, is associated with LSD1, a lysine (K)-specific histone demethylase. It inhibits LSD1-mediated histone demethylation in vitro. PHF21A is predominantly present in the central nervous system and spermatogenic cells and is one of the six components of BRAF-HDAC complex (BHC) involved in REST-dependent transcriptional repression of neuron-specific genes in non-neuronal cells. It acts as a scaffold protein in BHC in neuronal as well as non-neuronal cells and also plays a role in spermatogenesis. PHF21A contains a C-terminal plant homeodomain (PHD) finger that is responsible for the binding directly to each of five other components of BHC, and of organizing BHC mediating transcriptional repression.


Pssm-ID: 276998 [Multi-domain]  Cd Length: 43  Bit Score: 40.46  E-value: 6.37e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  229 CAVCEGPGELcdlFFCTSCGHHYHGACLDTALTARKRAGWQCPEC 273
Cdd:cd15523      2 CSVCRKSGEL---LMCDTCSLVYHLDCLDPPLKTIPKGMWICPKC 43
PHD_PHF21B cd15524
PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) ...
 1425-1469 6.47e-04

PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) finger-containing protein whose biological function remains unclear. It shows high sequence similarity with PHF21A, which is associated with LSD1, a lysine (K)-specific histone demethylase and inhibits LSD1-mediated histone demethylation in vitro. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins.


Pssm-ID: 276999 [Multi-domain]  Cd Length: 43  Bit Score: 40.26  E-value: 6.47e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313 1425 CEVCGQASDpsrLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1469
Cdd:cd15524      2 CAACKRGGN---LQPCGTCPRAYHLDCLDPPLKTAPKGVWVCPKC 43
PHD3_KMT2B cd15593
PHD finger 3 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed ...
 1502-1536 6.95e-04

PHD finger 3 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed trithorax homolog 2 or WW domain-binding protein 7 (WBP-7), is encoded by the gene that was first named myeloid/lymphoid or mixed-lineage leukemia 2 (MLL2), a second human homolog of Drosophila trithorax, located on chromosome 19. It belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2) and is vital for normal mammalian embryonic development. KMT2B functions as the catalytic subunit in the MLL2 complex, which contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL2 complex is highly active and specific for histone 3 lysine 4 (H3K4) methylation, which stimulates chromatin transcription in a SAM- and H3K4-dependent manner. Moreover, KMT2B plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. KMT2B contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the third PHD finger.


Pssm-ID: 277068  Cd Length: 57  Bit Score: 40.60  E-value: 6.95e-04
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 1537972313 1502 CPVCHAPYVEEDL---LIQCRHCERWMHAGCESLFTED 1536
Cdd:cd15593      2 CPICLKCYEDNDYeskMMQCAKCDHWVHAKCEGLSDEL 39
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
 228-273 7.03e-04

PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED) protein, functions as a regulator of gene transcription in the thymus. It is essential for prevention of autoimmunity. AIRE plays a critical role in the induction of central tolerance. It promotes self-tolerance through tissue-specific antigen (TSA) expression. It also acts as an active regulator of chondrocyte differentiation. AIRE contains a homogeneously-staining region (HSR) or caspase-recruitment domain (CARD), a nuclear localization signal (NLS), a SAND (for Sp100, AIRE, nuclear phosphoprotein 41/75 or NucP41/75, and deformed epidermal auto regulatory factor 1 or Deaf1) domain, two plant homeodomain (PHD) fingers, and four LXXLL (where L stands for leucine) motifs. This model corresponds to the first PHD finger that recognizes the unmethylated tail of histone H3 and targets AIRE-dependent genes.


Pssm-ID: 277014 [Multi-domain]  Cd Length: 43  Bit Score: 40.13  E-value: 7.03e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1537972313  228 HCAVCEGPGELcdlFFCTSCGHHYHGACLDTALTARKRAGWQCPEC 273
Cdd:cd15539      1 ECAVCGDGGEL---LCCDGCPRAFHLACLVPPLTLIPSGTWRCSSC 43
PHD_ARID4_like cd15615
PHD finger found in Arabidopsis thaliana AT-rich interactive domain-containing protein 4 ...
 1501-1551 7.46e-04

PHD finger found in Arabidopsis thaliana AT-rich interactive domain-containing protein 4 (ARID4) and similar proteins; This family includes A. thaliana ARID4 (ARID domain-containing protein 4) and similar proteins. Their biological roles remain unclear, but they all contain an AT-rich interactive domain (ARID) and a plant homeodomain (PHD) finger at the C-terminus. ARID is a helix-turn-helix motif-based DNA-binding domain conserved in all eukaryotes. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins.


Pssm-ID: 277087  Cd Length: 57  Bit Score: 40.54  E-value: 7.46e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1537972313 1501 TCPVCHAPYVE----EDLLIQCRHCERWMHAGCESLFTEDEVEQAADEG--FDCVSC 1551
Cdd:cd15615      1 FCILCGQVYEEnegdEKEWVQCDSCSEWVHFECDGRTGLGAFKYAKSDGlqYVCPRC 57
PRK14948 PRK14948
DNA polymerase III subunit gamma/tau;
4236-4340 7.50e-04

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237862 [Multi-domain]  Cd Length: 620  Bit Score: 46.11  E-value: 7.50e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4236 QSGGFSGSQTGPLQELGAGPRPQGPPRLPVPQgaLSTGPVLGPVHPTPPPSSPQEPKRPSQLPSPSAQPTPTHPgtPKPQ 4315
Cdd:PRK14948   511 ESQSGSASNTAKTPPPPQKSPPPPAPTPPLPQ--PTATAPPPTPPPPPPTATQASSNAPAQIPADSSPPPPIPE--EPTP 586

                           90       100
                   ....*....|....*....|....*
gi 1537972313 4316 GPTLELPPGRVSPAAAQLADTFFGK 4340
Cdd:PRK14948   587 SPTKDSSPEEIDKAAKNLADFFNGE 611
PHD_BRPF2 cd15677
PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar ...
 1424-1471 8.25e-04

PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar proteins; BRPF2, also termed bromodomain-containing protein 1 (BRD1), or BR140-like protein, is encoded by BRL (BR140 Like gene). It is responsible for the bulk of the acetylation of H3K14 and forms a novel monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with HBO1 and ING4. The complex is required for full transcriptional activation of the erythroid-specific regulator genes essential for terminal differentiation and survival of erythroblasts in fetal liver. BRPF2 shows widespread expression and localizes to the nucleus within spermatocytes. It contains a cysteine rich region harboring a canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277147 [Multi-domain]  Cd Length: 54  Bit Score: 40.38  E-value: 8.25e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1537972313 1424 VCEVC--GQASDPSRLLLCDDCDISYHTYCLDPPLltVPKGGWKCKWCVS 1471
Cdd:cd15677      3 VCCICmdGECQNSNVILFCDMCNLAVHQECYGVPY--IPEGQWLCRHCLQ 50
PHD1_MTF2 cd15578
PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also ...
 1424-1471 8.44e-04

PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also termed metal regulatory transcription factor 2, or metal-response element DNA-binding protein M96, or polycomb-like protein 2 (PCL2), complexes with the polycomb repressive complex-2 (PRC2) in embryonic stem cells and regulates the transcriptional networks during embryonic stem cell self-renewal and differentiation. It recruits the PRC2 complex to the inactive X chromosome and target loci in embryonic stem cells. Moreover, MTF2 is required for PRC2-mediated Hox cluster repression. It activates the Cdkn2a gene and promotes cellular senescence, thus suppressing the catalytic activity of PRC2 locally. MTF2 consists of an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. This model corresponds to the first PHD finger.


Pssm-ID: 277053  Cd Length: 53  Bit Score: 40.46  E-value: 8.44e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1537972313 1424 VCEVC--GQASDPSRLLLCDDCDISYHTYCLDPPLLTV---PKGGWKCKWCVS 1471
Cdd:cd15578      1 VCTVCqdGSSESPNEIVLCDKCGQGYHQLCHNPKIDSSvldPDVPWLCRQCVF 53
PHA03247 PHA03247
large tegument protein UL36; Provisional
 2080-2307 8.97e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 46.08  E-value: 8.97e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2080 AKVGDIARKTDRPALHLRIPSQPGALGSPPPAAAPtifigsptTPAGLSTSADGFLKPPAGTVPGPDSPgelfLKLPPQV 2159
Cdd:PHA03247  2774 APAAGPPRRLTRPAVASLSESRESLPSPWDPADPP--------AAVLAPAAALPPAASPAGPLPPPTSA----QPTAPPP 2841

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2160 PAQvPSQDPFGLAPAYAPEPRFSAAPPTYPPYPTPSgAPAQPPIlGTTTRPGTGQPGEFHTTPPGTPRHQPsTPDPFLKP 2239
Cdd:PHA03247  2842 PPG-PPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPA-APARPPV-RRLARPAVSRSTESFALPPDQPERPP-QPQAPPPP 2917

