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Conserved domains on  [gi|148762969|ref|NP_003473|]
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histone-lysine N-methyltransferase 2D [Homo sapiens]

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) ...
 5382-5536 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 148762969 5382 HSKSSQYRRLRTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVI 5461
Cdd:cd19209     1 HSKSSQYRRLKTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVI 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 148762969 5462 DATLTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWM 5536
Cdd:cd19209    81 DATLTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWM 155
ePHD2_KMT2D cd15698
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 5032-5138 9.73e-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: 9.73e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5032 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQRTGATSSCNRMRCPN 5111
Cdd:cd15698     1 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQKTGATNSCNRLRCPN 80

                          90       100
                  ....*....|....*....|....*..
gi 148762969 5112 VYHFACAIRAKCMFFKDKTMLCPMHKI 5138
Cdd:cd15698    81 VYHFACAIRAKCMFFKDKTMLCPMHKL 107
HMG-box_KMT2D cd22027
high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2D (KMT2D) and ...
 1995-2078 9.87e-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: 200.70  E-value: 9.87e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 1995 GLSYNQRSLQRWEKDEELGQLSTISPVLYANINFPNLKQDYPDWSSRCKQIMKLWRKVPAADKAPYLQKAKDNRAAHRIN 2074
Cdd:cd22027     1 GLSYNQRSLQRWEKDEELGELSTISPVLYANINFPNLKQDYPDWSSRCKQIMKLWRKVPAADKAPYLQKAKDNRAAHRIN 80


                  ....
gi 148762969 2075 KVQK 2078
Cdd:cd22027    81 KVQK 84
ePHD1_KMT2D cd15695
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 134-217 4.62e-53

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: 182.04  E-value: 4.62e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  134 GSCWAHHWCAAWSAGVWGQEGPELCGVDKAIFSGISQRCSHCTRLGASIPCRSPGCPRLYHFPCATASGSFLSMKTLQLL 213
Cdd:cd15695     7 GECWVHHWCAAWSAGVKQHEGDGLIGVDKAVFSGISQKCEHCKRLGATIQCHAEGCPRFYHFPCAAASGSFQSMKTLLLL 86


                  ....
gi 148762969  214 CPEH 217
Cdd:cd15695    87 CPEH 90
PHD5_KMT2D cd15601
PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 1506-1556 7.01e-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: 123.09  E-value: 7.01e-33
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 148762969 1506 TCPICHAPYVEEDLLIQCRHCERWMHAGCESLFTEDDVEQAADEGFDCVSC 1556
Cdd:cd15601     1 TCPVCRAKYVEEDLLIQCRHCDRWVHAVCESLFTEDEVEQAADEGFDCSSC 51
PHD3_KMT2D cd15597
PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 1378-1428 8.25e-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: 8.25e-33
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 148762969 1378 DMCVVCGSFGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVECI 1428
Cdd:cd15597     1 DMCVVCGSFGRGSEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVECI 51
FYRC smart00542
FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region ...
 5240-5327 1.96e-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: 1.96e-32
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969   5240 EFVIKVIEQGleDLVFTDASPQAVWNRIIEPVAAMRKEADMLRLFPEYLKGEELFGLTVHAVLRIAESLPGVESCQNYLF 5319
Cdd:smart00542    1 LFRVEIESDP--GEVFKGESPEKCWEMVLERVQEARIAADLLQLLPEGVSGEEMFGLSSPAVVKLIEALPGVHQCTNYWF 78


                    ....*...
gi 148762969   5320 RYGRHPLM 5327
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 ...
 1429-1475 6.62e-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: 111.41  E-value: 6.62e-29
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 148762969 1429 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWCV 1475
Cdd:cd15513     1 VCEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 47
PHD_SF super family cl22851
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 275-320 1.51e-27

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: 107.77  E-value: 1.51e-27
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969  275 VCQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15595     1 VCQTCRKPGEDSKMLVCEACDKGYHTFCLKPAMESLPTDSWKCKAC 46
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 228-273 1.32e-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: 1.32e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 148762969  228 RCAVCEGPGELCDLFFCTSCGHHYHGACLDTAL--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 ...
 5181-5232 3.63e-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: 3.63e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 148762969  5181 GGLVFHAIGQLLPHQMAdFHSATALYPVGYEATRIYWSLRTNNRRCCYRCSI 5232
Cdd:pfam05964    1 GSLTVLSLGEIVPDRPA-FHTERYIYPVGYKSTRLYWSTKDPRKRCRYTCEI 51
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 2108-2600 2.27e-12

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 74.59  E-value: 2.27e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2108 PQPGALGSPPPAA-------APTIFIGSPT---TPAGLSTSADGFLKPPAGSVPGPDSPgelflkLPPQVPAQVPSQDPF 2177
Cdd:PHA03247 2496 PDPGGGGPPDPDAppapsrlAPAILPDEPVgepVHPRMLTWIRGLEELASDDAGDPPPP------LPPAAPPAAPDRSVP 2569

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2178 GLAPA-YPLEPrfptappTYPPYPSPTGAPAQPpmlgasSRPGAgqPGEFHTTPPGTPRHQPSTPDPFlKPRCPSLDNLA 2256
Cdd:PHA03247 2570 PPRPApRPSEP-------AVTSRARRPDAPPQS------ARPRA--PVDDRGDPRGPAPPSPLPPDTH-APDPPPPSPSP 2633

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2257 VPESPGVGGGKASEPLLSP-----PPFGESRKALEVKKEELGASSPSYGPPNLGFVDSPSSGTHLGGLELKTPDVFKAPL 2331
Cdd:PHA03247 2634 AANEPDPHPPPTVPPPERPrddpaPGRVSRPRRARRLGRAAQASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAPH 2713

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2332 TPRASQVEPQSPGLGLRPQEPPPAQALAPSPPSHPDIfrPGSYTDPYAQPPLTPRPQPPPPESCCALPPRSLPSDPFSRV 2411
Cdd:PHA03247 2714 ALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPAT--PGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASL 2791

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2412 PASPQSQSSSQSpltPRPLSAEAFCPSPVTPRFQSPDPYSRPPSRPQSRDPFAPLHKPPRPQPPEVAFKAG---SLAHTS 2488
Cdd:PHA03247 2792 SESRESLPSPWD---PADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGgdvRRRPPS 2868

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2489 LGAGGFPAALPAGPAGELHAKVPSGQPPNFVRSPgtgafvgtPSPMRFTFPQAVGEPSLKPPVPQPGLPPPhginshfgP 2568
Cdd:PHA03247 2869 RSPAAKPAAPARPPVRRLARPAVSRSTESFALPP--------DQPERPPQPQAPPPPQPQPQPPPPPQPQP--------P 2932

                         490       500       510
                  ....*....|....*....|....*....|....
gi 148762969 2569 GPTLGKPQS--TNYTVATGNFHPSGSPLGPSSGS 2600
Cdd:PHA03247 2933 PPPPPRPQPplAPTTDPAGAGEPSGAVPQPWLGA 2966
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 690-1272 1.07e-11

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 72.28  E-value: 1.07e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  690 SPPPEDSPTSPPPEDSPASPPPEDSLMSLPLEESPLLPLP----------EE----------PQLCPRSEGPHLSPRPEE 749
Cdd:PHA03247 2491 AAGAAPDPGGGGPPDPDAPPAPSRLAPAILPDEPVGEPVHprmltwirglEElasddagdppPPLPPAAPPAAPDRSVPP 2570

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  750 PHLSPRPEEPHLSPQAEEPHLSPQPEEPclcAVPEEPHLSPQAEGPHLSPQPEelhlspqteephlSPVPEEPCLSPQPE 829
Cdd:PHA03247 2571 PRPAPRPSEPAVTSRARRPDAPPQSARP---RAPVDDRGDPRGPAPPSPLPPD-------------THAPDPPPPSPSPA 2634

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  830 EShlSPQSEEPCLSPRPEESHLSPELEKPPLSPRPEKPPEEPG-QCPAPEELPLFPPPGEPSLSPLLGEPALSEPGEPPL 908
Cdd:PHA03247 2635 AN--EPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQaSSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAP 2712

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  909 SPLPEELPLsPSGEPSLSPQLMPPDPLPPPLSPIITAAAPPALSPLGELEYPFGAKGDSDPESPLAAPILETPisPPPEA 988
Cdd:PHA03247 2713 HALVSATPL-PPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLT--RPAVA 2789

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  989 NCTDPEPVPPmilPPSPGSPVGPASPILMEPLPPQCSPllqHSLVPQNSPPSQCSPPALPLSVPSPLSPIGKVVGVSDEA 1068
Cdd:PHA03247 2790 SLSESRESLP---SPWDPADPPAAVLAPAAALPPAASP---AGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVR 2863

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 1069 elhemeteKVSEPECPALEPsATSPLPsPMGDLSCPAPSPAPalddfsglgeDTAPLDGiDAPGSQPEPGQTPGSLASEL 1148
Cdd:PHA03247 2864 --------RRPPSRSPAAKP-AAPARP-PVRRLARPAVSRST----------ESFALPP-DQPERPPQPQAPPPPQPQPQ 2922

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 1149 KGSPVLLDPEELAPVTPMEVYPECKQTAGQGSPCEEQEEPR-APVAPTPPTLIKSDIVNeisnlSQGDASASFPGSEPLL 1227
Cdd:PHA03247 2923 PPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWlGALVPGRVAVPRFRVPQ-----PAPSREAPASSTPPLT 2997

                         570       580       590       600
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969 1228 GSPDPE-GGGSLSMELGVSTDVSPARDEGSLRLCTDSLPETDDSLL 1272
Cdd:PHA03247 2998 GHSLSRvSSWASSLALHEETDPPPVSLKQTLWPPDDTEDSDADSLF 3043
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 469-860 9.21e-07

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 56.10  E-value: 9.21e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  469 PPPEELPASPLPEALHlsRPLEESPLSPPPEESPLSPPPESSPFSPLEESPLSPPEESPPSPALETPLSPPPEASPLSPP 548
Cdd:PHA03247 2607 DPRGPAPPSPLPPDTH--APDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQRPR 2684

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  549 FEESPLSPPPEELPTSPPPEasrlSPPPEESPMSPPPEESPMSPPPEASRLFPPFEESPLSPPPEESPLSPPPEASRLSP 628
Cdd:PHA03247 2685 RRAARPTVGSLTSLADPPPP----PPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARP 2760

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  629 PpedSPMSPPPEESPMSPPPEVSRLSPLPVVSRLSPPPEESPLSPPPEESPTSPPPEASRLSPPPEDSPTSPPPEDS--- 705
Cdd:PHA03247 2761 P---TTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAqpt 2837

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  706 PASPPPEDSLMSLPLEES--PLLPLPEEPQLCPRSEGPHLSPRPEEPHLSPRPEEPHLSPQAEEPHLSPQPEEPCLCAVP 783
Cdd:PHA03247 2838 APPPPPGPPPPSLPLGGSvaPGGDVRRRPPSRSPAAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPP 2917

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 148762969  784 EEPHLSPQAEGPHLSPQPEELHLSPQTEEPHLSPVPEEPCLSPQPEESHLSPQSEEP--CLSPRPEESHLSPELEKPPL 860
Cdd:PHA03247 2918 QPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVprFRVPQPAPSREAPASSTPPL 2996
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 4162-4426 5.17e-06

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 53.40  E-value: 5.17e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 4162 RPMQNNTGPQPPKPGPVLQSGQGLPGVGIMPTVGQLRAQLQGVLAKNPQLRH---LSPQQQQQLQALLMQRQLQQSQAVR 4238
Cdd:PHA03247 2756 RPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPpaaVLAPAAALPPAASPAGPLPPPTSAQ 2835

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 4239 QTPPYQEPGTQTSPLQGLLGCQPqlgGFPGPQTGPLQELGAGP-RPQGPP--RLPAPPGALSTGPVLGPVHPTPPPSSPQ 4315
Cdd:PHA03247 2836 PTAPPPPPGPPPPSLPLGGSVAP---GGDVRRRPPSRSPAAKPaAPARPPvrRLARPAVSRSTESFALPPDQPERPPQPQ 2912

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 4316 EPKRPsqLPSPSSQLPTEAQLPPTHPGTPKPQGPTLEPPPGRVSPAAAQLADTLFSKGLGPWDPPDNLAETQKPEQ---S 4392
Cdd:PHA03247 2913 APPPP--QPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRVPQPAPSReapA 2990

                         250       260       270
                  ....*....|....*....|....*....|....
gi 148762969 4393 SLVPGHLDQVNGQVVPEASQLSIKQEPREEPCAL 4426
Cdd:PHA03247 2991 SSTPPLTGHSLSRVSSWASSLALHEETDPPPVSL 3024
 
Name Accession Description Interval E-value
SET_KMT2D cd19209
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2D (KMT2D) ...
 5382-5536 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 148762969 5382 HSKSSQYRRLRTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVI 5461
Cdd:cd19209     1 HSKSSQYRRLKTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVI 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 148762969 5462 DATLTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWM 5536
Cdd:cd19209    81 DATLTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWM 155
ePHD2_KMT2D cd15698
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 5032-5138 9.73e-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: 9.73e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5032 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQRTGATSSCNRMRCPN 5111
Cdd:cd15698     1 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQKTGATNSCNRLRCPN 80

                          90       100
                  ....*....|....*....|....*..
gi 148762969 5112 VYHFACAIRAKCMFFKDKTMLCPMHKI 5138
Cdd:cd15698    81 VYHFACAIRAKCMFFKDKTMLCPMHKL 107
HMG-box_KMT2D cd22027
high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2D (KMT2D) and ...
 1995-2078 9.87e-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: 200.70  E-value: 9.87e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 1995 GLSYNQRSLQRWEKDEELGQLSTISPVLYANINFPNLKQDYPDWSSRCKQIMKLWRKVPAADKAPYLQKAKDNRAAHRIN 2074
Cdd:cd22027     1 GLSYNQRSLQRWEKDEELGELSTISPVLYANINFPNLKQDYPDWSSRCKQIMKLWRKVPAADKAPYLQKAKDNRAAHRIN 80


                  ....
gi 148762969 2075 KVQK 2078
Cdd:cd22027    81 KVQK 84
ePHD1_KMT2D cd15695
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 134-217 4.62e-53

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: 182.04  E-value: 4.62e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  134 GSCWAHHWCAAWSAGVWGQEGPELCGVDKAIFSGISQRCSHCTRLGASIPCRSPGCPRLYHFPCATASGSFLSMKTLQLL 213
Cdd:cd15695     7 GECWVHHWCAAWSAGVKQHEGDGLIGVDKAVFSGISQKCEHCKRLGATIQCHAEGCPRFYHFPCAAASGSFQSMKTLLLL 86


                  ....
gi 148762969  214 CPEH 217
Cdd:cd15695    87 CPEH 90
PHD5_KMT2D cd15601
PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 1506-1556 7.01e-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: 123.09  E-value: 7.01e-33
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 148762969 1506 TCPICHAPYVEEDLLIQCRHCERWMHAGCESLFTEDDVEQAADEGFDCVSC 1556
Cdd:cd15601     1 TCPVCRAKYVEEDLLIQCRHCDRWVHAVCESLFTEDEVEQAADEGFDCSSC 51
PHD3_KMT2D cd15597
PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 1378-1428 8.25e-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: 8.25e-33
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 148762969 1378 DMCVVCGSFGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVECI 1428
Cdd:cd15597     1 DMCVVCGSFGRGSEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVECI 51
FYRC smart00542
FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region ...
 5240-5327 1.96e-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: 1.96e-32
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969   5240 EFVIKVIEQGleDLVFTDASPQAVWNRIIEPVAAMRKEADMLRLFPEYLKGEELFGLTVHAVLRIAESLPGVESCQNYLF 5319
Cdd:smart00542    1 LFRVEIESDP--GEVFKGESPEKCWEMVLERVQEARIAADLLQLLPEGVSGEEMFGLSSPAVVKLIEALPGVHQCTNYWF 78


                    ....*...
gi 148762969   5320 RYGRHPLM 5327
Cdd:smart00542   79 RYHRSPLL 86
SET COG2940
SET domain-containing protein (function unknown) [General function prediction only];
5398-5535 9.63e-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: 9.63e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5398 NVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRgiYMFRINNEHVIDATLTGGPARYINHSC 5477
Cdd:COG2940     7 RIEVRPSPIHGRGVFATRDIPKGTLIGEYPGEVITWAEAERREPHKEPLHT--YLFELDDDGVIDGALGGNPARFINHSC 84

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 148762969 5478 APNCVAEVVTFD-----KEDkiiiissrrIPKGEELTYDYQFDFEDDQHkiPCHCGawNCRKW 5535
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 ...
 5397-5519 4.42e-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: 4.42e-31
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969   5397 NNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYE-EQNRGIYMFRINNEHVIDATLTGGPARYINH 5475
Cdd:smart00317    1 NKLEVFKSPGKGWGVRATEDIPKGEFIGEYVGEIITSEEAEERPKAYDtDGAKAFYLFDIDSDLCIDARRKGNLARFINH 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....
gi 148762969   5476 SCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDD 5519
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 ...
 1429-1475 6.62e-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: 111.41  E-value: 6.62e-29
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 148762969 1429 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWCV 1475
Cdd:cd15513     1 VCEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 47
PHD2_KMT2D cd15595
PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 275-320 1.51e-27

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: 107.77  E-value: 1.51e-27
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969  275 VCQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15595     1 VCQTCRKPGEDSKMLVCEACDKGYHTFCLKPAMESLPTDSWKCKAC 46
FYRC pfam05965
F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 5238-5322 2.41e-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: 2.41e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  5238 RPEFVIKVIEQglEDLVFTDASPQAVWNRIIEPVAAMRKEADMLRLFPEYLKGEELFGLTVHAVLRIAESLPGVESCQNY 5317
Cdd:pfam05965    1 GPLFRVTVEED--PDESFEGSSPTKCWSMVLERVQELRREAGLKLKLPESISGEDMFGLTHPAVVRLIESLPGAEKCTNY 78


                   ....*
gi 148762969  5318 LFRYG 5322
Cdd:pfam05965   79 KFRYG 83
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 228-273 1.32e-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: 1.32e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 148762969  228 RCAVCEGPGELCDLFFCTSCGHHYHGACLDTAL--TARKRAGWQCPEC 273
Cdd:cd15509     1 NCAVCDSPGDLSDLLFCTSCGQHYHGSCLDPAVrpTPLVRAGWQCPEC 48
SET pfam00856
SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be ...
 5408-5512 6.38e-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: 91.05  E-value: 6.38e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  5408 GLGLYAAKDLEKHTMVIEYIGT-IIRNEVANRREKIYEEQNR----GIYMFRIN--NEHVIDATLT--GGPARYINHSCA 5478
Cdd:pfam00856    1 GRGLFATEDIPKGEFIGEYVEVlLITKEEADKRELLYYDKLElrlwGPYLFTLDedSEYCIDARALyyGNWARFINHSCD 80

                           90       100       110
                   ....*....|....*....|....*....|....
gi 148762969  5479 PNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDY 5512
Cdd:pfam00856   81 PNCEVRVVYVNGGPRIVIFALRDIKPGEELTIDY 114
FYRN pfam05964
F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 5181-5232 3.63e-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: 3.63e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 148762969  5181 GGLVFHAIGQLLPHQMAdFHSATALYPVGYEATRIYWSLRTNNRRCCYRCSI 5232
Cdd:pfam05964    1 GSLTVLSLGEIVPDRPA-FHTERYIYPVGYKSTRLYWSTKDPRKRCRYTCEI 51
FYRN smart00541
FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region ...
 5191-5234 2.33e-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: 2.33e-16
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....
gi 148762969   5191 LLPHQMADFHSATALYPVGYEATRIYWSLRTNNRRCCYRCSIGE 5234
Cdd:smart00541    1 LLPIQGKLFHSESAIFPVGYKSTRKYWSVKDPNRRCLYSCVIDE 44
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1429-1477 2.53e-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: 2.53e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 148762969  1429 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPL--LTVPKGGWKCKWCVSC 1477
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 ...
 275-323 2.71e-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: 2.71e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 148762969   275 VCQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEELPAHS--WKCKACRVC 323
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPAEIPSgeWLCPECKPK 51
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 5059-5136 3.85e-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: 3.85e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  5059 HLNCALWSTEVY----ETQGGALMNVEVALHRGLLTKCSLC-QRTGATSSCNRMRCPNVYHFACAIRAKCMF-FKDKT-- 5130
Cdd:pfam13771    1 HVVCALWSPELVqrgnDSMGFPIEDIEKIPKRRWKLKCYLCkKKGGACIQCSKKNCRRAFHVTCALEAGLLMqFDEDNgt 80


                   ....*...
gi 148762969  5131 --MLCPMH 5136
Cdd:pfam13771   81 fkSYCKKH 88
PHA03247 PHA03247
large tegument protein UL36; Provisional
 2108-2600 2.27e-12

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 74.59  E-value: 2.27e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2108 PQPGALGSPPPAA-------APTIFIGSPT---TPAGLSTSADGFLKPPAGSVPGPDSPgelflkLPPQVPAQVPSQDPF 2177
Cdd:PHA03247 2496 PDPGGGGPPDPDAppapsrlAPAILPDEPVgepVHPRMLTWIRGLEELASDDAGDPPPP------LPPAAPPAAPDRSVP 2569

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2178 GLAPA-YPLEPrfptappTYPPYPSPTGAPAQPpmlgasSRPGAgqPGEFHTTPPGTPRHQPSTPDPFlKPRCPSLDNLA 2256
Cdd:PHA03247 2570 PPRPApRPSEP-------AVTSRARRPDAPPQS------ARPRA--PVDDRGDPRGPAPPSPLPPDTH-APDPPPPSPSP 2633

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2257 VPESPGVGGGKASEPLLSP-----PPFGESRKALEVKKEELGASSPSYGPPNLGFVDSPSSGTHLGGLELKTPDVFKAPL 2331
Cdd:PHA03247 2634 AANEPDPHPPPTVPPPERPrddpaPGRVSRPRRARRLGRAAQASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAPH 2713

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2332 TPRASQVEPQSPGLGLRPQEPPPAQALAPSPPSHPDIfrPGSYTDPYAQPPLTPRPQPPPPESCCALPPRSLPSDPFSRV 2411
Cdd:PHA03247 2714 ALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPAT--PGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASL 2791

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2412 PASPQSQSSSQSpltPRPLSAEAFCPSPVTPRFQSPDPYSRPPSRPQSRDPFAPLHKPPRPQPPEVAFKAG---SLAHTS 2488
Cdd:PHA03247 2792 SESRESLPSPWD---PADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGgdvRRRPPS 2868

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2489 LGAGGFPAALPAGPAGELHAKVPSGQPPNFVRSPgtgafvgtPSPMRFTFPQAVGEPSLKPPVPQPGLPPPhginshfgP 2568
Cdd:PHA03247 2869 RSPAAKPAAPARPPVRRLARPAVSRSTESFALPP--------DQPERPPQPQAPPPPQPQPQPPPPPQPQP--------P 2932

                         490       500       510
                  ....*....|....*....|....*....|....
gi 148762969 2569 GPTLGKPQS--TNYTVATGNFHPSGSPLGPSSGS 2600
Cdd:PHA03247 2933 PPPPPRPQPplAPTTDPAGAGEPSGAVPQPWLGA 2966
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1429-1474 2.31e-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: 64.54  E-value: 2.31e-12
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 148762969   1429 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLT-VPKGGWKCKWC 1474
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 275-320 5.84e-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: 63.38  E-value: 5.84e-12
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 148762969    275 VCQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEE-LPAHSWKCKAC 320
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
PHA03247 PHA03247
large tegument protein UL36; Provisional
 690-1272 1.07e-11

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 72.28  E-value: 1.07e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  690 SPPPEDSPTSPPPEDSPASPPPEDSLMSLPLEESPLLPLP----------EE----------PQLCPRSEGPHLSPRPEE 749
Cdd:PHA03247 2491 AAGAAPDPGGGGPPDPDAPPAPSRLAPAILPDEPVGEPVHprmltwirglEElasddagdppPPLPPAAPPAAPDRSVPP 2570

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  750 PHLSPRPEEPHLSPQAEEPHLSPQPEEPclcAVPEEPHLSPQAEGPHLSPQPEelhlspqteephlSPVPEEPCLSPQPE 829
Cdd:PHA03247 2571 PRPAPRPSEPAVTSRARRPDAPPQSARP---RAPVDDRGDPRGPAPPSPLPPD-------------THAPDPPPPSPSPA 2634

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  830 EShlSPQSEEPCLSPRPEESHLSPELEKPPLSPRPEKPPEEPG-QCPAPEELPLFPPPGEPSLSPLLGEPALSEPGEPPL 908
Cdd:PHA03247 2635 AN--EPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQaSSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAP 2712

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  909 SPLPEELPLsPSGEPSLSPQLMPPDPLPPPLSPIITAAAPPALSPLGELEYPFGAKGDSDPESPLAAPILETPisPPPEA 988
Cdd:PHA03247 2713 HALVSATPL-PPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLT--RPAVA 2789

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  989 NCTDPEPVPPmilPPSPGSPVGPASPILMEPLPPQCSPllqHSLVPQNSPPSQCSPPALPLSVPSPLSPIGKVVGVSDEA 1068
Cdd:PHA03247 2790 SLSESRESLP---SPWDPADPPAAVLAPAAALPPAASP---AGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVR 2863

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 1069 elhemeteKVSEPECPALEPsATSPLPsPMGDLSCPAPSPAPalddfsglgeDTAPLDGiDAPGSQPEPGQTPGSLASEL 1148
Cdd:PHA03247 2864 --------RRPPSRSPAAKP-AAPARP-PVRRLARPAVSRST----------ESFALPP-DQPERPPQPQAPPPPQPQPQ 2922

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 1149 KGSPVLLDPEELAPVTPMEVYPECKQTAGQGSPCEEQEEPR-APVAPTPPTLIKSDIVNeisnlSQGDASASFPGSEPLL 1227
Cdd:PHA03247 2923 PPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWlGALVPGRVAVPRFRVPQ-----PAPSREAPASSTPPLT 2997

                         570       580       590       600
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969 1228 GSPDPE-GGGSLSMELGVSTDVSPARDEGSLRLCTDSLPETDDSLL 1272
Cdd:PHA03247 2998 GHSLSRvSSWASSLALHEETDPPPVSLKQTLWPPDDTEDSDADSLF 3043
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 228-276 3.51e-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: 61.35  E-value: 3.51e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 148762969   228 RCAVCEGPGELCDLFFCTSCGHHYHGACLDTALTARKRA--GWQCPECKVC 276
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPAEIPsgEWLCPECKPK 51
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 691-1096 6.47e-11

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: 69.41  E-value: 6.47e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969   691 PPPEDSPTSPPPEDSPASPPPEDSLMSLPLEESPLLPlpeePQLCPRSEGPHLSPRPEEPHLSPRPEEPHLSPQ---AEE 767
Cdd:pfam03154  171 PPVLQAQSGAASPPSPPPPGTTQAATAGPTPSAPSVP----PQGSPATSQPPNQTQSTAAPHTLIQQTPTLHPQrlpSPH 246

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969   768 PHLSPQPEEPCLCAVPEEPHLSPQAEGPhLSPQPEELHLSPqteePHLS-PVPEEPCLSPQPeeshlSPQSEEPcLSPRP 846
Cdd:pfam03154  247 PPLQPMTQPPPPSQVSPQPLPQPSLHGQ-MPPMPHSLQTGP----SHMQhPVPPQPFPLTPQ-----SSQSQVP-PGPSP 315

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969   847 EESHLSPELEKPPLSPRPEKPPEEPGQCPAPEELPLFPPPGEPSLSPLLGEPALSEPGEPPLSPLPEELPLSPSGEPsls 926
Cdd:pfam03154  316 AAPGQSQQRIHTPPSQSQLQSQQPPREQPLPPAPLSMPHIKPPPTTPIPQLPNPQSHKHPPHLSGPSPFQMNSNLPP--- 392

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969   927 pqlmppdplppplspiitaaaPPALSPLGELeypfgakgdSDPESPLAAPileTPISPPPEANCTDPEPVPPMILPPSPG 1006
Cdd:pfam03154  393 ---------------------PPALKPLSSL---------STHHPPSAHP---PPLQLMPQSQQLPPPPAQPPVLTQSQS 439

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  1007 SPVGPAS---PILMEPLPPQcSPLLQHSLVPQNSP---PSQCSPPALPLSVPSPLSPIGKVVGVS-----------DEAE 1069
Cdd:pfam03154  440 LPPPAAShppTSGLHQVPSQ-SPFPQHPFVPGGPPpitPPSGPPTSTSSAMPGIQPPSSASVSSSgpvpaavscplPPVQ 518

