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Conserved domains on  [gi|767904604|ref|XP_011539870|]
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E3 ubiquitin-protein ligase TRIM33 isoform X2 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
981-1106 5.43e-59

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


:

Pssm-ID: 99934 [Multi-domain]  Cd Length: 109  Bit Score: 197.51  E-value: 5.43e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604  981 LSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCER 1060
Cdd:cd05502     1 LSPIDQRKCERLLLELYCHELSLPFHEPVSPSVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYK 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 767904604 1061 FNEMmkvvqvyadtqeinlkaDSEVAQAGKAVALYFEDKLTEIYSD 1106
Cdd:cd05502    81 FNEE-----------------DSEVAQAGKELELFFEEQLKEILPD 109
BBC smart00502
B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
319-445 5.70e-39

B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains


:

Pssm-ID: 128778  Cd Length: 127  Bit Score: 141.25  E-value: 5.70e-39
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604    319 QKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQ 398
Cdd:smart00502    1 QREALEELLTKLRKKAAELEDALKQLISIIQEVEENAADVEAQIKAAFDELRNALNKRKKQLLEDLEEQKENKLKVLEQQ 80
                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*..
gi 767904604    399 QNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKA 445
Cdd:smart00502   81 LESLTQKQEKLSHAINFTEEALNSGDPTELLLSKKLIIERLQNLLKQ 127
RING-HC_TIF1gamma cd16766
RING finger, HC subclass, found in transcriptional inknown asiary factor 1 gamma (TIF1gamma); ...
121-188 1.58e-37

RING finger, HC subclass, found in transcriptional inknown asiary factor 1 gamma (TIF1gamma); TIF1gamma, also known as tripartite motif-containing 33 (TRIM33), ectodermin, RFG7, or PTC7, belongs to the C-VI subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. It is an E3-ubiquitin ligase that functions as a regulator of transforming growth factor beta (TGFbeta) signaling, inhibiting 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 actor of tumorigenesis. Like other TIF1 proteins, 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.


:

Pssm-ID: 438422  Cd Length: 67  Bit Score: 134.99  E-value: 1.58e-37
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767904604  121 LLDTCAVCQQSLQSRReAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQEC 188
Cdd:cd16766     1 LLDTCAVCKQSLQSRD-AEPKLLPCLHSFCRRCLPEPERQLSVPVPGGSNGDIQQVGVIRCPVCRQEC 67
Bbox2_TIF1g_C-VI cd19830
B-box-type 2 zinc finger found in transcription intermediary factor 1 gamma (TIF1-gamma); ...
268-320 1.02e-32

B-box-type 2 zinc finger found in transcription intermediary factor 1 gamma (TIF1-gamma); TIF1-gamma, also known as tripartite motif-containing 33 (TRIM33), ectodermin, RFG7, or PTC7, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TIF1-gamma 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 actor of tumorigenesis. Like other TIF1 family members, TIF1-gamma 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.


:

Pssm-ID: 380888  Cd Length: 53  Bit Score: 120.55  E-value: 1.02e-32
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 767904604  268 ASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQK 320
Cdd:cd19830     1 ASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQK 53
Bbox1_TIF1g_C-VI cd19847
B-box-type 1 zinc finger found in transcriptional intermediary factor 1 gamma (TIF1-gamma); ...
210-263 5.58e-29

B-box-type 1 zinc finger found in transcriptional intermediary factor 1 gamma (TIF1-gamma); TIF1-gamma, also known as tripartite motif-containing 33 (TRIM33), ectodermin, RFG7, or PTC7, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. TIF1-gamma 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, TIF1-gamma is an important regulator of transcription during hematopoiesis, as well as a key actor of tumorigenesis. Like other TIF1 family members, TIF1-gamma 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.


:

Pssm-ID: 380905  Cd Length: 54  Bit Score: 109.85  E-value: 5.58e-29
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 767904604  210 DEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVS 263
Cdd:cd19847     1 DEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHMIRKKEDVS 54
PHD_TIF1gamma cd15624
PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also ...
912-957 3.29e-27

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: 104.74  E-value: 3.29e-27
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 767904604  912 WCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDI 957
Cdd:cd15624     1 WCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDI 46
Herpes_BLLF1 super family cl37540
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
603-763 5.65e-06

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


The actual alignment was detected with superfamily member pfam05109:

Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 50.69  E-value: 5.65e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604   603 PRHSGPQYS---MMQPHLQRQHSNPGHAGPFPVVSVhnTTINPTSPTTATMANANrGPTSPSVTAIELIPSVTNPE---N 676
Cdd:pfam05109  494 PRDNGTESKapdMTSPTSAVTTPTPNATSPTPAVTT--PTPNATSPTLGKTSPTS-AVTTPTPNATSPTPAVTTPTpnaT 570
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604   677 LPSLPDIPPIQANVVPMMHSWY----EFGAREKTQDQNLEDAGSSSL-----DNLLSRYISGSH-LPPQPTSTMN--PSP 744
Cdd:pfam05109  571 IPTLGKTSPTSAVTTPTPNATSptvgETSPQANTTNHTLGGTSSTPVvtsppKNATSAVTTGQHnITSSSTSSMSlrPSS 650
                          170
                   ....*....|....*....
gi 767904604   745 GPSALSPGSSGLSNSHTPV 763
Cdd:pfam05109  651 ISETLSPSTSDNSTSHMPL 669
 
Name Accession Description Interval E-value
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
981-1106 5.43e-59

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99934 [Multi-domain]  Cd Length: 109  Bit Score: 197.51  E-value: 5.43e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604  981 LSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCER 1060
Cdd:cd05502     1 LSPIDQRKCERLLLELYCHELSLPFHEPVSPSVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYK 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 767904604 1061 FNEMmkvvqvyadtqeinlkaDSEVAQAGKAVALYFEDKLTEIYSD 1106
Cdd:cd05502    81 FNEE-----------------DSEVAQAGKELELFFEEQLKEILPD 109
BBC smart00502
B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
319-445 5.70e-39

B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains


Pssm-ID: 128778  Cd Length: 127  Bit Score: 141.25  E-value: 5.70e-39
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604    319 QKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQ 398
Cdd:smart00502    1 QREALEELLTKLRKKAAELEDALKQLISIIQEVEENAADVEAQIKAAFDELRNALNKRKKQLLEDLEEQKENKLKVLEQQ 80
                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*..
gi 767904604    399 QNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKA 445
Cdd:smart00502   81 LESLTQKQEKLSHAINFTEEALNSGDPTELLLSKKLIIERLQNLLKQ 127
RING-HC_TIF1gamma cd16766
RING finger, HC subclass, found in transcriptional inknown asiary factor 1 gamma (TIF1gamma); ...
121-188 1.58e-37

RING finger, HC subclass, found in transcriptional inknown asiary factor 1 gamma (TIF1gamma); TIF1gamma, also known as tripartite motif-containing 33 (TRIM33), ectodermin, RFG7, or PTC7, belongs to the C-VI subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. It is an E3-ubiquitin ligase that functions as a regulator of transforming growth factor beta (TGFbeta) signaling, inhibiting 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 actor of tumorigenesis. Like other TIF1 proteins, 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.


Pssm-ID: 438422  Cd Length: 67  Bit Score: 134.99  E-value: 1.58e-37
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767904604  121 LLDTCAVCQQSLQSRReAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQEC 188
Cdd:cd16766     1 LLDTCAVCKQSLQSRD-AEPKLLPCLHSFCRRCLPEPERQLSVPVPGGSNGDIQQVGVIRCPVCRQEC 67
Bbox2_TIF1g_C-VI cd19830
B-box-type 2 zinc finger found in transcription intermediary factor 1 gamma (TIF1-gamma); ...
268-320 1.02e-32

B-box-type 2 zinc finger found in transcription intermediary factor 1 gamma (TIF1-gamma); TIF1-gamma, also known as tripartite motif-containing 33 (TRIM33), ectodermin, RFG7, or PTC7, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TIF1-gamma 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 actor of tumorigenesis. Like other TIF1 family members, TIF1-gamma 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.


Pssm-ID: 380888  Cd Length: 53  Bit Score: 120.55  E-value: 1.02e-32
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 767904604  268 ASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQK 320
Cdd:cd19830     1 ASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQK 53
Bbox1_TIF1g_C-VI cd19847
B-box-type 1 zinc finger found in transcriptional intermediary factor 1 gamma (TIF1-gamma); ...
210-263 5.58e-29

B-box-type 1 zinc finger found in transcriptional intermediary factor 1 gamma (TIF1-gamma); TIF1-gamma, also known as tripartite motif-containing 33 (TRIM33), ectodermin, RFG7, or PTC7, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. TIF1-gamma 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, TIF1-gamma is an important regulator of transcription during hematopoiesis, as well as a key actor of tumorigenesis. Like other TIF1 family members, TIF1-gamma 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.