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1537972313 2240 RCPSLDNLAVPESPGVAGGKASEPLLSPP--PFGESRKTLEVKKEELGASSPGY-------GPPNLGCVDSPSSGSH 2307
Cdd:PHA03247  2918 QPQPQPPPPPQPQPPPPPPPRPQPPLAPTtdPAGAGEPSGAVPQPWLGALVPGRvavprfrVPQPAPSREAPASSTP 2994
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 2102-2508 9.01e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 45.75  E-value: 9.01e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2102 PGALGSPPPAAAPTIFIGSPTTPAGLSTSADGFLKPPAGTVPGPDSPGELFLKLPPQVPAQVPSQdpfglAPAYAPEPRF 2181
Cdd:PRK07764   365 PSASDDERGLLARLERLERRLGVAGGAGAPAAAAPSAAAAAPAAAPAPAAAAPAAAAAPAPAAAP-----QPAPAPAPAP 439

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2182 SAAPPTYPPYPTPSGAPAQPPILGTTTRPGTGQPGEFHTTPPGTPRHQPSTPDPFLKPRCPSldnlAVPESPGVAGGKAS 2261
Cdd:PRK07764   440 APPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAAPEPTAAPAPAPPAAPAPAAAPAAPAAPA----APAGADDAATLRER 515

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2262 EPLLSPPPFGESRKTLEVKKEELGASSP-------GYGPPNLG---------------------------CVDSPSSGSH 2307
Cdd:PRK07764   516 WPEILAAVPKRSRKTWAILLPEATVLGVrgdtlvlGFSTGGLArrfaspgnaevlvtalaeelggdwqveAVVGPAPGAA 595

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2308 LGglelkAPDVFKAPLTPRASQVEPQSPGlglrAQEPPAAQALAPSPPSHSDVFRSASYPDPYAQPPLTPRPQPPPPESC 2387
Cdd:PRK07764   596 GG-----EGPPAPASSGPPEEAARPAAPA----APAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGG 666

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2388 CALPPRSLPSDPFSRVPASPQSQSSSQsplTPRPLSAEAFCPSPVTPRFQSPDPYSRPPSRPQSRDPFAPLHKPPRPQPP 2467
Cdd:PRK07764   667 DGWPAKAGGAAPAAPPPAPAPAAPAAP---AGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPP 743

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|.
gi 1537972313 2468 EVAFKAGPLAHTPLGAGGFPAALPSGPAGELHAKVPSGQPP 2508
Cdd:PRK07764   744 EPDDPPDPAGAPAQPPPPPAPAPAAAPAAAPPPSPPSEEEE 784
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
2099-2355 9.20e-04

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 45.64  E-value: 9.20e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2099 PSQPGALGSPPPAAAPTIfigSPTTPAglstsadgfLKPPAGTVPGPDSPGelflKLPPQVPAQVPSQDPFGLAPAYAPE 2178
Cdd:PRK12323   365 PGQSGGGAGPATAAAAPV---AQPAPA---------AAAPAAAAPAPAAPP----AAPAAAPAAAAAARAVAAAPARRSP 428

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2179 PRFSAAPPTYPPYPTPSGAPAQPPilgtttrpgtgqpgefhtTPPGTPRHQPSTPDPFLKPRCPSLDNLAVPESPGVAGG 2258
Cdd:PRK12323   429 APEALAAARQASARGPGGAPAPAP------------------APAAAPAAAARPAAAGPRPVAAAAAAAPARAAPAAAPA 490

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2259 KASEpllSPPPFGESRKTLEVkkEELGASSPGYGPPNLGCVDSPSSGSHLGGLELKAPDVFKAPLTPRASQVEPQSPGLG 2338
Cdd:PRK12323   491 PADD---DPPPWEELPPEFAS--PAPAQPDAAPAGWVAESIPDPATADPDDAFETLAPAPAAAPAPRAAAATEPVVAPRP 565

                          250
                   ....*....|....*..
gi 1537972313 2339 LRAQEPPAAQALAPSPP 2355
Cdd:PRK12323   566 PRASASGLPDMFDGDWP 582
PHD3_KMT2A cd15592
PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, ...
 1502-1551 9.53e-04

PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, CXXC-type zinc finger protein 7, myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), trithorax-like protein (Htrx), or zinc finger protein HRX) is a histone methyltransferase that belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2). It regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex, which also contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL1 complex is highly active and specific for H3K4 methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, a Bromodomain domain, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the third PHD finger.


Pssm-ID: 277067  Cd Length: 57  Bit Score: 40.36  E-value: 9.53e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1537972313 1502 CPVCHAPYVEEDL---LIQCRHCERWMHAGCESLfTEDEVEQAAD----EGFDCVSC 1551
Cdd:cd15592      2 CPLCDKCYDDDDYeskMMQCGKCDRWVHSKCENL-SDEMYEILSNlpesVAYTCINC 57
PHA03247 PHA03247
large tegument protein UL36; Provisional
 2390-2995 9.84e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 46.08  E-value: 9.84e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2390 LPPRSLPSDPFSRVPASPQSQSSSQSPLTPRPLSAEAfCPSPVTPRfqSPDPYSRPPSRPQSRDPFAPLHKPPRPQPPev 2469
Cdd:PHA03247  2555 LPPAAPPAAPDRSVPPPRPAPRPSEPAVTSRARRPDA-PPQSARPR--APVDDRGDPRGPAPPSPLPPDTHAPDPPPP-- 2629

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2470 afkaGPLAHTPLGAGGFPAALPSGPAGELHAKVPSGQPPNFARSPGTGAFVGTPspmrftfPQGVGEPSLKPPvpqpglp 2549
Cdd:PHA03247  2630 ----SPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSP-------PQRPRRRAARPT------- 2691

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2550 pphginshFGPGPTLGKPQSTNYTVATGNfhPSGSPLGPNTGPTGEGYGLSPLRPASVMPPPTPEGslpylshgASQRAG 2629
Cdd:PHA03247  2692 --------VGSLTSLADPPPPPPTPEPAP--HALVSATPLPPGPAAARQASPALPAAPAPPAVPAG--------PATPGG 2753

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2630 ITSPVEKREDAGATmSSSSLATPELSSAQDAGMPSLSqtelekqrqrqrlrellirqqiqrnNLRQEKETAAAAASAVGP 2709
Cdd:PHA03247  2754 PARPARPPTTAGPP-APAPPAAPAAGPPRRLTRPAVA-------------------------SLSESRESLPSPWDPADP 2807

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2710 PGnwgaePSSPAFEQLSRGQTPFTGSQDKSSIVGLPSSKLGGPI-----LGPGAFSSDDRLSRPLPPATPSSMDMNSRQL 2784
Cdd:PHA03247  2808 PA-----AVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPppslpLGGSVAPGGDVRRRPPSRSPAAKPAAPARPP 2882

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2785 VggsqafyQRTPYPgsLPLQQQQQQQQQPLWQQQQQQATVATsmrlamsarfPSTPGPELGRQALGSPLAGIPTRLPGPA 2864
Cdd:PHA03247  2883 V-------RRLARP--AVSRSTESFALPPDQPERPPQPQAPP----------PPQPQPQPPPPPQPQPPPPPPPRPQPPL 2943

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2865 EPVPGPAGPAQfielrhnVQKGLGPGGPPFPGQGPPQRPRFYPVSEEPHRLAPeglrgvAISGLPPQKPSAPPVPELNNS 2944
Cdd:PHA03247  2944 APTTDPAGAGE-------PSGAVPQPWLGALVPGRVAVPRFRVPQPAPSREAP------ASSTPPLTGHSLSRVSSWASS 3010

                          570       580       590       600       610
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1537972313 2945 LhqTSHTKSPALPTGLELVSRPPSSTELSRP-------PLALEAGKLPCEDPELDDDF 2995
Cdd:PHA03247  3011 L--ALHEETDPPPVSLKQTLWPPDDTEDSDAdslfdsdSERSDLEALDPLPPEPHDPF 3066
PHD_TAF3 cd15522
PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed ...
 276-320 1.00e-03

PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed 140 kDa TATA box-binding protein-associated factor, TBP-associated factor 3, transcription initiation factor TFIID 140 kDa subunit (TAF140), or TAFII-140, is an integral component of TFIID) is a general initiation factor (GTF) that plays a key role in preinitiation complex (PIC) assembly through core promoter recognition. The interaction of H3K4me3 with TAF3 directs global TFIID recruitment to active genes, which regulates gene-selective functions of p53 in response to genotoxic stress. TAF3 is highly enriched in embryonic stem cells and is required for endoderm lineage differentiation and prevents premature specification of neuroectoderm and mesoderm. Moreover, TAF3, along with TRF3, forms a complex that is essential for myogenic differentiation. TAF3 contains a plant homeodomain (PHD) finger. This family also includes Drosophila melanogaster BIP2 (Bric-a-brac interacting protein 2) protein, which functions as an interacting partner of D. melanogaster p53 (Dmp53).