                          410       420
                   ....*....|....*....|....*..
gi 148762969  1070 LHEMETEKVSEPECPALEPSATSPLPS 1096
Cdd:pfam03154  519 IKEEALDEAEEPESPPPPPRSPSPEPT 545
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 139-217 8.44e-11

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: 61.19  E-value: 8.44e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969   139 HHWCAAWSAGVWgQEGPE-----LCGVDKAIFSGISQRCSHC-TRLGASIPCRSPGCPRLYHFPCATASGSFLSMK---- 208
Cdd:pfam13771    1 HVVCALWSPELV-QRGNDsmgfpIEDIEKIPKRRWKLKCYLCkKKGGACIQCSKKNCRRAFHVTCALEAGLLMQFDedng 79


                   ....*....
gi 148762969   209 TLQLLCPEH 217
Cdd:pfam13771   80 TFKSYCKKH 88
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1380-1430 4.25e-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: 58.27  E-value: 4.25e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 148762969  1380 CVVCGsfGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKG-WRCVECIVC 1430
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 ...
 1379-1427 9.33e-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: 57.22  E-value: 9.33e-10
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*....
gi 148762969   1379 MCVVCGsfGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVEC 1427
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 ...
 228-273 7.72e-09

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: 54.53  E-value: 7.72e-09
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 148762969    228 RCAVCEGPGELCDLFFCTSCGHHYHGACLDTALT-ARKRAGWQCPEC 273
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLeEEPDGKWYCPKC 47
PspC_subgroup_2 NF033839
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 691-927 3.13e-07

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: 57.09  E-value: 3.13e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  691 PPPEDSPTSPPPEDSPASPPPEdslmslplEESPLLPLPEEPQLCPRSE--GPHLSPRPEEPHLSPRPEephlsPQAEEP 768
Cdd:NF033839  286 EPGNKKPSAPKPGMQPSPQPEK--------KEVKPEPETPKPEVKPQLEkpKPEVKPQPEKPKPEVKPQ-----LETPKP 352

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  769 HLSPQPEEPclcavpeEPHLSPQAEG--PHLSPQPE----ELHLSPQTEEPHLSPVPEEPCLSPQPEeshlsPQSEEPCL 842
Cdd:NF033839  353 EVKPQPEKP-------KPEVKPQPEKpkPEVKPQPEtpkpEVKPQPEKPKPEVKPQPEKPKPEVKPQ-----PEKPKPEV 420

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  843 SPRPE--ESHLSPELEKPplsprpekppeepgqcpapeelplfpppgEPSLSPLLGEPALSEPGEPPlSPLPEELPLSPS 920
Cdd:NF033839  421 KPQPEkpKPEVKPQPEKP-----------------------------KPEVKPQPEKPKPEVKPQPE-TPKPEVKPQPEK 470


                  ....*..
gi 148762969  921 GEPSLSP 927
Cdd:NF033839  471 PKPEVKP 477
HMG smart00398
high mobility group;
2021-2072 5.31e-07

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 50.01  E-value: 5.31e-07
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....
gi 148762969   2021 VLYANINFPNLKQDYPDWSS--RCKQIMKLWRKVPAADKAPYLQKAKDNRAAHR 2072
Cdd:smart00398   10 MLFSQENRAKIKAENPDLSNaeISKKLGERWKLLSEEEKAPYEEKAKKDKERYE 63
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1506-1556 7.49e-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: 7.49e-07
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|.
gi 148762969   1506 TCPICHAPYvEEDLLIQCRHCERWMHAGCESLFTEDDVEqaaDEGFDCVSC 1556
Cdd:smart00249    1 YCSVCGKPD-DGGELLQCDGCDRWYHQTCLGPPLLEEEP---DGKWYCPKC 47
PHA03247 PHA03247
large tegument protein UL36; Provisional
 469-860 9.21e-07

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 56.10  E-value: 9.21e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  469 PPPEELPASPLPEALHlsRPLEESPLSPPPEESPLSPPPESSPFSPLEESPLSPPEESPPSPALETPLSPPPEASPLSPP 548
Cdd:PHA03247 2607 DPRGPAPPSPLPPDTH--APDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQRPR 2684

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  549 FEESPLSPPPEELPTSPPPEasrlSPPPEESPMSPPPEESPMSPPPEASRLFPPFEESPLSPPPEESPLSPPPEASRLSP 628
Cdd:PHA03247 2685 RRAARPTVGSLTSLADPPPP----PPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARP 2760

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  629 PpedSPMSPPPEESPMSPPPEVSRLSPLPVVSRLSPPPEESPLSPPPEESPTSPPPEASRLSPPPEDSPTSPPPEDS--- 705
Cdd:PHA03247 2761 P---TTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAqpt 2837

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  706 PASPPPEDSLMSLPLEES--PLLPLPEEPQLCPRSEGPHLSPRPEEPHLSPRPEEPHLSPQAEEPHLSPQPEEPCLCAVP 783
Cdd:PHA03247 2838 APPPPPGPPPPSLPLGGSvaPGGDVRRRPPSRSPAAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPP 2917

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 148762969  784 EEPHLSPQAEGPHLSPQPEELHLSPQTEEPHLSPVPEEPCLSPQPEESHLSPQSEEP--CLSPRPEESHLSPELEKPPL 860
Cdd:PHA03247 2918 QPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVprFRVPQPAPSREAPASSTPPL 2996
PHA03247 PHA03247
large tegument protein UL36; Provisional
 4162-4426 5.17e-06

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 53.40  E-value: 5.17e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 4162 RPMQNNTGPQPPKPGPVLQSGQGLPGVGIMPTVGQLRAQLQGVLAKNPQLRH---LSPQQQQQLQALLMQRQLQQSQAVR 4238
Cdd:PHA03247 2756 RPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPpaaVLAPAAALPPAASPAGPLPPPTSAQ 2835

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 4239 QTPPYQEPGTQTSPLQGLLGCQPqlgGFPGPQTGPLQELGAGP-RPQGPP--RLPAPPGALSTGPVLGPVHPTPPPSSPQ 4315
Cdd:PHA03247 2836 PTAPPPPPGPPPPSLPLGGSVAP---GGDVRRRPPSRSPAAKPaAPARPPvrRLARPAVSRSTESFALPPDQPERPPQPQ 2912

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 4316 EPKRPsqLPSPSSQLPTEAQLPPTHPGTPKPQGPTLEPPPGRVSPAAAQLADTLFSKGLGPWDPPDNLAETQKPEQ---S 4392
Cdd:PHA03247 2913 APPPP--QPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRVPQPAPSReapA 2990

                         250       260       270
                  ....*....|....*....|....*....|....
gi 148762969 4393 SLVPGHLDQVNGQVVPEASQLSIKQEPREEPCAL 4426
Cdd:PHA03247 2991 SSTPPLTGHSLSRVSSWASSLALHEETDPPPVSL 3024
HMG_box pfam00505
HMG (high mobility group) box;
2021-2072 1.88e-05

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 45.68  E-value: 1.88e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 148762969  2021 VLYANINFPNLKQDYPDWSSR--CKQIMKLWRKVPAADKAPYLQKAKDNRAAHR 2072
Cdd:pfam00505    9 FLFSKEQRAKLKAENPGLKNAeiSKILGEKWKALSEEEKKPYEEKAEKEKARYE 62
PspC_subgroup_2 NF033839
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 691-840 1.89e-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: 51.31  E-value: 1.89e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  691 PPPEDSPTSPPPEDSPASPPPEDSLMSLPLEESPLL-PLPEEP----QLCPRSEGPHLSPRPE--EPHLSPRPE--EPHL 761
Cdd:NF033839  352 PEVKPQPEKPKPEVKPQPEKPKPEVKPQPETPKPEVkPQPEKPkpevKPQPEKPKPEVKPQPEkpKPEVKPQPEkpKPEV 431

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  762 SPQAEEP--HLSPQPEEPclcavpeEPHLSPQAEGPHLSPQPEelhlsPQTEEPHLSPVPEepclSPQPEESHLSPQSEE 839
Cdd:NF033839  432 KPQPEKPkpEVKPQPEKP-------KPEVKPQPETPKPEVKPQ-----PEKPKPEVKPQPE----KPKPDNSKPQADDKK 495


                  .
gi 148762969  840 P 840
Cdd:NF033839  496 P 496
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1507-1558 8.98e-05

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: 43.25  E-value: 8.98e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 148762969  1507 CPICHAPyVEEDLLIQCRHCERWMHAGCESLftEDDVEQAADEGFDCVSCQP 1558
Cdd:pfam00628    2 CAVCGKS-DDGGELVQCDGCDDWFHLACLGP--PLDPAEIPSGEWLCPECKP 50
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 4170-4366 2.30e-04

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: 47.72  E-value: 2.30e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  4170 PQPPKPGPvLQSGQGLPGVGIMP---TVGQLRAQlqgvlAKNPQlrhlspqqqqQLQALLMQRQLQQSQAVRQTPPYQEP 4246
Cdd:pfam09770  174 APAPQPAA-QPASLPAPSRKMMSleeVEAAMRAQ-----AKKPA----------QQPAPAPAQPPAAPPAQQAQQQQQFP 237

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  4247 gtQTSPLQGLLGCQPQLGGFPGPQTGPLQELGAGPRPQGPPRLPAPPgalsTGPVLGPVHPTPPPSSP----QEPKRPSQ 4322
Cdd:pfam09770  238 --PQIQQQQQPQQQPQQPQQHPGQGHPVTILQRPQSPQPDPAQPSIQ----PQAQQFHQQPPPVPVQPtqilQNPNRLSA 311

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 148762969  4323 LPSPSSQLPTEAQLP-PTHPGTPKPQGPtlePPPGRVSPAAAQLA 4366
Cdd:pfam09770  312 ARVGYPQNPQPGVQPaPAHQAHRQQGSF---GRQAPIITHPQQLA 353
PspC_subgroup_1 NF033838
pneumococcal surface protein PspC, choline-binding form; The pneumococcal surface protein PspC, ...
 730-822 3.48e-04

pneumococcal surface protein PspC, choline-binding 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 1, has variable numbers of a choline-binding repeat in the C-terminal region, and is also known as choline-binding protein A. The other form, subgroup 2, is anchored covalently after cleavage by sortase at a C-terminal LPXTG site.


Pssm-ID: 468201 [Multi-domain]  Cd Length: 684  Bit Score: 47.32  E-value: 3.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  730 EEPQLCPrsegphlSPRPEEPhlSPRPEEPHLSPQAEEPHlSPQPEEPCLCAVPEEPHLSPQAegphlspQPeelhlsPQ 809
Cdd:NF033838  418 EQPQPAP-------APQPEKP--APKPEKPAEQPKAEKPA-DQQAEEDYARRSEEEYNRLTQQ-------QP------PK 474

                          90
                  ....*....|...
gi 148762969  810 TEEPhlsPVPEEP 822
Cdd:NF033838  475 TEKP---AQPSTP 484
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 5092-5136 4.34e-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: 4.34e-04
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 148762969   5092 CSLCQRTGATS---SCNRmrCPNVYHFACAIRAKCMFFKDKTMLCPMH 5136
Cdd:smart00249    2 CSVCGKPDDGGellQCDG--CDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
half-pint TIGR01645
poly-U binding splicing factor, half-pint family; The proteins represented by this model ...
 4272-4468 2.09e-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: 44.68  E-value: 2.09e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  4272 GPLQELGAGPRPQGPPRLPAPPgALSTGPVLGPVHPTPPPSSPQ-EPKRPSQLPSPS--SQLPTEAQLPPthpgtPKPQG 4348
Cdd:TIGR01645  325 GPRAQSPATPSSSLPTDIGNKA-VVSSAKKEAEEVPPLPQAAPAvVKPGPMEIPTPVppPGLAIPSLVAP-----PGLVA 398

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  4349 PTLEPPPGRVSPAAAQLADTLfSKGLGPWDPPDNLAETQKPEQSSlVPGHLDQVNGQVVPEASQLSIKQEPREEpcalGA 4428
Cdd:TIGR01645  399 PTEINPSFLASPRKKMKREKL-PVTFGALDDTLAWKEPSKEDQTS-EDGKMLAIMGEAAAALALEPKKKKKEKE----GE 472

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|
gi 148762969  4429 QSVKREANGEPIGAPGTSNHLLLAGprSEAGHLLLQKLLR 4468
Cdd:TIGR01645  473 ELQPKLVMNSEDASLASQEGMSIRG--NSARHLVMQKLMR 510
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 2210-2522 2.47e-03

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: 44.37  E-value: 2.47e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  2210 PMLGASSRPGAGQPGEFHTTPPGTPRHQPSTPDPFLKPRCPSLDNLAVPESPGVGGGKASEPLLSPPPfgeSRKALEVKK 2289
Cdd:pfam03154  151 PQDNESDSDSSAQQQILQTQPPVLQAQSGAASPPSPPPPGTTQAATAGPTPSAPSVPPQGSPATSQPP---NQTQSTAAP 227

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  2290 EELGASSPSYGPPNLGFVDSPSSGthlgglelktpdvfkAPLTPRASQVEPQS-PGLGLRPQEPPPAQALAPSPPSHPDI 2368
Cdd:pfam03154  228 HTLIQQTPTLHPQRLPSPHPPLQP---------------MTQPPPPSQVSPQPlPQPSLHGQMPPMPHSLQTGPSHMQHP 292

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  2369 FRPGSYTDPyaqPPLTPRPQPPPPESCCALPPRSLPSDPFSRvPASPQSQSSSQSPLTPRPLSAEAFCPSPVTPRFQSPD 2448
Cdd:pfam03154  293 VPPQPFPLT---PQSSQSQVPPGPSPAAPGQSQQRIHTPPSQ-SQLQSQQPPREQPLPPAPLSMPHIKPPPTTPIPQLPN 368

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 148762969  2449 PYS-RPPSRPQSRDPFaplhKPPRPQPPEVAFKAGSLAHTSLGAGGFPAALPAGPAGElHAKVPSGQPPNFVRSP 2522
Cdd:pfam03154  369 PQShKHPPHLSGPSPF----QMNSNLPPPPALKPLSSLSTHHPPSAHPPPLQLMPQSQ-QLPPPPAQPPVLTQSQ 438
 
Name Accession Description Interval E-value
SET_KMT2D cd19209
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2D (KMT2D) ...
 5382-5536 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 148762969 5382 HSKSSQYRRLRTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVI 5461
Cdd:cd19209     1 HSKSSQYRRLKTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVI 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 148762969 5462 DATLTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWM 5536
Cdd:cd19209    81 DATLTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWM 155
SET_KMT2C_2D cd19171
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C), ...
 5384-5536 2.22e-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: 345.57  E-value: 2.22e-109
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5384 KSSQYRRLRTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVIDA 5463
Cdd:cd19171     1 KSSQYRKLKTEWRSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGEIIRNEVANRREKIYESQNRGIYMFRIDNDWVIDA 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 148762969 5464 TLTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWM 5536
Cdd:cd19171    81 TMTGGPARYINHSCNPNCVAEVVTFDKEKKIIIISNRRIAKGEELTYDYKFDFEDDQHKIPCLCGAPNCRKWM 153
SET_KMT2C cd19208
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C) ...
 5383-5536 6.02e-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: 6.02e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5383 SKSSQYRRLRTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVID 5462
Cdd:cd19208     1 SKSSQYRKMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGVYMFRIDNDHVID 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 148762969 5463 ATLTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWM 5536
Cdd:cd19208    81 ATLTGGPARYINHSCAPNCVAEVVTFEKGHKIIISSSRRIQKGEELCYDYKFDFEDDQHKIPCHCGAVNCRKWM 154
ePHD2_KMT2D cd15698
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 5032-5138 9.73e-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: 9.73e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5032 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQRTGATSSCNRMRCPN 5111
Cdd:cd15698     1 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQKTGATNSCNRLRCPN 80

                          90       100
                  ....*....|....*....|....*..
gi 148762969 5112 VYHFACAIRAKCMFFKDKTMLCPMHKI 5138
Cdd:cd15698    81 VYHFACAIRAKCMFFKDKTMLCPMHKL 107
ePHD2_KMT2C_like cd15666
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
 5032-5136 6.37e-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: 6.37e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5032 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQRTGATSSCNRMRCPN 5111
Cdd:cd15666     1 CVLCGGEGDGDTDGPGRLLNLDVDKWVHLNCALWSYEVYETQNGALMNVEEALRRALTTTCSHCGRTGATVPCFKPRCAN 80

                          90       100
                  ....*....|....*....|....*
gi 148762969 5112 VYHFACAIRAKCMFFKDKTMLCPMH 5136
Cdd:cd15666    81 VYHLPCAIKDGCMFFKDKTMLCPSH 105
SET_SETD1-like cd10518
SET domain (including post-SET domain) found in SET domain-containing proteins (SETD1A/SETD1B), ...
 5385-5533 5.59e-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: 5.59e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5385 SSQYRRLRTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQN-RGIYMFRINNEHVIDA 5463
Cdd:cd10518     2 SKRFRQLRSRLKERLRVGKSGIHGWGLFAKRPIAAGEMVIEYVGEVIRPIVADKREKRYDEEGgGGTYMFRIDEDLVIDA 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5464 TLTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQhKIPCHCGAWNCR 5533
Cdd:cd10518    82 TKKGNIARFINHSCDPNCYAKIITVDGEKHIVIFAKRDIAPGEELTYDYKFPIEDEE-KIPCLCGAPNCR 150
ePHD2_KMT2C cd15697
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 5032-5136 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 148762969 5032 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQRTGATSSCNRMRCPN 5111
Cdd:cd15697     1 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRLRCTN 80

                          90       100
                  ....*....|....*....|....*
gi 148762969 5112 VYHFACAIRAKCMFFKDKTMLCPMH 5136
Cdd:cd15697    81 VYHFTCAIKAQCMFFKDKTMLCPMH 105
HMG-box_KMT2D cd22027
high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2D (KMT2D) and ...
 1995-2078 9.87e-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: 200.70  E-value: 9.87e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 1995 GLSYNQRSLQRWEKDEELGQLSTISPVLYANINFPNLKQDYPDWSSRCKQIMKLWRKVPAADKAPYLQKAKDNRAAHRIN 2074
Cdd:cd22027     1 GLSYNQRSLQRWEKDEELGELSTISPVLYANINFPNLKQDYPDWSSRCKQIMKLWRKVPAADKAPYLQKAKDNRAAHRIN 80


                  ....
gi 148762969 2075 KVQK 2078
Cdd:cd22027    81 KVQK 84
ePHD1_KMT2D cd15695
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 134-217 4.62e-53

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: 182.04  E-value: 4.62e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  134 GSCWAHHWCAAWSAGVWGQEGPELCGVDKAIFSGISQRCSHCTRLGASIPCRSPGCPRLYHFPCATASGSFLSMKTLQLL 213
Cdd:cd15695     7 GECWVHHWCAAWSAGVKQHEGDGLIGVDKAVFSGISQKCEHCKRLGATIQCHAEGCPRFYHFPCAAASGSFQSMKTLLLL 86


                  ....
gi 148762969  214 CPEH 217
Cdd:cd15695    87 CPEH 90
SET_KMT2A_2B cd19170
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A), ...
 5385-5537 1.56e-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: 1.56e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5385 SSQYRRLRTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVIDAT 5464
Cdd:cd19170     2 AMRFRHLRKTAKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGEVIRSVLTDKREKYYESKGIGCYMFRIDDDEVVDAT 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 148762969 5465 LTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDqhKIPCHCGAWNCRKWMN 5537
Cdd:cd19170    82 MHGNAARFINHSCEPNCYSRVVNIDGKKHIVIFALRRILRGEELTYDYKFPIEDV--KIPCTCGSKKCRKYLN 152
SET_SETD1 cd19169
SET domain (including post-SET domain) found in SET domain-containing protein 1 (SETD1) and ...
 5396-5533 1.23e-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: 1.23e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5396 KNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEqnRGI---YMFRINNEHVIDATLTGGPARY 5472
Cdd:cd19169    12 KKQLKFAKSRIHDWGLFALEPIAADEMVIEYVGQVIRQSVADEREKRYEA--IGIgssYLFRVDDDTIIDATKCGNLARF 89

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 148762969 5473 INHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDqhKIPCHCGAWNCR 5533
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 3.33e-46

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: 162.49  E-value: 3.33e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  134 GSCWAHHWCAAWSAGVWGQEGPELCGVDKAIFSGISQRCSHCTRLGASIPCRSPGCPRLYHFPCATASGSFLSMKTLQLL 213
Cdd:cd15665     7 GEVYAHHCCAAWSEGVCQTEDGALENVDKAVAKALSQKCSFCLRYGASISCRMPSCSKSFHFPCAAAAGCFQDIKTLTLF 86


                  ....
gi 148762969  214 CPEH 217
Cdd:cd15665    87 CPEH 90
SET_KMT2A cd19206
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A) ...
 5387-5537 1.31e-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: 1.31e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5387 QYRRLRTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVIDATLT 5466
Cdd:cd19206     4 RFRHLKKTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYSGNVIRSILTDKREKYYDSKGIGCYMFRIDDSEVVDATMH 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 148762969 5467 GGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWMN 5537
Cdd:cd19206    84 GNAARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDASNKLPCNCGAKKCRKFLN 154
SET_SET1 cd20072
SET domain (including post-SET domain) found in catalytic component of the Saccharomyces ...
 5396-5533 1.68e-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: 1.68e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5396 KNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRG-IYMFRINNEHVIDATLTGGPARYIN 5474
Cdd:cd20072    12 KKQLKFARSAIHNWGLYAMENISAKDMVIEYVGEVIRQQVADEREKRYLRQGIGsSYLFRIDDDTVVDATKKGNIARFIN 91

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 148762969 5475 HSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDqhKIPCHCGAWNCR 5533
Cdd:cd20072    92 HCCDPNCTAKIIKVEGEKRIVIYAKRDIAAGEELTYDYKFPREED--KIPCLCGAPNCR 148
HMG_KMT2C-like cd21997
high mobility group (HMG)-box found in histone-lysine N-methyltransferases KMT2C, KMT2D and ...
 2005-2071 7.34e-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: 7.34e-42
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 148762969 2005 RWEKDEELGQLSTISPVLYANINFPNLKQDYPDWSSRCKQIMKLWRKVPAADKAPYLQKAKDNRAAH 2071
Cdd:cd21997     1 KWEKDEPLGDMATISPVLYANINHPNLKQEYPDWTDRAKQIAKLWRKLSAEERAPYLQKARENRAAL 67
HMG-box_KMT2C cd22026
high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2C (KMT2C) and ...
 2000-2077 6.94e-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: 6.94e-38
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 148762969 2000 QRSLQRWEKDEELGQLSTISPVLYANINFPNLKQDYPDWSSRCKQIMKLWRKVPAADKAPYLQKAKDNRAAHRINKVQ 2077
Cdd:cd22026     1 QRSTLKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIAKLWRKASSQERAPYVQKARDNRAALRINKVQ 78
SET_KMT2B cd19207
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2B (KMT2B) ...
 5387-5537 1.95e-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: 139.77  E-value: 1.95e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5387 QYRRLRTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVIDATLT 5466
Cdd:cd19207     4 RFRHLKKTSKEAVGVYRSAIHGRGLFCKRNIDAGEMVIEYSGIVIRSVLTDKREKFYDSKGIGCYMFRIDDFDVVDATMH 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 148762969 5467 GGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWMN 5537
Cdd:cd19207    84 GNAARFINHSCEPNCYSRVIHVEGQKHIVIFALRKIYRGEELTYDYKFPIEDASNKLPCNCGAKRCRRFLN 154
ePHD_KMT2A_like cd15664
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); The ...
 5032-5136 4.03e-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: 4.03e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5032 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQRTGATSSCNRMRCPN 5111
Cdd:cd15664     1 CALCGVYGDDEPNDAGRLLYCGQDEWVHINCALWSAEVFEEDDGSLQNVHSAVSRGRMMKCELCGKPGATVGCCLKSCPA 80

                          90       100
                  ....*....|....*....|....*
gi 148762969 5112 VYHFACAIRAKCMFFKDKTMLCPMH 5136
Cdd:cd15664    81 NYHFMCARKAECVFQDDKKVFCPAH 105
SET_SETD1A cd19204
SET domain (including post-SET domain) found in SET domain-containing protein 1A (SETD1A) and ...
 5396-5537 1.30e-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: 1.30e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5396 KNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGI-YMFRINNEHVIDATLTGGPARYIN 5474
Cdd:cd19204    13 KKKLRFGRSRIHEWGLFAMEPIAADEMVIEYVGQNIRQVVADMREKRYVQEGIGSsYLFRVDHDTIIDATKCGNLARFIN 92

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 148762969 5475 HSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDqhKIPCHCGAWNCRKWMN 5537
Cdd:cd19204    93 HCCTPNCYAKVITIESQKKIVIYSKQPIGVNEEITYDYKFPIEDN--KIPCLCGTENCRGTLN 153
SET_SETD1B cd19205
SET domain (including post-SET domain) found in SET domain-containing protein 1B (SETD1B) and ...
 5396-5537 5.39e-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: 5.39e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5396 KNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGI-YMFRINNEHVIDATLTGGPARYIN 5474
Cdd:cd19205    13 KKKLKFCKSHIHDWGLFAMEPIAADEMVIEYVGQNIRQVIADMREKRYEDEGIGSsYMFRVDHDTIIDATKCGNFARFIN 92

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 148762969 5475 HSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDqhKIPCHCGAWNCRKWMN 5537
Cdd:cd19205    93 HSCNPNCYAKVITVESQKKIVIYSKQHINVNEEITYDYKFPIEDV--KIPCLCGSENCRGTLN 153
PHD5_KMT2D cd15601
PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 1506-1556 7.01e-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: 123.09  E-value: 7.01e-33
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 148762969 1506 TCPICHAPYVEEDLLIQCRHCERWMHAGCESLFTEDDVEQAADEGFDCVSC 1556
Cdd:cd15601     1 TCPVCRAKYVEEDLLIQCRHCDRWVHAVCESLFTEDEVEQAADEGFDCSSC 51
PHD3_KMT2D cd15597
PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 1378-1428 8.25e-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: 8.25e-33
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 148762969 1378 DMCVVCGSFGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVECI 1428
Cdd:cd15597     1 DMCVVCGSFGRGSEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVECI 51
FYRC smart00542
FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region ...
 5240-5327 1.96e-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: 1.96e-32
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969   5240 EFVIKVIEQGleDLVFTDASPQAVWNRIIEPVAAMRKEADMLRLFPEYLKGEELFGLTVHAVLRIAESLPGVESCQNYLF 5319
Cdd:smart00542    1 LFRVEIESDP--GEVFKGESPEKCWEMVLERVQEARIAADLLQLLPEGVSGEEMFGLSSPAVVKLIEALPGVHQCTNYWF 78


                    ....*...
gi 148762969   5320 RYGRHPLM 5327
Cdd:smart00542   79 RYHRSPLL 86
SET_SETD2 cd19172
SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2) and ...
 5392-5536 5.13e-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: 5.13e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5392 RTEWKnnvylarsriqGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYE-EQNRGIYMFRINNEHVIDATLTGGPA 5470
Cdd:cd19172     8 RTEKK-----------GWGLRAAEDLPKGTFVIEYVGEVLDEKEFKRRMKEYArEGNRHYYFMALKSDEIIDATKKGNLS 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 148762969 5471 RYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFD--FEDDQhkiPCHCGAWNCRKWM 5536
Cdd:cd19172    77 RFINHSCEPNCETQKWTVNGELRVGFFAKRDIPAGEELTFDYQFEryGKEAQ---KCYCGSPNCRGYI 141
SET COG2940
SET domain-containing protein (function unknown) [General function prediction only];
5398-5535 9.63e-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: 9.63e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5398 NVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRgiYMFRINNEHVIDATLTGGPARYINHSC 5477
Cdd:COG2940     7 RIEVRPSPIHGRGVFATRDIPKGTLIGEYPGEVITWAEAERREPHKEPLHT--YLFELDDDGVIDGALGGNPARFINHSC 84