Pssm-ID: 380905  Cd Length: 54  Bit Score: 109.85  E-value: 5.58e-29
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 767904604  210 DEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVS 263
Cdd:cd19847     1 DEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHMIRKKEDVS 54
BROMO smart00297
bromo domain;
982-1103 5.95e-29

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 111.60  E-value: 5.95e-29
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604    982 SPVDQRKCERLLLYLYC----HELSIEFQEPVPAS-IPNYYKIIKKPMDLSTVKKKLQKkhsQHYQIPDDFVADVRLIFK 1056
Cdd:smart00297    1 DPKLQKKLQELLKAVLDkldsHPLSWPFLKPVSRKeAPDYYDIIKKPMDLKTIKKKLEN---GKYSSVEEFVADFNLMFS 77
                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*..
gi 767904604   1057 NCERFNEmmkvvqvyadtqeinlkADSEVAQAGKAVALYFEDKLTEI 1103
Cdd:smart00297   78 NARTYNG-----------------PDSEVYKDAKKLEKFFEKKLREL 107
PHD_TIF1gamma cd15624
PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also ...
912-957 3.29e-27

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: 104.74  E-value: 3.29e-27
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 767904604  912 WCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDI 957
Cdd:cd15624     1 WCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDI 46
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
989-1074 5.17e-23

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 93.92  E-value: 5.17e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604   989 CERLLLYLYCHELSIEFQEPV-PASIPNYYKIIKKPMDLSTVKKKLqkkHSQHYQIPDDFVADVRLIFKNCERFNEMMKV 1067
Cdd:pfam00439    1 CLEILDKLMEHPIAAPFLEPVdPDEYPDYYSVIKKPMDLSTIKKKL---ENGEYKSLAEFLADVKLIFSNARTYNGPGSV 77

                   ....*..
gi 767904604  1068 VQVYADT 1074
Cdd:pfam00439   78 IYKAAEK 84
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
967-1128 1.28e-12

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 70.99  E-value: 1.28e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604  967 DNLQHSKKGKTAQGLSPVDQRK-----CERLLLYLYC----HELSIEFQE------------PVPASIPNYYKIIKKPMD 1025
Cdd:COG5076   111 SVTPESGLGSLLMAHLKTSVKKrktpkIEDELLYADNkaiaKFKKQLFLRdgrflssiflglPSKREYPDYYEIIKSPMD 190
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604 1026 LSTVKKKLQkkhSQHYQIPDDFVADVRLIFKNCERFNEmmKVVQVYADTQEINlKADSEVAQagkavalyfedKLTEIYS 1105
Cdd:COG5076   191 LLTIQKKLK---NGRYKSFEEFVSDLNLMFDNCKLYNG--PDSSVYVDAKELE-KYFLKLIE-----------EIPEEML 253
                         170       180
                  ....*....|....*....|...
gi 767904604 1106 DRTFAPLPEFEQEEDDGEVTEDS 1128
Cdd:COG5076   254 ELSIKPGREEREERESVLITNSQ 276
BBOX smart00336
B-Box-type zinc finger;
271-312 1.31e-11

B-Box-type zinc finger;


Pssm-ID: 197662 [Multi-domain]  Cd Length: 42  Bit Score: 60.04  E-value: 1.31e-11
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|..
gi 767904604    271 QRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFL 312
Cdd:smart00336    1 QRAPKCDSHGDEPAEFFCEECGALLCRTCDEAEHRGHTVVLL 42
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
912-955 1.34e-10

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


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 57.50  E-value: 1.34e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 767904604   912 WCAVCQ---NGGDLLCCEKCPKVFHLTCHVPTLLS--FPSGDWICTFCR 955
Cdd:pfam00628    1 YCAVCGksdDGGELVQCDGCDDWFHLACLGPPLDPaeIPSGEWLCPECK 49
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
912-954 4.67e-10

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


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 56.07  E-value: 4.67e-10
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 767904604    912 WCAVCQ---NGGDLLCCEKCPKVFHLTCHVPTLLSF-PSGDWICTFC 954
Cdd:smart00249    1 YCSVCGkpdDGGELLQCDGCDRWYHQTCLGPPLLEEePDGKWYCPKC 47
zf-B_box pfam00643
B-box zinc finger;
271-312 8.53e-09

B-box zinc finger;


Pssm-ID: 459886 [Multi-domain]  Cd Length: 42  Bit Score: 52.09  E-value: 8.53e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 767904604   271 QRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFL 312
Cdd:pfam00643    1 SKERLCPEHEEEPLTLYCNDCQELLCEECSVGEHRGHTVVPL 42
CC_brat-like cd20482
coiled-coil (CC) domain of Drosophila brain tumor (brat) and similar proteins; This family ...
319-440 4.89e-06

coiled-coil (CC) domain of Drosophila brain tumor (brat) and similar proteins; This family contains the coiled-coil (CC) region of Drosophila brain tumor (Brat), a translational repressor that belongs to the tripartite motif (TRIM) protein superfamily. TRIM proteins play important roles in various cellular processes and are involved in many diseases which consists of two B-box domains and a coiled-coil (CC) domain at the N-terminal region, and an NHL domain at the C-terminus. Brat localizes at the basal cortex during asymmetric division of Drosophila neuroblasts by directly interacting with the scaffolding protein Miranda (Mira), which it does through the CC-NHL domain tandem, indicating that the function of the Brat CC domain is to assemble Brat-NHL in dimeric form which is necessary for Mira binding. Brat CC forms an elongated antiparallel dimer similar to its other TRIM protein counterparts, but the overall length of Brat CC dimer is shorter than the TRIMs.


Pssm-ID: 467844 [Multi-domain]  Cd Length: 122  Bit Score: 46.76  E-value: 4.89e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604  319 QKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKL-LQ 397
Cdd:cd20482     1 HKESLQQLLEEARAKIPELRDALKNVEHALSRLQMQYHKAQNEINETFQFYRSMLEERKDELLKELESIYNAKQLSLnEQ 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 767904604  398 QQNDITGLSRqVKHVMNFTNWAIASGSSTALLYSKRLITFQLR 440
Cdd:cd20482    81 QQKLQETIEK-IQQGCEFTERLLKHGSETEVLLFKKLLEARLQ 122
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
603-763 5.65e-06

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 50.69  E-value: 5.65e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604   603 PRHSGPQYS---MMQPHLQRQHSNPGHAGPFPVVSVhnTTINPTSPTTATMANANrGPTSPSVTAIELIPSVTNPE---N 676
Cdd:pfam05109  494 PRDNGTESKapdMTSPTSAVTTPTPNATSPTPAVTT--PTPNATSPTLGKTSPTS-AVTTPTPNATSPTPAVTTPTpnaT 570
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604   677 LPSLPDIPPIQANVVPMMHSWY----EFGAREKTQDQNLEDAGSSSL-----DNLLSRYISGSH-LPPQPTSTMN--PSP 744
Cdd:pfam05109  571 IPTLGKTSPTSAVTTPTPNATSptvgETSPQANTTNHTLGGTSSTPVvtsppKNATSAVTTGQHnITSSSTSSMSlrPSS 650
                          170
                   ....*....|....*....
gi 767904604   745 GPSALSPGSSGLSNSHTPV 763
Cdd:pfam05109  651 ISETLSPSTSDNSTSHMPL 669
BBOX smart00336
B-Box-type zinc finger;
212-248 8.44e-06

B-Box-type zinc finger;


Pssm-ID: 197662 [Multi-domain]  Cd Length: 42  Bit Score: 43.87  E-value: 8.44e-06
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|.
gi 767904604    212 KSEQVCTSCEDNAsAVGFCVECGEWLCKTCIEA----HQRV 248
Cdd:smart00336    1 QRAPKCDSHGDEP-AEFFCEECGALLCRTCDEAehrgHTVV 40
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
312-417 1.76e-03

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 42.31  E-value: 1.76e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604   312 LEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVE------QEIKVAIFTLINE----INKKGKSLL 381
Cdd:TIGR04523  237 KQQEINEKTTEISNTQTQLNQLKDEQNKIKKQLSEKQKELEQNNKKIKelekqlNQLKSEISDLNNQkeqdWNKELKSEL 316
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 767904604   382 QQLENVTKERQMKLLQQQNDITGLSRQV----KHVMNFTN 417
Cdd:TIGR04523  317 KNQEKKLEEIQNQISQNNKIISQLNEQIsqlkKELTNSES 356
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
312-412 2.86e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 41.97  E-value: 2.86e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604  312 LEEAFQNQKGAIENLLAKLLEKKNYVHfAATQVQNRIKEVNETNKRVEQEikvaiftlINEINKKGKSLLQQLENVTKER 391
Cdd:PRK03918  160 YENAYKNLGEVIKEIKRRIERLEKFIK-RTENIEELIKEKEKELEEVLRE--------INEISSELPELREELEKLEKEV 230
                          90       100
                  ....*....|....*....|.
gi 767904604  392 QmKLLQQQNDITGLSRQVKHV 412
Cdd:PRK03918  231 K-ELEELKEEIEELEKELESL 250
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
125-184 5.42e-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: 35.95  E-value: 5.42e-03
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604    125 CAVCQQslqsRREAEPKLLPCLHSFCLRCLPEperqlsvpipggsngdIQQVGVIRCPVC 184
Cdd:smart00184    1 CPICLE----EYLKDPVILPCGHTFCRSCIRK----------------WLESGNNTCPIC 40
 
Name Accession Description Interval E-value
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
981-1106 5.43e-59