Pssm-ID: 276997 [Multi-domain]  Cd Length: 46  Bit Score: 39.96  E-value: 1.00e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15522      2 CPICKKPDDGSPMIGCDECDDWYHWECVGITDEPPEEDDWFCPKC 46
PHA03378 PHA03378
EBNA-3B; Provisional
 4145-4424 1.16e-03

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 45.44  E-value: 1.16e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4145 QPPKTGPVPQSGQGLPGVG---VMPTVGQLRAQLQGVLAKNPQLRHLSPQQQQQLQALLMQRQLQQSQAVRQTP------ 4215
Cdd:PHA03378   552 EPASTEPVHDQLLPAPGLGplqIQPLTSPTTSQLASSAPSYAQTPWPVPHPSQTPEPPTTQSHIPETSAPRQWPmplrpi 631

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4216 PIQEPGSQPSPLQGLLGCQPQ-----SGGFSGSQTGPLQELGAGPRPQGPPRLPVPQGALSTG--PVLGPVHPTPPPSSP 4288
Cdd:PHA03378   632 PMRPLRMQPITFNVLVFPTPHqppqvEITPYKPTWTQIGHIPYQPSPTGANTMLPIQWAPGTMqpPPRAPTPMRPPAAPP 711

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4289 QEPKRPSQLPSPSAQPTPTHPGTPKPQGPTLELPPGRVSPAAAQLADTFFGKGLGPWDPSDNLTEAQKPEqsslvsghle 4368
Cdd:PHA03378   712 GRAQRPAAATGRARPPAAAPGRARPPAAAPGRARPPAAAPGRARPPAAAPGRARPPAAAPGAPTPQPPPQ---------- 781

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1537972313 4369 qvNGQVVQESPQLSIKQEPREESCALGAQAVKREADGEPGGTPGTSNHLLLAGSRS 4424
Cdd:PHA03378   782 --APPAPQQRPRGAPTPQPPPQAGPTSMQLMPRAAPGQQGPTKQILRQLLTGGVKR 835
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 541-850 1.19e-03

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 45.55  E-value: 1.19e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  541 SSPALETPLSPPPEASPLSPPFEESPLSPPPE--ALPTSPPPEASRLSPPPEESPMSPPPEESPMSPPPEASRLFPPFEE 618
Cdd:PHA03307    61 ACDRFEPPTGPPPGPGTEAPANESRSTPTWSLstLAPASPAREGSPTPPGPSSPDPPPPTPPPASPPPSPAPDLSEMLRP 140

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  619 SPLSpppeesplspppeASRLSPPPEDSPMSPPPEDSPMSPPPEVSRFSPLPV-LSHLSPLPEVSRLspppeespLSPPP 697
Cdd:PHA03307   141 VGSP-------------GPPPAASPPAAGASPAAVASDAASSRQAALPLSSPEeTARAPSSPPAEPP--------PSTPP 199

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  698 EDSPTSPPPEASRLSPPPEDSPVSPPPEDSLMSLPLEESPLSPLPEGPRLCPQPEEPYLSPQPEEPRLCPQPEELPLSPR 777
Cdd:PHA03307   200 AAASPRPPRRSSPISASASSPAPAPGRSAADDAGASSSDSSSSESSGCGWGPENECPLPRPAPITLPTRIWEASGWNGPS 279

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1537972313  778 SEEPCLSPVLAEPCLSSQPEE------PHLSPVPQEQHLSPQPEEPHLSPQPkephlSPQSEEPCLSPMLEEPCLSPKP 850
Cdd:PHA03307   280 SRPGPASSSSSPRERSPSPSPsspgsgPAPSSPRASSSSSSSRESSSSSTSS-----SSESSRGAAVSPGPSPSRSPSP 353
half-pint TIGR01645
poly-U binding splicing factor, half-pint family; The proteins represented by this model ...
 4243-4436 1.43e-03

poly-U binding splicing factor, half-pint family; The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.


Pssm-ID: 130706 [Multi-domain]  Cd Length: 612  Bit Score: 45.06  E-value: 1.43e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4243 SQTGPLQELGAGPRPQGPPrlPVPQGALSTGPVLGPVHPTPPPSSPQEpkrPSQLPSPSAQPTPTHPGTPKPQG---PTl 4319
Cdd:TIGR01645  327 RAQSPATPSSSLPTDIGNK--AVVSSAKKEAEEVPPLPQAAPAVVKPG---PMEIPTPVPPPGLAIPSLVAPPGlvaPT- 400

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4320 ELPPGRVSPAAAQLADTFFGKGLGPWDPSDNLTEAQKPEQSSlVSGHLEQVNGQVVQESPQLSIKQEPREEscalGAQAV 4399
Cdd:TIGR01645  401 EINPSFLASPRKKMKREKLPVTFGALDDTLAWKEPSKEDQTS-EDGKMLAIMGEAAAALALEPKKKKKEKE----GEELQ 475

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 1537972313 4400 KREADGEPGGTPGTSNHLLLAGsrSEAGHLLLQKLLR 4436
Cdd:TIGR01645  476 PKLVMNSEDASLASQEGMSIRG--NSARHLVMQKLMR 510
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 4144-4322 1.45e-03

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 45.41  E-value: 1.45e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4144 PQPPKTGPVPqSGQGLPGVGVMP---TVGQLRAQlqgvlAKNPQlrhlspqqqqQLQALLMQRQLQQSQAVRQTPPIQEP 4220
Cdd:pfam09770  174 APAPQPAAQP-ASLPAPSRKMMSleeVEAAMRAQ-----AKKPA----------QQPAPAPAQPPAAPPAQQAQQQQQFP 237

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4221 GSQPSPLQglLGCQPQSGGFSGSQTGPLQELGAGPRPQGPPRLPVPQgalsTGPVLGPVHPTPPPSSP----QEPKRPS- 4295
Cdd:pfam09770  238 PQIQQQQQ--PQQQPQQPQQHPGQGHPVTILQRPQSPQPDPAQPSIQ----PQAQQFHQQPPPVPVQPtqilQNPNRLSa 311

                          170       180       190
                   ....*....|....*....|....*....|...
gi 1537972313 4296 ------QLPSPSAQPTPTHPGTPKPQGPTLELP 4322
Cdd:pfam09770  312 arvgypQNPQPGVQPAPAHQAHRQQGSFGRQAP 344
PHD_JADE3 cd15681
PHD finger found in protein Jade-3 and similar proteins; Jade-3, also termed PHD finger ...
 1424-1470 1.51e-03

PHD finger found in protein Jade-3 and similar proteins; Jade-3, also termed PHD finger protein 16 (PHF16), is a plant homeodomain (PHD) zinc finger protein that is closely related to Jade-1, which functions as an essential regulator of multiple cell signaling pathways. Like Jade-1, Jade-3 is required for ING4 and ING5 to associate with histone acetyl transferase (HAT) HBO1 and Eaf6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. Jade-3 contains a canonical Cys4HisCys3 PHD domain followed by a non-canonical extended PHD (ePHD) domain, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277151 [Multi-domain]  Cd Length: 50  Bit Score: 39.57  E-value: 1.51e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1537972313 1424 VCEVCGQ--ASDPSRLLLCDDCDISYHTYCLDppLLTVPKGGWKCKWCV 1470
Cdd:cd15681      1 ICDVCRSpdSEEGNDMVFCDKCNICVHQACYG--ILKVPEGSWLCRTCV 47
PHD1_KMT2A_like cd15506
PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 276-320 1.60e-03

PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the first PHD finger.


Pssm-ID: 276981  Cd Length: 47  Bit Score: 39.26  E-value: 1.60e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1537972313  276 CQACRKPGNDsKMLVCETCDKGYHTFCLKPPIEELPAH--SWKCMTC 320
Cdd:cd15506      2 CFLCGSAGLN-ELLYCSVCCEPYHTFCLEEAERPLNINkdNWCCRRC 47
zf-HC5HC2H_2 pfam13832
PHD-zinc-finger like domain;
137-202 1.61e-03

PHD-zinc-finger like domain;


Pssm-ID: 463991 [Multi-domain]  Cd Length: 109  Bit Score: 41.18  E-value: 1.61e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1537972313  137 WAHHWCAVWSagvwgqegPELCGVD-----KAIFSGI-----SQRCSHC-TRFGASIPCRSPGCPRLYHFPCATASG 202
Cdd:pfam13832   21 WVHVLCAIFV--------PEVRFGNvatmePIDVSRIpperwKLKCVFCkKRSGACIQCSKGRCTTAFHVTCAQAAG 89
RING-H2_RNF167 cd16797
RING finger, H2 subclass, found in RING finger protein 167 (RNF167) and similar proteins; ...
 229-275 1.81e-03

RING finger, H2 subclass, found in RING finger protein 167 (RNF167) and similar proteins; RNF167, also known as RING105, is an endosomal/lysosomal E3 ubiquitin-protein ligase involved in alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) ubiquitination. It ubiquitinates AMPA-type glutamate receptor subunit GluA2 and regulates its surface expression, and thus acts as a selective regulator of AMPAR-mediated neurotransmission. It acts as an endosomal membrane protein which ubiquitylates vesicle-associated membrane protein 3 (VAMP3) and regulates endosomal trafficking. Moreover, RNF167 plays a role in the regulation of TSSC5 (tumor-suppressing subchromosomal transferable fragment cDNA, also known as ORCTL2/IMPT1/BWR1A/SLC22A1L), which can function in concert with the ubiquitin-conjugating enzyme UbcH6. RNF167 is widely conserved in metazoans and contains an N-terminal signal peptide, a protease-associated (PA) domain, two transmembrane domains (TM1 and TM2), and a C-terminal C3H2C3-type RING-H2 finger domain followed by a putative PEST sequence.