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 148762969 5478 APNCVAEVVTFD-----KEDkiiiissrrIPKGEELTYDYQFDFEDDQHkiPCHCGawNCRKW 5535
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 ...
 5397-5519 4.42e-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: 4.42e-31
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969   5397 NNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYE-EQNRGIYMFRINNEHVIDATLTGGPARYINH 5475
Cdd:smart00317    1 NKLEVFKSPGKGWGVRATEDIPKGEFIGEYVGEIITSEEAEERPKAYDtDGAKAFYLFDIDSDLCIDARRKGNLARFINH 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....
gi 148762969   5476 SCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDD 5519
Cdd:smart00317   81 SCEPNCELLFVEVNGDDRIVIFALRDIKPGEELTIDYGSDYANE 124
ePHD_KMT2A cd15693
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A); The extended plant ...
 5030-5140 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 148762969 5030 RRCCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQRTGATSSCNRMRC 5109
Cdd:cd15693     1 RQCALCLKYGDDSANDAGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSC 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 148762969 5110 PNVYHFACAIRAKCMFFKDKTMLCPMHK--IKG 5140
Cdd:cd15693    81 TSNYHFMCSRAKNCVFLEDKKVYCQRHKdlIKG 113
PHD4_KMT2C cd15596
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 1372-1427 2.22e-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: 2.22e-30
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 148762969 1372 KFVLMQDMCVVCGSFGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVEC 1427
Cdd:cd15596     1 KFTLNQDMCVVCGSFGQGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLEC 56
SET_SETD2-like cd10531
SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2), ...
 5398-5533 2.32e-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: 2.32e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5398 NVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRR-EKIYEEQNRGIYMFRINNEHVIDATLTGGPARYINHS 5476
Cdd:cd10531     1 KLELFRTEKKGWGVKAKEDIQKGEFIIEYVGEVIDKKEFKERlDEYEELGKSNFYILSLSDDVVIDATRKGNLSRFINHS 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 148762969 5477 CAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQhKIPCHCGAWNCR 5533
Cdd:cd10531    81 CEPNCETQKWIVNGEYRIGIFALRDIPAGEELTFDYNFVNYNEA-KQVCLCGAQNCR 136
ePHD1_KMT2C cd15696
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 134-217 6.68e-30

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: 115.81  E-value: 6.68e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  134 GSCWAHHWCAAWSAGVWGQEGPELCGVDKAIFSGISQRCSHCTRLGASIPCRSPGCPRLYHFPCATASGSFLSMKTLQLL 213
Cdd:cd15696     7 GECWAHLRCAEWSLGVCQGEEQLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQDFSRRLLL 86


                  ....
gi 148762969  214 CPEH 217
Cdd:cd15696    87 CPTH 90
SET_ASHR3-like cd19175
SET domain (including post-SET domain) found in Arabidopsis thaliana ASH1-related protein 3 ...
 5408-5536 4.88e-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: 4.88e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5408 GLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQ-NRGIYMFRINNEHVIDATLTGGPARYINHSCAPNCVAEVV 5486
Cdd:cd19175    11 GWGLVADEDINAGEFIIEYVGEVIDDKTCEERLWDMKHKgEKNFYMCEIDKDMVIDATFKGNLSRFINHSCDPNCELQKW 90

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 148762969 5487 TFDKEDKIIIISSRRIPKGEELTYDYQF-DFEDDQHkipCHCGAWNCRKWM 5536
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 ...
 1429-1475 6.62e-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: 111.41  E-value: 6.62e-29
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 148762969 1429 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWCV 1475
Cdd:cd15513     1 VCEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 47
ePHD cd15571
Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is ...
 5032-5136 8.81e-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: 8.81e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5032 CCFCHEEGdGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALM--NVEVALHRGLLTKCSLCQRT-GATSSCNRMR 5108
Cdd:cd15571     1 CALCPRSG-GALKGGGALKTTSDGLWVHVVCALWSPEVYFDDGTLLEveGVSKIPKRRKKLKCSICGKRgGACIQCSYPG 79

                          90       100       110
                  ....*....|....*....|....*....|...
gi 148762969 5109 CPNVYHFACAIRAKCMF-----FKDKTMLCPMH 5136
Cdd:cd15571    80 CPRSFHVSCAIRAGCLFefedgPGNFVVYCPKH 112
PHD4_KMT2C_like cd15512
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD domain 3 found in ...
 1379-1427 2.82e-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: 109.86  E-value: 2.82e-28
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 148762969 1379 MCVVCGSFGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVEC 1427
Cdd:cd15512     1 MCVSCGSFGRGAEGRLIACSQCGQCYHPYCVNVKVTKVILSKGWRCLDC 49
SET_EZH cd10519
SET domain found in enhancer of zeste homolog 1 (EZH1), zeste homolog 2 (EZH2) and similar ...
 5399-5514 8.40e-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: 8.40e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5399 VYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGiYMFRINNEHVIDATLTGGPARYINHSCA 5478
Cdd:cd10519     3 LLLGKSDVAGWGLFLKEPIKKDEFIGEYTGELISQDEADRRGKIYDKYNSS-YLFNLNDQFVVDATRKGNKIRFANHSSN 81

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 148762969 5479 PNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQF 5514
Cdd:cd10519    82 PNCYAKVMMVNGDHRIGIFAKRDIEAGEELFFDYGY 117
PHD2_KMT2D cd15595
PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 275-320 1.51e-27

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: 107.77  E-value: 1.51e-27
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969  275 VCQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15595     1 VCQTCRKPGEDSKMLVCEACDKGYHTFCLKPAMESLPTDSWKCKAC 46
SET_NSD cd19173
SET domain (including post-SET domain) found in nuclear SET domain-containing proteins, NSD1, ...
 5408-5532 8.50e-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: 8.50e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5408 GLGLYAAKDLEKHTMVIEYIGTIIRNEVANRR-EKIYEEQNRGIYMFRINNEHVIDATLTGGPARYINHSCAPNCVAEVV 5486
Cdd:cd19173    13 GWGLRTKRDIKKGDFVIEYVGELIDEEECRRRlKKAHENNITNFYMLTLDKDRIIDAGPKGNLSRFMNHSCQPNCETQKW 92

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969 5487 TFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQhKIPCHCGAWNC 5532
Cdd:cd19173    93 TVNGDTRVGLFAVRDIPAGEELTFNYNLDCLGNE-KKVCRCGAPNC 137
PHD6_KMT2C_like cd15514
PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 5 found in ...
 1506-1556 2.15e-26

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: 104.29  E-value: 2.15e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 148762969 1506 TCPICHAPYVEEDLLIQCRHCERWMHAGCESLFTEDDVEQAADEGFDCVSC 1556
Cdd:cd15514     1 KCPVCSRSYNEGELIIQCSQCERWLHGACDSLRTEEEAERAADNGYRCLLC 51
FYRC pfam05965
F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 5238-5322 2.41e-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: 2.41e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  5238 RPEFVIKVIEQglEDLVFTDASPQAVWNRIIEPVAAMRKEADMLRLFPEYLKGEELFGLTVHAVLRIAESLPGVESCQNY 5317
Cdd:pfam05965    1 GPLFRVTVEED--PDESFEGSSPTKCWSMVLERVQELRREAGLKLKLPESISGEDMFGLTHPAVVRLIESLPGAEKCTNY 78


                   ....*
gi 148762969  5318 LFRYG 5322
Cdd:pfam05965   79 KFRYG 83
PHD2_KMT2C_like cd15510
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 275-320 3.81e-26

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: 103.67  E-value: 3.81e-26
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969  275 VCQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15510     1 VCQACRQPGDDTKMLVCETCDKGYHTSCLRPVMSSIPKYGWKCKNC 46
ePHD_KMT2B cd15694
Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B); The extended plant ...
 5032-5136 4.29e-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: 4.29e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5032 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQRTGATSSCNRMRCPN 5111
Cdd:cd15694     1 CALCLKYGDADSKDAGRLLYIGQNEWTHVNCAIWSAEVFEENDGSLKNVHAAVARGRQMRCEHCQKIGATVGCCLSACLS 80

                          90       100
                  ....*....|....*....|....*
gi 148762969 5112 VYHFACAIRAKCMFFKDKTMLCPMH 5136
Cdd:cd15694    81 NFHFMCARASRCCFQDDKKVFCQKH 105
SET_SUV39H cd10542
SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 ...
 5408-5536 8.82e-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: 8.82e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5408 GLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRgIYMFRIN-----NEHVIDATLTGGPARYINHSCAPN-- 5480
Cdd:cd10542    99 GWGVKTLEDIKKGTFVMEYVGEIITSEEAERRGKIYDANGR-TYLFDLDyndddCEYTVDAAYYGNISHFINHSCDPNla 177

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 148762969 5481 ---CVAE--------VVTFDKEDkiiiissrrIPKGEELTYDYQFDFEDDQH----------KIPCHCGAWNCRKWM 5536
Cdd:cd10542   178 vyaVWINhldprlprIAFFAKRD---------IKAGEELTFDYLMTGTGGSSestipkpkdvRVPCLCGSKNCRKYL 245
PHD2_KMT2C cd15594
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 275-320 3.77e-23

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: 95.01  E-value: 3.77e-23
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969  275 VCQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15594     1 VCQTCRQPGDDNKMLVCDTCDKGYHTFCLQPVMTTIPKNGWKCKNC 46
SET_ASH1L cd19174
SET domain (including post-SET domain) found in ASH1-like protein (ASH1L) and similar proteins; ...
 5408-5537 4.54e-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: 4.54e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5408 GLGLYAAKDLEKHTMVIEYIGTII-RNEVANRREKIYEeQNRGIYMFRINNEHVIDATLTGGPARYINHSCAPNC----- 5481
Cdd:cd19174    11 GWGVRTKEPIKAGQFIIEYVGEVVsEQEFRRRMIEQYH-NHSHHYCLNLDSGMVIDGYRMGNEARFVNHSCDPNCemqkw 89

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5482 ----VAEVVTFDKEDkiiiissrrIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWMN 5537
Cdd:cd19174    90 svngVYRIGLFALKD---------IPAGEELTYDYNFHSFNVEKQQPCKCGSPNCRGVIG 140
PHD6_KMT2C cd15600
PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 1506-1556 6.12e-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: 6.12e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 148762969 1506 TCPICHAPYVEEDLLIQCRHCERWMHAGCESLFTEDDVEQAADEGFDCVSC 1556
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 1.32e-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: 1.32e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 148762969  228 RCAVCEGPGELCDLFFCTSCGHHYHGACLDTAL--TARKRAGWQCPEC 273
Cdd:cd15509     1 NCAVCDSPGDLSDLLFCTSCGQHYHGSCLDPAVrpTPLVRAGWQCPEC 48
ePHD cd15571
Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is ...
 129-217 5.27e-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: 91.49  E-value: 5.27e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  129 LGEPGGSCWAHHWCAAWSAGVWGQEG--PELCGVDKAIFSGISQRCSHC-TRLGASIPCRSPGCPRLYHFPCATASGSFL 205
Cdd:cd15571    17 LKTTSDGLWVHVVCALWSPEVYFDDGtlLEVEGVSKIPKRRKKLKCSICgKRGGACIQCSYPGCPRSFHVSCAIRAGCLF 96

                          90
                  ....*....|....*.
gi 148762969  206 SMKT----LQLLCPEH 217
Cdd:cd15571    97 EFEDgpgnFVVYCPKH 112
SET pfam00856
SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be ...
 5408-5512 6.38e-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: 91.05  E-value: 6.38e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  5408 GLGLYAAKDLEKHTMVIEYIGT-IIRNEVANRREKIYEEQNR----GIYMFRIN--NEHVIDATLT--GGPARYINHSCA 5478
Cdd:pfam00856    1 GRGLFATEDIPKGEFIGEYVEVlLITKEEADKRELLYYDKLElrlwGPYLFTLDedSEYCIDARALyyGNWARFINHSCD 80

                           90       100       110
                   ....*....|....*....|....*....|....
gi 148762969  5479 PNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDY 5512
Cdd:pfam00856   81 PNCEVRVVYVNGGPRIVIFALRDIKPGEELTIDY 114
ePHD1_KMT2C_like cd15665
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
 5032-5136 6.76e-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: 6.76e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5032 CCFCheegdgatdgparllNLDlDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQRTGATSSCNRMRCPN 5111
Cdd:cd15665     1 CALC---------------NLG-EVYAHHCCAAWSEGVCQTEDGALENVDKAVAKALSQKCSFCLRYGASISCRMPSCSK 64

                          90       100
                  ....*....|....*....|....*..
gi 148762969 5112 VYHFACAIRAKCmF--FKDKTMLCPMH 5136
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 3.82e-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: 3.82e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  137 WAHHWCAAWSAGVWGQEGPELCGVDKAIFSGISQRCSHCTRLGASIPCRSPGCPRLYHFPCATASG-SFLSMKTlqLLCP 215
Cdd:cd15666    26 WVHLNCALWSYEVYETQNGALMNVEEALRRALTTTCSHCGRTGATVPCFKPRCANVYHLPCAIKDGcMFFKDKT--MLCP 103


                  ..
gi 148762969  216 EH 217
Cdd:cd15666   104 SH 105
SET_NSD2 cd19211
SET domain (including post-SET domain) found in nuclear SET domain-containing protein 2 (NSD2) ...
 5401-5532 4.19e-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: 4.19e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5401 LARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQN-RGIYMFRINNEHVIDATLTGGPARYINHSCAP 5479
Cdd:cd19211     6 IIKTEGKGWGLIAKRDIKKGEFVNEYVGELIDEEECMARIKHAHENDiTHFYMLTIDKDRIIDAGPKGNYSRFMNHSCQP 85

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 148762969 5480 NCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIpCHCGAWNC 5532
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) ...
 5395-5514 8.29e-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: 8.29e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5395 WKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEqnrgiYM----FRINNEHVIDATLTGGPA 5470
Cdd:cd19218     2 SKKHLLLAPSDVAGWGIFIKDPVQKNEFISEYCGEIISQDEADRRGKVYDK-----YMcsflFNLNNDFVVDATRKGNKI 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 148762969 5471 RYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQF 5514
Cdd:cd19218    77 RFANHSVNPNCYAKVMMVNGDHRIGIFAKRAIQTGEELFFDYRY 120
FYRN pfam05964
F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 5181-5232 3.63e-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: 3.63e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 148762969  5181 GGLVFHAIGQLLPHQMAdFHSATALYPVGYEATRIYWSLRTNNRRCCYRCSI 5232
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) ...
 5396-5518 7.65e-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: 7.65e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5396 KNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGiYMFRINNEHVIDATLTGGPARYINH 5475
Cdd:cd19217     5 KKHLLLAPSDVAGWGTFIKESVQKNEFISEYCGELISQDEADRRGKVYDKYMSS-FLFNLNNDFVVDATRKGNKIRFANH 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 148762969 5476 SCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFED 5518
Cdd:cd19217    84 SVNPNCYAKVVMVNGDHRIGIFAKRAIQQGEELFFDYRYSQAD 126
ePHD_RAI1_like cd15668
Extended PHD finger found in retinoic acid-induced protein 1 (RAI1), transcription factor 20 ...
 5032-5136 1.01e-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: 1.01e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5032 CCFC----HEEGDGATDGPArllnldLDLWVHLNCALWSTEVYETqGGALMNVEVALHRGLLTKCSLCQRTGATSSCNRM 5107
Cdd:cd15668     1 CVFCkrgpHYKGLGDLFGPY------YEVWVHEDCAVWAPGVYLV-GGKLYGLEEAVWVAKQSVCSSCQQTGATIGCLHK 73

                          90       100       110
                  ....*....|....*....|....*....|
gi 148762969 5108 RCPNVYHFACAIRAKCMFFKDK-TMLCPMH 5136
Cdd:cd15668    74 GCKAKYHYPCAVESGCQLDEENfSLLCPKH 103
SET_NSD3 cd19212
SET domain (including post-SET domain) found in nuclear receptor-binding SET domain-containing ...
 5407-5532 2.78e-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: 2.78e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5407 QGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQN-RGIYMFRINNEHVIDATLTGGPARYINHSCAPNCVAEV 5485
Cdd:cd19212    12 RGWGLRTKRSIKKGEFVNEYVGELIDEEECRLRIKRAHENSvTNFYMLTVTKDRIIDAGPKGNYSRFMNHSCNPNCETQK 91

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 148762969 5486 VTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIpCHCGAWNC 5532
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) ...
 5403-5513 4.86e-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: 83.19  E-value: 4.86e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5403 RSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEeQNRGIYMFRINN---------EHVIDATLTGGPARYI 5473
Cdd:cd10538    95 RTSKKGWGVRSLEFIPKGSFVCEYVGEVITTSEADRRGKIYD-KSGGSYLFDLDEfsdsdgdgeELCVDATFCGNVSRFI 173

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 148762969 5474 NHSCAPNCVAEVVTFDKEDKIIII----SSRRIPKGEELTYDYQ 5513
Cdd:cd10538   174 NHSCDPNLFPFNVVIDHDDLRYPRialfATRDILPGEELTFDYG 217
FYRN smart00541
FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region ...
 5191-5234 2.33e-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: 2.33e-16
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....
gi 148762969   5191 LLPHQMADFHSATALYPVGYEATRIYWSLRTNNRRCCYRCSIGE 5234
Cdd:smart00541    1 LLPIQGKLFHSESAIFPVGYKSTRKYWSVKDPNRRCLYSCVIDE 44
SET_NSD1 cd19210
SET domain (including post-SET domain) found in nuclear receptor-binding SET domain-containing ...
 5399-5532 2.92e-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: 2.92e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5399 VYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQN-RGIYMFRINNEHVIDATLTGGPARYINHSC 5477
Cdd:cd19210     4 VEIFRTLGRGWGLRCKTDIKKGEFVNEYVGELIDEEECRARIRYAQEHDiTNFYMLTLDKDRIIDAGPKGNYARFMNHCC 83

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 148762969 5478 APNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQhKIPCHCGAWNC 5532
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 1.63e-15

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: 75.42  E-value: 1.63e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  137 WAHHWCAAWSAGVWgQEGPELCGVDKAIFSGISQRCSHCTRLGASIPCRSPGCPRLYHFPCATASGSFLSMKTLQLLCPE 216
Cdd:cd15668    24 WVHEDCAVWAPGVY-LVGGKLYGLEEAVWVAKQSVCSSCQQTGATIGCLHKGCKAKYHYPCAVESGCQLDEENFSLLCPK 102


                  .
gi 148762969  217 H 217
Cdd:cd15668   103 H 103
PHD2_KMT2C cd15594
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 1429-1474 1.79e-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: 73.43  E-value: 1.79e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969 1429 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1474
Cdd:cd15594     1 VCQTCRQPGDDNKMLVCDTCDKGYHTFCLQPVMTTIPKNGWKCKNC 46
ePHD_RAI1 cd15700
Extended PHD finger (ePHD) found in retinoic acid-induced protein 1 (RAI1); The extended plant ...
 126-217 4.72e-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: 74.14  E-value: 4.72e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  126 PAHLGEPGGSC-------WAHHWCAAWSAGVWGQEGpELCGVDKAIFSGISQRCSHCTRLGASIPCRSPGCPRLYHFPCA 198
Cdd:cd15700     7 PANYKDLGDLCgpyypehWVHEACAVWTTGVYLVAG-KLFGLQEAVQKAADAKCSSCQGAGATVGCCHKGCTQSYHYICA 85

                          90
                  ....*....|....*....
gi 148762969  199 TASGSFLSMKTLQLLCPEH 217
Cdd:cd15700    86 VEAGCLFEEENFSLRCPKH 104
SET_SUV39H_Clr4-like cd20073
SET domain (including pre-SET and post-SET domains) found in of Schizosaccharomyces pombe H3K9 ...
 5407-5536 6.77e-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: 78.38  E-value: 6.77e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5407 QGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEeqNRGI-YMF-------RINNEHVIDATLTGGPARYINHSCA 5478
Cdd:cd20073   103 KGWGLRCPRFIKAGTFIGVYLGEVITQSEAEIRGKKYD--NVGVtYLFdldlfedQVDEYYTVDAQYCGDVTRFINHSCD 180

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 148762969 5479 PNCVAEVVTFDKEDKIIIISS----RRIPKGEELTYDYQFDFEDDQ----------------HKIPCHCGAWNCRKWM 5536
Cdd:cd20073   181 PNLAIYSVLRDKSDSKIYDLAffaiKDIPALEELTFDYSGRNNFDQlgfignrsnskyinlkNKRPCYCGSANCRGWL 258
SET_SETD8 cd10528
SET domain found in SET domain-containing protein 8 (SETD8) and similar proteins; SETD8 (EC 2. ...
 5405-5512 7.60e-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: 74.54  E-value: 7.60e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5405 RIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEE-QNRGIYM--FRINNE-HVIDATL-TGGPARYINHSC-A 5478
Cdd:cd10528    25 DGKGRGVIATRPFEKGDFVVEYHGDLITITEAKKREALYAKdPSTGCYMyyFQYKGKtYCVDATKeSGRLGRLINHSKkK 104

                          90       100       110
                  ....*....|....*....|....*....|....
gi 148762969 5479 PNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDY 5512
Cdd:cd10528   105 PNLKTKLLVIDGVPHLILVAKRDIKPGEELLYDY 138
PHD_BAZ2A_like cd15545
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B ...
 276-320 9.18e-15

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: 71.19  E-value: 9.18e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15545     2 CQICRSGDNEDQLLLCDGCDRGYHTYCFKPKMTNVPEGDWFCPEC 46
PHD_BAZ1A cd15627
PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also ...
 276-320 9.20e-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: 71.27  E-value: 9.20e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15627     2 CRICRRKGDAEKMLLCDGCDRGHHMYCLRPPLKKVPEGDWFCPDC 46
PHD2_KMT2C_like cd15510
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 1429-1474 1.84e-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: 1.84e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969 1429 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1474
Cdd:cd15510     1 VCQACRQPGDDTKMLVCETCDKGYHTSCLRPVMSSIPKYGWKCKNC 46
PHD1_KDM5B cd15603
PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
 1429-1474 1.97e-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: 1.97e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969 1429 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1474
Cdd:cd15603     1 VCLVCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 46
SET_SETMAR cd10544
SET domain (including pre-SET and post-SET domains) found in SET domain and mariner ...
 5408-5536 2.56e-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: 2.56e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5408 GLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKiyeEQNRGI--YMFRINnEHV---------IDATLTGGPARYINHS 5476
Cdd:cd10544   101 GWGLRTLEFIPKGRFVCEYAGEVIGFEEARRRTK---SQTKGDmnYIIVLR-EHLssgkvletfVDPTYIGNIGRFLNHS 176

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5477 CAPNC----------VAEVVTFDKEDkiiiissrrIPKGEELTYDY------------QFDFEDDQHKIPCHCGAWNCRK 5534
Cdd:cd10544   177 CEPNLfmvpvrvdsmVPKLALFAARD---------IVAGEELSFDYsgefsnsvesvtLARQDESKSRKPCLCGAENCRG 247


                  ..
gi 148762969 5535 WM 5536
Cdd:cd10544   248 FL 249
PHD_RSF1 cd15543
PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV ...
 1430-1474 2.93e-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: 69.61  E-value: 2.93e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969 1430 CEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1474
Cdd:cd15543     2 CRKCGLSDHPEWILLCDRCDAGYHTACLRPPLMIIPDGNWFCPPC 46
PHD_BAZ1A_like cd15544
PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, ...
 276-320 3.49e-14

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: 69.36  E-value: 3.49e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15544     2 CKVCRKKGDPDNMILCDGCDKAFHLYCLRPALREVPSGDWFCPAC 46
PHD1_KDM5A_like cd15515
PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar ...
 1429-1474 5.18e-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: 68.96  E-value: 5.18e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969 1429 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1474
Cdd:cd15515     1 ICQVCGRGDDEDKLLLCDGCDDSYHTFCLIPPLPDIPPGDWRCPKC 46
PHD1_Lid2p_like cd15519
PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
 1429-1474 7.06e-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: 68.65  E-value: 7.06e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969 1429 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1474
Cdd:cd15519     1 GCEVCGLDDNEGEVLLCDGCDAEYHTSCLDPPLGEIPPGTWFCPSC 46
ePHD1_KMT2D cd15695
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 5055-5136 7.63e-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: 69.94  E-value: 7.63e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5055 DLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQRTGATSSCNRMRCPNVYHFACAIrAKCMFFKDKT--ML 5132
Cdd:cd15695     8 ECWVHHWCAAWSAGVKQHEGDGLIGVDKAVFSGISQKCEHCKRLGATIQCHAEGCPRFYHFPCAA-ASGSFQSMKTllLL 86


                  ....
gi 148762969 5133 CPMH 5136
Cdd:cd15695    87 CPEH 90
PHD_BAZ1A cd15627
PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also ...
 1430-1474 8.19e-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: 8.19e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969 1430 CEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1474
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; ...
 5408-5536 8.29e-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: 8.29e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5408 GLGLYAAKDLEKHTMVIEYIGTIIRNEVAN-RREKIYEEQNRGIYMF-------------RINNE-HVIDATLTGGPARY 5472
Cdd:cd19473   117 GWGVRSTVDIKRGQFVDCYVGEIITPEEAQrRRDAATIAQRKDVYLFaldkfsdpdsldpRLRGDpYEIDGEFMSGPTRF 196

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 148762969 5473 INHSCAPNC-VAEVVTfDKEDKIIII----SSRRIPKGEELTYDY----------QFDFEDDQHKIPCHCGAWNCRKWM 5536
Cdd:cd19473   197 INHSCDPNLrIFARVG-DHADKHIHDlaffAIKDIPRGTELTFDYvdgvtgldddAGDEEKEKEMTKCLCGSPKCRGYL 274
ePHD1_KMT2C cd15696
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 5055-5136 1.49e-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: 1.49e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5055 DLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQRTGATSSCNRMRCPNVYHFACAIRAKCMF-FKDKTMLC 5133
Cdd:cd15696     8 ECWAHLRCAEWSLGVCQGEEQLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQdFSRRLLLC 87


                  ...
gi 148762969 5134 PMH 5136
Cdd:cd15696    88 PTH 90
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1429-1477 2.53e-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: 2.53e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 148762969  1429 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPL--LTVPKGGWKCKWCVSC 1477
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 ...
 275-323 2.71e-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: 2.71e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 148762969   275 VCQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEELPAHS--WKCKACRVC 323
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPAEIPSgeWLCPECKPK 51
ePHD_TCF20 cd15699
Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20); The extended plant ...
 128-217 3.59e-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: 68.79  E-value: 3.59e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  128 HLGE---PGGSCWAHHWCAAWSAGVWGQEGpELCGVDKAIFSGISQRCSHCTRLGASIPCRSPGCPRLYHFPCATASGSF 204
Cdd:cd15699    12 NLGDlfgPFYEFWVHEGCILWANGIYLVCG-RLYGLQEALDIAREMKCSHCQEAGATLGCYNKGCSFRYHYPCAIDADCL 90

                          90
                  ....*....|...
gi 148762969  205 LSMKTLQLLCPEH 217
Cdd:cd15699    91 LNEENFSVRCPKH 103
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 5059-5136 3.85e-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: 3.85e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  5059 HLNCALWSTEVY----ETQGGALMNVEVALHRGLLTKCSLC-QRTGATSSCNRMRCPNVYHFACAIRAKCMF-FKDKT-- 5130
Cdd:pfam13771    1 HVVCALWSPELVqrgnDSMGFPIEDIEKIPKRRWKLKCYLCkKKGGACIQCSKKNCRRAFHVTCALEAGLLMqFDEDNgt 80


                   ....*...
gi 148762969  5131 --MLCPMH 5136
Cdd:pfam13771   81 fkSYCKKH 88
PHD_BAZ1A_like cd15544
PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, ...
 1430-1474 5.70e-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: 5.70e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969 1430 CEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1474
Cdd:cd15544     2 CKVCRKKGDPDNMILCDGCDKAFHLYCLRPALREVPSGDWFCPAC 46
PHD1_KDM5A cd15602
PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone ...
 1429-1476 6.29e-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: 6.29e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 148762969 1429 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWCVS 1476
Cdd:cd15602     1 VCLFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKCVA 48
ePHD2_KMT2D cd15698
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 126-217 6.81e-13

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: 68.16  E-value: 6.81e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  126 PAHLGEPGGSCWAHHWCAAWSAGVWGQEGPELCGVDKAIFSGISQRCSHCTRLGASIPCRSPGCPRLYHFPCAT-ASGSF 204
Cdd:cd15698    15 PARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQKTGATNSCNRLRCPNVYHFACAIrAKCMF 94

                          90
                  ....*....|...
gi 148762969  205 LSMKTlqLLCPEH 217
Cdd:cd15698    95 FKDKT--MLCPMH 105
SET_EHMT cd10543
SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine ...
 5401-5533 7.28e-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: 7.28e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5401 LARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKiyeeqnrGIYMFRINNE----HVIDATLTGGPARYINHS 5476
Cdd:cd10543    95 LFRTRGMGWGVRALQDIPKGTFVCEYIGELISDSEADSRED-------DSYLFDLDNKdgetYCIDARRYGNISRFINHL 167