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99934 [Multi-domain]  Cd Length: 109  Bit Score: 197.51  E-value: 5.43e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604  981 LSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCER 1060
Cdd:cd05502     1 LSPIDQRKCERLLLELYCHELSLPFHEPVSPSVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYK 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 767904604 1061 FNEMmkvvqvyadtqeinlkaDSEVAQAGKAVALYFEDKLTEIYSD 1106
Cdd:cd05502    81 FNEE-----------------DSEVAQAGKELELFFEEQLKEILPD 109
BBC smart00502
B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
319-445 5.70e-39

B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains


Pssm-ID: 128778  Cd Length: 127  Bit Score: 141.25  E-value: 5.70e-39
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604    319 QKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQ 398
Cdd:smart00502    1 QREALEELLTKLRKKAAELEDALKQLISIIQEVEENAADVEAQIKAAFDELRNALNKRKKQLLEDLEEQKENKLKVLEQQ 80
                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*..
gi 767904604    399 QNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKA 445
Cdd:smart00502   81 LESLTQKQEKLSHAINFTEEALNSGDPTELLLSKKLIIERLQNLLKQ 127
RING-HC_TIF1gamma cd16766
RING finger, HC subclass, found in transcriptional inknown asiary factor 1 gamma (TIF1gamma); ...
121-188 1.58e-37

RING finger, HC subclass, found in transcriptional inknown asiary factor 1 gamma (TIF1gamma); TIF1gamma, also known as tripartite motif-containing 33 (TRIM33), ectodermin, RFG7, or PTC7, belongs to the C-VI subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. It is an E3-ubiquitin ligase that functions as a regulator of transforming growth factor beta (TGFbeta) signaling, inhibiting 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 actor of tumorigenesis. Like other TIF1 proteins, 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.


Pssm-ID: 438422  Cd Length: 67  Bit Score: 134.99  E-value: 1.58e-37
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767904604  121 LLDTCAVCQQSLQSRReAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQEC 188
Cdd:cd16766     1 LLDTCAVCKQSLQSRD-AEPKLLPCLHSFCRRCLPEPERQLSVPVPGGSNGDIQQVGVIRCPVCRQEC 67
Bbox2_TIF1g_C-VI cd19830
B-box-type 2 zinc finger found in transcription intermediary factor 1 gamma (TIF1-gamma); ...
268-320 1.02e-32

B-box-type 2 zinc finger found in transcription intermediary factor 1 gamma (TIF1-gamma); TIF1-gamma, also known as tripartite motif-containing 33 (TRIM33), ectodermin, RFG7, or PTC7, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TIF1-gamma 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 actor of tumorigenesis. Like other TIF1 family members, TIF1-gamma 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.


Pssm-ID: 380888  Cd Length: 53  Bit Score: 120.55  E-value: 1.02e-32
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 767904604  268 ASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQK 320
Cdd:cd19830     1 ASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQK 53
Bbox1_TIF1g_C-VI cd19847
B-box-type 1 zinc finger found in transcriptional intermediary factor 1 gamma (TIF1-gamma); ...
210-263 5.58e-29

B-box-type 1 zinc finger found in transcriptional intermediary factor 1 gamma (TIF1-gamma); TIF1-gamma, also known as tripartite motif-containing 33 (TRIM33), ectodermin, RFG7, or PTC7, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. TIF1-gamma 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, TIF1-gamma is an important regulator of transcription during hematopoiesis, as well as a key actor of tumorigenesis. Like other TIF1 family members, TIF1-gamma 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.


Pssm-ID: 380905  Cd Length: 54  Bit Score: 109.85  E-value: 5.58e-29
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 767904604  210 DEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVS 263
Cdd:cd19847     1 DEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHMIRKKEDVS 54
BROMO smart00297
bromo domain;
982-1103 5.95e-29

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 111.60  E-value: 5.95e-29
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604    982 SPVDQRKCERLLLYLYC----HELSIEFQEPVPAS-IPNYYKIIKKPMDLSTVKKKLQKkhsQHYQIPDDFVADVRLIFK 1056
Cdd:smart00297    1 DPKLQKKLQELLKAVLDkldsHPLSWPFLKPVSRKeAPDYYDIIKKPMDLKTIKKKLEN---GKYSSVEEFVADFNLMFS 77
                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*..
gi 767904604   1057 NCERFNEmmkvvqvyadtqeinlkADSEVAQAGKAVALYFEDKLTEI 1103
Cdd:smart00297   78 NARTYNG-----------------PDSEVYKDAKKLEKFFEKKLREL 107
PHD_TIF1gamma cd15624
PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also ...
912-957 3.29e-27

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: 104.74  E-value: 3.29e-27
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 767904604  912 WCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDI 957
Cdd:cd15624     1 WCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDI 46
Bbox2_TIF1a_C-VI cd19828
B-box-type 2 zinc finger found in transcription intermediary factor 1-alpha (TIF1-alpha); ...
271-327 1.30e-26

B-box-type 2 zinc finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also known as tripartite motif-containing protein 24 (TRIM24), E3 ubiquitin-protein ligase TRIM24, or RING finger protein 82, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TIF1-alpha interacts specifically and in a ligand-dependent manner with the ligand binding domain (LBD) of several nuclear receptors (NRs), including retinoid X (RXR), retinoic acid (RAR), vitamin D3 (VDR), estrogen (ER), and progesterone (PR) receptors. It also associates with heterochromatin-associated factors HP1alpha, MOD1 (HP1beta), and MOD2 (HP1gamma), as well as the vertebrate Kruppel-type (C2H2) zinc finger proteins that contain the transcriptional silencing domain KRAB. TIF1-alpha is a ligand-dependent co-repressor of retinoic acid receptor (RAR) that interacts with multiple nuclear receptors in vitro via an LXXLL motif and further acts as a gatekeeper of liver carcinogenesis. It also functions as an E3-ubiquitin ligase targeting p53, and is broadly associated with chromatin silencing. Moreover, it is a chromatin regulator that recognizes specific, combinatorial histone modifications through its C-terminal PHD-Bromo region. In addition, it interacts with chromatin and estrogen receptor to activate estrogen-dependent genes associated with cellular proliferation and tumor development.


Pssm-ID: 380886  Cd Length: 57  Bit Score: 103.20  E-value: 1.30e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 767904604  271 QRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLL 327
Cdd:cd19828     1 QRPVFCPFHKKEQLKLYCETCDKLTCRDCQLLEHKEHRYQFIEEAFQNQKVIIDTLI 57
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
989-1099 4.45e-26

Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99935  Cd Length: 97  Bit Score: 103.22  E-value: 4.45e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604  989 CERLLLYLYCHELSIEFQEPV-PASIPNYYKIIKKPMDLSTVKKKLQKKhsqHYQIPDDFVADVRLIFKNCERFNEmmkv 1067
Cdd:cd05503     5 CETILDEMEAHEDAWPFLEPVnTKLVPGYRKIIKKPMDFSTIREKLESG---QYKTLEEFAEDVRLVFDNCETFNE---- 77
                          90       100       110
                  ....*....|....*....|....*....|..
gi 767904604 1068 vqvyadtqeinlkADSEVAQAGKAVALYFEDK 1099
Cdd:cd05503    78 -------------DDSEVGRAGHNMRKFFEKR 96
Bbox2_TIF1_C-VI cd19775
B-box-type 2 zinc finger found in transcription intermediary factor 1 (TIF1) family; This ...
273-315 1.49e-25

B-box-type 2 zinc finger found in transcription intermediary factor 1 (TIF1) family; This family corresponds to the TIF1 family of transcriptional cofactors including TIF1-alpha (TRIM24), TIF1-beta (TRIM28), and TIF1-gamma (TRIM33), which belong to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 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 and TIF1beta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. They bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. 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).


Pssm-ID: 380833  Cd Length: 43  Bit Score: 99.71  E-value: 1.49e-25
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 767904604  273 PVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEA 315
Cdd:cd19775     1 PLFCPVHPQEPLKLFCETCDKLTCRDCQLLEHKDHKYQFAEEA 43
RING-HC_TIF1_C-VI cd16585
RING finger, HC subclass, found in the transcriptional inknown asiary factor 1 (TIF1) ...
122-188 4.12e-25

RING finger, HC subclass, found in the transcriptional inknown asiary factor 1 (TIF1) subfamily and similar proteins; The TIF1 subfamily of transcriptional cofactors containing RING-HC fingers includes TIF1alpha (TRIM24), TIF1beta (TRIM28), and TIF1gamma (TRIM33), which belong to the C-VI subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. 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 and TIF1beta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. They bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. 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 heterochromatin proteins HP1alpha, beta and gamma. It cannot bind to nuclear receptors (NRs). TIF1delta (TRIM66) doesn't have a RING-HC finger and is not included in this model.