Pssm-ID: 319711 [Multi-domain]  Cd Length: 46  Bit Score: 39.26  E-value: 1.81e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1537972313  229 CAVCEGPGELCDLFFCTSCGHHYHGACLDTALTARKRAgwqCPECKE 275
Cdd:cd16797      3 CAICLDEYEEGDKLRVLPCSHAYHSKCVDPWLTQTKKT---CPVCKQ 46
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 5060-5104 1.88e-03

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 39.22  E-value: 1.88e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1537972313 5060 CSLCQRTGATS----SCNRmrCPNVYHFACAIRAKCMFFKDKTMLCPMH 5104
Cdd:cd15489      2 CIVCGKGGDLGgellQCDG--CGKWFHADCLGPPLSSFVPNGKWICPVC 48
PHD5_NSD cd15568
PHD finger 5 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
 5060-5104 1.99e-03

PHD finger 5 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the fifth PHD finger.


Pssm-ID: 277043 [Multi-domain]  Cd Length: 43  Bit Score: 38.85  E-value: 1.99e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313 5060 CSLCQRTGATSSCNRMRCPNVYHFACAIRAKcmfFKDKTMLCPMH 5104
Cdd:cd15568      2 CFRCGDGGDLVLCDFKGCPKVYHLSCLGLEK---PPGGKWICPWH 43
PHD1_MOZ_d4 cd15526
PHD finger 1 found in monocytic leukemia zinc-finger protein (MOZ), its factor (MORF), and d4 ...
 229-273 2.10e-03

PHD finger 1 found in monocytic leukemia zinc-finger protein (MOZ), its factor (MORF), and d4 gene family proteins; MOZ is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity and to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ-related factor (MORF) is a ubiquitously expressed transcriptional regulator with intrinsic HAT activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. Both MOZ and MORF are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are implicated in human leukemias. MOZ is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphoma genesis and bone development, and its homologs. This family also includes three members of the d4 gene family, DPF1 (neuro-d4), DPF2 (ubi-d4/Requiem), and DPF3 (cer-d4), which function as transcription factors and are involved in transcriptional regulation of genes via changing the condensed/decondensed state of chromatin in nucleus. DPF2 is ubiquitously expressed and it acts as a transcription factor that may participate in developmentally programmed cell death. DPF1 and DPF3 are expressed predominantly in neural tissues, and they may be involved in the transcription regulation of neuro specific gene clusters. All family members contain two plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277001  Cd Length: 56  Bit Score: 39.26  E-value: 2.10e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1537972313  229 CAVCEGPGELC-------DLFFCTSCGHHYHGACLD---TALTARKRAGWQCPEC 273
Cdd:cd15526      2 CDFCLGTDEKNnktgepeELISCADCGSSGHPSCLKfspGLTDAVKSYRWQCIEC 56
PHD3_KMT2D cd15597
PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 229-273 2.13e-03

PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the third PHD finger.


Pssm-ID: 277072  Cd Length: 51  Bit Score: 39.25  E-value: 2.13e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1537972313  229 CAVCE--GPGELCDLFFCTSCGHHYHGACLDTALTARK-RAGWQCPEC 273
Cdd:cd15597      3 CVVCGsfGRGSEGHLLACSQCSQCYHPYCVNSKITKVMlLKGWRCVEC 50
SP2_N cd22540
N-terminal domain of transcription factor Specificity Protein (SP) 2; Specificity Proteins ...
 4040-4336 2.33e-03

N-terminal domain of transcription factor Specificity Protein (SP) 2; Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. SP2 contains the least conserved DNA-binding domain within the SP subfamily of proteins, and its DNA sequence specificity differs from the other SP proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate, or in some cases, repress expression from different promoters. The transcription factor SP2 serves as a paradigm for indirect genomic binding. It does not require its DNA-binding domain for genomic DNA binding and occupies target promoters independently of whether they contain a cognate DNA-binding motif. SP2 belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. SP1-4 have similar N-terminal transactivation domains characterized by glutamine-rich regions, which, in most cases, have adjacent serine/threonine-rich regions. This model represents the N-terminal domain of SP2.


Pssm-ID: 411776 [Multi-domain]  Cd Length: 511  Bit Score: 44.15  E-value: 2.33e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4040 PSVSGDSQLLLVQSQAQAQPIPVQLQPPLRlpGQPQQQQVNLLHTTGGGNHGQQLGSSsevpsvphLLNQPSVSLGEQPG 4119
Cdd:cd22540    138 INNSGQIQIIPGTNQAIITPVQVLQQPQQA--HKPVPIKPAPLQTSNTNSASLQVPGN--------VIKLQSGGNVALTL 207

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4120 PMtQNLLGSQqplglDRPIQNNTGPQPPKTGPVpQSGQGLPGVGVMPTVGQlraQLQGVLAKNPQLRHLSPQQQQQLQAL 4199
Cdd:cd22540    208 PV-NNLVGTQ-----DGATQLQLAAAPSKPSKK-IRKKSAQAAQPAVTVAE---QVETVLIETTADNIIQAGNNLLIVQS 277

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4200 LMQRQLQQSQAVRQTPPIQEPGSQPSPLQGLLGCQPQSGGFSGSQTGPLQ--ELGAGPRPQGPPRLPVPQGALSTgpVLG 4277
Cdd:cd22540    278 PGTGQPAVLQQVQVLQPKQEQQVVQIPQQALRVVQAASATLPTVPQKPLQniQIQNSEPTPTQVYIKTPSGEVQT--VLL 355

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1537972313 4278 PVHPTPPPSSPQEPKRPSQLPSPSAQPTPTHPGTPKPQGPTLELPP---GRVSPAAAQLADT 4336
Cdd:cd22540    356 QEAPAATATPSSSTSTVQQQVTANNGTGTSKPNYNVRKERTLPKIApagGIISLNAAQLAAA 417
SET_Suv4-20-like cd10524
SET domain (including post-SET domain) found in Drosophila melanogaster suppressor of ...
 5452-5518 2.39e-03

SET domain (including post-SET domain) found in Drosophila melanogaster suppressor of variegation 4-20 (Suv4-20) and similar proteins; Suv4-20 (also termed Su(var)4-20) is a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-20' of histone H4. It acts as a dominant suppressor of position-effect variegation. The family also includes Suv4-20 homologs, lysine N-methyltransferase 5B (KMT5B) and lysine N-methyltransferase 5C (KMT5C). Both KMT5B (also termed lysine-specific methyltransferase 5B, or suppressor of variegation 4-20 homolog 1, or Su(var)4-20 homolog 1, or Suv4-20h1) and KMT5C (also termed lysine-specific methyltransferase 5C, or suppressor of variegation 4-20 homolog 2, or Su(var)4-20 homolog 2, or Suv4-20h2) are histone methyltransferases that specifically trimethylate 'Lys-20' of histone H4 (H4K20me3). They play central roles in the establishment of constitutive heterochromatin in pericentric heterochromatin regions.


Pssm-ID: 380922 [Multi-domain]  Cd Length: 141  Bit Score: 41.50  E-value: 2.39e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1537972313 5452 GPARYINHSCAPNCVaevvtFDKEDKIIIISSRRIP--KGEELTYDYQFDFEDDQHkipCHCGAWNCRK 5518
Cdd:cd10524     75 GPAAFINHDCRPNCK-----FVPTGKSTACVKVLRDiePGEEITVYYGDNYFGENN---EECECETCER 135
PHD1_NSD cd15564
PHD finger 1 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
 229-274 2.53e-03

PHD finger 1 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the first PHD finger.