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 148762969 5477 CAPNCVAEVVTFDKED----KIIIISSRRIPKGEELTYDYQFDFEDDQHK-IPCHCGAWNCR 5533
Cdd:cd10543   168 CEPNLIPVRVFVEHQDlrfpRIAFFASRDIKAGEELGFDYGEKFWRIKGKyFTCRCGSPKCK 229
ePHD_TCF20 cd15699
Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20); The extended plant ...
 5032-5136 7.52e-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: 7.52e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5032 CCFCHEEGD----GATDGPArllnldLDLWVHLNCALWSTEVYETQGgALMNVEVALHRGLLTKCSLCQRTGATSSCNRM 5107
Cdd:cd15699     1 CCLCGKWANyrnlGDLFGPF------YEFWVHEGCILWANGIYLVCG-RLYGLQEALDIAREMKCSHCQEAGATLGCYNK 73

                          90       100       110
                  ....*....|....*....|....*....|
gi 148762969 5108 RCPNVYHFACAIRAKCMFFKDK-TMLCPMH 5136
Cdd:cd15699    74 GCSFRYHYPCAIDADCLLNEENfSVRCPKH 103
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
 275-320 7.62e-13

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: 65.96  E-value: 7.62e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969  275 VCQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15513     1 VCEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 46
SET_SUV39H1 cd10525
SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 ...
 5407-5536 8.49e-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: 8.49e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5407 QGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNrGIYMFR---INNEHVIDATLTGGPARYINHSCAPNCVA 5483
Cdd:cd10525    97 RGWGVRTLEKIRKNSFVMEYVGEIITSEEAERRGQIYDRQG-ATYLFDldyVEDVYTVDAAYYGNISHFVNHSCDPNLQV 175

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 148762969 5484 EVVTFDKEDKIIIISSRRIPK----GEELTYDYQF-----DFEDDQH-----------------KIPCHCGAWNCRKWM 5536
Cdd:cd10525   176 YNVFIDNLDERLPRIALFATRtiraGEELTFDYNMqvdpvDAESTKMdsnfglaglpgspkkrvRIECKCGVRSCRKYL 254
PHD_UHRF1_2 cd15525
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and ...
 1430-1474 9.41e-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: 65.47  E-value: 9.41e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969 1430 CEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGG-WKCKWC 1474
Cdd:cd15525     2 CHVCGGKQDPEKQLLCDECDMAYHLYCLDPPLTSLPDDDeWYCPDC 47
SET_EZH-like cd19168
SET domain found in enhancer of zeste homolog 1 (EZH1) and zeste homolog 2 (EZH2) of polycomb ...
 5399-5516 1.01e-12

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: 1.01e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5399 VYLARSRIQ-GLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRgIYMFRINNEHVIDATLTGGPARYINH-- 5475
Cdd:cd19168     3 VVLGKSQLEcGLGLFAAEDIKEGEFVIEYTGELISHDEGVRREHRRGDVSY-LYLFEEQEGIWVDAAIYGNLSRYINHat 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 148762969 5476 --SCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDF 5516
Cdd:cd19168    82 dkVKTGNCMPKIMYVNHEWRIKFTAIKDIKIGEELFFNYGDNF 124
SET_SUV39H2 cd10532
SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 ...
 5407-5536 1.05e-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: 1.05e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5407 QGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEeqNRGI-YMFRIN---NEHVIDATLTGGPARYINHSCAPNCV 5482
Cdd:cd10532    95 RGWGVKTLQKIKKNSFVMEYVGEVITSEEAERRGQFYD--SKGItYLFDLDyesDEFTVDAARYGNVSHFVNHSCDPNLQ 172

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 148762969 5483 AEVVTFDKED----KIIIISSRRIPKGEELTYDYQFDFEDD-------------QHKIPCHCGAWNCRKWM 5536
Cdd:cd10532   173 VFNVFIDNLDtrlpRIALFSTRTIKAGEELTFDYQMKGSGDlssdsidnspakkRVRTVCKCGAVTCRGYL 243
PHD1_Lid_like cd15605
PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar ...
 1429-1474 1.14e-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: 1.14e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969 1429 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1474
Cdd:cd15605     1 VCHTCGRGDGEESMLLCDGCDDSYHTFCLLPPLSEVPKGDWRCPKC 46
ePHD_KMT2A_like cd15664
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); The ...
 133-217 1.52e-12

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: 67.05  E-value: 1.52e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  133 GGSCWAHHWCAAWSAGVWGQEGPELCGVDKAIFSGISQRCSHCTRLGASIPCRSPGCPRLYHFPCA-TASGSFLSMKtlQ 211
Cdd:cd15664    22 GQDEWVHINCALWSAEVFEEDDGSLQNVHSAVSRGRMMKCELCGKPGATVGCCLKSCPANYHFMCArKAECVFQDDK--K 99


                  ....*.
gi 148762969  212 LLCPEH 217
Cdd:cd15664   100 VFCPAH 105
ePHD_RAI1 cd15700
Extended PHD finger (ePHD) found in retinoic acid-induced protein 1 (RAI1); The extended plant ...
 5032-5136 1.98e-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: 66.44  E-value: 1.98e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5032 CCFCHEegdgatdgPARLLNL-DL------DLWVHLNCALWSTEVYETqGGALMNVEVALHRGLLTKCSLCQRTGATSSC 5104
Cdd:cd15700     1 CCLCRN--------PANYKDLgDLcgpyypEHWVHEACAVWTTGVYLV-AGKLFGLQEAVQKAADAKCSSCQGAGATVGC 71

                          90       100       110
                  ....*....|....*....|....*....|...
gi 148762969 5105 NRMRCPNVYHFACAIRAKCMFFKDK-TMLCPMH 5136
Cdd:cd15700    72 CHKGCTQSYHYICAVEAGCLFEEENfSLRCPKH 104
PHD1_KDM5C_5D cd15604
PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family ...
 1429-1474 2.24e-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: 2.24e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969 1429 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1474
Cdd:cd15604     1 VCRMCSRGDEDDKLLLCDGCDDNYHTFCLLPPLPEPPKGIWRCPKC 46
PHA03247 PHA03247
large tegument protein UL36; Provisional
 2108-2600 2.27e-12

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 74.59  E-value: 2.27e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2108 PQPGALGSPPPAA-------APTIFIGSPT---TPAGLSTSADGFLKPPAGSVPGPDSPgelflkLPPQVPAQVPSQDPF 2177
Cdd:PHA03247 2496 PDPGGGGPPDPDAppapsrlAPAILPDEPVgepVHPRMLTWIRGLEELASDDAGDPPPP------LPPAAPPAAPDRSVP 2569

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2178 GLAPA-YPLEPrfptappTYPPYPSPTGAPAQPpmlgasSRPGAgqPGEFHTTPPGTPRHQPSTPDPFlKPRCPSLDNLA 2256
Cdd:PHA03247 2570 PPRPApRPSEP-------AVTSRARRPDAPPQS------ARPRA--PVDDRGDPRGPAPPSPLPPDTH-APDPPPPSPSP 2633

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2257 VPESPGVGGGKASEPLLSP-----PPFGESRKALEVKKEELGASSPSYGPPNLGFVDSPSSGTHLGGLELKTPDVFKAPL 2331
Cdd:PHA03247 2634 AANEPDPHPPPTVPPPERPrddpaPGRVSRPRRARRLGRAAQASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAPH 2713

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2332 TPRASQVEPQSPGLGLRPQEPPPAQALAPSPPSHPDIfrPGSYTDPYAQPPLTPRPQPPPPESCCALPPRSLPSDPFSRV 2411
Cdd:PHA03247 2714 ALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPAT--PGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASL 2791

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2412 PASPQSQSSSQSpltPRPLSAEAFCPSPVTPRFQSPDPYSRPPSRPQSRDPFAPLHKPPRPQPPEVAFKAG---SLAHTS 2488
Cdd:PHA03247 2792 SESRESLPSPWD---PADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGgdvRRRPPS 2868

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2489 LGAGGFPAALPAGPAGELHAKVPSGQPPNFVRSPgtgafvgtPSPMRFTFPQAVGEPSLKPPVPQPGLPPPhginshfgP 2568
Cdd:PHA03247 2869 RSPAAKPAAPARPPVRRLARPAVSRSTESFALPP--------DQPERPPQPQAPPPPQPQPQPPPPPQPQP--------P 2932

                         490       500       510
                  ....*....|....*....|....*....|....
gi 148762969 2569 GPTLGKPQS--TNYTVATGNFHPSGSPLGPSSGS 2600
Cdd:PHA03247 2933 PPPPPRPQPplAPTTDPAGAGEPSGAVPQPWLGA 2966
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1429-1474 2.31e-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: 64.54  E-value: 2.31e-12
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 148762969   1429 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLT-VPKGGWKCKWC 1474
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
PHA03247 PHA03247
large tegument protein UL36; Provisional
 2107-2533 2.82e-12

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 74.20  E-value: 2.82e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2107 PPQPGALGSPPPAAAPTIFIGSPTTPAGLSTSADGFLKPPAGSVPGPDSPGELFLKLPPQVPAQVPSQDPFGLAPAYPLE 2186
Cdd:PHA03247 2570 PPRPAPRPSEPAVTSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPP 2649

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2187 PRFPTAPPTYPPYPS----PTGAPAQPPMLGASSRPGAGQPGEFHTTPPGTPRHQPSTPDPFLKPRCPSldnLAVPESPG 2262
Cdd:PHA03247 2650 ERPRDDPAPGRVSRPrrarRLGRAAQASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAPHALVSA---TPLPPGPA 2726

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2263 VGGGKASEPLLSP-PPFGESRKALEVKKEELGASSPSYGPPNLGFVDSPSSGthlgglelkTPDVFKAPLTPRASQVEPQ 2341
Cdd:PHA03247 2727 AARQASPALPAAPaPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAG---------PPRRLTRPAVASLSESRES 2797

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2342 SPglGLRPQEPPPAQALAPSPPSHPDIFRPGSYTDPYAQPPLTPRPQPPPPESCCALPPRSLPSDPFSRVPASPQSQSSS 2421
Cdd:PHA03247 2798 LP--SPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKP 2875

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2422 QSPLTPRPLSAEAFCPSPVTPRF-QSPDPYSRP--PSRPQSRDPFAPLHKPPRPQP-PEVAFKAGSLAHTSLGAGGFPAA 2497
Cdd:PHA03247 2876 AAPARPPVRRLARPAVSRSTESFaLPPDQPERPpqPQAPPPPQPQPQPPPPPQPQPpPPPPPRPQPPLAPTTDPAGAGEP 2955

                         410       420       430
                  ....*....|....*....|....*....|....*.
gi 148762969 2498 LPAGPAGELHAKVPSGQPPNFVRSPGTGAFVGTPSP 2533
Cdd:PHA03247 2956 SGAVPQPWLGALVPGRVAVPRFRVPQPAPSREAPAS 2991
PHD2_PHF10 cd15529
PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
 275-320 3.74e-12

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: 63.86  E-value: 3.74e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969  275 VCQACRKPGNDSKMLVCETCDKGYHTFCLKppMEELPAHSWKCKAC 320
Cdd:cd15529     1 TCTKCGDPHDEDKMMFCDQCDRGYHTFCVG--LRSIPDGRWICPLC 44
PHD_UHRF1 cd15616
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); ...
 1430-1474 4.09e-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: 4.09e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969 1430 CEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVP-KGGWKCKWC 1474
Cdd:cd15616     2 CHVCGGKQDPDKQLMCDECDMAFHIYCLNPPLSSIPdDEDWYCPEC 47
ePHD2_KMT2C cd15697
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 120-217 5.39e-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: 65.45  E-value: 5.39e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  120 FPEGLT--PAHLGEPGGSCWAHHWCAAWSAGVWGQEGPELCGVDKAIFSGISQRCSHCTRLGASIPCRSPGCPRLYHFPC 197
Cdd:cd15697     7 EGDGLTdgPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRLRCTNVYHFTC 86

                          90       100
                  ....*....|....*....|.
gi 148762969  198 A-TASGSFLSMKTlqLLCPEH 217
Cdd:cd15697    87 AiKAQCMFFKDKT--MLCPMH 105
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 275-320 5.84e-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: 63.38  E-value: 5.84e-12
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 148762969    275 VCQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEE-LPAHSWKCKAC 320
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
PHD_PHRF1 cd15536
PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also ...
 1430-1474 7.71e-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: 62.82  E-value: 7.71e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969 1430 CEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1474
Cdd:cd15536     2 CEVCGRSDREDRLLLCDGCDAGYHMECLTPPLDEVPIEEWFCPEC 46
SET_LegAS4-like cd10522
SET domain found in Legionella pneumophila type IV secretion system effector LegAS4 and ...
 5408-5518 8.67e-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: 8.67e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5408 GLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNrgiYMFRINNEH-VIDATLTGGPARYINHSCAPNCVAEVV 5486
Cdd:cd10522    14 GLGLFAAETIAKGEFVGEYTGEVLDRWEEDRDSVYHYDPL---YPFDLNGDIlVIDAGKKGNLTRFINHSDQPNLELIVR 90

                          90       100       110
                  ....*....|....*....|....*....|..
gi 148762969 5487 TFDKEDKIIIISSRRIPKGEELTYDYQFDFED 5518
Cdd:cd10522    91 TLKGEQHIGFVAIRDIKPGEELFISYGPKYWK 122
PHD_BAZ2A_like cd15545
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B ...
 1430-1474 9.97e-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: 9.97e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969 1430 CEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1474
Cdd:cd15545     2 CQICRSGDNEDQLLLCDGCDRGYHTYCFKPKMTNVPEGDWFCPEC 46
PHA03247 PHA03247
large tegument protein UL36; Provisional
 690-1272 1.07e-11

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 72.28  E-value: 1.07e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  690 SPPPEDSPTSPPPEDSPASPPPEDSLMSLPLEESPLLPLP----------EE----------PQLCPRSEGPHLSPRPEE 749
Cdd:PHA03247 2491 AAGAAPDPGGGGPPDPDAPPAPSRLAPAILPDEPVGEPVHprmltwirglEElasddagdppPPLPPAAPPAAPDRSVPP 2570

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  750 PHLSPRPEEPHLSPQAEEPHLSPQPEEPclcAVPEEPHLSPQAEGPHLSPQPEelhlspqteephlSPVPEEPCLSPQPE 829
Cdd:PHA03247 2571 PRPAPRPSEPAVTSRARRPDAPPQSARP---RAPVDDRGDPRGPAPPSPLPPD-------------THAPDPPPPSPSPA 2634

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  830 EShlSPQSEEPCLSPRPEESHLSPELEKPPLSPRPEKPPEEPG-QCPAPEELPLFPPPGEPSLSPLLGEPALSEPGEPPL 908
Cdd:PHA03247 2635 AN--EPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQaSSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAP 2712

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  909 SPLPEELPLsPSGEPSLSPQLMPPDPLPPPLSPIITAAAPPALSPLGELEYPFGAKGDSDPESPLAAPILETPisPPPEA 988
Cdd:PHA03247 2713 HALVSATPL-PPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLT--RPAVA 2789

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  989 NCTDPEPVPPmilPPSPGSPVGPASPILMEPLPPQCSPllqHSLVPQNSPPSQCSPPALPLSVPSPLSPIGKVVGVSDEA 1068
Cdd:PHA03247 2790 SLSESRESLP---SPWDPADPPAAVLAPAAALPPAASP---AGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVR 2863

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 1069 elhemeteKVSEPECPALEPsATSPLPsPMGDLSCPAPSPAPalddfsglgeDTAPLDGiDAPGSQPEPGQTPGSLASEL 1148
Cdd:PHA03247 2864 --------RRPPSRSPAAKP-AAPARP-PVRRLARPAVSRST----------ESFALPP-DQPERPPQPQAPPPPQPQPQ 2922

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 1149 KGSPVLLDPEELAPVTPMEVYPECKQTAGQGSPCEEQEEPR-APVAPTPPTLIKSDIVNeisnlSQGDASASFPGSEPLL 1227
Cdd:PHA03247 2923 PPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWlGALVPGRVAVPRFRVPQ-----PAPSREAPASSTPPLT 2997

                         570       580       590       600
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969 1228 GSPDPE-GGGSLSMELGVSTDVSPARDEGSLRLCTDSLPETDDSLL 1272
Cdd:PHA03247 2998 GHSLSRvSSWASSLALHEETDPPPVSLKQTLWPPDDTEDSDADSLF 3043
SET_EHMT1 cd10535
SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine ...
 5384-5533 1.16e-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: 1.16e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5384 KSSQYRRLRTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKiyeeqnrGIYMFRINNE----H 5459
Cdd:cd10535    78 RNCRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEYVGELISDSEADVREE-------DSYLFDLDNKdgevY 150

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 148762969 5460 VIDATLTGGPARYINHSCAPNCVAEVVTFDKED----KIIIISSRRIPKGEELTYDYQFDFEDDQHKI-PCHCGAWNCR 5533
Cdd:cd10535   151 CIDARFYGNVSRFINHHCEPNLVPVRVFMAHQDlrfpRIAFFSTRLIEAGEQLGFDYGERFWDIKGKLfSCRCGSPKCR 229
PHD_BAZ2A cd15629
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also ...
 276-320 1.24e-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: 62.18  E-value: 1.24e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15629     2 CLVCRKGDNDEYLLLCDGCDRGCHMYCHRPKMLQVPEGDWFCPNC 46
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
 1430-1474 1.31e-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: 1.31e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969 1430 CEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1474
Cdd:cd15527     2 CSVCQDSGNADNLLFCDACDKGFHMECHDPPLTRMPKGKWVCQIC 46
PHD2_KMT2D cd15595
PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 1429-1474 2.16e-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: 2.16e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969 1429 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1474
Cdd:cd15595     1 VCQTCRKPGEDSKMLVCEACDKGYHTFCLKPAMESLPTDSWKCKAC 46
PHD_BAZ1B cd15628
PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also ...
 276-320 3.32e-11

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: 60.91  E-value: 3.32e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15628     2 CKVCRKKGEDDKLILCDECNQAFHLFCLRPALYEVPDGEWMCPAC 46
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 228-276 3.51e-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: 61.35  E-value: 3.51e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 148762969   228 RCAVCEGPGELCDLFFCTSCGHHYHGACLDTALTARKRA--GWQCPECKVC 276
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPAEIPsgEWLCPECKPK 51
PHD1_KDM5A_like cd15515
PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar ...
 275-320 3.56e-11

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: 60.87  E-value: 3.56e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969  275 VCQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15515     1 ICQVCGRGDDEDKLLLCDGCDDSYHTFCLIPPLPDIPPGDWRCPKC 46
PHD_RSF1 cd15543
PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV ...
 276-320 4.11e-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: 60.75  E-value: 4.11e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15543     2 CRKCGLSDHPEWILLCDRCDAGYHTACLRPPLMIIPDGNWFCPPC 46
PHD2_d4 cd15530
PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three ...
 276-320 5.40e-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: 5.40e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15530     2 CSLCGTSENDDQLLFCDDCDRGYHMYCLSPPMSEPPEGSWSCHLC 46
PHD2_d4 cd15530
PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three ...
 1430-1474 5.62e-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: 5.62e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969 1430 CEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1474
Cdd:cd15530     2 CSLCGTSENDDQLLFCDDCDRGYHMYCLSPPMSEPPEGSWSCHLC 46
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 691-1096 6.47e-11

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: 69.41  E-value: 6.47e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969   691 PPPEDSPTSPPPEDSPASPPPEDSLMSLPLEESPLLPlpeePQLCPRSEGPHLSPRPEEPHLSPRPEEPHLSPQ---AEE 767
Cdd:pfam03154  171 PPVLQAQSGAASPPSPPPPGTTQAATAGPTPSAPSVP----PQGSPATSQPPNQTQSTAAPHTLIQQTPTLHPQrlpSPH 246

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969   768 PHLSPQPEEPCLCAVPEEPHLSPQAEGPhLSPQPEELHLSPqteePHLS-PVPEEPCLSPQPeeshlSPQSEEPcLSPRP 846
Cdd:pfam03154  247 PPLQPMTQPPPPSQVSPQPLPQPSLHGQ-MPPMPHSLQTGP----SHMQhPVPPQPFPLTPQ-----SSQSQVP-PGPSP 315

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969   847 EESHLSPELEKPPLSPRPEKPPEEPGQCPAPEELPLFPPPGEPSLSPLLGEPALSEPGEPPLSPLPEELPLSPSGEPsls 926
Cdd:pfam03154  316 AAPGQSQQRIHTPPSQSQLQSQQPPREQPLPPAPLSMPHIKPPPTTPIPQLPNPQSHKHPPHLSGPSPFQMNSNLPP--- 392

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969   927 pqlmppdplppplspiitaaaPPALSPLGELeypfgakgdSDPESPLAAPileTPISPPPEANCTDPEPVPPMILPPSPG 1006
Cdd:pfam03154  393 ---------------------PPALKPLSSL---------STHHPPSAHP---PPLQLMPQSQQLPPPPAQPPVLTQSQS 439

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  1007 SPVGPAS---PILMEPLPPQcSPLLQHSLVPQNSP---PSQCSPPALPLSVPSPLSPIGKVVGVS-----------DEAE 1069
Cdd:pfam03154  440 LPPPAAShppTSGLHQVPSQ-SPFPQHPFVPGGPPpitPPSGPPTSTSSAMPGIQPPSSASVSSSgpvpaavscplPPVQ 518

                          410       420
                   ....*....|....*....|....*..
gi 148762969  1070 LHEMETEKVSEPECPALEPSATSPLPS 1096
Cdd:pfam03154  519 IKEEALDEAEEPESPPPPPRSPSPEPT 545
ePHD_PHF7_G2E3_like cd15669
Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ...
 138-217 8.40e-11

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: 62.27  E-value: 8.40e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  138 AHHWCAAWSAGVWgQEGPELCGVDKAIFSGIS--------QRCSHCTRLGASIPCRSPGCPRLYHFPCATASGS-FLSMK 208
Cdd:cd15669    25 AHYFCLLFSSGLP-QRGEDNEGIYGFLPEDIRkevrrasrLRCFYCKKKGASIGCAVKGCRRSFHFPCGLENGCvTQFFG 103


                  ....*....
gi 148762969  209 TLQLLCPEH 217
Cdd:cd15669   104 EYRSFCWEH 112
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 139-217 8.44e-11

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: 61.19  E-value: 8.44e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969   139 HHWCAAWSAGVWgQEGPE-----LCGVDKAIFSGISQRCSHC-TRLGASIPCRSPGCPRLYHFPCATASGSFLSMK---- 208
Cdd:pfam13771    1 HVVCALWSPELV-QRGNDsmgfpIEDIEKIPKRRWKLKCYLCkKKGGACIQCSKKNCRRAFHVTCALEAGLLMQFDedng 79


                   ....*....
gi 148762969   209 TLQLLCPEH 217
Cdd:pfam13771   80 TFKSYCKKH 88
SET_SETDB1 cd10517
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) ...
 5408-5534 1.02e-10

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: 1.02e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5408 GLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIY-------------EEQNRGIYMfRINNEH--VIDATLTGGPARY 5472
Cdd:cd10517   140 GWGIRCLDDIPKGSFVCIYAGQILTEDEANEEGLQYgdeyfaeldyievVEKLKEGYE-SDVEEHcyIIDAKSEGNLGRY 218

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 148762969 5473 INHSCAPNCVAEVVTFDKEDKIIII----SSRRIPKGEELTYDYQFDFEDDQHKI-PCHCGAWNCRK 5534
Cdd:cd10517   219 LNHSCSPNLFVQNVFVDTHDLRFPWvaffASRYIRAGTELTWDYNYEVGSVPGKVlYCYCGSSNCRG 285
zf-HC5HC2H_2 pfam13832
PHD-zinc-finger like domain;
5030-5125 1.02e-10

PHD-zinc-finger like domain;


Pssm-ID: 463991 [Multi-domain]  Cd Length: 109  Bit Score: 61.98  E-value: 1.02e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  5030 RRCCFCHEEGdGAtdgparLLNLDLDLWVHLNCALWSTEV----YETQggALMNVEVALHRGLLTKCSLC-QRTGATSSC 5104
Cdd:pfam13832    1 VRCCLCPLRG-GA------LKQTSDGRWVHVLCAIFVPEVrfgnVATM--EPIDVSRIPPERWKLKCVFCkKRSGACIQC 71

                           90       100
                   ....*....|....*....|.
gi 148762969  5105 NRMRCPNVYHFACAIRAKCMF 5125
Cdd:pfam13832   72 SKGRCTTAFHVTCAQAAGVYM 92
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
 276-320 1.14e-10

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: 59.70  E-value: 1.14e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15527     2 CSVCQDSGNADNLLFCDACDKGFHMECHDPPLTRMPKGKWVCQIC 46
PHD_UHRF2 cd15617
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); ...
 1430-1474 1.30e-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: 1.30e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969 1430 CEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKG-GWKCKWC 1474
Cdd:cd15617     2 CYVCGGKQDAHMQLLCDECNMAYHIYCLNPPLDKIPEDeDWYCPSC 47
PHD1_KDM5C_5D cd15604
PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family ...
 275-320 1.32e-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: 59.47  E-value: 1.32e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969  275 VCQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15604     1 VCRMCSRGDEDDKLLLCDGCDDNYHTFCLLPPLPEPPKGIWRCPKC 46
SET_EHMT2 cd10533
SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine ...
 5384-5533 1.82e-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: 1.82e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5384 KSSQYRRLRTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKiyeeqnrGIYMFRINNE----H 5459
Cdd:cd10533    78 RNCKNRVVQSGIKVRLQLYRTAKMGWGVRALQTIPQGTFICEYVGELISDAEADVRED-------DSYLFDLDNKdgevY 150

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 148762969 5460 VIDATLTGGPARYINHSCAPNCVAEVVTFDKED----KIIIISSRRIPKGEELTYDYQFDFEDDQHK-IPCHCGAWNCR 5533
Cdd:cd10533   151 CIDARYYGNISRFINHLCDPNIIPVRVFMLHQDlrfpRIAFFSSRDIRTGEELGFDYGDRFWDIKSKyFTCQCGSEKCK 229
PHD1_Lid2p_like cd15519
PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
 275-320 1.97e-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: 59.02  E-value: 1.97e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969  275 VCQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15519     1 GCEVCGLDDNEGEVLLCDGCDAEYHTSCLDPPLGEIPPGTWFCPSC 46
PHD1_KDM5A cd15602
PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone ...
 275-320 3.98e-10

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: 58.04  E-value: 3.98e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969  275 VCQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15602     1 VCLFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKC 46
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1380-1430 4.25e-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: 58.27  E-value: 4.25e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 148762969  1380 CVVCGsfGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKG-WRCVECIVC 1430
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 ...
 5032-5136 5.75e-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: 5.75e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5032 CCFCHEEgDGATDGPARLLNLDlDLWVHLNCALWSTEV----YETQG--GALMN-VEVALHRGLLTKCSLCQRTGATSSC 5104
Cdd:cd15669     1 CVLCGRS-DDDPDKYGEKLQKD-GICAHYFCLLFSSGLpqrgEDNEGiyGFLPEdIRKEVRRASRLRCFYCKKKGASIGC 78

                          90       100       110
                  ....*....|....*....|....*....|....
gi 148762969 5105 NRMRCPNVYHFACAIRAKC--MFFKDKTMLCPMH 5136
Cdd:cd15669    79 AVKGCRRSFHFPCGLENGCvtQFFGEYRSFCWEH 112
PHD2_PHF10 cd15529
PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
 1429-1474 5.84e-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: 5.84e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969 1429 VCEVCGQASDPSRLLLCDDCDISYHTYCLDppLLTVPKGGWKCKWC 1474
Cdd:cd15529     1 TCTKCGDPHDEDKMMFCDQCDRGYHTFCVG--LRSIPDGRWICPLC 44
PHD2_PHF14 cd15562
PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 1429-1474 6.90e-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: 6.90e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 148762969 1429 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKG----GWKCKWC 1474
Cdd:cd15562     1 SCGICKKSNDQHLLALCDTCKLYYHLGCLDPPLTRMPKKtknsGWQCSEC 50
SET_SETDB2 cd10523
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 2 (SETDB2) ...
 5407-5536 8.88e-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: 62.93  E-value: 8.88e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5407 QGLGLYAAKDLEKHTMVIEYIGTIIRNEVA--------------NRREKIYEEQNRGIYMFRINNEHVIDATLTGGPARY 5472
Cdd:cd10523   118 KGWGVRCLDDIDKGTFVCIYAGRVLSRARSpteplppklelpseNEVEVVTSWLILSKKRKLRENVCFLDASKEGNVGRF 197

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5473 INHSCAPNCVAEVVTFDKEDKIIII----SSRRIPKGEELTYDYQFDF--EDDQhKIPCHCGAWNCRKWM 5536
Cdd:cd10523   198 LNHSCCPNLFVQNVFVDTHDKNFPWvaffTNRVVKAGTELTWDYSYDAgtSPEQ-EIPCLCGVNKCQKKI 266
PHD1_Lid_like cd15605
PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar ...
 275-320 8.97e-10