Pssm-ID: 438247 [Multi-domain]  Cd Length: 62  Bit Score: 99.20  E-value: 4.12e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767904604  122 LDTCAVCQQSLQSRreaEPKLLPCLHSFCLRCLPEPERQLSVPIPggSNGDIQQVGVIRCPVCRQEC 188
Cdd:cd16585     1 LDTCAVCKQSFQSR---EPKLLPCLHSFCKRCLPPADRAAANPSP--SGGAAGQVGVIRCPVCKQEC 62
Bbox1_TIF1a_C-VI cd19845
B-box-type 1 zinc finger found in transcription intermediary factor 1-alpha (TIF1-alpha); ...
215-259 4.58e-25

B-box-type 1 zinc finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also known as tripartite motif-containing protein 24 (TRIM24), E3 ubiquitin-protein ligase TRIM24, or RING finger protein 82, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. TIF1-alpha interacts specifically and in a ligand-dependent manner with the ligand binding domain (LBD) of several nuclear receptors (NRs), including retinoic X (RXR), retinoic acid (RAR), vitamin D3 (VDR), estrogen (ER), and progesterone (PR) receptors. It also associates with heterochromatin-associated factors HP1alpha, MOD1 (HP1beta), and MOD2 (HP1gamma), as well as the vertebrate Kruppel-type (C2H2) zinc finger proteins that contain the transcriptional silencing domain KRAB. TIF1-alpha is a ligand-dependent co-repressor of retinoic acid receptor (RAR) that interacts with multiple nuclear receptors in vitro via an LXXLL motif and further acts as a gatekeeper of liver carcinogenesis. It also functions as an E3-ubiquitin ligase targeting p53, and is broadly associated with chromatin silencing. Moreover, it is a chromatin regulator that recognizes specific, combinatorial histone modifications through its C-terminal PHD-Bromo region. In addition, it interacts with chromatin and estrogen receptor to activate estrogen-dependent genes associated with cellular proliferation and tumor development.


Pssm-ID: 380903  Cd Length: 45  Bit Score: 98.60  E-value: 4.58e-25
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 767904604  215 QVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKK 259
Cdd:cd19845     1 QVCTSCEDNAEANGFCVECVEWLCKTCIEAHQRVKFTKDHTVRQK 45
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
985-1100 1.17e-24

Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.


Pssm-ID: 99922 [Multi-domain]  Cd Length: 99  Bit Score: 99.37  E-value: 1.17e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604  985 DQRKCERLLLYLYCH--ELSIEFQEPV-PASIPNYYKIIKKPMDLSTVKKKLQKKhsqHYQIPDDFVADVRLIFKNCERF 1061
Cdd:cd04369     1 LKKKLRSLLDALKKLkrDLSEPFLEPVdPKEAPDYYEVIKNPMDLSTIKKKLKNG---EYKSLEEFEADVRLIFSNAKTY 77
                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 767904604 1062 NEmmkvvqvyadtqeinlkADSEVAQAGKAVALYFEDKL 1100
Cdd:cd04369    78 NG-----------------PGSPIYKDAKKLEKLFEKLL 99
PHD_TIF1alpha cd15622
PHD finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also ...
912-954 6.11e-24

PHD finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also termed tripartite motif-containing protein 24 (TRIM24), or E3 ubiquitin-protein ligase TRIM24, or RING finger protein 82, belongs to the TRIM/RBCC protein family. It interacts specifically and in a ligand-dependent manner with the ligand binding domain (LBD) of several nuclear receptors (NRs), including retinoid X (RXR), retinoic acid (RAR), vitamin D3 (VDR), estrogen (ER), and progesterone (PR) receptors. It also associates with heterochromatin-associated factors HP1alpha, MOD1 (HP1beta) and MOD2 (HP1gamma), as well as vertebrate Kruppel-type (C2H2) zinc finger proteins that contain transcriptional silencing domain KRAB. TIF1-alpha is a ligand-dependent co-repressor of retinoic acid receptor (RAR) that interacts with multiple nuclear receptors in vitro via an LXXLL motif, and further acts as a gatekeeper of liver carcinogenesis. It also functions as an E3-ubiquitin ligase targeting p53 and is broadly associated with chromatin silencing. Moreover, it is a chromatin regulator that recognizes specific, combinatorial histone modifications through its C-terminal plant homeodomain (PHD)-Bromodomain (Bromo) region. In addition, it interacts with chromatin and estrogen receptor to activate estrogen-dependent genes associated with cellular proliferation and tumor development. TIF1-alpha 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: 277092  Cd Length: 43  Bit Score: 95.52  E-value: 6.11e-24
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 767904604  912 WCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 954
Cdd:cd15622     1 WCAVCQNGGELLCCEKCPKVFHLSCHVPTLMNFPSGEWICTFC 43
Bbox1_TIF1 cd19805
B-box-type 1 zinc finger found in transcription intermediary factor 1 (TIF1) family; This ...
216-259 9.48e-24

B-box-type 1 zinc finger found in transcription intermediary factor 1 (TIF1) family; This family corresponds to the TIF1 family of transcriptional cofactors including TIF1-alpha (TRIM24), TIF1-beta (TRIM28), and TIF1-gamma (TRIM33), which belongs to the C-VI subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. 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. TIF1-alpha and TIF1-beta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. They bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. TIF1-gamma is structurally closely related to TIF1-alpha and TIF1-beta, 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).


Pssm-ID: 380863  Cd Length: 44  Bit Score: 94.76  E-value: 9.48e-24
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 767904604  216 VCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKK 259
Cdd:cd19805     1 VCTSCEDNAPATSFCVECSEWLCDTCVQAHQRVKVTKDHTIRSK 44
PHD_TIF1delta cd15625
PHD finger found in transcriptional intermediary factor 1 delta (TIF1delta); TIF1delta, also ...
909-957 1.71e-23

PHD finger found in transcriptional intermediary factor 1 delta (TIF1delta); TIF1delta, also termed tripartite motif-containing protein 66 (TRIM66), is a novel heterochromatin protein 1 (HP1)-interacting member of the transcriptional intermediary factor1 (TIF1) family expressed by elongating spermatids. Like other TIF1 proteins, TIF1delta displays a potent trichostatin A (TSA)-sensitive repression function; TSA is a specific inhibitor of histone deacetylases. Moreover, TIF1delta plays an important role in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. It functions as a negative regulator of postmeiotic genes acting through HP1 isotype gamma (HP1gamma) complex formation and centromere association. TIF1delta 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: 277095 [Multi-domain]  Cd Length: 49  Bit Score: 94.26  E-value: 1.71e-23
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 767904604  909 NEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDI 957
Cdd:cd15625     1 NEDFCAVCLNGGELLCCDRCPKVFHLSCHVPALLSFPVGEWVCTLCRNL 49
PHD_TIF1_like cd15541
PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar ...
912-954 3.44e-23

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: 93.18  E-value: 3.44e-23
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 767904604  912 WCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 954
Cdd:cd15541     1 WCAVCQNGGELLCCDKCPRVFHLDCHIPPIPEFPSGEWSCSLC 43
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
989-1074 5.17e-23

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 93.92  E-value: 5.17e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604   989 CERLLLYLYCHELSIEFQEPV-PASIPNYYKIIKKPMDLSTVKKKLqkkHSQHYQIPDDFVADVRLIFKNCERFNEMMKV 1067
Cdd:pfam00439    1 CLEILDKLMEHPIAAPFLEPVdPDEYPDYYSVIKKPMDLSTIKKKL---ENGEYKSLAEFLADVKLIFSNARTYNGPGSV 77

                   ....*..
gi 767904604  1068 VQVYADT 1074
Cdd:pfam00439   78 IYKAAEK 84
RING-HC_TIF1alpha cd16764
RING finger, HC subclass, found in transcription inknown asiary factor 1-alpha (TIF1-alpha); ...
122-188 5.95e-23

RING finger, HC subclass, found in transcription inknown asiary factor 1-alpha (TIF1-alpha); TIF1-alpha, also known as tripartite motif-containing protein 24 (TRIM24), E3 ubiquitin-protein ligase TRIM24, or RING finger protein 82, belongs to the C-VI subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. It interacts specifically and in a ligand-dependent manner with the ligand binding domain (LBD) of several nuclear receptors (NRs), including retinoid X (RXR), retinoic acid (RAR), vitamin D3 (VDR), estrogen (ER), and progesterone (PR) receptors. It also associates with heterochromatin-associated factors HP1alpha, MOD1 (HP1beta), and MOD2 (HP1gamma), as well as the vertebrate Kruppel-type (C2H2) zinc finger proteins that contain the transcriptional silencing domain KRAB. TIF1-alpha is a ligand-dependent co-repressor of RAR that interacts with multiple nuclear receptors in vitro via an LXXLL motif and further acts as a gatekeeper of liver carcinogenesis. It also functions as an E3-ubiquitin ligase targeting p53, and is broadly associated with chromatin silencing. Moreover, it is a chromatin regulator that recognizes specific, combinatorial histone modifications through its C-terminal PHD-Bromo region. In addition, it interacts with chromatin and estrogen receptor to activate estrogen-dependent genes associated with cellular proliferation and tumor development.