Pssm-ID: 277039  Cd Length: 43  Bit Score: 38.86  E-value: 2.53e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1537972313  229 CAVCEGPGElcdLFFCT-SCGHHYHGACLdtALTARKRAGWQCPECK 274
Cdd:cd15564      2 CQICEKPGK---LLTCEgPCCGHFHLDCL--GLSEQPDEPFKCDECT 43
PHD_TCF19_like cd15517
PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and ...
 1502-1551 2.66e-03

PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and KDM5B, and other similar proteins; TCF-19 was identified as a putative trans-activating factor with expression beginning at the late G1-S boundary in dividing cells. It functions as a novel islet factor necessary for proliferation and survival in the INS-1 beta cell line. It plays an important role in susceptibility to both Type 1 Diabetes Mellitus (T1DM) and Type 2 Diabetes Mellitus (T2DM); it has been suggested that it may positively impact beta cell mass under conditions of beta cell stress and increased insulin demand. KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interaction with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK, and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. This family also includes Caenorhabditis elegans Lysine-specific demethylase 7 homolog (ceKDM7A). ceKDM7A (also termed JmjC domain-containing protein 1.2, PHD finger protein 8 homolog, or PHF8 homolog) is a plant homeodomain (PHD)- and JmjC domain-containing protein that functions as a histone demethylase specific for H3K9me2 and H3K27me2. The binding of the PHD finger to H3K4me3 guides H3K9me2- and H3K27me2-specific demethylation by its catalytic JmjC domain in a trans-histone regulation mechanism. In addition, this family includes plant protein OBERON 1 and OBERON 2, Alfin1-like (AL) proteins, histone acetyltransferases (HATs) HAC, and AT-rich interactive domain-containing protein 4 (ARID4).


Pssm-ID: 276992 [Multi-domain]  Cd Length: 49  Bit Score: 38.68  E-value: 2.66e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1537972313 1502 CPVCHAPYVEEDLL-IQCRHCERWMHAGCESLftedEVEQAADEG-FDCVSC 1551
Cdd:cd15517      2 CGICNLETAAVDELwVQCDGCDKWFHQFCLGL----SNERYADEDkFKCPNC 49
PHD2_KMT2C_like cd15510
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 1375-1422 2.70e-03

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 276985  Cd Length: 46  Bit Score: 38.57  E-value: 2.70e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1537972313 1375 CVVCGSfgRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLkGWRCVEC 1422
Cdd:cd15510      2 CQACRQ--PGDDTKMLVCETCDKGYHTSCLRPVMSSIPKY-GWKCKNC 46
PRK14950 PRK14950
DNA polymerase III subunits gamma and tau; Provisional
 4235-4334 2.71e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237864 [Multi-domain]  Cd Length: 585  Bit Score: 44.03  E-value: 2.71e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4235 PQSGGFSGSQTGPLQElgaGPRPQGPPRLPVPQGALSTGPVLGPVHPTPPPSSPQEPKRPSQLPSPSAQPTPTHPGTPKP 4314
Cdd:PRK14950   366 PQPAKPTAAAPSPVRP---TPAPSTRPKAAAAANIPPKEPVRETATPPPVPPRPVAPPVPHTPESAPKLTRAAIPVDEKP 442

                           90       100
                   ....*....|....*....|
gi 1537972313 4315 QGPTLELPPGRVSPAAAQLA 4334
Cdd:PRK14950   443 KYTPPAPPKEEEKALIADGD 462
PHD_BRPF cd15572
PHD finger found in bromodomain and PHD finger-containing (BRPF) proteins; The family of BRPF ...
 1424-1470 3.12e-03

PHD finger found in bromodomain and PHD finger-containing (BRPF) proteins; The family of BRPF proteins includes BRPF1, BRD1/BRPF2, and BRPF3. They are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277047 [Multi-domain]  Cd Length: 54  Bit Score: 38.75  E-value: 3.12e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1537972313 1424 VCEVC--GQASDPSRLLLCDDCDISYHTYCLDPPLltVPKGGWKCKWCV 1470
Cdd:cd15572      3 VCCICldGECQNSNVILFCDMCNLAVHQECYGVPY--IPEGQWLCRRCL 49
ePHD_BRPF3 cd15703
Extended PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and ...
 5025-5089 3.21e-03

Extended PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of BRPF3. BRF3 is a homolog of BRPF1 and BRPF2. It is a scaffold protein that forms a novel monocytic leukemic zinc finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with other regulatory subunits. BRPF3 contains a plant homeodomain (PHD) finger followed by this non-canonical ePHD finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain.


Pssm-ID: 277173 [Multi-domain]  Cd Length: 118  Bit Score: 40.81  E-value: 3.21e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1537972313 5025 WVHLNCALWSTEVYETQGGALMNVE----VALHRGLLTkCSLCQRT--GATSSCNRMRCPNVYHFACAIRA 5089
Cdd:cd15703     19 WAHVVCAIWIPEVCFANTVFLEPVEgvnnIPPARWKLT-CYLCKQKgrGAAIQCHKVNCYTAFHVTCAQRA 88
PHA03369 PHA03369
capsid maturational protease; Provisional
 700-780 3.47e-03

capsid maturational protease; Provisional


Pssm-ID: 223061 [Multi-domain]  Cd Length: 663  Bit Score: 43.83  E-value: 3.47e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  700 SPTSPP--PEASRLSPPPEDSPVSPPPEDSLMSLPLEESPLSPLPEGPRLCPQPEEPYlSPQPEEPRLCPQ------PEE 771
Cdd:PHA03369   379 ADRQRPqrPDGIPYSVPARSPMTAYPPVPQFCGDPGLVSPYNPQSPGTSYGPEPVGPV-PPQPTNPYVMPIsmanmvYPG 457


                   ....*....
gi 1537972313  772 LPlSPRSEE 780
Cdd:PHA03369   458 HP-QEHGHE 465
PHD_PRKCBP1 cd15538
PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed ...
 276-320 3.71e-03

PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed cutaneous T-cell lymphoma-associated antigen se14-3 (CTCL-associated antigen se14-3), or Rack7, or zinc finger MYND domain-containing protein 8 (ZMYND8), is a novel receptor for activated C-kinase (RACK)-like protein that may play an important role in the activation and regulation of PKC-beta I, and the PKC signaling cascade. It also has been identified as a formin homology-2-domain containing protein 1 (FHOD1)-binding protein that may be involved in FHOD1-regulated actin polymerization and transcription. Moreover, PRKCBP1 may function as a REST co-repressor 2 (RCOR2) interacting factor; the RCOR2/ZMYND8 complex which might be involved in the regulation of neural differentiation. PRKCBP1 contains a plant homeodomain (PHD) finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain.


Pssm-ID: 277013  Cd Length: 41  Bit Score: 38.08  E-value: 3.71e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGndsKMLVCETCDKGYHTFCLKPPIEelPAHSWKCMTC 320
Cdd:cd15538      2 CWRCHKEG---QVLCCSLCPRVYHKKCLKLTSE--PDEDWVCPEC 41
PHD1_Lid2p_like cd15519
PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
 229-273 3.84e-03

PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar proteins; Lid2p is a trimethyl H3K4 (H3K4me3) demethylase responsible for H3K4 hypomethylation in heterochromatin. It interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, and mediates H3K9 methylation and small RNA production. It also acts cooperatively with the histone modification enzymes Set1 and Lsd1 and plays an essential role in cross-talk between H3K4 and H3K9 methylation in euchromatin. Lid2p contains a JmjC domain, three PHD fingers and a JmjN domain. This model corresponds to the first PHD finger.


Pssm-ID: 276994 [Multi-domain]  Cd Length: 46  Bit Score: 38.22  E-value: 3.84e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1537972313  229 CAVC---EGPGELcdlFFCTSCGHHYHGACLDTALTARKRAGWQCPEC 273
Cdd:cd15519      2 CEVCgldDNEGEV---LLCDGCDAEYHTSCLDPPLGEIPPGTWFCPSC 46
PHD_UHRF1_2 cd15525
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and ...
 1375-1422 4.04e-03

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and UHRF2; UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277000  Cd Length: 47  Bit Score: 38.12  E-value: 4.04e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1537972313 1375 CVVCGsfGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVEC 1422
Cdd:cd15525      2 CHVCG--GKQDPEKQLLCDECDMAYHLYCLDPPLTSLPDDDEWYCPDC 47
PHD1_KMT2A_like cd15506
PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 1374-1422 4.11e-03

PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the first PHD finger.


Pssm-ID: 276981  Cd Length: 47  Bit Score: 38.11  E-value: 4.11e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1537972313 1374 MCVVCGSFGRGaegHLLACSQCSQCYHPYCVNSKITKVMLLKG-WRCVEC 1422
Cdd:cd15506      1 LCFLCGSAGLN---ELLYCSVCCEPYHTFCLEEAERPLNINKDnWCCRRC 47
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
 231-273 4.14e-03

PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger of KMT2C and the fourth PHD finger of KMT2D.


Pssm-ID: 276988  Cd Length: 47  Bit Score: 38.23  E-value: 4.14e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1537972313  231 VCEGPGELCD---LFFCTSCGHHYHGACLDTALTARKRAGWQCPEC 273
Cdd:cd15513      1 VCEGCGKASDesrLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 46
PHD2_3_BPTF cd15560
PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF); ...
 1504-1551 4.32e-03

PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, also termed nucleosome-remodeling factor subunit BPTF, or fetal Alz-50 clone 1 protein (FAC1), or fetal Alzheimer antigen, functions as a transcriptional regulator that exhibits altered expression and subcellular localization during neuronal development and neurodegenerative diseases such as Alzheimer's disease. It interacts with the human orthologue of the Kelch-like Ech-associated protein (Keap1). Its function and subcellular localization can be regulated by Keap1. Moreover, BPTF is a novel DNA-binding protein that recognizes the DNA sequence CACAACAC and represses transcription through this site in a phosphorylation-dependent manner. Furthermore, BPTF interacts with the Myc-associated zinc finger protein (ZF87/MAZ) and alters its transcriptional activity, which has been implicated in gene regulation in neurodegeneration. Some family members contain two or three plant homeodomain (PHD) fingers, which may be involved in complex formation with histone H3 trimethylated at K4 (H3K4me3). This family corresponds to the second and third PHD fingers.