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: 57.07  E-value: 8.97e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969  275 VCQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15605     1 VCHTCGRGDGEESMLLCDGCDDSYHTFCLLPPLSEVPKGDWRCPKC 46
SET_SETD5-like cd10529
SET domain found in SET domain-containing protein 5 (SETD5), inactive histone-lysine ...
 5410-5516 9.11e-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: 9.11e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5410 GLYAAKDLEKHTMVIEYIGTI-IRNEVanrrEKIYEEQNRGI-YMFRINNEH----VIDATLTGGPARYINHSCAPNCVA 5483
Cdd:cd10529    18 GLVATEDISPGEPILEYKGEVsLRSEF----KEDNGFFKRPSpFVFFYDGFEglplCVDARKYGNEARFIRRSCRPNAEL 93

                          90       100       110
                  ....*....|....*....|....*....|....
gi 148762969 5484 EVVTFDK-EDKIIIISSRRIPKGEELTYDYQFDF 5516
Cdd:cd10529    94 RHVVVSNgELRLFIFALKDIRKGTEITIPFDYDY 127
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1379-1427 9.33e-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: 57.22  E-value: 9.33e-10
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*....
gi 148762969   1379 MCVVCGsfGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVEC 1427
Cdd:smart00249    1 YCSVCG--KPDDGGELLQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
PHA03247 PHA03247
large tegument protein UL36; Provisional
 2105-2485 1.06e-09

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 65.73  E-value: 1.06e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2105 RIPPQPGALGSPPPAAAPTIFIGSPTTPAGLSTSADGFLKPPAGSVPGPDSPGelflkLPPQVPAQVPSQDPFGLAPAYP 2184
Cdd:PHA03247 2662 SRPRRARRLGRAAQASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAPHA-----LVSATPLPPGPAAARQASPALP 2736

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2185 LEPrfptAPPTYPPYPSPTGAPAQPPMLGASSRPGAGQPGefhTTPPGTPrhQPSTPDPFLKPRCPSLDNLAVPESPG-- 2262
Cdd:PHA03247 2737 AAP----APPAVPAGPATPGGPARPARPPTTAGPPAPAPP---AAPAAGP--PRRLTRPAVASLSESRESLPSPWDPAdp 2807

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2263 ---VGGGKASEPLLSPPPFGESRKALEVKKEELGASSPSYGPPNLGFVDSPSSGTHLGGLELKTPDVFKAPLTPRASQVE 2339
Cdd:PHA03247 2808 paaVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAPARPPVRRLA 2887

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2340 pqspglglRPQEPPPAQALAPSPPSHPDIFRPGSYTDPYAQPPLTPRPQPPPpesccALPPRSLPSDPFSrvPASPQSQS 2419
Cdd:PHA03247 2888 --------RPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQP-----PPPPPPRPQPPLA--PTTDPAGA 2952

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 148762969 2420 SSQSPLTPRPLSAEAFCPSPVTPRFQSPDPysrPPSRPQSRDPFAPLHKPPRPQppeVAFKAGSLA 2485
Cdd:PHA03247 2953 GEPSGAVPQPWLGALVPGRVAVPRFRVPQP---APSREAPASSTPPLTGHSLSR---VSSWASSLA 3012
PHD_PHRF1 cd15536
PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also ...
 276-320 1.13e-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: 56.65  E-value: 1.13e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15536     2 CEVCGRSDREDRLLLCDGCDAGYHMECLTPPLDEVPIEEWFCPEC 46
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 1429-1474 1.18e-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: 56.94  E-value: 1.18e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 148762969 1429 VCEVCGQASD-PSRLLLCDDCDISYHTYCLDPPLLT-VPKGGWKCKWC 1474
Cdd:cd15489     1 SCIVCGKGGDlGGELLQCDGCGKWFHADCLGPPLSSfVPNGKWICPVC 48
PHD_BAZ1B cd15628
PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also ...
 1430-1474 1.24e-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: 1.24e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969 1430 CEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1474
Cdd:cd15628     2 CKVCRKKGEDDKLILCDECNQAFHLFCLRPALYEVPDGEWMCPAC 46
PHD2_CHD_II cd15532
PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 1429-1474 1.75e-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: 1.75e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969 1429 VCEVCGQASDpsrLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1474
Cdd:cd15532     1 FCRVCKDGGE---LLCCDGCPSSYHLHCLNPPLAEIPDGDWFCPRC 43
ePHD_KMT2B cd15694
Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B); The extended plant ...
 133-201 2.17e-09

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: 58.13  E-value: 2.17e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 148762969  133 GGSCWAHHWCAAWSAGVWGQEGPELCGVDKAIFSGISQRCSHCTRLGASIPCRSPGCPRLYHFPCATAS 201
Cdd:cd15694    22 GQNEWTHVNCAIWSAEVFEENDGSLKNVHAAVARGRQMRCEHCQKIGATVGCCLSACLSNFHFMCARAS 90
ePHD_PHF6_like cd15673
Extended PHD finger found in PHD finger protein 6 (PHF6) and PHD finger protein 11 (PHF11); ...
 5032-5136 2.28e-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: 2.28e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5032 CCFCHEEGDGATDGParLLNLDLDLWVHLNCALWSTEVYETQ-------GGALMN-VEVALHRGLLTKCSLCQRTGATSS 5103
Cdd:cd15673     1 CGFCKSGEENKETGG--KLASGEKIAAHHNCMLFSSGLVQYVspnendfGGFDIEdVKKEIKRGRKLKCNLCKKTGATIG 78

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 148762969 5104 CNRMRCPNVYHFACAIRAKCMFFKDK-----TMLCPMH 5136
Cdd:cd15673    79 CDVKQCKKTYHYHCAKKDDAKIIERNsqgiyRVYCKNH 116
PHD1_KDM5B cd15603
PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
 275-320 2.99e-09

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: 55.73  E-value: 2.99e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969  275 VCQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15603     1 VCLVCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 46
PHD_BAZ2A cd15629
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also ...
 1430-1475 3.92e-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: 3.92e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969 1430 CEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWCV 1475
Cdd:cd15629     2 CLVCRKGDNDEYLLLCDGCDRGCHMYCHRPKMLQVPEGDWFCPNCV 47
SET_SETDB cd10541
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1), ...
 5407-5534 4.00e-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: 4.00e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5407 QGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVIDATLTGGPARYINHSCAPNCVAEVV 5486
Cdd:cd10541   102 KGWGIRCLDDIAKGTFVCIYAGKILTDDFADKEGLEMGDEYFANLDHIEESCYIIDAKLEGNLGRYLNHSCSPNLFVQNV 181

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 148762969 5487 TFDKEDKIIIISSRRIPK----GEELTYDYQFDFED-DQHKIPCHCGAWNCRK 5534
Cdd:cd10541   182 FVDTHDLRFPWVAFFASKrikaGTELTWDYNYEVGSvEGKELLCCCGSNECRG 234
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 275-320 6.05e-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: 54.63  E-value: 6.05e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 148762969  275 VCQACRKPGND-SKMLVCETCDKGYHTFCLKPPMEELPAH-SWKCKAC 320
Cdd:cd15489     1 SCIVCGKGGDLgGELLQCDGCGKWFHADCLGPPLSSFVPNgKWICPVC 48
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 228-273 7.72e-09

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: 54.53  E-value: 7.72e-09
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 148762969    228 RCAVCEGPGELCDLFFCTSCGHHYHGACLDTALT-ARKRAGWQCPEC 273
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLeEEPDGKWYCPKC 47
ePHD_KMT2A cd15693
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A); The extended plant ...
 133-219 7.94e-09

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: 56.55  E-value: 7.94e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  133 GGSCWAHHWCAAWSAGVWGQEGPELCGVDKAIFSGISQRCSHCTRLGASIPCRSPGCPRLYHFPCATASG-SFLSMKtlQ 211
Cdd:cd15693    24 GQNEWTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSCTSNYHFMCSRAKNcVFLEDK--K 101


                  ....*...
gi 148762969  212 LLCPEHSE 219
Cdd:cd15693   102 VYCQRHKD 109
PHD_BAZ2B cd15630
PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also ...
 276-320 1.07e-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: 54.21  E-value: 1.07e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15630     3 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPEGDWFCPAC 47
PHD2_CHD_II cd15532
PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 275-320 1.78e-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: 53.44  E-value: 1.78e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969  275 VCQACRKPGNdskMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15532     1 FCRVCKDGGE---LLCCDGCPSSYHLHCLNPPLAEIPDGDWFCPRC 43
PHD_UHRF1_2 cd15525
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and ...
 278-320 2.06e-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: 53.14  E-value: 2.06e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 148762969  278 ACRKPGN---DSKMLVCETCDKGYHTFCLKPPMEELPAHS-WKCKAC 320
Cdd:cd15525     1 ACHVCGGkqdPEKQLLCDECDMAYHLYCLDPPLTSLPDDDeWYCPDC 47
PHD_PHF21A cd15523
PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC ...
 1429-1474 2.17e-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: 2.17e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969 1429 VCEVCGQASDpsrLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1474
Cdd:cd15523     1 FCSVCRKSGE---LLMCDTCSLVYHLDCLDPPLKTIPKGMWICPKC 43
SET cd08161
SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily; The Su(var)3-9, ...
 5398-5512 3.05e-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: 3.05e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5398 NVYLARSRIQGLGLYAAKDLEKhtmvieyiGTIIrnevanrrekiyeeqnrgiymfrinnehvidatltgGPARYINHSC 5477
Cdd:cd08161     1 EIRPSTIPGAGFGLFATRDIPK--------GEVI------------------------------------GLARFINHSC 36

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 148762969 5478 APNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDY 5512
Cdd:cd08161    37 EPNCEFEEVYVGGKPRVFIVALRDIKAGEELTVDY 71
PHD_BAZ2B cd15630
PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also ...
 1428-1476 3.08e-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: 3.08e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 148762969 1428 IVCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWCVS 1476
Cdd:cd15630     1 VYCQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPEGDWFCPACIA 49
PHD3_PHF14 cd15563
PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 1429-1474 3.34e-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: 3.34e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 148762969 1429 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKG---GWKCKWC 1474
Cdd:cd15563     1 ECCVCKQTGDNSQLVRCDECKLCYHFGCLDPPLKKSPKQrgyGWVCEEC 49
PHA03247 PHA03247
large tegument protein UL36; Provisional
 538-1114 3.76e-08

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 60.72  E-value: 3.76e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  538 PPPEASPLSPPFEESPLSPPPEELPTSPPP----EASRLSPPPEESPMSPPPEESPMSPPPEASRLFPPFEESPLSPPPE 613
Cdd:PHA03247 2551 PPPPLPPAAPPAAPDRSVPPPRPAPRPSEPavtsRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPS 2630

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  614 ESPLSPPPEASRLSPPPEDSPMSPPPEESPMSPPPEVSRLsplpvvSRLSPPPEESPLSPPPEESPTSPPPEASRLSPPP 693
Cdd:PHA03247 2631 PSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRL------GRAAQASSPPQRPRRRAARPTVGSLTSLADPPPP 2704

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  694 EDSPTSPPPEDSPASP-PPEDSLMSLPLEESPLLPLPEEPQLCPRSE-GPHLSPRPEEPHLSPRPEEPHLSPQAEEPHLS 771
Cdd:PHA03247 2705 PPTPEPAPHALVSATPlPPGPAAARQASPALPAAPAPPAVPAGPATPgGPARPARPPTTAGPPAPAPPAAPAAGPPRRLT 2784

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  772 PQPEEPCLCAVPEEPhlSPQAEGPHLSPQPEELHLSPQTEEPhlsPVPEEPCLSPQPEESHLSPQSEEPCLSPRPEESHL 851
Cdd:PHA03247 2785 RPAVASLSESRESLP--SPWDPADPPAAVLAPAAALPPAASP---AGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPG 2859

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  852 SPELEKPPlsprpekppeePGQCPApeelplfpppgEPSLSPllgEPALSEPGEPPLSPLPEELPLSPSGEPSLSPQLMP 931
Cdd:PHA03247 2860 GDVRRRPP-----------SRSPAA-----------KPAAPA---RPPVRRLARPAVSRSTESFALPPDQPERPPQPQAP 2914

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  932 PDPLPpplspiiTAAAPPALSPLGELEYPFGAKGDSDPESPLAAPILETPISPPPEANCTDPEPVPpmilppspGSPVGP 1011
Cdd:PHA03247 2915 PPPQP-------QPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVA--------VPRFRV 2979

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 1012 ASPILMEPLPPQCSPLLQHSLVPQNSppSQCSPPALPLSVPSPLSPIGKVVGVSDEAELHEMETEKVSEPEcpALEPSAT 1091
Cdd:PHA03247 2980 PQPAPSREAPASSTPPLTGHSLSRVS--SWASSLALHEETDPPPVSLKQTLWPPDDTEDSDADSLFDSDSE--RSDLEAL 3055

                         570       580
                  ....*....|....*....|...
gi 148762969 1092 SPLPSPMGDLSCPAPSPAPALDD 1114
Cdd:PHA03247 3056 DPLPPEPHDPFAHEPDPATPEAG 3078
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 1506-1556 3.85e-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: 3.85e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 148762969 1506 TCPICHAPYVEEDLLIQCRHCERWMHAGCESLFTEddvEQAADEGFDCVSC 1556
Cdd:cd15489     1 SCIVCGKGGDLGGELLQCDGCGKWFHADCLGPPLS---SFVPNGKWICPVC 48
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
 1430-1474 4.06e-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: 4.06e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969 1430 CEVCGqasDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1474
Cdd:cd15539     2 CAVCG---DGGELLCCDGCPRAFHLACLVPPLTLIPSGTWRCSSC 43
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 228-273 5.21e-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: 52.32  E-value: 5.21e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 148762969  228 RCAVCEGPGELCD-LFFCTSCGHHYHGACLDTAL-TARKRAGWQCPEC 273
Cdd:cd15489     1 SCIVCGKGGDLGGeLLQCDGCGKWFHADCLGPPLsSFVPNGKWICPVC 48
PHD1_BPTF cd15559
PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, ...
 276-320 1.05e-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: 51.26  E-value: 1.05e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969  276 CQACRKPGNdskMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15559     2 CRVCHKLGD---LLCCETCSAVYHLECVDPPLEEVPEEDWQCEVC 43
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 1379-1427 1.35e-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: 51.16  E-value: 1.35e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 148762969 1379 MCVVCGSfGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVEC 1427
Cdd:cd15489     1 SCIVCGK-GGDLGGELLQCDGCGKWFHADCLGPPLSSFVPNGKWICPVC 48
PspC_subgroup_2 NF033839
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 691-927 3.13e-07

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: 57.09  E-value: 3.13e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  691 PPPEDSPTSPPPEDSPASPPPEdslmslplEESPLLPLPEEPQLCPRSE--GPHLSPRPEEPHLSPRPEephlsPQAEEP 768
Cdd:NF033839  286 EPGNKKPSAPKPGMQPSPQPEK--------KEVKPEPETPKPEVKPQLEkpKPEVKPQPEKPKPEVKPQ-----LETPKP 352

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  769 HLSPQPEEPclcavpeEPHLSPQAEG--PHLSPQPE----ELHLSPQTEEPHLSPVPEEPCLSPQPEeshlsPQSEEPCL 842
Cdd:NF033839  353 EVKPQPEKP-------KPEVKPQPEKpkPEVKPQPEtpkpEVKPQPEKPKPEVKPQPEKPKPEVKPQ-----PEKPKPEV 420

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  843 SPRPE--ESHLSPELEKPplsprpekppeepgqcpapeelplfpppgEPSLSPLLGEPALSEPGEPPlSPLPEELPLSPS 920
Cdd:NF033839  421 KPQPEkpKPEVKPQPEKP-----------------------------KPEVKPQPEKPKPEVKPQPE-TPKPEVKPQPEK 470


                  ....*..
gi 148762969  921 GEPSLSP 927
Cdd:NF033839  471 PKPEVKP 477
HMG smart00398
high mobility group;
2021-2072 5.31e-07

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 50.01  E-value: 5.31e-07
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....
gi 148762969   2021 VLYANINFPNLKQDYPDWSS--RCKQIMKLWRKVPAADKAPYLQKAKDNRAAHR 2072
Cdd:smart00398   10 MLFSQENRAKIKAENPDLSNaeISKKLGERWKLLSEEEKAPYEEKAKKDKERYE 63
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1506-1556 7.49e-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: 7.49e-07
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|.
gi 148762969   1506 TCPICHAPYvEEDLLIQCRHCERWMHAGCESLFTEDDVEqaaDEGFDCVSC 1556
Cdd:smart00249    1 YCSVCGKPD-DGGELLQCDGCDRWYHQTCLGPPLLEEEP---DGKWYCPKC 47
PHD2_PHF12_Rco1 cd15534
PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, ...
 1429-1471 7.77e-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: 7.77e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 148762969 1429 VCEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGG-WKC 1471
Cdd:cd15534     1 VCFKCNRSCRVAPLIQCDYCPLLFHLDCLDPPLTHPPATGrWMC 44
PHD1_Snt2p_like cd15497
PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and ...
 1430-1474 8.09e-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: 48.84  E-value: 8.09e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 148762969 1430 CEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGG--WKCKWC 1474
Cdd:cd15497     2 CKVCKEWCASDDSVRCDECKVSYHLLCVDPPLTKKPNRGfvWSCAPC 48
PHA03247 PHA03247
large tegument protein UL36; Provisional
 469-860 9.21e-07

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 56.10  E-value: 9.21e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  469 PPPEELPASPLPEALHlsRPLEESPLSPPPEESPLSPPPESSPFSPLEESPLSPPEESPPSPALETPLSPPPEASPLSPP 548
Cdd:PHA03247 2607 DPRGPAPPSPLPPDTH--APDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQRPR 2684

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  549 FEESPLSPPPEELPTSPPPEasrlSPPPEESPMSPPPEESPMSPPPEASRLFPPFEESPLSPPPEESPLSPPPEASRLSP 628
Cdd:PHA03247 2685 RRAARPTVGSLTSLADPPPP----PPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARP 2760

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  629 PpedSPMSPPPEESPMSPPPEVSRLSPLPVVSRLSPPPEESPLSPPPEESPTSPPPEASRLSPPPEDSPTSPPPEDS--- 705
Cdd:PHA03247 2761 P---TTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAqpt 2837

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  706 PASPPPEDSLMSLPLEES--PLLPLPEEPQLCPRSEGPHLSPRPEEPHLSPRPEEPHLSPQAEEPHLSPQPEEPCLCAVP 783
Cdd:PHA03247 2838 APPPPPGPPPPSLPLGGSvaPGGDVRRRPPSRSPAAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPP 2917

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 148762969  784 EEPHLSPQAEGPHLSPQPEELHLSPQTEEPHLSPVPEEPCLSPQPEESHLSPQSEEP--CLSPRPEESHLSPELEKPPL 860
Cdd:PHA03247 2918 QPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVprFRVPQPAPSREAPASSTPPL 2996
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 1430-1474 1.00e-06

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: 1.00e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969 1430 CEVCGQASDpsrLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1474
Cdd:cd15531     2 CEVCQQGGE---IILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 43
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 1430-1474 1.12e-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: 1.12e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 148762969 1430 CEVCGQASDPSRLLLCDDCDISYHTYCLDPPLLTVP--KGGWKCKWC 1474
Cdd:cd15509     2 CAVCDSPGDLSDLLFCTSCGQHYHGSCLDPAVRPTPlvRAGWQCPEC 48
PHD1_PHF12 cd15533
PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is ...
 1429-1474 1.13e-06

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: 48.12  E-value: 1.13e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 148762969 1429 VCEVCGQASDpsrLLLCDDCDISYHTYCLDPPL--LTVPKGGWKCKWC 1474
Cdd:cd15533     1 YCDSCGEGGD---LLCCDRCPASFHLQCCNPPLdeEDLPPGEWLCHRC 45
PHD_PRHA_like cd15504
PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and ...
 1429-1474 1.13e-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: 1.13e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 148762969 1429 VCEVC--GQASDPSRLLLCD-DCDISYHTYCLDPPLLT--VPKG--GWKCKWC 1474
Cdd:cd15504     1 FCAKCqsGEASPDNDILLCDgGCNRAYHQKCLEPPLLTedIPPEdeGWLCPLC 53
PHA03247 PHA03247
large tegument protein UL36; Provisional
 2117-2683 1.44e-06

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 55.33  E-value: 1.44e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2117 PPAAAPTIFIGSPTTP------------AGLSTSADGFLKPPAGSVP-------GPDSPGELFLKLPPQVP---AQVPSQ 2174
Cdd:PHA03247 2417 PPGPPDVRFVGSEEIEelpfvspggdvlAGLAADGDPFFARTILGAPfslslllGELFPGAPVYRRPAEARfpfAAGAAP 2496

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2175 DPFGLAPAYPLEPRFPTAPPTYPPYPSPTGAPAQPPMLG------ASSRPGAGQPgefhtTPPGTPRHQPSTPDPFLKPR 2248
Cdd:PHA03247 2497 DPGGGGPPDPDAPPAPSRLAPAILPDEPVGEPVHPRMLTwirgleELASDDAGDP-----PPPLPPAAPPAAPDRSVPPP 2571

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2249 CPSldnlAVPESPGVGGgKASEPLlSPPPFGESRKALEVKKEELGASSPSYGPPNLGFVDSPSSGTHLGGLELKTPDVFK 2328
Cdd:PHA03247 2572 RPA----PRPSEPAVTS-RARRPD-APPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPT 2645

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2329 APltPRASQVEPQSPGLGLRPQEPPpAQALAPSPPSHPDIFRPGSYTDPYAQPPLTPRPQPPPPESCCAlPPRSLPSDPF 2408
Cdd:PHA03247 2646 VP--PPERPRDDPAPGRVSRPRRAR-RLGRAAQASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPA-PHALVSATPL 2721

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2409 SRVPASPQSQSSSQSPL-TPRPLSAEAFCPSPVTPRFQSPDPySRPPSRPQSRDPFAPlhKPPRPQPPEVAFKAGSLAht 2487
Cdd:PHA03247 2722 PPGPAAARQASPALPAApAPPAVPAGPATPGGPARPARPPTT-AGPPAPAPPAAPAAG--PPRRLTRPAVASLSESRE-- 2796

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2488 SLGAGGFPAALPAgPAGELHAKVPSGQPPNFVRSPGTGAFVGTPSPmrftfPQAVGEPSLKPPvpqpglppphGINSHFG 2567
Cdd:PHA03247 2797 SLPSPWDPADPPA-AVLAPAAALPPAASPAGPLPPPTSAQPTAPPP-----PPGPPPPSLPLG----------GSVAPGG 2860

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2568 PGPTLGKPQSTNYTVATGNFHPSGSPLGPSSGSTGESYGLSPLRPPSVLPPPAPDGSLPYLSHGASQRSGITSPVEKRED 2647
Cdd:PHA03247 2861 DVRRRPPSRSPAAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQ 2940

                         570       580       590
                  ....*....|....*....|....*....|....*...
gi 148762969 2648 P--GTGMGSSLATAELPGTQDPGMSGLSQTELEKQRQR 2683
Cdd:PHA03247 2941 PplAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFR 2978
PHD_Phf1p_Phf2p_like cd15502
PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 ...
 1427-1474 1.76e-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: 1.76e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 148762969 1427 CIVCEvCGQASDPSRLLLCDDCDISYHTYCLDPP----LLTVPKGGWKCKWC 1474
Cdd:cd15502     2 CIVCQ-RGHSPKSNRIVFCDGCNTPYHQLCHDPSiddeVVEDPDAEWFCKKC 52
PHD_TIF1_like cd15541
PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar ...
 1429-1474 1.83e-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: 47.72  E-value: 1.83e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969 1429 VCEVCGqasDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1474
Cdd:cd15541     1 WCAVCQ---NGGELLCCDKCPRVFHLDCHIPPIPEFPSGEWSCSLC 43
PHD3_PHF14 cd15563
PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 275-320 1.95e-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: 47.77  E-value: 1.95e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 148762969  275 VCQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEELP---AHSWKCKAC 320
Cdd:cd15563     1 ECCVCKQTGDNSQLVRCDECKLCYHFGCLDPPLKKSPkqrGYGWVCEEC 49
SET_SpSET3-like cd19183
SET domain (including post-SET domain) found in Schizosaccharomyces pombe SET ...
 5409-5523 2.30e-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: 2.30e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5409 LGLYAAKDLEKHTMVIEYIGtiirnEVANRREKIYEEQNRgiY----------MFRINNEHVIDATLTGGPARYINHSCA 5478
Cdd:cd19183    14 FGLFADRPIPAGDPIQELLG-----EIGLQSEYIADPENQ--YqilgapkphvFFHPQSPLYIDTRRSGSVARFIRRSCR 86

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 148762969 5479 PNCVAEVVTFDK--EDKIIIISSRRIPKGEELTYDYQFDFEDDQHKI 5523
Cdd:cd19183    87 PNAELVTVASDSgsVLKFVLYASRDISPGEEITIGWDWDNPHPFRRF 133
SET_AtSUVH-like cd10545
SET domain found in Arabidopsis thaliana histone H3-K9 methyltransferases (SUVHs) and similar ...
 5423-5512 2.56e-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: 2.56e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5423 VIEYIGTIIRNEVANRREKiyeeqnRGIYMFRINN-------------------------------EHVIDATLTGGPAR 5471
Cdd:cd10545   112 ICEYVGELLDTSEADTRSG------NDDYLFDIDNrqtnrgwdggqrldvgmsdgerssaedeessEFTIDAGSFGNVAR 185

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 148762969 5472 YINHSCAPNCVAEVVTFDKEDKIIII----SSRRIPKGEELTYDY 5512
Cdd:cd10545   186 FINHSCSPNLFVQCVLYDHNDLRLPRvmlfAADNIPPLQELTYDY 230
PHD1_MTF2_PHF19_like cd15499
PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ...
 1429-1477 3.06e-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: 3.06e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 148762969 1429 VCEVCG--QASDPSRLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWCVSC 1477
Cdd:cd15499     1 TCSICGgaEARDGNEILICDKCDKGYHQLCHSPKVRTSPLEGDEKWFCSRC 51
ePHD1_PHF6 cd15710
Extended PHD finger 1 found in PHD finger protein 6 (PHF6); The extended plant homeodomain ...
 5059-5122 3.49e-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: 3.49e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 148762969 5059 HLNCALWSTEVYETQ-------GGALMNVEVALHRGLLTKCSLCQRTGATSSCNRMRCPNVYHFACAIRAK 5122
Cdd:cd15710    26 HHKCMLFSSALVSSHsdsenlgGFSIEDVQKEIKRGTKLMCSLCHCPGATIGCDVKTCHRTYHYYCALHDK 96
SET_SETD5 cd19181
SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and ...
 5411-5532 3.66e-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: 3.66e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5411 LYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINN--EHVIDATLTGGPARYINHSCAPNCVAEVVTF 5488
Cdd:cd19181    21 LRAARDLALDTLIIEYRGKVMLRQQFEVNGHFFKRPYPFVLFYSKFNgvEMCVDARTFGNDARFIRRSCTPNAEVRHMIA 100

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969 5489 DKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHC--GAWNC 5532
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 4.30e-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: 4.30e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 148762969  229 CAVCEGPGELCDLFFCTSCGHHYHGACLDTALT----ARKRAGWQCPEC 273
Cdd:cd15562     2 CGICKKSNDQHLLALCDTCKLYYHLGCLDPPLTrmpkKTKNSGWQCSEC 50
PHA03247 PHA03247
large tegument protein UL36; Provisional
 4162-4426 5.17e-06

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 53.40  E-value: 5.17e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 4162 RPMQNNTGPQPPKPGPVLQSGQGLPGVGIMPTVGQLRAQLQGVLAKNPQLRH---LSPQQQQQLQALLMQRQLQQSQAVR 4238
Cdd:PHA03247 2756 RPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPpaaVLAPAAALPPAASPAGPLPPPTSAQ 2835

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 4239 QTPPYQEPGTQTSPLQGLLGCQPqlgGFPGPQTGPLQELGAGP-RPQGPP--RLPAPPGALSTGPVLGPVHPTPPPSSPQ 4315
Cdd:PHA03247 2836 PTAPPPPPGPPPPSLPLGGSVAP---GGDVRRRPPSRSPAAKPaAPARPPvrRLARPAVSRSTESFALPPDQPERPPQPQ 2912

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 4316 EPKRPsqLPSPSSQLPTEAQLPPTHPGTPKPQGPTLEPPPGRVSPAAAQLADTLFSKGLGPWDPPDNLAETQKPEQ---S 4392
Cdd:PHA03247 2913 APPPP--QPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRVPQPAPSReapA 2990