Pssm-ID: 438420  Cd Length: 71  Bit Score: 93.39  E-value: 5.95e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767904604  122 LDTCAVCQQSLQSRReaePKLLPCLHSFCLRCLPEPERQLSVPIP-------GGSNGDIQQVGVIRCPVCRQEC 188
Cdd:cd16764     1 LDTCGVCKQHIQSRE---PRLLPCLHSFCQRCLPQPERYLMLPAPfspspgpRATSSANRQVGVVRCPVCSQEC 71
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
985-1103 1.11e-22

Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99941 [Multi-domain]  Cd Length: 101  Bit Score: 93.77  E-value: 1.11e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604  985 DQRKCERLLLYLYCHELSIEFQEPVPAS-IPNYYKIIKKPMDLSTVKKKLQKKhsqHYQIPDDFVADVRLIFKNCERFNe 1063
Cdd:cd05509     2 LYTQLKKVLDSLKNHKSAWPFLEPVDKEeAPDYYDVIKKPMDLSTMEEKLENG---YYVTLEEFVADLKLIFDNCRLYN- 77
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 767904604 1064 mmkvvqvyadtqeinlKADSEVAQAGKAVALYFEDKLTEI 1103
Cdd:cd05509    78 ----------------GPDTEYYKCANKLEKFFWKKLKEL 101
Bbox2_TIF1b_C-VI cd19829
B-box-type 2 zinc finger found in transcription intermediary factor 1-beta (TIF1-beta); ...
273-315 3.32e-22

B-box-type 2 zinc finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also known as Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), KRAB-interacting protein 1 (KRIP-1), nuclear co-repressor KAP-1, RING finger protein 96, tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD) and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TIF1-beta acts as a nuclear co-repressor that plays a role in transcription and in the 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 the DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. Moreover, 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. The N-terminal RBCC domains of TIF1-beta are responsible for the interaction with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and the regulation of homo- and heterodimerization. The C-terminal PHD/Bromo domains are involved in interacting with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity.


Pssm-ID: 380887  Cd Length: 44  Bit Score: 90.27  E-value: 3.32e-22
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 767904604  273 PVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEA 315
Cdd:cd19829     1 TVYCSIHKQEPLKLFCETCDTLTCRDCQLNAHKDHQYQFLEDA 43
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
987-1078 6.23e-22

Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99938  Cd Length: 99  Bit Score: 91.62  E-value: 6.23e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604  987 RKCERLLLYLYCHELSIEFQEPVPAS---IPNYYKIIKKPMDLSTVKKKLQKKhsqHYQIPDDFVADVRLIFKNCERFNE 1063
Cdd:cd05506     3 KQCGTLLRKLMKHKWGWVFNAPVDVValgLPDYFDIIKKPMDLGTVKKKLEKG---EYSSPEEFAADVRLTFANAMRYNP 79
                          90
                  ....*....|....*
gi 767904604 1064 mmKVVQVYADTQEIN 1078
Cdd:cd05506    80 --PGNDVHTMAKELL 92
Bbox1_TIF1b_C-VI cd19846
B-box-type 1 zinc finger found in transcription intermediary factor 1-beta (TIF1-beta); ...
213-259 1.02e-21

B-box-type 1 zinc finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also known as Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), KRAB-interacting protein 1 (KRIP-1), nuclear co-repressor KAP-1, RING finger protein 96, tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. TIF1-beta/KAP-1 acts as a nuclear co-repressor that plays a role in transcription and in the 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 the DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. Moreover, 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. The N-terminal RBCC domains of TIF1-beta are responsible for the interaction with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and the regulation of homo- and heterodimerization. The C-terminal PHD/Bromo domains are involved in interacting with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity.


Pssm-ID: 380904  Cd Length: 52  Bit Score: 89.37  E-value: 1.02e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 767904604  213 SEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKK 259
Cdd:cd19846     2 TIQCCTSCEDNAPATSYCVECSEPLCETCVEAHQRVKYTKDHTVRVK 48
Bromo_Brdt_II_like cd05498
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...
1005-1099 4.75e-20

Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99930  Cd Length: 102  Bit Score: 86.18  E-value: 4.75e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604 1005 FQEPVPAS---IPNYYKIIKKPMDLSTVKKKLQKKhsqHYQIPDDFVADVRLIFKNCERFNemmkvvqvyadtqeinlKA 1081
Cdd:cd05498    24 FYKPVDPEalgLHDYHDIIKHPMDLSTIKKKLDNR---EYADAQEFAADVRLMFSNCYKYN-----------------PP 83
                          90
                  ....*....|....*...
gi 767904604 1082 DSEVAQAGKAVALYFEDK 1099
Cdd:cd05498    84 DHPVHAMARKLQDVFEDR 101
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
999-1062 1.43e-18

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99931  Cd Length: 102  Bit Score: 81.95  E-value: 1.43e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767904604  999 HELSIEFQEPVPA---SIPNYYKIIKKPMDLSTVKKKLQkkhSQHYQIPDDFVADVRLIFKNCERFN 1062
Cdd:cd05499    18 SAYNWPFLDPVDPvalNIPNYFSIIKKPMDLGTISKKLQ---NGQYQSAKEFERDVRLIFKNCYTFN 81
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
1002-1100 6.99e-18

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99932  Cd Length: 103  Bit Score: 80.05  E-value: 6.99e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604 1002 SIEFQEPV-PA--SIPNYYKIIKKPMDLSTVKKKLQkkhSQHYQIPDDFVADVRLIFKNCERFNemmkvvqvyadtqein 1078
Cdd:cd05500    22 ARPFLVPVdPVklNIPHYPTIIKKPMDLGTIERKLK---SNVYTSVEEFTADFNLMVDNCLTFN---------------- 82
                          90       100
                  ....*....|....*....|..
gi 767904604 1079 lKADSEVAQAGKAVALYFEDKL 1100
Cdd:cd05500    83 -GPEHPVSQMGKRLQAAFEKHL 103
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
989-1062 3.65e-17

Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99942 [Multi-domain]  Cd Length: 112  Bit Score: 78.25  E-value: 3.65e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767904604  989 CERLLLYLYCH-ELSIEFQEPV-PASIPNYYKIIKKPMDLSTVKKKLQKKhsqHYQIPDDFVADVRLIFKNCERFN 1062
Cdd:cd05510    12 LDKVLNELKTYtEHSTPFLTKVsKREAPDYYDIIKKPMDLGTMLKKLKNL---QYKSKAEFVDDLNLIWKNCLLYN 84
Bbox2_TRIM66-like cd19794
B-box-type 2 zinc finger found in tripartite motif-containing protein 66 (TRIM66) and similar ...
274-315 7.10e-16

B-box-type 2 zinc finger found in tripartite motif-containing protein 66 (TRIM66) and similar proteins; TRIM66, also termed transcriptional intermediary factor 1 delta (TIF1delta), is a novel heterochromatin protein 1 (HP1)-interacting member of the transcriptional intermediary factor 1 (TIF1) family expressed by elongating spermatids. Like other TIF1 proteins, TRIM66 displays a potent trichostatin A (TSA)-sensitive repression function; TSA is a specific inhibitor of histone deacetylases. Moreover, TRIM66 plays an important role in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. It functions as a negative regulator of postmeiotic genes acting through HP1 isotype gamma (HP1gamma) complex formation and centromere association. TRIM66 belongs to an unclassified TRIM (tripartite motif) family of proteins that do not have RING fingers and thus lack the characteristic tripartite (RING (R), B-box, and coiled coil (CC)) RBCC motif. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380852  Cd Length: 43  Bit Score: 72.49  E-value: 7.10e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 767904604  274 VFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEA 315
Cdd:cd19794     1 LMCPLHNQEPLKLFCETCDVLVCRSCLLSEHKEHRFKHLDEA 42
Bbox2_TRIM45_C-X cd19785
B-box-type 2 zinc finger found in tripartite motif-containing protein 45 (TRIM45) and similar ...
273-315 2.97e-15

B-box-type 2 zinc finger found in tripartite motif-containing protein 45 (TRIM45) and similar proteins; TRIM45, also known as RING finger protein 99 (RNF99), is a novel receptor for activated C-kinase (RACK1)-interacting protein that suppresses transcriptional activities of Elk-1 and AP-1 and downregulates mitogen-activated protein kinase (MAPK) signal transduction by inhibiting RACK1/PKC (protein kinase C) complex formation. It also negatively regulates tumor necrosis factor alpha (TNFalpha)-induced nuclear factor-kappaB (NF-kappa B)-mediated transcription and suppresses cell proliferation. TRIM45 belongs to the C-X subclass of TRIM (tripartite motif) family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a filamin-type immunoglobulin (IG-FLMN) domain and NHL repeats positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380843  Cd Length: 43  Bit Score: 70.53  E-value: 2.97e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 767904604  273 PVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEA 315
Cdd:cd19785     1 PVLCPFHPAEELRLFCETCDKPVCRDCVLVEHRGHQCDFTSDV 43
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
1002-1062 1.30e-14

Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99943 [Multi-domain]  Cd Length: 112  Bit Score: 71.14  E-value: 1.30e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767904604 1002 SIEFQEPV-PASIPNYYKIIKKPMDLSTVKKKLqKKHSqhYQIPDDFVADVRLIFKNCERFN 1062
Cdd:cd05511    18 SWPFHTPVnKKKVPDYYKIIKRPMDLQTIRKKI-SKHK--YQSREEFLEDIELIVDNSVLYN 76
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
989-1103 1.48e-14

Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99936  Cd Length: 115  Bit Score: 70.89  E-value: 1.48e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604  989 CERLLLYLYCHELSIEFQEPVPAS-IPNYYKIIKKPMDLSTVKKKLQKkhsQHYQIPDDFVADVRLIFKNCERFNEmmkv 1067
Cdd:cd05504    17 LEQLLVEIVKHKDSWPFLRPVSKIeVPDYYDIIKKPMDLGTIKEKLNM---GEYKLAEEFLSDIQLVFSNCFLYNP---- 89
                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 767904604 1068 vqvyadtqeinlkADSEVAQAGKAVALYFEDKLTEI 1103
Cdd:cd05504    90 -------------EHTSVYKAGTRLQRFFIKRCRKL 112
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
913-954 2.13e-14

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: 68.25  E-value: 2.13e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 767904604  913 CAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 954
Cdd:cd15539     2 CAVCGDGGELLCCDGCPRAFHLACLVPPLTLIPSGTWRCSSC 43
Bromo_Brdt_I_like cd05497
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...
996-1063 2.69e-13

Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99929  Cd Length: 107  Bit Score: 67.06  E-value: 2.69e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767904604  996 LYCHELSIEFQEPVPA---SIPNYYKIIKKPMDLSTVKKKLQKKhsqHYQIPDDFVADVRLIFKNCERFNE 1063
Cdd:cd05497    17 LWKHKFAWPFQQPVDAvklNLPDYHKIIKTPMDLGTIKKRLENN---YYWSASECIQDFNTMFTNCYIYNK 84
Bromo_cbp_like cd05495
Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ...
1002-1071 3.79e-13

Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99927  Cd Length: 108  Bit Score: 66.70  E-value: 3.79e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767904604 1002 SIEFQEPVPA---SIPNYYKIIKKPMDLSTVKKKLQkkhSQHYQIPDDFVADVRLIFKNCERFNEmmKVVQVY 1071
Cdd:cd05495    22 SLPFRQPVDPkllGIPDYFDIVKNPMDLSTIRRKLD---TGQYQDPWQYVDDVWLMFDNAWLYNR--KTSRVY 89
Bbox1_TRIM71_C-VII cd19812
B-box-type 1 zinc finger found in tripartite motif-containing protein 71 (TRIM71) and similar ...
217-258 4.56e-13

B-box-type 1 zinc finger found in tripartite motif-containing protein 71 (TRIM71) and similar proteins; TRIM71, also known as protein lineage variant 41 (lin-41), is an E3 ubiquitin-protein ligase that may play essential roles in embryonic stem cells, cellular reprogramming, and the timing of embryonic neurogenesis. It was first identified in the nematode Caenorhabditis elegans as a target of the differentiation-associated microRNA (miRNA) let-7 (lethal 7) and therefore part of a heterochronic gene network that controls larval development. In humans, it regulates let-7 microRNA biogenesis via modulation of Lin28B protein polyubiquitination. TRIM71 localizes to cytoplasmic P-bodies and directly interacts with the miRNA pathway proteins Argonaute 2 (AGO2) and DICER. It represses miRNA activity by promoting degradative ubiquitination of AGO2. Moreover, TRIM71 associates with SHCBP1, a novel component of the fibroblast growth factor (FGF) signaling pathway, and regulates its non-degradative polyubiquitination. It is also involved in the post-transcriptional regulation of the CDKN1A, RBL1 and RBL2 or EGR1 mRNAs by mediating RNA-binding in embryonic stem cells. TRIM71 belongs to the C-VII subclass of the TRIM (tripartite motif) family of proteins that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif.


Pssm-ID: 380870  Cd Length: 44  Bit Score: 64.34  E-value: 4.56e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 767904604  217 CTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRK 258
Cdd:cd19812     2 CSSCDEGNAATSRCKDCNEYLCDNCVRAHQRVRLTKDHFIVR 43
PHD2_CHD_II cd15532
PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
913-954 5.50e-13

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: 64.22  E-value: 5.50e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 767904604  913 CAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 954
Cdd:cd15532     2 CRVCKDGGELLCCDGCPSSYHLHCLNPPLAEIPDGDWFCPRC 43
Bromo_SP100C_like cd05501
Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major ...
983-1070 5.61e-13

Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major component of PML-SP100 nuclear bodies (NBs), which are poorly understood. It is covalently modified by SUMO-1 and may play a role in processes at the chromatin level. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99933  Cd Length: 102  Bit Score: 65.91  E-value: 5.61e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604  983 PVDQRKCERLLLYLYCHELSIEFQePVPASIPNYYKIIKKPMDLSTVKKKLqkkHSQHYQIPDDFVADVRLIFKNCERFN 1062
Cdd:cd05501     1 PEELLKCEFLLLKVYCMSKSGFFI-SKPYYIRDYCQGIKEPMWLNKVKERL---NERVYHTVEGFVRDMRLIFHNHKLFY 76

                  ....*...
gi 767904604 1063 EMMKVVQV 1070
Cdd:cd05501    77 KDDDFGQV 84
PHD1_PHF12 cd15533
PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is ...
913-954 7.17e-13

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: 63.91  E-value: 7.17e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 767904604  913 CAVCQNGGDLLCCEKCPKVFHLTCHVPTL--LSFPSGDWICTFC 954
Cdd:cd15533     2 CDSCGEGGDLLCCDRCPASFHLQCCNPPLdeEDLPPGEWLCHRC 45
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
967-1128 1.28e-12

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 70.99  E-value: 1.28e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604  967 DNLQHSKKGKTAQGLSPVDQRK-----CERLLLYLYC----HELSIEFQE------------PVPASIPNYYKIIKKPMD 1025
Cdd:COG5076   111 SVTPESGLGSLLMAHLKTSVKKrktpkIEDELLYADNkaiaKFKKQLFLRdgrflssiflglPSKREYPDYYEIIKSPMD 190
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604 1026 LSTVKKKLQkkhSQHYQIPDDFVADVRLIFKNCERFNEmmKVVQVYADTQEINlKADSEVAQagkavalyfedKLTEIYS 1105
Cdd:COG5076   191 LLTIQKKLK---NGRYKSFEEFVSDLNLMFDNCKLYNG--PDSSVYVDAKELE-KYFLKLIE-----------EIPEEML 253
                         170       180
                  ....*....|....*....|...
gi 767904604 1106 DRTFAPLPEFEQEEDDGEVTEDS 1128
Cdd:COG5076   254 ELSIKPGREEREERESVLITNSQ 276
Bbox2_BRAT-like cd19798
B-box-type 2 zinc finger found in Drosophila melanogaster brain tumor protein (BRAT) and ...
271-312 2.84e-12

B-box-type 2 zinc finger found in Drosophila melanogaster brain tumor protein (BRAT) and similar proteins; BRAT is a NHL-domain family protein that functions as a translational repressor to inhibit cell proliferation. This family also contains Caenorhabditis elegans B-box type zinc finger protein ncl-1, a C. elegans Brat homolog which functions as a translational repressor that inhibits protein synthesis. BRAT contains Bbox1 and Bbox2 zinc fingers and NHL repeats. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380856  Cd Length: 44  Bit Score: 61.93  E-value: 2.84e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 767904604  271 QRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHK--EHRYQFL 312
Cdd:cd19798     1 EKPVFCPKHPNEVLKFFCKTCNIPICKDCTLLDHNkgLHDYEYL 44
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
985-1063 5.76e-12

Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99937  Cd Length: 97  Bit Score: 62.94  E-value: 5.76e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604  985 DQRKCERLLLYLYCHELSIEFQEPVPAS-IPNYYKIIKKPMDLSTVKKKLQKKHSQHYQipdDFVADVRLIFKNCERFNE 1063
Cdd:cd05505     1 ELQKCEEILSKILKYRFSWPFREPVTADeAEDYKKVITNPMDLQTMQTKCSCGSYSSVQ---EFLDDMKLVFSNAEKYYE 77
RING-HC_TIF1beta cd16765
RING finger, HC subclass, found in transcription inknown asiary factor 1-beta (TIF1-beta); ...
122-188 5.95e-12

RING finger, HC subclass, found in transcription inknown asiary factor 1-beta (TIF1-beta); TIF1-beta, also known as Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), KRAB-interacting protein 1 (KRIP-1), nuclear co-repressor KAP-1, RING finger protein 96, tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, belongs to the C-VI subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. It acts as a nuclear co-repressor that plays a role in transcription and in the 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 the DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. Moreover, 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. The N-terminal RBCC domain of TIF1-beta is responsible for the interaction with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and the regulation of homo- and heterodimerization. The C-terminal PHD/Bromo domains are involved in interacting with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity.