Pssm-ID: 277035  Cd Length: 47  Bit Score: 38.10  E-value: 4.32e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1537972313 1504 VCHAPYVEEDLLIQCRHCERWMHAGCESLfTEDEVEQAADegFDCVSC 1551
Cdd:cd15560      3 ICRTPYDESQFYIGCDRCQDWFHGRCVGI-LQSEAEKIDE--YVCPQC 47
RING-HC_CHFR cd16503
RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein ...
 225-274 4.42e-03

RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein (CHFR); CHFR, also known as RING finger protein 196 (RNF196), is a checkpoint protein that delays entry into mitosis in response to stress. It functions as an E3 ubiquitin ligase that ubiquitinates and degrades its target proteins, such as Aurora-A, Plk1, Kif22, and PARP-1, which are critical for proper mitotic transitions. It also plays an important role in cell cycle progression and tumor suppression, and is negatively regulated by SUMOylation-mediated proteasomal ubiquitylation. Moreover, CHFR is involved in the early stage of the DNA damage response, which mediates the crosstalk between ubiquitination and poly-ADP-ribosylation. CHFR contains a fork head associated (FHA) domain and a C3HC4-type RING-HC finger.


Pssm-ID: 438166 [Multi-domain]  Cd Length: 55  Bit Score: 38.50  E-value: 4.42e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1537972313  225 EEAHCAVCegpgelCDLFF-CTS---CGHHYHGACLDTALtarKRAGWQCPECK 274
Cdd:cd16503      1 ENLTCSIC------QDLLHdCVSlqpCMHNFCAACYSDWM---ERSNTECPTCR 45
PHD_PRHA_like cd15504
PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and ...
 273-320 4.46e-03

PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and similar proteins; PRHA is a homeodomain protein encoded by a single-copy Arabidopsis thaliana homeobox gene, prha. It shows the capacity to bind to TAATTG core sequence elements but requires additional adjacent bases for high-affinity binding. PRHA contains a plant homeodomain (PHD) finger, a homeodomain, peptide repeats and a putative leucine zipper dimerization domain.


Pssm-ID: 276979  Cd Length: 53  Bit Score: 38.18  E-value: 4.46e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1537972313  273 CKECQAcRKPGNDSKMLVCE-TCDKGYHTFCLKPPI--EELPA--HSWKCMTC 320
Cdd:cd15504      2 CAKCQS-GEASPDNDILLCDgGCNRAYHQKCLEPPLltEDIPPedEGWLCPLC 53
PHD1_PHF12 cd15533
PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is ...
 276-320 4.50e-03

PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is a plant homeodomain (PHD) zinc finger-containing protein that bridges the transducin-like enhancer of split (TLE) corepressor to the mSin3A-histone deacetylase (HDAC)-complex, and further represses transcription at targeted genes. PHF12 also interacts with MRG15 (mortality factor-related genes on chromosome 15), a member of the mortality factor (MORF) family of proteins implicated in regulating cellular senescence. PHF12 contains two plant-homeodomain (PHD) zinc fingers followed by a polybasic region. The PHD fingers function downstream of phosphoinositide signaling triggered by the interaction between polybasic regions and phosphoinositides. This model corresponds to the first PHD finger.


Pssm-ID: 277008 [Multi-domain]  Cd Length: 45  Bit Score: 38.11  E-value: 4.50e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1537972313  276 CQACRKPGNdskMLVCETCDKGYHTFCLKPPIEE--LPAHSWKCMTC 320
Cdd:cd15533      2 CDSCGEGGD---LLCCDRCPASFHLQCCNPPLDEedLPPGEWLCHRC 45
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
 229-273 4.73e-03

Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)


Pssm-ID: 214546 [Multi-domain]  Cd Length: 40  Bit Score: 37.87  E-value: 4.73e-03
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*
gi 1537972313   229 CAVCEGpgELCDLFFCTSCGHHYHGACLDTALtarKRAGWQCPEC 273
Cdd:smart00184    1 CPICLE--EYLKDPVILPCGHTFCRSCIRKWL---ESGNNTCPIC 40
PHD4_KMT2C cd15596
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 224-273 4.84e-03

PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the fourth PHD finger.


Pssm-ID: 277071  Cd Length: 57  Bit Score: 38.46  E-value: 4.84e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1537972313  224 LEEAHCAVCE--GPGELCDLFFCTSCGHHYHGACLDTALT-ARKRAGWQCPEC 273
Cdd:cd15596      4 LNQDMCVVCGsfGQGAEGRLLACSQCGQCYHPYCVSIKITkVVLSKGWRCLEC 56
PHD_BAZ1B cd15628
PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also ...
 229-273 5.01e-03

PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. BAZ1B contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277098  Cd Length: 46  Bit Score: 37.80  E-value: 5.01e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  229 CAVCEGPGELCDLFFCTSCGHHYHGACLDTALTARKRAGWQCPEC 273
Cdd:cd15628      2 CKVCRKKGEDDKLILCDECNQAFHLFCLRPALYEVPDGEWMCPAC 46
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 1375-1422 5.01e-03

PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the first PHD finger.


Pssm-ID: 276984  Cd Length: 48  Bit Score: 38.06  E-value: 5.01e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1537972313 1375 CVVCGSFGRGAEghLLACSQCSQCYHPYCVNSKITKVMLL-KGWRCVEC 1422
Cdd:cd15509      2 CAVCDSPGDLSD--LLFCTSCGQHYHGSCLDPAVRPTPLVrAGWQCPEC 48
PHD_PHF2_like cd15554
PHD finger found in PHF2, PHF8 and KDM7; This family includes PHF2, PHF8, KDM7, and similar ...
 1504-1551 5.02e-03

PHD finger found in PHF2, PHF8 and KDM7; This family includes PHF2, PHF8, KDM7, and similar proteins. PHF2, also termed GRC5, or PHD finger protein 2, is a histone lysine demethylase ubiquitously expressed in various tissues. PHF8, also termed PHD finger protein 8, or KDM7B, is a monomethylated histone H4 lysine 20(H4K20me1) demethylase that transcriptionally regulates many cell cycle genes. It also preferentially acts on H3K9me2 and H3K9me1. PHF8 is modulated by CDC20-containing anaphase-promoting complex (APC (cdc20)) and plays an important role in the G2/M transition. It acts as a critical molecular sensor for mediating retinoic acid (RA) treatment response in RAR alpha-fusion-induced leukemia. Moreover, PHF8 is essential for cytoskeleton dynamics and is associated with X-linked mental retardation. KDM7, also termed JmjC domain-containing histone demethylation protein 1D (JHDM1D), or KIAA1718, is a dual histone demethylase that catalyzes demethylation of monomethylated and dimethylated H3K9 (H3K9me2/me1) and H3K27 (H3K27me2/me1), which functions as an eraser of silencing marks on chromatin during brain development. It also plays a tumor-suppressive role by regulating angiogenesis. All family members contain a plant homeodomain (PHD) finger and a JmjC domain.


Pssm-ID: 277029  Cd Length: 47  Bit Score: 38.13  E-value: 5.02e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1537972313 1504 VCHAPYVEEDLLIQCRHCERWMHAGCeslfTEDEVEQAAD-EGFDCVSC 1551
Cdd:cd15554      3 ICRQPYDVTRFMIECDVCKDWFHGSC----VGVEEHQANDiERYHCPNC 47
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 228-273 5.05e-03

PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the first PHD finger.


Pssm-ID: 277006 [Multi-domain]  Cd Length: 43  Bit Score: 37.97  E-value: 5.05e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1537972313  228 HCAVCEGPGELcdlFFCTSCGHHYHGACLDTALTARKRAGWQCPEC 273
Cdd:cd15531      1 YCEVCQQGGEI---ILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 43
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
 4256-4348 5.25e-03

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 43.52  E-value: 5.25e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4256 RPQGP--PRLPV-PQGALSTGPVLGPVHPTPPPSS--------PQEPKRPSQLPSPSAQPTPTHPGTP-KPQGPtlELPP 4323
Cdd:PTZ00449   578 KPEFPkdPKHPKdPEEPKKPKRPRSAQRPTRPKSPklpelldiPKSPKRPESPKSPKRPPPPQRPSSPeRPEGP--KIIK 655

                           90       100
                   ....*....|....*....|....*
gi 1537972313 4324 GRVSPAAAQLadtffgkglgPWDPS 4348
Cdd:PTZ00449   656 SPKPPKSPKP----------PFDPK 670
ePHD_JADE cd15671
Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins; The extended ...
 133-217 5.39e-03

Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-1 (PHF17), Jade-2 (PHF15), and Jade-3 (PHF16); each of these proteins is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, has reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. This family also contains Drosophila melanogaster PHD finger protein rhinoceros (RNO). It is a novel plant homeodomain (PHD)-containing nuclear protein that may function as a transcription factor that antagonizes Ras signaling by regulating transcription of key EGFR/Ras pathway regulators in the Drosophila eye. All Jade proteins contain a canonical PHD finger followed by this non-canonical ePHD finger, both of which are zinc-binding motifs.