                         250       260       270
                  ....*....|....*....|....*....|....
gi 148762969 4393 SLVPGHLDQVNGQVVPEASQLSIKQEPREEPCAL 4426
Cdd:PHA03247 2991 SSTPPLTGHSLSRVSSWASSLALHEETDPPPVSL 3024
ePHD_PHF6_like cd15673
Extended PHD finger found in PHD finger protein 6 (PHF6) and PHD finger protein 11 (PHF11); ...
 136-217 5.20e-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: 48.54  E-value: 5.20e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  136 CWAHHWCAAWSAGVWGQEGP---ELCG-----VDKAIFSGISQRCSHCTRLGASIPCRSPGCPRLYHFPCATASGSFLSM 207
Cdd:cd15673    23 IAAHHNCMLFSSGLVQYVSPnenDFGGfdiedVKKEIKRGRKLKCNLCKKTGATIGCDVKQCKKTYHYHCAKKDDAKIIE 102

                          90
                  ....*....|....
gi 148762969  208 KTLQ----LLCPEH 217
Cdd:cd15673   103 RNSQgiyrVYCKNH 116
PHD1_Rco1 cd15535
PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and ...
 276-320 5.91e-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: 46.26  E-value: 5.91e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 148762969  276 CQACRKPGNdskMLVCETCDKGYHTFCLKPPMEE--LPAHSWKCKAC 320
Cdd:cd15535     2 CSACGGYGS---FLCCDGCPRSFHFSCLDPPLEEdnLPDDEWFCNEC 45
PHD2_KMT2A_like cd15507
PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 1427-1477 6.41e-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: 6.41e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 148762969 1427 CIVCEVCGQASDPsrLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWCVSC 1477
Cdd:cd15507     2 CHVCGRKGQAQKQ--LLECEKCQRGYHVDCLGPSYPTKPTRKKKTWICSKC 50
PHD_Phf1p_Phf2p_like cd15502
PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 ...
 273-320 7.31e-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: 46.28  E-value: 7.31e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 148762969  273 CKVCQACRKPGNDsKMLVCETCDKGYHTFCLKPPME----ELPAHSWKCKAC 320
Cdd:cd15502     2 CIVCQRGHSPKSN-RIVFCDGCNTPYHQLCHDPSIDdevvEDPDAEWFCKKC 52
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 2098-2516 7.96e-06

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 52.87  E-value: 7.96e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2098 DRPALHLRIPPQPGALGSPPPAAAPTIFIGSPTTPAGLSTSadgflKPPAGSVPGPDSPGELFLKLPPQVPAQVPSQDPF 2177
Cdd:PHA03307   29 GDAADDLLSGSQGQLVSDSAELAAVTVVAGAAACDRFEPPT-----GPPPGPGTEAPANESRSTPTWSLSTLAPASPARE 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2178 GL---APAYPLEPRFPTAPPTYPPYPSPTGAPAQPPMLGASSRPGAGQPGEFHTTPPGTPRHQPSTPDPFLkprcpsLDN 2254
Cdd:PHA03307  104 GSptpPGPSSPDPPPPTPPPASPPPSPAPDLSEMLRPVGSPGPPPAASPPAAGASPAAVASDAASSRQAAL------PLS 177

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2255 LAVPESPGVGGGKASEPLLSPPPFGESRKALEVKKEELGASSPSYGPP---NLGFVDSPSSGTHLGGLELKTPDVFKAPL 2331
Cdd:PHA03307  178 SPEETARAPSSPPAEPPPSTPPAAASPRPPRRSSPISASASSPAPAPGrsaADDAGASSSDSSSSESSGCGWGPENECPL 257

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2332 TPRASQVEPQSPGLGLRPQEPPPaqaLAPSPPSHPDIFRPGSYTDPyaqppltprpqppPPESCCALPPRSLPSDPFSRV 2411
Cdd:PHA03307  258 PRPAPITLPTRIWEASGWNGPSS---RPGPASSSSSPRERSPSPSP-------------SSPGSGPAPSSPRASSSSSSS 321

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2412 PASPQSQSSSQSPlTPRPLSAEAFCPSPVTPRFQSPDPYSRPPSRPQ----SRDPFAPLHKPPRPQPPEVAFKAGSLAHT 2487
Cdd:PHA03307  322 RESSSSSTSSSSE-SSRGAAVSPGPSPSRSPSPSRPPPPADPSSPRKrprpSRAPSSPAASAGRPTRRRARAAVAGRARR 400

                         410       420
                  ....*....|....*....|....*....
gi 148762969 2488 SLGAGGFPAALPagPAGELHAKVPSGQPP 2516
Cdd:PHA03307  401 RDATGRFPAGRP--RPSPLDAGAASGAFY 427
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
 229-273 8.20e-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: 8.20e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969  229 CAVCEGPGELCDLFFCTSCGHHYHGACLDTALTARKRAGWQCPEC 273
Cdd:cd15527     2 CSVCQDSGNADNLLFCDACDKGFHMECHDPPLTRMPKGKWVCQIC 46
PHD2_PHF14 cd15562
PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 275-320 1.01e-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: 45.86  E-value: 1.01e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 148762969  275 VCQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEELPAHS----WKCKAC 320
Cdd:cd15562     1 SCGICKKSNDQHLLALCDTCKLYYHLGCLDPPLTRMPKKTknsgWQCSEC 50
PHD1_MTF2_PHF19_like cd15499
PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ...
 273-320 1.22e-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: 45.57  E-value: 1.22e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 148762969  273 CKVCQACR-KPGNDskMLVCETCDKGYHTFCLKPPMEELPAHS---WKCKAC 320
Cdd:cd15499     2 CSICGGAEaRDGNE--ILICDKCDKGYHQLCHSPKVRTSPLEGdekWFCSRC 51
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
 276-320 1.31e-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: 1.31e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969  276 CQACRKPGNdskMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15539     2 CAVCGDGGE---LLCCDGCPRAFHLACLVPPLTLIPSGTWRCSSC 43
PHD_PHF21A cd15523
PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC ...
 275-320 1.33e-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: 45.08  E-value: 1.33e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969  275 VCQACRKPGndsKMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15523     1 FCSVCRKSG---ELLMCDTCSLVYHLDCLDPPLKTIPKGMWICPKC 43
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 276-320 1.67e-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: 44.90  E-value: 1.67e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969  276 CQACRKPGndsKMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15531     2 CEVCQQGG---EIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 43
PHD1_Rco1 cd15535
PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and ...
 1430-1474 1.69e-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: 1.69e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 148762969 1430 CEVCGQasdPSRLLLCDDCDISYHTYCLDPPL--LTVPKGGWKCKWC 1474
Cdd:cd15535     2 CSACGG---YGSFLCCDGCPRSFHFSCLDPPLeeDNLPDDEWFCNEC 45
HMG_box pfam00505
HMG (high mobility group) box;
2021-2072 1.88e-05

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 45.68  E-value: 1.88e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 148762969  2021 VLYANINFPNLKQDYPDWSSR--CKQIMKLWRKVPAADKAPYLQKAKDNRAAHR 2072
Cdd:pfam00505    9 FLFSKEQRAKLKAENPGLKNAeiSKILGEKWKALSEEEKKPYEEKAEKEKARYE 62
PspC_subgroup_2 NF033839
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 691-840 1.89e-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: 51.31  E-value: 1.89e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  691 PPPEDSPTSPPPEDSPASPPPEDSLMSLPLEESPLL-PLPEEP----QLCPRSEGPHLSPRPE--EPHLSPRPE--EPHL 761
Cdd:NF033839  352 PEVKPQPEKPKPEVKPQPEKPKPEVKPQPETPKPEVkPQPEKPkpevKPQPEKPKPEVKPQPEkpKPEVKPQPEkpKPEV 431

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  762 SPQAEEP--HLSPQPEEPclcavpeEPHLSPQAEGPHLSPQPEelhlsPQTEEPHLSPVPEepclSPQPEESHLSPQSEE 839
Cdd:NF033839  432 KPQPEKPkpEVKPQPEKP-------KPEVKPQPETPKPEVKPQ-----PEKPKPEVKPQPE----KPKPDNSKPQADDKK 495


                  .
gi 148762969  840 P 840
Cdd:NF033839  496 P 496
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 693-860 2.08e-05

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 51.62  E-value: 2.08e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  693 PEDSPTSPPPEDSPASPPPEdslmslPLEESPLLPLPEEPQlcprsegPHLSPRPEEphLSPRPEEPHLSPQAEEPHLSP 772
Cdd:PRK10263  336 PVEPVTQTPPVASVDVPPAQ------PTVAWQPVPGPQTGE-------PVIAPAPEG--YPQQSQYAQPAVQYNEPLQQP 400

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  773 QPEEPCLCAVPEEPHLSPQAEGPHLSPQPEELHLSPQTEEPHLS----PVPEEPCLSPQP--------------EESHLS 834
Cdd:PRK10263  401 VQPQQPYYAPAAEQPAQQPYYAPAPEQPAQQPYYAPAPEQPVAGnawqAEEQQSTFAPQStyqteqtyqqpaaqEPLYQQ 480

                         170       180
                  ....*....|....*....|....*.
gi 148762969  835 PQSEEPCLSPRPEESHLSPELEKPPL 860
Cdd:PRK10263  481 PQPVEQQPVVEPEPVVEETKPARPPL 506
PHD1_BPTF cd15559
PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, ...
 1430-1474 2.12e-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: 2.12e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969 1430 CEVCGQASDpsrLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1474
Cdd:cd15559     2 CRVCHKLGD---LLCCETCSAVYHLECVDPPLEEVPEEDWQCEVC 43
PHD1_Snt2p_like cd15497
PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and ...
 273-320 2.32e-05

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: 44.61  E-value: 2.32e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 148762969  273 CKVC-QACrkPGNDSkmLVCETCDKGYHTFCLKPPMEELPAH--SWKCKAC 320
Cdd:cd15497     2 CKVCkEWC--ASDDS--VRCDECKVSYHLLCVDPPLTKKPNRgfVWSCAPC 48
PHD_UHRF1 cd15616
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); ...
 276-320 2.33e-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: 44.57  E-value: 2.33e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969  276 CQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEELPA-HSWKCKAC 320
Cdd:cd15616     2 CHVCGGKQDPDKQLMCDECDMAFHIYCLNPPLSSIPDdEDWYCPEC 47
PHA03247 PHA03247
large tegument protein UL36; Provisional
 4238-4448 2.50e-05

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 51.48  E-value: 2.50e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 4238 RQTPPYQEPGTQTSPLQGllgcqPQLGGFPgPQTGPLQELgAGPRPQGPPRLPAPPGALS-----TGPVLGPVHPTPPPS 4312
Cdd:PHA03247 2665 RRARRLGRAAQASSPPQR-----PRRRAAR-PTVGSLTSL-ADPPPPPPTPEPAPHALVSatplpPGPAAARQASPALPA 2737

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 4313 SPQEPKRPSQLPSPSSQLPTEAQLPPTHPGTPKPQGPTLEPPPGRVSPAAAQLADTLFSKGLGPWDPPDNLAETQKP--- 4389
Cdd:PHA03247 2738 APAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPaaa 2817

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 148762969 4390 EQSSLVPGHLDQVNGQVVPEASQLSikQEPREEPCALGAQSV------KREANGEPIGAPGTSNH 4448
Cdd:PHA03247 2818 LPPAASPAGPLPPPTSAQPTAPPPP--PGPPPPSLPLGGSVApggdvrRRPPSRSPAAKPAAPAR 2880
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 2022-2071 2.75e-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: 2.75e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 148762969 2022 LYANINFPNLKQDYPDWSSrcKQIMKL----WRKVPAADKAPYLQKAKDNRAAH 2071
Cdd:cd00084     8 LFSKEKRPKLKKENPDLSF--TEISKLlgerWKELSEEEKQPYEEKAKEDKERY 59
ePHD_PHF11 cd15712
Extended PHD finger found in PHD finger protein 11 (PHF11); The extended plant homeodomain ...
 5055-5136 3.73e-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: 3.73e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5055 DLWVHLNCALWSTEVYETQGGALMNVEVA---------LHRGLLTKCSLCQRTGATSSCNRMRCPNVYHFACAIRAKCMF 5125
Cdd:cd15712    20 NIAAHQNCLLYSSGFVESEEYNPLNLDRRfdvesvlneIKRGKRLKCNFCRKKGATVGCEERACRRSYHYFCALCDDAAI 99

                          90
                  ....*....|....*.
gi 148762969 5126 FKDKT-----MLCPMH 5136
Cdd:cd15712   100 ETDEVrgiyrVFCQKH 115
PHD3_PHF14 cd15563
PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 229-273 6.67e-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: 43.54  E-value: 6.67e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 148762969  229 CAVCEGPGELCDLFFCTSCGHHYHGACLDTAL--TARKRA-GWQCPEC 273
Cdd:cd15563     2 CCVCKQTGDNSQLVRCDECKLCYHFGCLDPPLkkSPKQRGyGWVCEEC 49
PHD_ARID4_like cd15615
PHD finger found in Arabidopsis thaliana AT-rich interactive domain-containing protein 4 ...
 1506-1556 6.80e-05

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: 43.62  E-value: 6.80e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 148762969 1506 TCPICHAPYVE----EDLLIQCRHCERWMHAGCESLFTEDDVEQAADEG--FDCVSC 1556
Cdd:cd15615     1 FCILCGQVYEEnegdEKEWVQCDSCSEWVHFECDGRTGLGAFKYAKSDGlqYVCPRC 57
PHD_UHRF2 cd15617
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); ...
 273-320 6.94e-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: 6.94e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 148762969  273 CKVCQACRKPgndSKMLVCETCDKGYHTFCLKPPMEELPA-HSWKCKAC 320
Cdd:cd15617     2 CYVCGGKQDA---HMQLLCDECNMAYHIYCLNPPLDKIPEdEDWYCPSC 47
SET_SMYD cd20071
SET domain (including SET domain and post-SET domain) found in SET and MYND domain-containing ...
 5408-5512 8.31e-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: 8.31e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5408 GLGLYAAKDLEKhtmvieyiGTIIRNE------VANRREKIYEEQNRGIYMFRInnehvidatltggpARYINHSCAPNC 5481
Cdd:cd20071    10 GRGLVATRDIEP--------GELILVEkplvsvPSNSFSLTDGLNEIGVGLFPL--------------ASLLNHSCDPNA 67

                          90       100       110
                  ....*....|....*....|....*....|.
gi 148762969 5482 VaevVTFDKEDKIIIISSRRIPKGEELTYDY 5512
Cdd:cd20071    68 V---VVFDGNGTLRVRALRDIKAGEELTISY 95
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1507-1558 8.98e-05

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: 43.25  E-value: 8.98e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 148762969  1507 CPICHAPyVEEDLLIQCRHCERWMHAGCESLftEDDVEQAADEGFDCVSCQP 1558
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 ...
 1507-1558 9.17e-05

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: 43.20  E-value: 9.17e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 148762969 1507 CPICHAPYVEEDL---LIQCRHCERWMHAGCESLfteddveqaADEGFDCVSCQP 1558
Cdd:cd15508     2 CPLCEKCYDDDDYdskMMQCSQCDHWVHAKCEGL---------SDEMYEILSYLP 47
PHD2_KMT2C cd15594
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 229-273 9.19e-05

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: 43.00  E-value: 9.19e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969  229 CAVCEGPGELCDLFFCTSCGHHYHGACLDTALTARKRAGWQCPEC 273
Cdd:cd15594     2 CQTCRQPGDDNKMLVCDTCDKGYHTFCLQPVMTTIPKNGWKCKNC 46
PHD_TCF19_like cd15517
PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and ...
 275-320 9.60e-05

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: 42.92  E-value: 9.60e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 148762969  275 VCQACRKPGNDSKML--VCETCDKGYHTFCLK--PPMEELPAhSWKCKAC 320
Cdd:cd15517     1 VCGICNLETAAVDELwvQCDGCDKWFHQFCLGlsNERYADED-KFKCPNC 49
PRK14954 PRK14954
DNA polymerase III subunits gamma and tau; Provisional
 4273-4362 1.02e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184918 [Multi-domain]  Cd Length: 620  Bit Score: 48.79  E-value: 1.02e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 4273 PLQELGAGPRPQGPPRLPAPPGALSTGPVlgpvhpTPPPSSPQEP-KRPSQLPSPSSQlPTEAQLPPTHPGTPKPQGPTL 4351
Cdd:PRK14954  376 NDGGVAPSPAGSPDVKKKAPEPDLPQPDR------HPGPAKPEAPgARPAELPSPASA-PTPEQQPPVARSAPLPPSPQA 448

                          90
                  ....*....|.
gi 148762969 4352 EPPPGRVSPAA 4362
Cdd:PRK14954  449 SAPRNVASGKP 459
dnaA PRK14086
chromosomal replication initiator protein DnaA;
4236-4439 1.03e-04

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 48.67  E-value: 1.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 4236 AVRQTPPYQEPGTQTSPLQGLLGCQPqLGGFPGPQtgplqelgAGPRPQGPPRlpappgalstgpvlGPVHPTPPPSSPQ 4315
Cdd:PRK14086   92 AGEPAPPPPHARRTSEPELPRPGRRP-YEGYGGPR--------ADDRPPGLPR--------------QDQLPTARPAYPA 148

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 4316 EPKRPSQLPSPSSQLPTEAQLPPTHPGTPKPQGPTLEPPPGRV---SPAAAQLADTLFSKGLGPWDPPD----NLAETQK 4388
Cdd:PRK14086  149 YQQRPEPGAWPRAADDYGWQQQRLGFPPRAPYASPASYAPEQErdrEPYDAGRPEYDQRRRDYDHPRPDwdrpRRDRTDR 228

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 148762969 4389 PEQSslvPG-HLDQVNGQVVPEASQLSIKQEPREEPCALGAQSVKREANGEP 4439
Cdd:PRK14086  229 PEPP---PGaGHVHRGGPGPPERDDAPVVPIRPSAPGPLAAQPAPAPGPGEP 277
PHD_TIF1beta cd15623
PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also ...
 276-320 1.08e-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: 42.48  E-value: 1.08e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969  276 CQACRKPGNdskMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15623     2 CRVCQKAGA---LVMCDQCEFCFHLDCHLPALQEVPGEDWKCLLC 43
PHD2_KMT2B cd15591
PHD domain 2 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed ...
 1380-1427 1.11e-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: 42.62  E-value: 1.11e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 148762969 1380 CVVCGSFGRGAEgHLLACSQCSQCYHPYCVNSKITKVMLLK--GWRCVEC 1427
Cdd:cd15591     2 CHVCGRKNKESK-PLLECERCRNCYHPACLGPNYPKPANRKkrPWICSAC 50
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 899-1258 1.28e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 49.01  E-value: 1.28e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  899 ALSEPGEPPLSPLPEELPLSPSGEPSlspqlmppDPLPPPLSPIITAAAPPALSPlgeleypfgakGDSDPESPLAAPIL 978
Cdd:PHA03307   60 AACDRFEPPTGPPPGPGTEAPANESR--------STPTWSLSTLAPASPAREGSP-----------TPPGPSSPDPPPPT 120

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  979 ETPISPPPeancTDPEPVPPMILPPSPGSPVGPASPILmEPLPPQCSPllqhslvpqnSPPSQCSPPALPLSVPSPLSPI 1058
Cdd:PHA03307  121 PPPASPPP----SPAPDLSEMLRPVGSPGPPPAASPPA-AGASPAAVA----------SDAASSRQAALPLSSPEETARA 185

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 1059 GKVVGVSDeaelhemetekvsEPECPALEPSATSPLPSPMGDLSCPAPSPAPALDDFSGLGEDTAPLDGIDAPGSQPEP- 1137
Cdd:PHA03307  186 PSSPPAEP-------------PPSTPPAAASPRPPRRSSPISASASSPAPAPGRSAADDAGASSSDSSSSESSGCGWGPe 252

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 1138 GQTPGSLAselkgSPVLLDPEELAPVTPMEVYPECKQTAGQGSPCEEQEEPRAPVAPTPPTLIKSDIVNEISNLSQGDAS 1217
Cdd:PHA03307  253 NECPLPRP-----APITLPTRIWEASGWNGPSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSS 327

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|.
gi 148762969 1218 ASFPGSEPLLGSPDPegGGSLSMELGVSTDVSPARDEGSLR 1258
Cdd:PHA03307  328 STSSSSESSRGAAVS--PGPSPSRSPSPSRPPPPADPSSPR 366
dnaA PRK14086
chromosomal replication initiator protein DnaA;
727-906 1.37e-04

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 48.28  E-value: 1.37e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  727 PLPEEPQlcPRSEGPHLSPRPEEPHLSPRPEEPHLSPQAEE--PHLSPQPEEPclCAVPEEPHLSPQAE-GPHLSPQ--- 800
Cdd:PRK14086   90 PSAGEPA--PPPPHARRTSEPELPRPGRRPYEGYGGPRADDrpPGLPRQDQLP--TARPAYPAYQQRPEpGAWPRAAddy 165

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  801 -PEELHLSPQTEEPHLSPVPEEPCLSPQPEESHLSPQSEEPclsPRPEESHLSPELEKP-------PLSPRPEKPPEEPG 872
Cdd:PRK14086  166 gWQQQRLGFPPRAPYASPASYAPEQERDREPYDAGRPEYDQ---RRRDYDHPRPDWDRPrrdrtdrPEPPPGAGHVHRGG 242

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 148762969  873 QCPAPEELPLFPPPGEPSLSPLLGEPA-LSEPGEP 906
Cdd:PRK14086  243 PGPPERDDAPVVPIRPSAPGPLAAQPApAPGPGEP 277
PHD_TIF1_like cd15541
PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar ...
 275-320 1.70e-04

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: 41.95  E-value: 1.70e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969  275 VCQACRKPGNdskMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15541     1 WCAVCQNGGE---LLCCDKCPRVFHLDCHIPPIPEFPSGEWSCSLC 43
ePHD2_PHF6 cd15711
Extended PHD finger 2 found in PHD finger protein 6 (PHF6); The extended plant homeodomain ...
 5032-5128 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 148762969 5032 CCFCHE-EGDGATDGPARLLNLDlDLWVHLNCALWST---EVYETQGGALMNVEVA-----LHRGLLTKCSLCQRTGATS 5102
Cdd:cd15711     1 CGFCHAgEEENETRGKLHIFNAK-KAAAHYKCMLFSSgtvQLTTTSRAEFGDFDIKtviqeIKRGKRMKCTLCSQLGATI 79

                          90       100
                  ....*....|....*....|....*.
gi 148762969 5103 SCNRMRCPNVYHFACAIRAKCMFFKD 5128
Cdd:cd15711    80 GCEIKACVKTYHYHCGVQDKAKYIEN 105
PLN03209 PLN03209
translocon at the inner envelope of chloroplast subunit 62; Provisional
 687-926 2.19e-04

translocon at the inner envelope of chloroplast subunit 62; Provisional


Pssm-ID: 178748 [Multi-domain]  Cd Length: 576  Bit Score: 47.61  E-value: 2.19e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  687 SRLSPPPEDSPTSPPPEDSPASPPPEDSlmSLPLEESPllplPEEPQLCPRSEGPHLSPRPEEPHLSPRPEEPHLSPQAE 766
Cdd:PLN03209  325 SQRVPPKESDAADGPKPVPTKPVTPEAP--SPPIEEEP----PQPKAVVPRPLSPYTAYEDLKPPTSPIPTPPSSSPASS 398

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  767 EPHLSPQ-PEEPCLCAVPEEPHLSPQAEgPHLSPQPEELHLSPQTEEPHLSPvPEEPclSPQPEESHLSPQSEEPCLSPR 845
Cdd:PLN03209  399 KSVDAVAkPAEPDVVPSPGSASNVPEVE-PAQVEAKKTRPLSPYARYEDLKP-PTSP--SPTAPTGVSPSVSSTSSVPAV 474

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  846 PE--------ESHLSPELEKPPLSPRPEKPPEEPGQCPAPEELPLFPPPGEPSLSPLLGEPAL----------SEPGEPP 907
Cdd:PLN03209  475 PDtapataatDAAAPPPANMRPLSPYAVYDDLKPPTSPSPAAPVGKVAPSSTNEVVKVGNSAPptaladeqhhAQPKPRP 554

                         250
                  ....*....|....*....
gi 148762969  908 LSPLPEELPLSPSGEPSLS 926
Cdd:PLN03209  555 LSPYTMYEDLKPPTSPTPS 573
PHD_BRPF_JADE_like cd15492
PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; ...
 1429-1474 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 148762969 1429 VCEVCGQAS--DPSRLLLCDDCDISYHTYCLDppLLTVPKGGWKCKWC 1474
Cdd:cd15492     1 VCDVCLDGEseDDNEIVFCDGCNVAVHQSCYG--IPLIPEGDWFCRKC 46
PHD_JADE2 cd15680
PHD finger found in protein Jade-2 and similar proteins; Jade-2, also termed PHD finger ...
 1429-1474 2.27e-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: 41.92  E-value: 2.27e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 148762969 1429 VCEVC--GQASDPSRLLLCDDCDISYHTYCLDppLLTVPKGGWKCKWC 1474
Cdd:cd15680     1 VCDVCrsPEGEDGNEMVFCDKCNVCVHQACYG--ILKVPTGSWLCRTC 46
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 4170-4366 2.30e-04

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: 47.72  E-value: 2.30e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  4170 PQPPKPGPvLQSGQGLPGVGIMP---TVGQLRAQlqgvlAKNPQlrhlspqqqqQLQALLMQRQLQQSQAVRQTPPYQEP 4246
Cdd:pfam09770  174 APAPQPAA-QPASLPAPSRKMMSleeVEAAMRAQ-----AKKPA----------QQPAPAPAQPPAAPPAQQAQQQQQFP 237

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  4247 gtQTSPLQGLLGCQPQLGGFPGPQTGPLQELGAGPRPQGPPRLPAPPgalsTGPVLGPVHPTPPPSSP----QEPKRPSQ 4322
Cdd:pfam09770  238 --PQIQQQQQPQQQPQQPQQHPGQGHPVTILQRPQSPQPDPAQPSIQ----PQAQQFHQQPPPVPVQPtqilQNPNRLSA 311

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 148762969  4323 LPSPSSQLPTEAQLP-PTHPGTPKPQGPtlePPPGRVSPAAAQLA 4366
Cdd:pfam09770  312 ARVGYPQNPQPGVQPaPAHQAHRQQGSF---GRQAPIITHPQQLA 353
PHD_PRHA_like cd15504
PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and ...
 275-320 2.36e-04

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: 42.04  E-value: 2.36e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 148762969  275 VCQACRKP--GNDSKMLVCE-TCDKGYHTFCLKPPM--EELPA--HSWKCKAC 320
Cdd:cd15504     1 FCAKCQSGeaSPDNDILLCDgGCNRAYHQKCLEPPLltEDIPPedEGWLCPLC 53
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 4278-4400 2.38e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 47.67  E-value: 2.38e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 4278 GAGPRPQGPPRLPAPPGALSTGPvlGPVHPTPPPSSPQEPKRPSQLPSPSSQLPTEAQLPPTHPGTPKPQGPTLEPPPGr 4357
Cdd:PRK07764  391 AGAPAAAAPSAAAAAPAAAPAPA--AAAPAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGGAPSPPPAAAPSAQPA- 467

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 148762969 4358 vsPAAAQLADTLFSKGLGPWDPPDNLAETQKPEQSSLVPGHLD 4400
Cdd:PRK07764  468 --PAPAAAPEPTAAPAPAPPAAPAPAAAPAAPAAPAAPAGADD 508
ePHD_BRPF cd15670
Extended PHD finger found in BRPF proteins; The extended plant homeodomain (ePHD) zinc finger ...
 5032-5121 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 148762969 5032 CCFCHEEGdGA----TDGParllnldldlWVHLNCALWSTEVY-------EtqggALMNVE-VALHRGLLTkCSLC-QRT 5098
Cdd:cd15670     1 CVLCPNKG-GAfkqtDDGR----------WAHVVCALWIPEVSfantvflE----PIDGIQnIPKARWKLT-CYICkKRM 64

                          90       100
                  ....*....|....*....|...
gi 148762969 5099 GATSSCNRMRCPNVYHFACAIRA 5121
Cdd:cd15670    65 GACIQCHKKNCYTAFHVTCAQQA 87
PHD3_KMT2B cd15593
PHD finger 3 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed ...
 1507-1544 2.71e-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: 41.76  E-value: 2.71e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 148762969 1507 CPICHAPYVEEDL---LIQCRHCERWMHAGCESLfTEDDVE 1544
Cdd:cd15593     2 CPICLKCYEDNDYeskMMQCAKCDHWVHAKCEGL-SDELYE 41
PHD_TCF19_like cd15517
PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and ...
 1507-1556 2.97e-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: 41.38  E-value: 2.97e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 148762969 1507 CPICHAPYVEEDLL-IQCRHCERWMHAGCESLftedDVEQAADEG-FDCVSC 1556
Cdd:cd15517     2 CGICNLETAAVDELwVQCDGCDKWFHQFCLGL----SNERYADEDkFKCPNC 49
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
960-1165 3.09e-04

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 47.18  E-value: 3.09e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  960 PFGAKGDSDPESPLAAPIL-ETPISPPPEANCTDPEPVPPMILPPSPGSPVGPASPILMEPLPPQCSPLLQHSLVPQNSP 1038
Cdd:PRK12323  365 PGQSGGGAGPATAAAAPVAqPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQASARGP 444

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 1039 PSQCSPPALPLSVPSPLS--PIGKVVGVSDEAelhemetEKVSEPECPALEPSATSPLPSPMGDLSCPAPSPAPALDDFS 1116
Cdd:PRK12323  445 GGAPAPAPAPAAAPAAAArpAAAGPRPVAAAA-------AAAPARAAPAAAPAPADDDPPPWEELPPEFASPAPAQPDAA 517

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 148762969 1117 GLGEDTAPL-DGIDAPGSQPEPGQTPGSLASELkgSPVLLDPEELAPVTP 1165
Cdd:PRK12323  518 PAGWVAESIpDPATADPDDAFETLAPAPAAAPA--PRAAAATEPVVAPRP 565
PHD_PRKCBP1 cd15538
PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed ...
 1391-1427 3.15e-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: 3.15e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 148762969 1391 EGHLLACSQCSQCYHPYCVNSKItkvMLLKGWRCVEC 1427
Cdd:cd15538     8 EGQVLCCSLCPRVYHKKCLKLTS---EPDEDWVCPEC 41
PspC_subgroup_1 NF033838
pneumococcal surface protein PspC, choline-binding form; The pneumococcal surface protein PspC, ...
 730-822 3.48e-04

pneumococcal surface protein PspC, choline-binding 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 1, has variable numbers of a choline-binding repeat in the C-terminal region, and is also known as choline-binding protein A. The other form, subgroup 2, is anchored covalently after cleavage by sortase at a C-terminal LPXTG site.