Pssm-ID: 438421 [Multi-domain]  Cd Length: 63  Bit Score: 61.86  E-value: 5.95e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604  122 LDTCAVCQQSLQSRREaePKLLPCLHSFCLRCLPeperqLSVPIPGGSNGDIQQVG---VIRCPVCRQEC 188
Cdd:cd16765     1 LEHCGVCRERLRPERE--PRLLPCLHSVCSACLG-----PAAPAAANSSGDGGAAGdgtVVDCPVCKQQC 63
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
999-1063 1.00e-11

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99946  Cd Length: 105  Bit Score: 62.71  E-value: 1.00e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767904604  999 HELSIEFQE-PVPASIPNYYKIIKKPMDLSTVKKKLQkkhSQHYQIPDDFVADVRLIFKNCERFNE 1063
Cdd:cd05515    21 RRLSLIFMRlPSKSEYPDYYDVIKKPIDMEKIRSKIE---GNQYQSLDDMVSDFVLMFDNACKYNE 83
BBOX smart00336
B-Box-type zinc finger;
271-312 1.31e-11

B-Box-type zinc finger;


Pssm-ID: 197662 [Multi-domain]  Cd Length: 42  Bit Score: 60.04  E-value: 1.31e-11
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|..
gi 767904604    271 QRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFL 312
Cdd:smart00336    1 QRAPKCDSHGDEPAEFFCEECGALLCRTCDEAEHRGHTVVLL 42
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
1005-1062 1.51e-11

Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99944  Cd Length: 98  Bit Score: 62.03  E-value: 1.51e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 767904604 1005 FQEPVPAS-IPNYYKIIKKPMDLSTVKKKLQkkhSQHYQIPDDFVADVRLIFKNCERFN 1062
Cdd:cd05512    22 FSEPVDLSeVPDYLDHIKQPMDFSTMRKKLE---SQRYRTLEDFEADFNLIINNCLAYN 77
PHD1_BPTF cd15559
PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, ...
913-954 1.65e-11

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: 60.12  E-value: 1.65e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 767904604  913 CAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 954
Cdd:cd15559     2 CRVCHKLGDLLCCETCSAVYHLECVDPPLEEVPEEDWQCEVC 43
Bromo_WDR9_II cd05496
Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
987-1062 2.91e-11

Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99928  Cd Length: 119  Bit Score: 61.70  E-value: 2.91e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767904604  987 RKCERLLLYLYCHELSIEFQEPVPA-SIPNYYKIIKKPMDLSTVKKKLQkkhSQHYQIPDDFVADVRLIFKNCERFN 1062
Cdd:cd05496     8 KQCKELVNLMWDCEDSEPFRQPVDLlKYPDYRDIIDTPMDLGTVKETLF---GGNYDDPMEFAKDVRLIFSNSKSYT 81
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
1004-1062 6.75e-11

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver


Pssm-ID: 99957  Cd Length: 112  Bit Score: 60.45  E-value: 6.75e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604 1004 EFQEPV-PASIPNYYKIIKKPMDLSTVKKKLQkkhSQHYQIPDDFVADVRLIFKNCERFN 1062
Cdd:cd05528    23 AFTKPVdEEEVPDYYEIIKQPMDLQTILQKLD---THQYLTAKDFLKDIDLIVTNALEYN 79
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
912-955 1.34e-10

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


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 57.50  E-value: 1.34e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 767904604   912 WCAVCQ---NGGDLLCCEKCPKVFHLTCHVPTLLS--FPSGDWICTFCR 955
Cdd:pfam00628    1 YCAVCGksdDGGELVQCDGCDDWFHLACLGPPLDPaeIPSGEWLCPECK 49
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
913-954 3.19e-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: 56.23  E-value: 3.19e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 767904604  913 CAVCQNGGD---LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 954
Cdd:cd15527     2 CSVCQDSGNadnLLFCDACDKGFHMECHDPPLTRMPKGKWVCQIC 46
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
912-954 4.67e-10

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


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 56.07  E-value: 4.67e-10
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 767904604    912 WCAVCQ---NGGDLLCCEKCPKVFHLTCHVPTLLSF-PSGDWICTFC 954
Cdd:smart00249    1 YCSVCGkpdDGGELLQCDGCDRWYHQTCLGPPLLEEePDGKWYCPKC 47
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
1005-1073 5.23e-10

Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99949 [Multi-domain]  Cd Length: 103  Bit Score: 57.46  E-value: 5.23e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604 1005 FQE-PVPASIPNYYKIIKKPMDLSTVKKKLQkkhSQHYQIPDDFVADVRLIFKNCERFNEmmKVVQVYAD 1073
Cdd:cd05518    27 FMEkPSKKDYPDYYKIILEPIDLKTIEHNIR---NDKYATEEELMDDFKLMFRNARHYNE--EGSQVYED 91
PHD_TIF1beta cd15623
PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also ...
913-954 9.77e-10

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: 54.81  E-value: 9.77e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 767904604  913 CAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 954
Cdd:cd15623     2 CRVCQKAGALVMCDQCEFCFHLDCHLPALQEVPGEDWKCLLC 43
Bbox2_TRIM71_C-VII cd19796
B-box-type 2 zinc finger found in tripartite motif-containing protein 71 (TRIM71) and similar ...
273-320 1.68e-09

B-box-type 2 zinc finger found in tripartite motif-containing protein 71 (TRIM71) and similar proteins; TRIM71, also known as protein lineage variant 41 (lin-41), is an E3 ubiquitin-protein ligase that may play essential roles in embryonic stem cells, cellular reprogramming, and the timing of embryonic neurogenesis. It was first identified in the nematode Caenorhabditis elegans as a target of the differentiation-associated microRNA (miRNA) let-7 (lethal 7), and therefore part of a heterochronic gene network that controls larval development. In humans, it regulates let-7 microRNA biogenesis via modulation of Lin28B protein polyubiquitination. TRIM71 localizes to cytoplasmic P-bodies and directly interacts with the miRNA pathway proteins Argonaute 2 (AGO2) and DICER. It represses miRNA activity by promoting degradative ubiquitination of AGO2. Moreover, TRIM71 associates with SHCBP1, a novel component of the fibroblast growth factor (FGF) signaling pathway, and regulates its non-degradative polyubiquitination. It is also involved in the post-transcriptional regulation of the CDKN1A, RBL1 and RBL2 or EGR1 mRNAs through mediating RNA-binding in embryonic stem cells. TRIM71 belongs to the C-VII subclass of TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380854 [Multi-domain]  Cd Length: 48  Bit Score: 54.23  E-value: 1.68e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 767904604  273 PVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQK 320
Cdd:cd19796     1 PSYCEIHEHEVLRLYCDTCSVPICRECTMGEHRGHSFIYLQEAVQDSK 48
PHD_PHF21A cd15523
PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC ...
913-954 1.73e-09

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: 54.32  E-value: 1.73e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 767904604  913 CAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 954
Cdd:cd15523     2 CSVCRKSGELLMCDTCSLVYHLDCLDPPLKTIPKGMWICPKC 43
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
912-954 2.39e-09

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: 53.76  E-value: 2.39e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 767904604  912 WCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 954
Cdd:cd15531     1 YCEVCQQGGEIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 43
Bbox2 cd19756
B-box-type 2 zinc finger (Bbox2); The B-box-type zinc finger is a short zinc binding domain of ...
275-312 4.63e-09

B-box-type 2 zinc finger (Bbox2); The B-box-type zinc finger is a short zinc binding domain of around 40 amino acid residues in length. It has been found in transcription factors, ribonucleoproteins and proto-oncoproteins, such as in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). The B-box-type zinc finger often presents in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction. Based on different consensus sequence and the spacing of the 7-8 zinc-binding residues, B-box-type zinc fingers can be divided into two groups, type 1 (Bbox1: C6H2) and type 2 (Bbox2: CHC3H2). The family corresponds to type 2 B-box (Bbox2).


Pssm-ID: 380814 [Multi-domain]  Cd Length: 39  Bit Score: 52.80  E-value: 4.63e-09
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 767904604  275 FCPVHKQEQLKLFCETCDRLTCRDCQLL-EHKEHRYQFL 312
Cdd:cd19756     1 LCPEHPEEPLKLFCETCQELVCVLCLLSgEHRGHKVVPL 39
PHD4_NSD2 cd15657
PHD finger 4 found in nuclear SET domain-containing protein 2 (NSD2); NSD2, also termed ...
912-955 5.22e-09

PHD finger 4 found in nuclear SET domain-containing protein 2 (NSD2); NSD2, also termed histone-lysine N-methyltransferase NSD2, or multiple myeloma SET domain-containing protein (MMSET), or protein trithorax-5 Wolf-Hirschhorn syndrome candidate 1 protein (WHSC1), is overexpressed frequently in the t(4;14) translocation in 15% to 20% of multiple myeloma. It plays important roles in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. It also enhances androgen receptor (AR)-mediated transcription. The principal chromatin-regulatory activity of NSD2 is dimethylation of histone H3 at lysine 36 (H3K36me2). NSD2 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, a high mobility group (HMG) box, five PHD (plant-homeodomain) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP, HMG, and PHD fingers mediate chromatin interaction and recognition of histone marks. This model corresponds to the fourth PHD finger.