Pssm-ID: 277141  Cd Length: 112  Bit Score: 39.73  E-value: 5.39e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  133 GGHCWAHHWCAVWSAGVWGQEgPE----LCGVDKAIFSGISQRCSHC-TRFGASIPCRSPGCPRLYHFPCATASGsfLSM 207
Cdd:cd15671     16 SGTKWVHVSCALWIPEVSIGC-PEkmepITKISHIPMSRWALVCVLCkEKTGACIQCSVKSCKTAFHVTCAFQHG--LEM 92

                           90       100
                   ....*....|....*....|
gi 1537972313  208 KT--------LQLL--CPDH 217
Cdd:cd15671     93 KTilededdeVKFKsyCPKH 112
PHD1_MOZ_d4 cd15526
PHD finger 1 found in monocytic leukemia zinc-finger protein (MOZ), its factor (MORF), and d4 ...
 1389-1422 5.40e-03

PHD finger 1 found in monocytic leukemia zinc-finger protein (MOZ), its factor (MORF), and d4 gene family proteins; MOZ is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity and to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ-related factor (MORF) is a ubiquitously expressed transcriptional regulator with intrinsic HAT activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. Both MOZ and MORF are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are implicated in human leukemias. MOZ is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphoma genesis and bone development, and its homologs. This family also includes three members of the d4 gene family, DPF1 (neuro-d4), DPF2 (ubi-d4/Requiem), and DPF3 (cer-d4), which function as transcription factors and are involved in transcriptional regulation of genes via changing the condensed/decondensed state of chromatin in nucleus. DPF2 is ubiquitously expressed and it acts as a transcription factor that may participate in developmentally programmed cell death. DPF1 and DPF3 are expressed predominantly in neural tissues, and they may be involved in the transcription regulation of neuro specific gene clusters. All family members contain two plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277001  Cd Length: 56  Bit Score: 38.11  E-value: 5.40e-03
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1537972313 1389 LLACSQCSQCYHPYCVN--SKITKVMLLKGWRCVEC 1422
Cdd:cd15526     21 LISCADCGSSGHPSCLKfsPGLTDAVKSYRWQCIEC 56
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
636-840 5.87e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 43.33  E-value: 5.87e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  636 ASRLSPPPEDSPMSPPPEDSPMSPPPEVSRFSPLPVLSHLSPLPEVSRLSPPPEESPLSPPPEDSPTSPPPEASRLSPPP 715
Cdd:PRK12323   387 PAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQASARGPGGAPAPAPAPAAAPAAAARPAA 466

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  716 edSPVSPPPEDSLMSLPLEESPLSPLPEGPRLCPQPEEP--YLSPQPEEPRLCPQPEELPLSPRSeepclSPVLAEPCLS 793
Cdd:PRK12323   467 --AGPRPVAAAAAAAPARAAPAAAPAPADDDPPPWEELPpeFASPAPAQPDAAPAGWVAESIPDP-----ATADPDDAFE 539

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 1537972313  794 SQPEEPHLSPVPqeqhlspqpeEPHLSPQPKEPHLSPQSEEPCLSPM 840
Cdd:PRK12323   540 TLAPAPAAAPAP----------RAAAATEPVVAPRPPRASASGLPDM 576
PHD_UHRF2 cd15617
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); ...
 1375-1422 5.91e-03

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); UHRF2 (also termed Np95/ICBP90-like RING finger protein (NIRF), Np95-like RING finger protein, nuclear protein 97, nuclear zinc finger protein Np97, RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2) was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs,p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277089  Cd Length: 47  Bit Score: 38.01  E-value: 5.91e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1537972313 1375 CVVCGsfGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVEC 1422
Cdd:cd15617      2 CYVCG--GKQDAHMQLLCDECNMAYHIYCLNPPLDKIPEDEDWYCPSC 47
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
 539-826 6.06e-03

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 43.14  E-value: 6.06e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  539 SPSSPAL----------------ETPLSPPPEASPLSPPFEESPLSPPPEALPTSP-PPEASRLSPPPEESPMSPPPEES 601
Cdd:PTZ00449   608 RPKSPKLpelldipkspkrpespKSPKRPPPPQRPSSPERPEGPKIIKSPKPPKSPkPPFDPKFKEKFYDDYLDAAAKSK 687

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  602 PMSPPPEASRLFPPFEESPLSPPPEESPLSPPPEASRLsPPPEDSPMSPPPEdsPMSPPPEVSRFSPLPV--------LS 673
Cdd:PTZ00449   688 ETKTTVVLDESFESILKETLPETPGTPFTTPRPLPPKL-PRDEEFPFEPIGD--PDAEQPDDIEFFTPPEeertffheTP 764

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  674 HLSPLPEVSRLSPPPEESPLSPPPEDSPTSPPPEASRLSP-PPEDSPVSPPPEDSLMSLPLEESPLSplPEGPRLCPQPE 752
Cdd:PTZ00449   765 ADTPLPDILAEEFKEEDIHAETGEPDEAMKRPDSPSEHEDkPPGDHPSLPKKRHRLDGLALSTTDLE--SDAGRIAKDAS 842

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313  753 -EPY----------LSPQPEEPRLCPQPEELPLSPRSEEpclspvlAEPCLSSQPEEPHLSPV-----PQEQHLSPQPEE 816
Cdd:PTZ00449   843 gKIVklkrsksfddLTTVEEAEEMGAEARKIVVDDDGTE-------ADDEDTHPPEEKHKSEVrrrrpPKKPSKPKKPSK 915

                          330
                   ....*....|
gi 1537972313  817 PHlspQPKEP 826
Cdd:PTZ00449   916 PK---KPKKP 922
PHD_TIF1gamma cd15624
PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also ...
 1425-1469 6.20e-03

PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also termed tripartite motif-containing 33 (trim33), or ectodermin, or RFG7, or PTC7, is an E3-ubiquitin ligase that functions as a regulator of transforming growth factor beta (TGFbeta) signaling; it inhibits the Smad4-mediated TGFbeta response by interaction with Smad2/3 or ubiquitylation of Smad4. Moreover, TIF1gamma is an important regulator of transcription during hematopoiesis, as well as a key factor of tumorigenesis. Like other TIF1 family members, TIF1gamma also contains an intrinsic transcriptional silencing function. It can control erythroid cell fate by regulating transcription elongation. It can bind to the anaphase-promoting complex/cyclosome (APC/C) and promotes mitosis. TIF1gamma contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region.


Pssm-ID: 277094  Cd Length: 46  Bit Score: 37.72  E-value: 6.20e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313 1425 CEVCGQASDpsrLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1469
Cdd:cd15624      2 CAVCQNGGD---LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 43
PHD_PHF21B cd15524
PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) ...
 276-320 6.28e-03

PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) finger-containing protein whose biological function remains unclear. It shows high sequence similarity with PHF21A, which is associated with LSD1, a lysine (K)-specific histone demethylase and inhibits LSD1-mediated histone demethylation in vitro. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins.


Pssm-ID: 276999 [Multi-domain]  Cd Length: 43  Bit Score: 37.57  E-value: 6.28e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  276 CQACRKPGNdskMLVCETCDKGYHTFCLKPPIEELPAHSWKCMTC 320
Cdd:cd15524      2 CAACKRGGN---LQPCGTCPRAYHLDCLDPPLKTAPKGVWVCPKC 43
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 2088-2482 6.55e-03

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 43.24  E-value: 6.55e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2088 KTDRPALHLRIPSQPGALGSPPPAAAPTIFIGSPTTPAGLStsadgflkPPAGTVPGPDSPGELFLKLPPQVPAQVPSQD 2167
Cdd:PHA03307    95 LAPASPAREGSPTPPGPSSPDPPPPTPPPASPPPSPAPDLS--------EMLRPVGSPGPPPAASPPAAGASPAAVASDA 166

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2168 PFGLAPAYA------PEPRFSAAPPTYPPYPTPSGAPAQPPILGTTTRPGTGQPGefhttpPGTPRHQPStpdpflkPRC 2241
Cdd:PHA03307   167 ASSRQAALPlsspeeTARAPSSPPAEPPPSTPPAAASPRPPRRSSPISASASSPA------PAPGRSAAD-------DAG 233

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2242 PSLDNLAVPESPGVAGGKASE-PLLSPPPFgesrktleVKKEELGASSPGYGPPnlgcVDSPSSGSHlgglelkapdvfk 2320
Cdd:PHA03307   234 ASSSDSSSSESSGCGWGPENEcPLPRPAPI--------TLPTRIWEASGWNGPS----SRPGPASSS------------- 288

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2321 APLTPRASQVEPQSPGLGLRAQEPPAAQALAPSPPSHSDVFRSASYPDpyaqppltPRPQPPPPESCCALPPRSLPSDPF 2400
Cdd:PHA03307   289 SSPRERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSSSSESS--------RGAAVSPGPSPSRSPSPSRPPPPA 360

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 2401 SrvpaspqsqsssqsplTPRPLSAEAFCPSPVTPRFQSPDPYSR-------PPSRPQSRDPFAPLHKPPRPQPPEVAFKA 2473
Cdd:PHA03307   361 D----------------PSSPRKRPRPSRAPSSPAASAGRPTRRraraavaGRARRRDATGRFPAGRPRPSPLDAGAASG 424


                   ....*....
gi 1537972313 2474 GPLAHTPLG 2482
Cdd:PHA03307   425 AFYARYPLL 433
ePHD_PHF14 cd15674
Extended PHD finger found in PHD finger protein 14 (PHF14) and similar proteins; The extended ...
 5025-5088 6.79e-03

Extended PHD finger found in PHD finger protein 14 (PHF14) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of PHF14. PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and this non-canonical ePHD finger. It can interact with histones through its PHD fingers.