Pssm-ID: 468201 [Multi-domain]  Cd Length: 684  Bit Score: 47.32  E-value: 3.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  730 EEPQLCPrsegphlSPRPEEPhlSPRPEEPHLSPQAEEPHlSPQPEEPCLCAVPEEPHLSPQAegphlspQPeelhlsPQ 809
Cdd:NF033838  418 EQPQPAP-------APQPEKP--APKPEKPAEQPKAEKPA-DQQAEEDYARRSEEEYNRLTQQ-------QP------PK 474

                          90
                  ....*....|...
gi 148762969  810 TEEPhlsPVPEEP 822
Cdd:NF033838  475 TEKP---AQPSTP 484
PHA03247 PHA03247
large tegument protein UL36; Provisional
 2107-2495 3.58e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 47.63  E-value: 3.58e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2107 PPQPGALGSPPPAAAPTIFIGSPttPAGLSTSADGFLKPPAGSVPGPDSPGELFLKLPPQVPAQVPSQDPFGLAPAYPle 2186
Cdd:PHA03247 2757 PARPPTTAGPPAPAPPAAPAAGP--PRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPT-- 2832

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2187 prfptapptyppYPSPTGAPAQPPMLGASSRPGAGQP--GEFHTTPPgtPRHQPSTPDPFLKPRCPSLDNLAVPESPgvg 2264
Cdd:PHA03247 2833 ------------SAQPTAPPPPPGPPPPSLPLGGSVApgGDVRRRPP--SRSPAAKPAAPARPPVRRLARPAVSRST--- 2895

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2265 ggkasEPLLSPPPfgesrkalevkkeelgasspsyGPPNLGFVDSPSSgthlgglelktPDVFKAPLTPRASQVEPQSPG 2344
Cdd:PHA03247 2896 -----ESFALPPD----------------------QPERPPQPQAPPP-----------PQPQPQPPPPPQPQPPPPPPP 2937

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2345 LGLRPQEPPPAQALAPSPPSHPDIFRPGSYTDPYAQPPLTPRPQPPPPESCCALPPRSLPSDPFSRVPASPQSQSSSQSP 2424
Cdd:PHA03247 2938 RPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRVPQPAPSREAPASSTPPLTGHSLSRVSSWASSLALHEET 3017

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 148762969 2425 lTPRPLSAEAFCPSP--------VTPRFQSPDPYSRPPSRPQSRDPFAPLHKPPRPQPPEvafkAGSLAHTSLGAGGFP 2495
Cdd:PHA03247 3018 -DPPPVSLKQTLWPPddtedsdaDSLFDSDSERSDLEALDPLPPEPHDPFAHEPDPATPE----AGARESPSSQFGPPP 3091
PHD_JADE1 cd15679
PHD finger found in protein Jade-1 and similar proteins; Jade-1, also termed PHD finger ...
 1429-1474 3.62e-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: 3.62e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 148762969 1429 VCEVCGQ--ASDPSRLLLCDDCDISYHTYCLDppLLTVPKGGWKCKWC 1474
Cdd:cd15679     1 VCDVCQSpdGEDGNEMVFCDKCNICVHQACYG--ILKVPEGSWLCRTC 46
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 4267-4423 4.06e-04

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: 47.07  E-value: 4.06e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  4267 PGPQTGPLQELGAGPRPqGPPRLPAPPGALSTGPVLGPVHPTPPPS--------------SPQEPKRPSQLPSPSSQLPT 4332
Cdd:pfam03154  185 SPPPPGTTQAATAGPTP-SAPSVPPQGSPATSQPPNQTQSTAAPHTliqqtptlhpqrlpSPHPPLQPMTQPPPPSQVSP 263

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  4333 EAQLPPTHPGTPKPQGPTLEPPPGRVS-PAAAQladtlfskglgPWDPPDNLAETQKPEQSSLVPGHLDQVNGQVVPEAS 4411
Cdd:pfam03154  264 QPLPQPSLHGQMPPMPHSLQTGPSHMQhPVPPQ-----------PFPLTPQSSQSQVPPGPSPAAPGQSQQRIHTPPSQS 332

                          170
                   ....*....|..
gi 148762969  4412 QLSIKQEPREEP 4423
Cdd:pfam03154  333 QLQSQQPPREQP 344
RING-H2 cd16448
H2 subclass of RING (RING-H2) fingers and its variants; The RING finger is a specialized type ...
 229-274 4.33e-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: 4.33e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969  229 CAVCEGPGELCDLFFCTSCGHHYHGACLDTALTARKRagwQCPECK 274
Cdd:cd16448     1 CVICLEEFEEGDVVRLLPCGHVFHLACILRWLESGNN---TCPLCR 43
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 5092-5136 4.34e-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: 4.34e-04
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 148762969   5092 CSLCQRTGATS---SCNRmrCPNVYHFACAIRAKCMFFKDKTMLCPMH 5136
Cdd:smart00249    2 CSVCGKPDDGGellQCDG--CDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
PHD_TIF1beta cd15623
PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also ...
 1430-1474 4.56e-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: 4.56e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969 1430 CEVCGQASDpsrLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1474
Cdd:cd15623     2 CRVCQKAGA---LVMCDQCEFCFHLDCHLPALQEVPGEDWKCLLC 43
ePHD_JMJD2A cd15713
Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A); The ...
 5032-5128 5.11e-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: 5.11e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5032 CCFCHEEGdGAtdgparLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVA---LHRGLLtKCSLCQR-----TGATSS 5103
Cdd:cd15713     1 CCLCSLRG-GA------LQRANDDKWVHVMCAVAVLEARFVNIAERSPVDVSkipLQRFKL-KCIFCKKrrkrtAGCCVQ 72

                          90       100
                  ....*....|....*....|....*
gi 148762969 5104 CNRMRCPNVYHFACAIRAKCMFFKD 5128
Cdd:cd15713    73 CSHGRCPTSFHASCAQAAGVMMQPD 97
PHD1_KMT2A_like cd15506
PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 275-320 5.17e-04

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: 40.81  E-value: 5.17e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 148762969  275 VCQACRKPGNDsKMLVCETCDKGYHTFCLKPPMEELPAH--SWKCKAC 320
Cdd:cd15506     1 LCFLCGSAGLN-ELLYCSVCCEPYHTFCLEEAERPLNINkdNWCCRRC 47
PHA03247 PHA03247
large tegument protein UL36; Provisional
 458-1056 5.31e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 46.86  E-value: 5.31e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  458 TSPPPeaSRLSP---------------------------------PPEELPASPLPEALHLSRPLEESPLSPPPEESPLS 504
Cdd:PHA03247 2508 APPAP--SRLAPailpdepvgepvhprmltwirgleelasddagdPPPPLPPAAPPAAPDRSVPPPRPAPRPSEPAVTSR 2585

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  505 PPPESSPFSPLEESPLSPPEESPPSPALETPLsPPPEASPLSPPFEESPLSPPPEELPTSPPPEASRLSPPPEESPMSPP 584
Cdd:PHA03247 2586 ARRPDAPPQSARPRAPVDDRGDPRGPAPPSPL-PPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRP 2664

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  585 PEESPMSPPPEASRlfPPFEESPLSPPPEESPLSPPPEASRLSPPPEDSPMSPPPEESPMSPPPEVSRLSPLPVVSRLSP 664
Cdd:PHA03247 2665 RRARRLGRAAQASS--PPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPP 2742

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  665 PPEESPLSPPPEESPTSPPPEASRLSPPPEDSPTSPPPedsPASPPPEDSLMSLPLEESPLLPLPEEPQLCPRSEGPHLS 744
Cdd:PHA03247 2743 AVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPP---RRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALP 2819

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  745 PRPEEPHLSPRPEEPHLSPQAEEPHLSPQPEEPCLCAVP-----EEPHLSPQAEGPHLSPQPEELHLSpqteEPHLSPVP 819
Cdd:PHA03247 2820 PAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPggdvrRRPPSRSPAAKPAAPARPPVRRLA----RPAVSRST 2895

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  820 EEPCLSPQPEESHLSPQSEEPclsPRPEESHLSPELEKPPLSPRPEKPPEEPGQCPAPEELPLFPPPGEPSLSPLL-GEP 898
Cdd:PHA03247 2896 ESFALPPDQPERPPQPQAPPP---PQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVpGRV 2972

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  899 ALSEPGEPPLSPlPEELPLSPSgePSLSPQLMPPDPLPPPLSPIITAAAPPALSPLGELeYPFGAKGDSDPESPLAAPil 978
Cdd:PHA03247 2973 AVPRFRVPQPAP-SREAPASST--PPLTGHSLSRVSSWASSLALHEETDPPPVSLKQTL-WPPDDTEDSDADSLFDSD-- 3046

                         570       580       590       600       610       620       630
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 148762969  979 etpiSPPPEANCTDPEPVPPmilppspgspvgpASPILMEPLPPqcSPLLQHslvpQNSPPSQCSPPalPLSVPSPLS 1056
Cdd:PHA03247 3047 ----SERSDLEALDPLPPEP-------------HDPFAHEPDPA--TPEAGA----RESPSSQFGPP--PLSANAALS 3099
SET_KMT2E cd19182
SET domain found in inactive histone-lysine N-methyltransferase 2E (KMT2E) and similar ...
 5411-5516 6.20e-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: 6.20e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 5411 LYAAKDLEKHTMVIEYIGTIIRNEV--AN----RREK---IYEEQNRGIYMfrinnehVIDATLTGGPARYINHSCAPNC 5481
Cdd:cd19182    21 LKAAKDLPPDTLIIEYRGKFMLREQfeANgyffKRPYpfvLFYSKFHGLEM-------CVDARTFGNEARFIRRSCTPNA 93

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 148762969 5482 VAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDF 5516
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 6.64e-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: 6.64e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969  229 CAVCEGPGELcdlFFCTSCGHHYHGACLDTALTARKRAGWQCPEC 273
Cdd:cd15523     2 CSVCRKSGEL---LMCDTCSLVYHLDCLDPPLKTIPKGMWICPKC 43
PHD_BRPF2 cd15677
PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar ...
 1429-1476 7.35e-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: 40.77  E-value: 7.35e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 148762969 1429 VCEVC--GQASDPSRLLLCDDCDISYHTYCLDPPLltVPKGGWKCKWCVS 1476
Cdd:cd15677     3 VCCICmdGECQNSNVILFCDMCNLAVHQECYGVPY--IPEGQWLCRHCLQ 50
PHD1_MTF2 cd15578
PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also ...
 1429-1476 7.37e-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: 7.37e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 148762969 1429 VCEVC--GQASDPSRLLLCDDCDISYHTYCLDPPLLTV---PKGGWKCKWCVS 1476
Cdd:cd15578     1 VCTVCqdGSSESPNEIVLCDKCGQGYHQLCHNPKIDSSvldPDVPWLCRQCVF 53
PHD_PHF21B cd15524
PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) ...
 1430-1474 8.29e-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: 8.29e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969 1430 CEVCGQASDpsrLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1474
Cdd:cd15524     2 CAACKRGGN---LQPCGTCPRAYHLDCLDPPLKTAPKGVWVCPKC 43
PHD_BAZ1A cd15627
PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also ...
 228-273 9.25e-04

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: 40.07  E-value: 9.25e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969  228 RCAVCEGPGELCDLFFCTSCGHHYHGACLDTALTARKRAGWQCPEC 273
Cdd:cd15627     1 RCRICRRKGDAEKMLLCDGCDRGHHMYCLRPPLKKVPEGDWFCPDC 46
ePHD1_PHF6 cd15710
Extended PHD finger 1 found in PHD finger protein 6 (PHF6); The extended plant homeodomain ...
 138-198 9.26e-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: 42.26  E-value: 9.26e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 148762969  138 AHHWCAAWSAG-VWGQEGPELCG------VDKAIFSGISQRCSHCTRLGASIPCRSPGCPRLYHFPCA 198
Cdd:cd15710    25 AHHKCMLFSSAlVSSHSDSENLGgfsiedVQKEIKRGTKLMCSLCHCPGATIGCDVKTCHRTYHYYCA 92
PHD3_KMT2A cd15592
PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, ...
 1507-1556 1.07e-03

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: 1.07e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 148762969 1507 CPICHAPYVEEDL---LIQCRHCERWMHAGCESLftEDDVEQAADE-----GFDCVSC 1556
Cdd:cd15592     2 CPLCDKCYDDDDYeskMMQCGKCDRWVHSKCENL--SDEMYEILSNlpesvAYTCINC 57
PHD1_MOZ_d4 cd15526
PHD finger 1 found in monocytic leukemia zinc-finger protein (MOZ), its factor (MORF), and d4 ...
 228-273 1.07e-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: 40.03  E-value: 1.07e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 148762969  228 RCAVCEGPGELC-------DLFFCTSCGHHYHGACLD---TALTARKRAGWQCPEC 273
Cdd:cd15526     1 ICDFCLGTDEKNnktgepeELISCADCGSSGHPSCLKfspGLTDAVKSYRWQCIEC 56
PHD_JADE3 cd15681
PHD finger found in protein Jade-3 and similar proteins; Jade-3, also termed PHD finger ...
 1429-1475 1.33e-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: 1.33e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 148762969 1429 VCEVCGQ--ASDPSRLLLCDDCDISYHTYCLDppLLTVPKGGWKCKWCV 1475
Cdd:cd15681     1 ICDVCRSpdSEEGNDMVFCDKCNICVHQACYG--ILKVPEGSWLCRTCV 47
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 781-997 1.42e-03

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 45.46  E-value: 1.42e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  781 AVPEEPHLS----PQAEGPHLSPQPE-ELHLSPQTEEPHLSPVPEEpcLSPQPEESHLSPQSEEPCLSP-RPEESHLSPE 854
Cdd:PRK10263  334 AAPVEPVTQtppvASVDVPPAQPTVAwQPVPGPQTGEPVIAPAPEG--YPQQSQYAQPAVQYNEPLQQPvQPQQPYYAPA 411

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  855 LEKPPLSPRPEKPPEEPGQCPAPEELPLfpppgepslSPLLGEPALSEPGEPPLSPLPEELPLSPSGEPSLSPQLMPPDP 934
Cdd:PRK10263  412 AEQPAQQPYYAPAPEQPAQQPYYAPAPE---------QPVAGNAWQAEEQQSTFAPQSTYQTEQTYQQPAAQEPLYQQPQ 482

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 148762969  935 LPPPLSPI----ITAAAPPALSPLGELE----------YPFGAKGDSDPEsPLAAPILETPISPPPEANCTDP-EPVP 997
Cdd:PRK10263  483 PVEQQPVVepepVVEETKPARPPLYYFEeveekrarerEQLAAWYQPIPE-PVKEPEPIKSSLKAPSVAAVPPvEAAA 559
PTZ00441 PTZ00441
sporozoite surface protein 2 (SSP2); Provisional
 691-819 1.48e-03

sporozoite surface protein 2 (SSP2); Provisional


Pssm-ID: 240420 [Multi-domain]  Cd Length: 576  Bit Score: 44.95  E-value: 1.48e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  691 PPPEDSPTSPPPEDSpASPPPEDSLMslplEESPLLPLPEEPQLCPRSEGPHLSPRPEEPhlsPRPEEPHLSPQAEEPHL 770
Cdd:PTZ00441  331 PPPNEGKDGNPNEEN-LFPPGDDEVP----DESNVPPNPPNVPGGSNSEFSSDVENPPNP---PNPDIPEQEPNIPEDSN 402

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 148762969  771 SPQPEEpclcaVPEEPHLsPQAEGPHLSPQPEELHlspQTEEPHLSPVP 819
Cdd:PTZ00441  403 KEVPED-----VPMEPED-DRDNNFNEPKKPENKG---DGQNEPVIPKP 442
PHD_BAZ1B cd15628
PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also ...
 228-273 1.50e-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: 39.34  E-value: 1.50e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969  228 RCAVCEGPGELCDLFFCTSCGHHYHGACLDTALTARKRAGWQCPEC 273
Cdd:cd15628     1 KCKVCRKKGEDDKLILCDECNQAFHLFCLRPALYEVPDGEWMCPAC 46
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 5092-5136 1.67e-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: 39.61  E-value: 1.67e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 148762969 5092 CSLCQRTGATS----SCNRmrCPNVYHFACAIRAKCMFFKDKTMLCPMH 5136
Cdd:cd15489     2 CIVCGKGGDLGgellQCDG--CGKWFHADCLGPPLSSFVPNGKWICPVC 48
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 3978-4352 1.77e-03

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: 45.00  E-value: 1.77e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  3978 LNQSRTLLSPQQQQQQQVALGPGMPAKPLQHFSSPGALGPTLLLTGKEQNTVDPAVSSEATEGPSTHQGGPLAIGTTPES 4057
Cdd:pfam09606   83 INALQNLAGQGTRPQMMGPMGPGPGGPMGQQMGGPGTASNLLASLGRPQMPMGGAGFPSQMSRVGRMQPGGQAGGMMQPS 162

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  4058 MAtEPGEVKPSLSGdSQLLLVQPQPQPQPSSLQLQPPLRLPGQQQQQVSLLHTAGGGSHGQLGSGSSSEASSVPHLlAQP 4137
Cdd:pfam09606  163 SG-QPGSGTPNQMG-PNGGPGQGQAGGMNGGQQGPMGGQMPPQMGVPGMPGPADAGAQMGQQAQANGGMNPQQMGG-APN 239

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  4138 SVSLGDQPGSMT----QNLLGPQQPMLERPMQNNTGPQ--PPKPGPVLQSGQGLPGVGIMPTVGQLRAQLQGvlaKNPQL 4211
Cdd:pfam09606  240 QVAMQQQQPQQQgqqsQLGMGINQMQQMPQGVGGGAGQggPGQPMGPPGQQPGAMPNVMSIGDQNNYQQQQT---RQQQQ 316

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  4212 RhlspqqqqQLQALLMQRQLQQSQAVRQ------TPPYQEPGTQTSPLQGLLGCQPQLGGFP----GPQTGPLQELGA-- 4279
Cdd:pfam09606  317 Q--------QGGNHPAAHQQQMNQSVGQggqvvaLGGLNHLETWNPGNFGGLGANPMQRGQPgmmsSPSPVPGQQVRQvt 388

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  4280 ---GPRPQGPPRLPAPPGALSTGPVLGPVHPTPPP-----SSPQEPKRPSQLPSPSSQLPTEAQLPPTHPGTPKPQGPTL 4351
Cdd:pfam09606  389 pnqFMRQSPQPSVPSPQGPGSQPPQSHPGGMIPSPalipsPSPQMSQQPAQQRTIGQDSPGGSLNTPGQSAVNSPLNPQE 468


                   .
gi 148762969  4352 E 4352
Cdd:pfam09606  469 E 469
PHD1_PHF12 cd15533
PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is ...
 275-320 1.82e-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: 39.26  E-value: 1.82e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 148762969  275 VCQACRKPGNdskMLVCETCDKGYHTFCLKPPMEE--LPAHSWKCKAC 320
Cdd:cd15533     1 YCDSCGEGGD---LLCCDRCPASFHLQCCNPPLDEedLPPGEWLCHRC 45
PHD_TAF3 cd15522
PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed ...
 275-320 2.00e-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: 39.19  E-value: 2.00e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969  275 VCQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15522     1 ICPICKKPDDGSPMIGCDECDDWYHWECVGITDEPPEEDDWFCPKC 46
half-pint TIGR01645
poly-U binding splicing factor, half-pint family; The proteins represented by this model ...
 4272-4468 2.09e-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: 44.68  E-value: 2.09e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  4272 GPLQELGAGPRPQGPPRLPAPPgALSTGPVLGPVHPTPPPSSPQ-EPKRPSQLPSPS--SQLPTEAQLPPthpgtPKPQG 4348
Cdd:TIGR01645  325 GPRAQSPATPSSSLPTDIGNKA-VVSSAKKEAEEVPPLPQAAPAvVKPGPMEIPTPVppPGLAIPSLVAP-----PGLVA 398

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  4349 PTLEPPPGRVSPAAAQLADTLfSKGLGPWDPPDNLAETQKPEQSSlVPGHLDQVNGQVVPEASQLSIKQEPREEpcalGA 4428
Cdd:TIGR01645  399 PTEINPSFLASPRKKMKREKL-PVTFGALDDTLAWKEPSKEDQTS-EDGKMLAIMGEAAAALALEPKKKKKEKE----GE 472

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|
gi 148762969  4429 QSVKREANGEPIGAPGTSNHLLLAGprSEAGHLLLQKLLR 4468
Cdd:TIGR01645  473 ELQPKLVMNSEDASLASQEGMSIRG--NSARHLVMQKLMR 510
PHD3_KMT2D cd15597
PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 229-273 2.14e-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: 2.14e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 148762969  229 CAVCE--GPGELCDLFFCTSCGHHYHGACLDTALTARK-RAGWQCPEC 273
Cdd:cd15597     3 CVVCGsfGRGSEGHLLACSQCSQCYHPYCVNSKITKVMlLKGWRCVEC 50
PHD5_NSD cd15568
PHD finger 5 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
 5092-5136 2.22e-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: 2.22e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969 5092 CSLCQRTGATSSCNRMRCPNVYHFACAIRAKcmfFKDKTMLCPMH 5136
Cdd:cd15568     2 CFRCGDGGDLVLCDFKGCPKVYHLSCLGLEK---PPGGKWICPWH 43
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 4249-4347 2.30e-03

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 44.41  E-value: 2.30e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  4249 QTSPLQGLLGcQPQLGGfpgpqTGPLQELGagPRPQGPPRLPAPPGALSTGPVLGPVHPTPPPSSPQEPK----RPSQLP 4324
Cdd:TIGR01628  387 MGSPMGGAMG-QPPYYG-----QGPQQQFN--GQPLGWPRMSMMPTPMGPGGPLRPNGLAPMNAVRAPSRnaqnAAQKPP 458

                           90       100
                   ....*....|....*....|...
gi 148762969  4325 SPSSQLPTEAQLPPTHPGTPKPQ 4347
Cdd:TIGR01628  459 MQPVMYPPNYQSLPLSQDLPQPQ 481
PRK14950 PRK14950
DNA polymerase III subunits gamma and tau; Provisional
 4286-4367 2.33e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237864 [Multi-domain]  Cd Length: 585  Bit Score: 44.42  E-value: 2.33e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 4286 PPRLPAPPGALSTGPVLGPVHPTPPPS-------SPQEPKRPSQLPSPSSQLPTEAQLPPTHPGTPK--------PQGPT 4350
Cdd:PRK14950  364 PAPQPAKPTAAAPSPVRPTPAPSTRPKaaaaaniPPKEPVRETATPPPVPPRPVAPPVPHTPESAPKltraaipvDEKPK 443

                          90
                  ....*....|....*..
gi 148762969 4351 LEPPPGRVSPAAAQLAD 4367
Cdd:PRK14950  444 YTPPAPPKEEEKALIAD 460
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 2210-2522 2.47e-03

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: 44.37  E-value: 2.47e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  2210 PMLGASSRPGAGQPGEFHTTPPGTPRHQPSTPDPFLKPRCPSLDNLAVPESPGVGGGKASEPLLSPPPfgeSRKALEVKK 2289
Cdd:pfam03154  151 PQDNESDSDSSAQQQILQTQPPVLQAQSGAASPPSPPPPGTTQAATAGPTPSAPSVPPQGSPATSQPP---NQTQSTAAP 227

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  2290 EELGASSPSYGPPNLGFVDSPSSGthlgglelktpdvfkAPLTPRASQVEPQS-PGLGLRPQEPPPAQALAPSPPSHPDI 2368
Cdd:pfam03154  228 HTLIQQTPTLHPQRLPSPHPPLQP---------------MTQPPPPSQVSPQPlPQPSLHGQMPPMPHSLQTGPSHMQHP 292

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  2369 FRPGSYTDPyaqPPLTPRPQPPPPESCCALPPRSLPSDPFSRvPASPQSQSSSQSPLTPRPLSAEAFCPSPVTPRFQSPD 2448
Cdd:pfam03154  293 VPPQPFPLT---PQSSQSQVPPGPSPAAPGQSQQRIHTPPSQ-SQLQSQQPPREQPLPPAPLSMPHIKPPPTTPIPQLPN 368

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 148762969  2449 PYS-RPPSRPQSRDPFaplhKPPRPQPPEVAFKAGSLAHTSLGAGGFPAALPAGPAGElHAKVPSGQPPNFVRSP 2522
Cdd:pfam03154  369 PQShKHPPHLSGPSPF----QMNSNLPPPPALKPLSSLSTHHPPSAHPPPLQLMPQSQ-QLPPPPAQPPVLTQSQ 438
SET_Suv4-20-like cd10524
SET domain (including post-SET domain) found in Drosophila melanogaster suppressor of ...
 5468-5534 2.49e-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: 2.49e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 148762969 5468 GPARYINHSCAPNCVaevvtFDKEDKIIIISSRRIP--KGEELTYDYQFDFEDDQHkipCHCGAWNCRK 5534
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 2.51e-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: 2.51e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 148762969  229 CAVCEGPGElcdLFFCT-SCGHHYHGACLdtALTARKRAGWQCPECK 274
Cdd:cd15564     2 CQICEKPGK---LLTCEgPCCGHFHLDCL--GLSEQPDEPFKCDECT 43
PHD2_KMT2C_like cd15510
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 1380-1427 2.55e-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: 38.95  E-value: 2.55e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 148762969 1380 CVVCGSfgRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLkGWRCVEC 1427
Cdd:cd15510     2 CQACRQ--PGDDTKMLVCETCDKGYHTSCLRPVMSSIPKY-GWKCKNC 46
PHA01929 PHA01929
putative scaffolding protein
 4284-4386 2.74e-03

putative scaffolding protein


Pssm-ID: 177328  Cd Length: 306  Bit Score: 43.51  E-value: 2.74e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 4284 QGPPRLP-----APPGALSTgPVLGPVHPTPPPSSPQEPKRPSQLPSPSSQlpteAQLPPTHPGTPK--PQGPTlEPPPG 4356
Cdd:PHA01929    7 QLPPGLAglvanVPPAAAPT-PQPNPVIQPQAPVQPGQPGAPQQLAIPTQQ----PQPVPTSAMTPHvvQQAPA-QPAPA 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 148762969 4357 RVSPAAAQLADTLFSKGLGPWDPPDNLAET 4386
Cdd:PHA01929   81 APPAAGAALPEALEVPPPPAFTPNGEIVGT 110
RING-H2_RNF167 cd16797
RING finger, H2 subclass, found in RING finger protein 167 (RNF167) and similar proteins; ...
 229-274 2.75e-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: 38.87  E-value: 2.75e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969  229 CAVCEGPGELCDLFFCTSCGHHYHGACLDTALTARKRAgwqCPECK 274
Cdd:cd16797     3 CAICLDEYEEGDKLRVLPCSHAYHSKCVDPWLTQTKKT---CPVCK 45
PHD2_PHF12_Rco1 cd15534
PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, ...
 275-317 2.75e-03

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: 38.87  E-value: 2.75e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 148762969  275 VCQACRKPGNDSKMLVCETCDKGYHTFCLKPPMEELPAHS-WKC 317
Cdd:cd15534     1 VCFKCNRSCRVAPLIQCDYCPLLFHLDCLDPPLTHPPATGrWMC 44
PHD_BRPF cd15572
PHD finger found in bromodomain and PHD finger-containing (BRPF) proteins; The family of BRPF ...
 1429-1475 2.84e-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: 39.14  E-value: 2.84e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 148762969 1429 VCEVC--GQASDPSRLLLCDDCDISYHTYCLDPPLltVPKGGWKCKWCV 1475
Cdd:cd15572     3 VCCICldGECQNSNVILFCDMCNLAVHQECYGVPY--IPEGQWLCRRCL 49
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
 4282-4560 3.10e-03

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 44.30  E-value: 3.10e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 4282 RPQGP-----PRLPAPPGAlSTGPVlGPVHPTPPPSspqePKRPSQLPSPSSQLPTEAQ------LPPTHPGTP-KPQGP 4349
Cdd:PTZ00449  578 KPEFPkdpkhPKDPEEPKK-PKRPR-SAQRPTRPKS----PKLPELLDIPKSPKRPESPkspkrpPPPQRPSSPeRPEGP 651

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 4350 ----TLEPPPGRVSPAAAQLADTLFSkglgpwDPPDNLAETQKPEQSSLVPGHLDQVNGQVVPEASQLSIKQEPREEPCA 4425
Cdd:PTZ00449  652 kiikSPKPPKSPKPPFDPKFKEKFYD------DYLDAAAKSKETKTTVVLDESFESILKETLPETPGTPFTTPRPLPPKL 725

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 4426 LGAQSVKREANGEPiGAPGTSNHLLLAGPRSEAGHL-----------LLQKLLRAKNVQLSTGRGSEGLraeinghidsk 4494
Cdd:PTZ00449  726 PRDEEFPFEPIGDP-DAEQPDDIEFFTPPEEERTFFhetpadtplpdILAEEFKEEDIHAETGEPDEAM----------- 793

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 148762969 4495 lagleqKLQGTPSNKEDAA-ARKPLTPKPKRvqkASDRLVSSRKKLRKEDGVRASEALLKQLKQELS 4560
Cdd:PTZ00449  794 ------KRPDSPSEHEDKPpGDHPSLPKKRH---RLDGLALSTTDLESDAGRIAKDASGKIVKLKRS 851
ePHD_BRPF3 cd15703
Extended PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and ...
 5057-5121 3.22e-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: 3.22e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 148762969 5057 WVHLNCALWSTEVYETQGGALMNVE----VALHRGLLTkCSLCQRT--GATSSCNRMRCPNVYHFACAIRA 5121
Cdd:cd15703    19 WAHVVCAIWIPEVCFANTVFLEPVEgvnnIPPARWKLT-CYLCKQKgrGAAIQCHKVNCYTAFHVTCAQRA 88
PHD1_KMT2A_like cd15506
PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 1379-1427 3.74e-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: 38.49  E-value: 3.74e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 148762969 1379 MCVVCGSFGRGaegHLLACSQCSQCYHPYCVNSKITKVMLLKG-WRCVEC 1427
Cdd:cd15506     1 LCFLCGSAGLN---ELLYCSVCCEPYHTFCLEEAERPLNINKDnWCCRRC 47
PHD_PHF2_like cd15554
PHD finger found in PHF2, PHF8 and KDM7; This family includes PHF2, PHF8, KDM7, and similar ...
 1509-1556 4.06e-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: 4.06e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 148762969 1509 ICHAPYVEEDLLIQCRHCERWMHAGCeslfTEDDVEQAAD-EGFDCVSC 1556
Cdd:cd15554     3 ICRQPYDVTRFMIECDVCKDWFHGSC----VGVEEHQANDiERYHCPNC 47
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
 229-273 4.09e-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: 4.09e-03
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*
gi 148762969    229 CAVCEGpgELCDLFFCTSCGHHYHGACLDTALtarKRAGWQCPEC 273
Cdd:smart00184    1 CPICLE--EYLKDPVILPCGHTFCRSCIRKWL---ESGNNTCPIC 40
PHA03247 PHA03247
large tegument protein UL36; Provisional
 362-926 4.17e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 44.16  E-value: 4.17e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  362 AEQHTPVCSRFSP-------PEPGDTPTDEPDALYVACQGQPKGGHVTSMQPKEPGPLQCEAKPLGKAGVQLEPQLEAPl 434
Cdd:PHA03247 2596 ARPRAPVDDRGDPrgpappsPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAA- 2674

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  435 neempllpPPEESPLSPPPEESPTSPPPEASRLSPPPEELPASPLPEALhLSRPLEESPLSPPPEESPLSPPPESSPFSP 514
Cdd:PHA03247 2675 --------QASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAPHAL-VSATPLPPGPAAARQASPALPAAPAPPAVP 2745

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  515 LEESPLSPPEESPPSPALETPLSPPPEASPLSPPfeesplspppeeLPTSPPPEASRLSPPPEESPMSPPPEESPMSPPP 594
Cdd:PHA03247 2746 AGPATPGGPARPARPPTTAGPPAPAPPAAPAAGP------------PRRLTRPAVASLSESRESLPSPWDPADPPAAVLA 2813

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  595 EASRLFPPFEESPLSPPPEESPLSPPPEASRLSPPPEdspmsppPEESPMSPPPEVSRLSPlpvvsrlspppeesplspp 674
Cdd:PHA03247 2814 PAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSL-------PLGGSVAPGGDVRRRPP------------------- 2867

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  675 peesptspppeaSRLSPPPEDSPTSPPPEDSPASPPPEdslmslPLEESPLLPLPEEPQLCPRSEGPHLSPRPEEPHLSP 754
Cdd:PHA03247 2868 ------------SRSPAAKPAAPARPPVRRLARPAVSR------STESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQP 2929

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  755 RPEEPhlSPQAEEPHLSPQPEEPclcAVPEEPHLSPQAEGPHLSPQPEELhlsPQTEEPHLSPVPEEPCLSPQPEESHLS 834
Cdd:PHA03247 2930 QPPPP--PPPRPQPPLAPTTDPA---GAGEPSGAVPQPWLGALVPGRVAV---PRFRVPQPAPSREAPASSTPPLTGHSL 3001

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  835 PQseepcLSPRPEESHLSPELEKPPLSPRPE--KPPEEPGQCPAPEELPLFPPPGEPSLSPLLGEPAlSEPGEPPLSPLP 912
Cdd:PHA03247 3002 SR-----VSSWASSLALHEETDPPPVSLKQTlwPPDDTEDSDADSLFDSDSERSDLEALDPLPPEPH-DPFAHEPDPATP 3075

                         570
                  ....*....|....*...
gi 148762969  913 E----ELPLSPSGEPSLS 926
Cdd:PHA03247 3076 EagarESPSSQFGPPPLS 3093
PHA03264 PHA03264
envelope glycoprotein D; Provisional
 4238-4366 4.28e-03

envelope glycoprotein D; Provisional


Pssm-ID: 223029 [Multi-domain]  Cd Length: 416  Bit Score: 43.46  E-value: 4.28e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 4238 RQTPPYQEPGTQTSPLQGLLGCQPQLGGFPGPQtgplqelgagPRPQGPPRLPAPPGALSTGPVLGPVHPTPPPSSPQEP 4317
Cdd:PHA03264  252 GVVPPYFEESKGYEPPPAPSGGSPAPPGDDRPE----------AKPEPGPVEDGAPGRETGGEGEGPEPAGRDGAAGGEP 321

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 148762969 4318 KRPSQLPSPSS-------QLPTEAQLPPThPGTPKPqgPTLEPPPGRVSPAAAQLA 4366
Cdd:PHA03264  322 KPGPPRPAPDAdrpegwpSLEAITFPPPT-PATPAV--PRARPVIVGTGIAAAAIA 374
PTZ00441 PTZ00441
sporozoite surface protein 2 (SSP2); Provisional
 689-801 4.33e-03

sporozoite surface protein 2 (SSP2); Provisional


Pssm-ID: 240420 [Multi-domain]  Cd Length: 576  Bit Score: 43.41  E-value: 4.33e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  689 LSPPPEDSPTSPPPEDSPASPPPEDSLM-----SLPlEESPLLPLPEEP------QLCPRSEGPHLSPRPEEPHLSPRPE 757
Cdd:PTZ00441  320 LDVPDNPQDPVPPPNEGKDGNPNEENLFppgddEVP-DESNVPPNPPNVpggsnsEFSSDVENPPNPPNPDIPEQEPNIP 398

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 148762969  758 EPHLSPQAEEPHLSPQPEEPCLCAVPEEPHLSPQAEGPHLSPQP 801
Cdd:PTZ00441  399 EDSNKEVPEDVPMEPEDDRDNNFNEPKKPENKGDGQNEPVIPKP 442
PHD1_Lid2p_like cd15519
PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
 229-273 4.33e-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: 4.33e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 148762969  229 CAVC---EGPGELcdlFFCTSCGHHYHGACLDTALTARKRAGWQCPEC 273
Cdd:cd15519     2 CEVCgldDNEGEV---LLCDGCDAEYHTSCLDPPLGEIPPGTWFCPSC 46
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
 231-273 4.36e-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: 4.36e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969  231 VCEGPGELCD---LFFCTSCGHHYHGACLDTALTARKRAGWQCPEC 273
Cdd:cd15513     1 VCEGCGKASDesrLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 46
PHA03247 PHA03247
large tegument protein UL36; Provisional
 2094-2434 4.38e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 43.77  E-value: 4.38e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2094 ARKTDRPALHLRIPPQPGALGSPPPAAAPTIFIGSPTTPAGLSTSADGfLKPPAGSVPGPdspgelflklPPQVPAQVPS 2173
Cdd:PHA03247 2780 PRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGP-LPPPTSAQPTA----------PPPPPGPPPP 2848

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2174 QDPFG--LAPAYPLEPRfptapPTYPPYPSPTGAPAQPPMlGASSRPGAGQPGEFHTTPPGTPRHQPsTPDPFLKPRCPs 2251
Cdd:PHA03247 2849 SLPLGgsVAPGGDVRRR-----PPSRSPAAKPAAPARPPV-RRLARPAVSRSTESFALPPDQPERPP-QPQAPPPPQPQ- 2920

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2252 ldnlAVPESPGVGGGKASEPLLSPPPFGESRKALEVKKEELGASSPSYGPPNLGFVDSPSSGTHLGGLELKTPDVFKAPL 2331
Cdd:PHA03247 2921 ----PQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRVPQPAPSREAPASSTPPL 2996

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2332 TPRA-SQVEPQSPGLGLRPQEPPPAQALAPSppshpdIFRPGSYTDPYAQPPLTPRPQPPPPESCCALPPRslPSDPFSR 2410
Cdd:PHA03247 2997 TGHSlSRVSSWASSLALHEETDPPPVSLKQT------LWPPDDTEDSDADSLFDSDSERSDLEALDPLPPE--PHDPFAH 3068

                         330       340
                  ....*....|....*....|....*...
gi 148762969 2411 VPASPQSQ----SSSQSPLTPRPLSAEA 2434
Cdd:PHA03247 3069 EPDPATPEagarESPSSQFGPPPLSANA 3096
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
 229-273 4.49e-03

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: 38.20  E-value: 4.49e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969  229 CAVCEGPGELcdlFFCTSCGHHYHGACLDTALTARKRAGWQCPEC 273
Cdd:cd15539     2 CAVCGDGGEL---LCCDGCPRAFHLACLVPPLTLIPSGTWRCSSC 43
PHD4_KMT2C cd15596
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 224-273 4.53e-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: 4.53e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 148762969  224 LEEARCAVCE--GPGELCDLFFCTSCGHHYHGACLDTALT-ARKRAGWQCPEC 273
Cdd:cd15596     4 LNQDMCVVCGsfGQGAEGRLLACSQCGQCYHPYCVSIKITkVVLSKGWRCLEC 56
PHD_UHRF1_2 cd15525
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and ...
 1380-1427 4.56e-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: 4.56e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 148762969 1380 CVVCGsfGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVEC 1427
Cdd:cd15525     2 CHVCG--GKQDPEKQLLCDECDMAYHLYCLDPPLTSLPDDDEWYCPDC 47
PHD_PHF21B cd15524
PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) ...
 276-320 4.64e-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: 37.95  E-value: 4.64e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969  276 CQACRKPGNdskMLVCETCDKGYHTFCLKPPMEELPAHSWKCKAC 320
Cdd:cd15524     2 CAACKRGGN---LQPCGTCPRAYHLDCLDPPLKTAPKGVWVCPKC 43
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 4143-4383 4.68e-03

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: 43.60  E-value: 4.68e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  4143 DQPGSMTQNLLGPQQPMLERPMQNNTGPQPPKPGPVLQSGQGLPgvgimPTVGQLRAQLQGVLAKNPQ--LRHLSPQQQQ 4220
Cdd:pfam03154  157 DSDSSAQQQILQTQPPVLQAQSGAASPPSPPPPGTTQAATAGPT-----PSAPSVPPQGSPATSQPPNqtQSTAAPHTLI 231

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  4221 QLQALLMQRQLQQSQAVRQTPPYQEPGTQTSPlQGLLgcQPQLGGFPGPQTGPLQELGAG-PRPQGPPRLPAPPGALSTG 4299
Cdd:pfam03154  232 QQTPTLHPQRLPSPHPPLQPMTQPPPPSQVSP-QPLP--QPSLHGQMPPMPHSLQTGPSHmQHPVPPQPFPLTPQSSQSQ 308

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  4300 PVLGPVHPTPPPSSPQEPKRPSQLPSPSSQLPTEAQLPPTHPGTPKPQGPTLEPPPGRVSPAAAQLADTLfsKGLGPWDP 4379
Cdd:pfam03154  309 VPPGPSPAAPGQSQQRIHTPPSQSQLQSQQPPREQPLPPAPLSMPHIKPPPTTPIPQLPNPQSHKHPPHL--SGPSPFQM 386


                   ....
gi 148762969  4380 PDNL 4383
Cdd:pfam03154  387 NSNL 390
ePHD_JADE cd15671
Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins; The extended ...
 133-217 4.68e-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: 40.12  E-value: 4.68e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  133 GGSCWAHHWCAAWSAGVWGQEgPE----LCGVDKAIFSGISQRCSHC-TRLGASIPCRSPGCPRLYHFPCATASGsfLSM 207
Cdd:cd15671    16 SGTKWVHVSCALWIPEVSIGC-PEkmepITKISHIPMSRWALVCVLCkEKTGACIQCSVKSCKTAFHVTCAFQHG--LEM 92

                          90       100
                  ....*....|....*....|
gi 148762969  208 KT--------LQLL--CPEH 217
Cdd:cd15671    93 KTilededdeVKFKsyCPKH 112
PHD_BAZ1A_like cd15544
PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, ...
 228-273 4.77e-03

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: 38.16  E-value: 4.77e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 148762969  228 RCAVCEGPGELCDLFFCTSCGHHYHGACLDTALTARKRAGWQCPEC 273
Cdd:cd15544     1 RCKVCRKKGDPDNMILCDGCDKAFHLYCLRPALREVPSGDWFCPAC 46
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 808-1213 4.80e-03

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: 43.60  E-value: 4.80e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969   808 PQTEEPHLSPVPEEPCLSPQPEESHLSPQSEEPCLSPRPeeshlSPELEKPPLSPRPEKPPEEPGQCpapeelplfpppg 887
Cdd:pfam03154  172 PVLQAQSGAASPPSPPPPGTTQAATAGPTPSAPSVPPQG-----SPATSQPPNQTQSTAAPHTLIQQ------------- 233

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969   888 epslSPLLGEPALSEPGEP----PLSPLPEELPLSPSGEPSLSPQLMPPDPLPPPLSPIITAAAPPalSPLGELEYPFGA 963
Cdd:pfam03154  234 ----TPTLHPQRLPSPHPPlqpmTQPPPPSQVSPQPLPQPSLHGQMPPMPHSLQTGPSHMQHPVPP--QPFPLTPQSSQS 307

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969   964 KGDSDPESPLAAPILETPISPPPEANCTDPEPVPPMILPPspgspvgpaSPILMEPL-PPQCSPLLQHSLVPQNSPPSQC 1042
Cdd:pfam03154  308 QVPPGPSPAAPGQSQQRIHTPPSQSQLQSQQPPREQPLPP---------APLSMPHIkPPPTTPIPQLPNPQSHKHPPHL 378

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  1043 SPPAlPLSVPSPLSPIGKVVGVSDEAELH---------EMETEKVSEPECPALEPSAT---------SPLPSPMGDLSCP 1104
Cdd:pfam03154  379 SGPS-PFQMNSNLPPPPALKPLSSLSTHHppsahppplQLMPQSQQLPPPPAQPPVLTqsqslpppaASHPPTSGLHQVP 457

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  1105 APSPAPALDDFSGLGEDTAPLDGIDAPGSQPEPGQTPGSLASELKGSPVLLDPEelAPVTPMEVYPEckqtagqgsPCEE 1184
Cdd:pfam03154  458 SQSPFPQHPFVPGGPPPITPPSGPPTSTSSAMPGIQPPSSASVSSSGPVPAAVS--CPLPPVQIKEE---------ALDE 526

                          410       420
                   ....*....|....*....|....*....
gi 148762969  1185 QEEPRAPVAPTPPTLIKSDIVNEISNLSQ 1213
Cdd:pfam03154  527 AEEPESPPPPPRSPSPEPTVVNTPSHASQ 555
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 1380-1427 5.03e-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: 5.03e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 148762969 1380 CVVCGSFGRGAEghLLACSQCSQCYHPYCVNSKITKVMLL-KGWRCVEC 1427
Cdd:cd15509     2 CAVCDSPGDLSD--LLFCTSCGQHYHGSCLDPAVRPTPLVrAGWQCPEC 48
PHD1_MOZ_d4 cd15526
PHD finger 1 found in monocytic leukemia zinc-finger protein (MOZ), its factor (MORF), and d4 ...
 1394-1427 5.36e-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: 5.36e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 148762969 1394 LLACSQCSQCYHPYCVN--SKITKVMLLKGWRCVEC 1427
Cdd:cd15526    21 LISCADCGSSGHPSCLKfsPGLTDAVKSYRWQCIEC 56
PHA03132 PHA03132
thymidine kinase; Provisional
 4266-4363 5.39e-03

thymidine kinase; Provisional


Pssm-ID: 222997 [Multi-domain]  Cd Length: 580  Bit Score: 43.21  E-value: 5.39e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 4266 FPGPQTGPLQELGAGPRPQgPPRLPAPPGALSTGPVLGPVHPTPPPS------------SPQEPKRPSQLPSPSSQLPTE 4333
Cdd:PHA03132   55 YPPRETGSGGGVATSTIYT-VPRPPRGPEQTLDKPDSLPASRELPPGptpvppggfrgaSSPRLGADSTSPRFLYQVNFP 133

                          90       100       110
                  ....*....|....*....|....*....|.
gi 148762969 4334 AQLPP-THPGTPKPQgPTLEPPPGRVSPAAA 4363
Cdd:PHA03132  134 VILAPiGESNSSSEE-LSEEEEHSRPPPSES 163
PHA03378 PHA03378
EBNA-3B; Provisional
 4267-4363 5.87e-03

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 43.13  E-value: 5.87e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 4267 PGPQTGPLQELGAGPRPQGPPRLPAPPGALSTG---PVLGPVHPTPPPSSPQEPKRPSQLPSPssqlpteAQLPPTHPGT 4343
Cdd:PHA03378  701 PTPMRPPAAPPGRAQRPAAATGRARPPAAAPGRarpPAAAPGRARPPAAAPGRARPPAAAPGR-------ARPPAAAPGA 773

                          90       100
                  ....*....|....*....|
gi 148762969 4344 PKPQGPTLEPPPGRVSPAAA 4363
Cdd:PHA03378  774 PTPQPPPQAPPAPQQRPRGA 793
PHD1_PHF10 cd15528
PHD finger 1 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
 228-273 6.02e-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: 38.16  E-value: 6.02e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 148762969  228 RCAVCE-----GPGELCDLFFCTSCGHHYHGACLDtaLTAR-----KRAGWQCPEC 273
Cdd:cd15528     1 VCGICEkggksNKGEPEELIHCSQCGNSGHPSCLE--MSDEmvaviKTYPWQCMEC 54
PHD_UHRF2 cd15617
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); ...
 1380-1427 6.10e-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: 37.63  E-value: 6.10e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 148762969 1380 CVVCGsfGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVEC 1427
Cdd:cd15617     2 CYVCG--GKQDAHMQLLCDECNMAYHIYCLNPPLDKIPEDEDWYCPSC 47
PHD_TIF1gamma cd15624
PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also ...
 1430-1474 6.22e-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: 6.22e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969 1430 CEVCGQASDpsrLLLCDDCDISYHTYCLDPPLLTVPKGGWKCKWC 1474
Cdd:cd15624     2 CAVCQNGGD---LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 43
PHD_TAF3 cd15522
PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed ...
 1507-1556 6.33e-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: 37.65  E-value: 6.33e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 148762969 1507 CPICHAPYvEEDLLIQCRHCERWMHAGCESLftedDVEQAADEGFDCVSC 1556
Cdd:cd15522     2 CPICKKPD-DGSPMIGCDECDDWYHWECVGI----TDEPPEEDDWFCPKC 46
ePHD_PHF14 cd15674
Extended PHD finger found in PHD finger protein 14 (PHF14) and similar proteins; The extended ...
 5057-5120 6.81e-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: 6.81e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 148762969 5057 WVHLNCALWstevyeTQGGALMNVE----VALHRGLLTK-----CSLCQ-----RTGATSSCNRMRCPNVYHFACAIR 5120
Cdd:cd15674    19 WVHLVCALY------TPGVAFGDVDklspVTLTEMNYSKwgareCSLCEdprfaRTGVCISCDAGMCKSYFHVTCAQR 90
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 680-923 6.97e-03

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 43.24  E-value: 6.97e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  680 TSPPPEASRLSPPPEDSPTSPPPEDSPASPPPEDSLMSLPLEESPLLPLPEEPQLCPRSEGPHLSPRPEEPHLSPRPEEP 759
Cdd:PHA03307  195 PSTPPAAASPRPPRRSSPISASASSPAPAPGRSAADDAGASSSDSSSSESSGCGWGPENECPLPRPAPITLPTRIWEASG 274

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  760 HLSPQAEEPHLSPQPEEPCLCAVPEEPHlspQAEGPHLSPQPEELHLSPQTE----EPHLSPVPEEPCLSPQPEESHLSP 835
Cdd:PHA03307  275 WNGPSSRPGPASSSSSPRERSPSPSPSS---PGSGPAPSSPRASSSSSSSREssssSTSSSSESSRGAAVSPGPSPSRSP 351

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969  836 QSEEPCLSPRPEESHLSPELEKPPLSPRPEKPPEEPGQCPAPEELPLFPPPGEPSLSPLLGEPALSEPGEPPLSPLPEEL 915
Cdd:PHA03307  352 SPSRPPPPADPSSPRKRPRPSRAPSSPAASAGRPTRRRARAAVAGRARRRDATGRFPAGRPRPSPLDAGAASGAFYARYP 431


                  ....*...
gi 148762969  916 PLSPSGEP 923
Cdd:PHA03307  432 LLTPSGEP 439
PHD2_3_BPTF cd15560
PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF); ...
 1509-1556 7.37e-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: 37.71  E-value: 7.37e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 148762969 1509 ICHAPYVEEDLLIQCRHCERWMHAGCESLfTEDDVEQAADegFDCVSC 1556
Cdd:cd15560     3 ICRTPYDESQFYIGCDRCQDWFHGRCVGI-LQSEAEKIDE--YVCPQC 47
PHD_TIF1gamma cd15624
PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also ...
 273-321 8.11e-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: 37.33  E-value: 8.11e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 148762969  273 CKVCQacrkpgNDSKMLVCETCDKGYHTFCLKPPMEELPAHSWKCKACR 321
Cdd:cd15624     2 CAVCQ------NGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCR 44
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 2321-2478 8.41e-03

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 42.76  E-value: 8.41e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 2321 LKTPDVFKAPLTPRASQVEPQS-PGlglrPQEPPPAqaLAPSPPSHPDIfrpGSYTDPYAQPPLTPRPQPPPPESCCALP 2399
Cdd:PRK10263  341 TQTPPVASVDVPPAQPTVAWQPvPG----PQTGEPV--IAPAPEGYPQQ---SQYAQPAVQYNEPLQQPVQPQQPYYAPA 411

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 148762969 2400 PRSLPSDPFSRVPASPQSQSSSQSPLTPRPLSAEAFCPSPVTPRFQsPDPYSRPPSRPQSRDPFAPLHKPPRPQPPEVA 2478
Cdd:PRK10263  412 AEQPAQQPYYAPAPEQPAQQPYYAPAPEQPVAGNAWQAEEQQSTFA-PQSTYQTEQTYQQPAAQEPLYQQPQPVEQQPV 489
PHD2_KMT2A_like cd15507
PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 1380-1427 8.81e-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: 8.81e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 148762969 1380 CVVCGSFGRGAEgHLLACSQCSQCYHPYCVN----SKITKVMllKGWRCVEC 1427
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 ...
 2021-2069 8.88e-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: 8.88e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 148762969 2021 VLYANINFPNLKQDYPDWSSrcKQIMK----LWRKVPAADKAPYLQKAKDNRA 2069
Cdd:cd21994     7 MLWLNENREKIKKENPGISV--TEISKkageIWKELDEEDKEKWEQKAEKAKE 57
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 229-273 9.06e-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: 37.20  E-value: 9.06e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 148762969  229 CAVCEGPGELcdlFFCTSCGHHYHGACLDTALTARKRAGWQCPEC 273
Cdd:cd15531     2 CEVCQQGGEI---ILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 43
RING-HC_ScPSH1-like cd16568
RING finger, HC subclass, found in Saccharomyces cerevisiae POB3/SPT16 histone-associated ...
 223-275 9.20e-03

RING finger, HC subclass, found in Saccharomyces cerevisiae POB3/SPT16 histone-associated protein 1 (ScPSH1) and similar proteins; ScPSH1 is a Cse4-specific E3 ubiquitin ligase that interacts with the kinetochore protein Pat1 and targets the degradation of budding yeast centromeric histone H3 variant, CENP-ACse4, which is essential for faithful chromosome segregation. ScPSH1 contains a C3HC4-type RING-HC finger and a DNA directed RNA polymerase domain.


Pssm-ID: 438230 [Multi-domain]  Cd Length: 54  Bit Score: 37.35  E-value: 9.20e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 148762969  223 YLEEARCAVCEgpgELCDLFFCTSCGHHYHGACLDTALTARKraGWQCPECKV 275
Cdd:cd16568     1 ILETQECIICH---EYLYEPMVTTCGHTYCYTCLNTWFKSNR--SLSCPDCRT 48
PostSET smart00508
Cysteine-rich motif following a subset of SET domains;
5521-5537 9.76e-03

Cysteine-rich motif following a subset of SET domains;


Pssm-ID: 214703  Cd Length: 17  Bit Score: 36.61  E-value: 9.76e-03
                            10
                    ....*....|....*..
gi 148762969   5521 HKIPCHCGAWNCRKWMN 5537
Cdd:smart00508    1 KKQPCLCGAPNCRGFLG 17
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
4279-4444 9.87e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 42.56  E-value: 9.87e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 4279 AGPRPQGPPRLPAPPGALSTGPVLGPVHPTPPP--------SSPQEPKRPSQLPSPSSQLPTEAQLPPTHPgtPKPQGPT 4350
Cdd:PRK12323  398 APAAPPAAPAAAPAAAAAARAVAAAPARRSPAPealaaarqASARGPGGAPAPAPAPAAAPAAAARPAAAG--PRPVAAA 475

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148762969 4351 LEPPPGRVSPAAAQLADtlfSKGLGPW-DPPDNLAEtqkPEQSSLVPGHLDQVNGQVVPEASQLSIKQEPREEPCALGAQ 4429
Cdd:PRK12323  476 AAAAPARAAPAAAPAPA---DDDPPPWeELPPEFAS---PAPAQPDAAPAGWVAESIPDPATADPDDAFETLAPAPAAAP 549

                         170
                  ....*....|....*
gi 148762969 4430 SVKREANGEPIGAPG 4444
Cdd:PRK12323  550 APRAAAATEPVVAPR 564
 
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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