Pssm-ID: 277144  Cd Length: 114  Bit Score: 39.67  E-value: 6.79e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1537972313 5025 WVHLNCALWstevyeTQGGALMNVE----VALHRGLLTK-----CSLCQ-----RTGATSSCNRMRCPNVYHFACAIR 5088
Cdd:cd15674     19 WVHLVCALY------TPGVAFGDVDklspVTLTEMNYSKwgareCSLCEdprfaRTGVCISCDAGMCKSYFHVTCAQR 90
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 4213-4337 7.52e-03

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 43.15  E-value: 7.52e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4213 QTPPIQEPGSQPSPLQGLLGCQPQSGGFSGSQTGPLQELGAGPRPQGPPRLPVPQGALSTGPVLGPVHPTPPPSSPQEPK 4292
Cdd:PRK10263   752 VQQPQQPVAPQQQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQ 831

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1537972313 4293 RPSQLPSPSAQPTPTHP-----GTPKP-QGPTLELPPGRV---SPAAAQLADTF 4337
Cdd:PRK10263   832 QPQQPVAPQPQDTLLHPllmrnGDSRPlHKPTTPLPSLDLltpPPSEVEPVDTF 885
PHD_BAZ1A cd15627
PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also ...
 229-273 7.66e-03

PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1A contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277097 [Multi-domain]  Cd Length: 46  Bit Score: 37.37  E-value: 7.66e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1537972313  229 CAVCEGPGELCDLFFCTSCGHHYHGACLDTALTARKRAGWQCPEC 273
Cdd:cd15627      2 CRICRRKGDAEKMLLCDGCDRGHHMYCLRPPLKKVPEGDWFCPDC 46
PHD_KDM7 cd15640
PHD finger found in lysine-specific demethylase 7 (KDM7); KDM7, also termed JmjC ...
 1504-1553 7.81e-03

PHD finger found in lysine-specific demethylase 7 (KDM7); KDM7, also termed JmjC domain-containing histone demethylation protein 1D (JHDM1D), or KIAA1718, is a dual histone demethylase that catalyzes demethylation of monomethylated and dimethylated H3K9 (H3K9me2/me1) and H3K27 (H3K27me2/me1), which functions as an eraser of silencing marks on chromatin during brain development. It also plays a tumor-suppressive role by regulating angiogenesis. KDM7 contains a plant homeodomain (PHD) that binds Lys4-trimethylated histone 3 (H3K4me3) and a jumonji domain that demethylates either H3K9me2 or H3K27me2.


Pssm-ID: 277110  Cd Length: 50  Bit Score: 37.66  E-value: 7.81e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1537972313 1504 VCHAPYVEEDLLIQCRHCERWMHAGCESLftedEVEQAAD-EGFDCVSCQP 1553
Cdd:cd15640      3 VCRQPYDVNRFMIECDICKDWFHGSCVQV----EEHHAADiDLYHCPNCEV 49
PHD1_PHF10 cd15528
PHD finger 1 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
 229-273 7.84e-03

PHD finger 1 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed BRG1-associated factor 45a (BAF45a), or XAP135, is a ubiquitously expressed transcriptional regulator that is required for maintaining the undifferentiated status of neuroblasts. It contains a SAY (supporter of activation of yellow) domain and two adjacent plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277003  Cd Length: 54  Bit Score: 37.78  E-value: 7.84e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1537972313  229 CAVCE-----GPGELCDLFFCTSCGHHYHGACLDtaLTAR-----KRAGWQCPEC 273
Cdd:cd15528      2 CGICEkggksNKGEPEELIHCSQCGNSGHPSCLE--MSDEmvaviKTYPWQCMEC 54
PHD2_KMT2A_like cd15507
PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 1375-1422 8.70e-03

PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger.


Pssm-ID: 276982  Cd Length: 50  Bit Score: 37.45  E-value: 8.70e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1537972313 1375 CVVCGSFGRGAEgHLLACSQCSQCYHPYCVN----SKITKVMllKGWRCVEC 1422
Cdd:cd15507      2 CHVCGRKGQAQK-QLLECEKCQRGYHVDCLGpsypTKPTRKK--KTWICSKC 50
HMG-box_SSRP1-like cd21994
high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and ...
 2013-2061 8.85e-03

high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and similar proteins; SSRP1, also called FACT complex subunit SSRP1, chromatin-specific transcription elongation factor 80 kDa subunit, facilitates chromatin transcription complex 80 kDa subunit (FACT 80 kDa subunit or FACTp80), facilitates chromatin transcription complex subunit SSRP1, recombination signal sequence recognition protein 1, or T160, is a factor that facilitates transcript elongation through nucleosomes. It is a component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication, and DNA repair.


Pssm-ID: 438810 [Multi-domain]  Cd Length: 67  Bit Score: 38.05  E-value: 8.85e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1537972313 2013 VLYANINFPNLKQDYPDWSSrcKQIMK----LWRKVPAADKAPYLQKAKDNRA 2061
Cdd:cd21994      7 MLWLNENREKIKKENPGISV--TEISKkageIWKELDEEDKEKWEQKAEKAKE 57
PHA03378 PHA03378
EBNA-3B; Provisional
 3978-4339 9.08e-03

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 42.75  E-value: 9.08e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 3978 PLQHFSSPGALgptLLLTGKEQNITEASLPSEVTEgPSTHQggPLAVGTTP----ESMSVEPGEVKPSVSGDSQLLLVQS 4053
Cdd:PHA03378   495 PAQGVQAHGSM---LDLLEKDDEDMEQRVMATLLP-PSPPQ--PRAGRRAPcvytEDLDIESDEPASTEPVHDQLLPAPG 568

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4054 --QAQAQPIPVQLQPPLRLPGQPQQQQVNLL---HTTGGGNHGQQLGSSSEVPSVPHLLNQPSVSLGEQPGPMTQNLLGS 4128
Cdd:PHA03378   569 lgPLQIQPLTSPTTSQLASSAPSYAQTPWPVphpSQTPEPPTTQSHIPETSAPRQWPMPLRPIPMRPLRMQPITFNVLVF 648

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4129 QQPlgldrpiqnntgPQPPKTGPVPQSGQglpgvgvMPTVGQLRAQLQGVLAKNPQLRHLSPQQQQQLQALLMQRQLQQS 4208
Cdd:PHA03378   649 PTP------------HQPPQVEITPYKPT-------WTQIGHIPYQPSPTGANTMLPIQWAPGTMQPPPRAPTPMRPPAA 709

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1537972313 4209 QAVRQTPPIQEPGSQPSPlQGLLGCQPQSGGFSGSQTGPLQELGAGPRPQGPP-RLPVPQGALstgpvlGPVHPTPPPSS 4287
Cdd:PHA03378   710 PPGRAQRPAAATGRARPP-AAAPGRARPPAAAPGRARPPAAAPGRARPPAAAPgRARPPAAAP------GAPTPQPPPQA 782

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1537972313 4288 PQEP-KRPSQLPSPSAQPTpthpGTPKPQGPTLELPPGRVSPAAAQLADTFFG 4339
Cdd:PHA03378   783 PPAPqQRPRGAPTPQPPPQ----AGPTSMQLMPRAAPGQQGPTKQILRQLLTG 831
PostSET smart00508
Cysteine-rich motif following a subset of SET domains;
5505-5521 9.73e-03

Cysteine-rich motif following a subset of SET domains;


Pssm-ID: 214703  Cd Length: 17  Bit Score: 36.61  E-value: 9.73e-03
                            10
                    ....*....|....*..
gi 1537972313  5505 HKIPCHCGAWNCRKWMN 5521
Cdd:smart00508    1 KKQPCLCGAPNCRGFLG 17
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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