Pssm-ID: 277127  Cd Length: 41  Bit Score: 52.70  E-value: 5.22e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 767904604  912 WCAVCQNGGDLLCCEKCPKVFHLTChvpTLLSFPSGDWICTFCR 955
Cdd:cd15657     1 WCFVCSKGGSLLCCESCPAAFHPDC---LNIEMPDGSWFCNDCR 41
Bromo_Rsc1_2_I cd05521
Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
999-1076 8.03e-09

Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99952  Cd Length: 106  Bit Score: 54.25  E-value: 8.03e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767904604  999 HELSIEFQE-PVPASIPNYYKIIKKPMDLSTVKKKLqkkhsQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQE 1076
Cdd:cd05521    22 IEIHPIFNVlPLRKDYPDYYKIIKNPLSLNTVKKRL-----PHYTNAQEFVNDLAQIPWNARLYNTKGSVIYKYALILE 95
zf-B_box pfam00643
B-box zinc finger;
271-312 8.53e-09

B-box zinc finger;


Pssm-ID: 459886 [Multi-domain]  Cd Length: 42  Bit Score: 52.09  E-value: 8.53e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 767904604   271 QRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFL 312
Cdd:pfam00643    1 SKERLCPEHEEEPLTLYCNDCQELLCEECSVGEHRGHTVVPL 42
Bromo_brd7_like cd05513
Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ...
1005-1062 1.42e-08

Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99945  Cd Length: 98  Bit Score: 53.57  E-value: 1.42e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 767904604 1005 FQEPVPASI-PNYYKIIKKPMDLSTVKKKLqKKHSqhYQIPDDFVADVRLIFKNCERFN 1062
Cdd:cd05513    22 FAFPVTDFIaPGYSSIIKHPMDFSTMKEKI-KNND--YQSIEEFKDDFKLMCENAMKYN 77
Bbox1 cd19757
B-box-type 1 zinc finger (Bbox1); The B-box-type zinc finger is a short zinc binding domain of ...
216-256 2.61e-08

B-box-type 1 zinc finger (Bbox1); The B-box-type zinc finger is a short zinc binding domain of around 40 amino acid residues in length. It has been found in transcription factors, ribonucleoproteins and proto-oncoproteins, such as in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). The B-box-type zinc finger often presents in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain, in functionally unrelated proteins, most likely mediating protein-protein interactions. Based on different consensus sequences and the spacing of the 7-8 zinc-binding residues, the B-box-type zinc fingers can be divided into two groups, type 1 (Bbox1: C6H2) and type 2 (Bbox2: CHC3H2). This family corresponds to the type 1 B-box (Bbox1).


Pssm-ID: 380815 [Multi-domain]  Cd Length: 44  Bit Score: 50.96  E-value: 2.61e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 767904604  216 VCTSCEDNaSAVGFCVECGEWLCKTCIEA-HQRVKFTKDHLI 256
Cdd:cd19757     1 LCDECEER-EATVYCLECEEFLCDDCSDAiHRRGKLTRSHKL 41
Bbox1_BRAT-like cd19813
B-box-type 1 zinc finger found in Drosophila melanogaster brain tumor protein (BRAT) and ...
216-256 2.94e-08

B-box-type 1 zinc finger found in Drosophila melanogaster brain tumor protein (BRAT) and similar proteins; BRAT is a NHL-domain family protein that functions as a translational repressor to inhibit cell proliferation. The family also contains Caenorhabditis elegans B-box type zinc finger protein ncl-1, a C. elegans Brat homolog which functions as a translational repressor that inhibits protein synthesis. BRAT contains Bbox1 and Bbox2 zinc fingers and NHL repeats. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif.


Pssm-ID: 380871  Cd Length: 44  Bit Score: 50.87  E-value: 2.94e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 767904604  216 VCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLI 256
Cdd:cd19813     1 HCTGCKSKETAVARCFDCQVLLCANCVTAHQFMHCFKDHRV 41
PHD5_NSD cd15568
PHD finger 5 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
912-951 3.34e-08

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: 50.41  E-value: 3.34e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 767904604  912 WCAVCQNGGDLLCCEK--CPKVFHLTChvPTLLSFPSGDWIC 951
Cdd:cd15568     1 ECFRCGDGGDLVLCDFkgCPKVYHLSC--LGLEKPPGGKWIC 40
PHD4_NSD3 cd15658
PHD finger 4 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed ...
912-954 3.56e-08

PHD finger 4 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed histone-lysine N-methyltransferase NSD3, or protein whistle, or WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, or Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1-like protein 1, or WHSC1L1), is a lysine methyltransferase encoded by gene NSD3, which is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD3 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, five plant-homeodomain (PHD) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the fourth PHD finger.


Pssm-ID: 277128  Cd Length: 40  Bit Score: 50.30  E-value: 3.56e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 767904604  912 WCAVCQNGGDLLCCEKCPKVFHLTChvpTLLSFPSGDWICTFC 954
Cdd:cd15658     1 FCFVCARGGRLLCCESCPASFHPEC---LSIEMPEGCWNCNEC 40
PHD4_NSD cd15567
PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
912-954 3.88e-08

PHD finger 4 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 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 fourth PHD finger.


Pssm-ID: 277042 [Multi-domain]  Cd Length: 41  Bit Score: 50.32  E-value: 3.88e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 767904604  912 WCAVCQNGGDLLCCEKCPKVFHLTCHvpTLLSFPSGDWICTFC 954
Cdd:cd15567     1 WCFICSEGGSLICCESCPASFHPECL--GLEPPPEGKFYCEDC 41
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
999-1063 4.70e-08

Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99953 [Multi-domain]  Cd Length: 104  Bit Score: 52.24  E-value: 4.70e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767904604  999 HELSIEFQE-PVPASIPNYYKIIKKPMDLSTVKKKLQKKhsqHYQIPDDFVADVRLIFKNCERFNE 1063
Cdd:cd05522    22 RLLTLHFEKlPDKAREPEYYQEISNPISLDDIKKKVKRR---KYKSFDQFLNDLNLMFENAKLYNE 84
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
913-954 7.82e-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: 49.62  E-value: 7.82e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 767904604  913 CAVCQNGGD----LLCCEKCPKVFHLTCHVPTLLSF-PSGDWICTFC 954
Cdd:cd15489     2 CIVCGKGGDlggeLLQCDGCGKWFHADCLGPPLSSFvPNGKWICPVC 48
PHD4_NSD1 cd15656
PHD finger 4 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1); NSD1, ...
912-954 9.11e-08

PHD finger 4 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1); NSD1, also termed H3 Lysine-36 and H4 Lysine-20 specific histone-lysine N-methyltransferase, or androgen receptor coactivator 267 kDa protein, or androgen receptor-associated protein of 267 kDa, or H3-K36-HMTase H4-K20-HMTase, or Lysine N-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein, is a lysine methyltransferase that preferentially methylates H3 on Lysine36 (H3-K36) and H4 on Lysine20 (H4-K20), which is primarily associated with active transcription. It plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. It can alter transcription by interacting with the protein NSD1-interacting zinc finger protein 1 (NIZP1). It also mitigates caspase-1 activation by listeriolysin o (LLO) in macrophages, and requires functional LLO for the regulation of IL-1beta secretion. Moreover, NSD1 regulates RNA polymerase II (RNAP II) recruitment to bone morphogenetic protein 4 (BMP4). NSD1 contains 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). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the fourth PHD finger.


Pssm-ID: 277126  Cd Length: 40  Bit Score: 49.24  E-value: 9.11e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 767904604  912 WCAVCQNGGDLLCCEKCPKVFHLTChvpTLLSFPSGDWICTFC 954
Cdd:cd15656     1 WCFVCSEGGSLLCCESCPAAFHREC---LNIDMPEGSWYCNDC 40
PHD_BAZ1A_like cd15544
PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, ...
913-954 9.48e-08

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: 49.33  E-value: 9.48e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 767904604  913 CAVCQNGGD---LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 954
Cdd:cd15544     2 CKVCRKKGDpdnMILCDGCDKAFHLYCLRPALREVPSGDWFCPAC 46
PHD_SP110_140 cd15626
PHD finger found in the Sp100/Sp140 family of nuclear body components; The Sp100/Sp140 family ...
913-954 1.12e-07

PHD finger found in the Sp100/Sp140 family of nuclear body components; The Sp100/Sp140 family includes nuclear body proteins SP100, SP140, and similar proteins. Sp110, also termed interferon-induced protein 41/75, or speckled 110 kDa, or transcriptional coactivator 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. Sp110 gene polymorphisms may be associated with susceptibility to tuberculosis in Chinese population. Sp110 contains a Sp100-like domain, a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD). SP140, also termed lymphoid-restricted homolog of Sp100 (LYSp100), or nuclear autoantigen Sp-140, or speckled 140 kDa, 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's viral infectivity factor (Vif) protein. Sp140 contains a nuclear localization signal, a dimerization domain (HSR or CARD domain), a SAND domain, a PHD finger, and a BRD.


Pssm-ID: 277096  Cd Length: 42  Bit Score: 48.96  E-value: 1.12e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 767904604  913 CAVCQNGGDLLCCEKCPKVFHLTCHVPTlLSFPSGDWICTFC 954
Cdd:cd15626     2 CEVCGQEGKLFCCCTCSRVFHEDCHIPP-VEAQRSPWSCTFC 42
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
1004-1063 1.34e-07

Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99958  Cd Length: 128  Bit Score: 51.57  E-value: 1.34e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767904604 1004 EFQEPV--PASIPNYYKIIKKPMDLSTVKKKLQkkhSQHYQIPDDFVADVRLIFKNCERFNE 1063
Cdd:cd05529    47 YFEYPVdlRAWYPDYWNRVPVPMDLETIRSRLE---NRYYRSLEALRHDVRLILSNAETFNE 105
PHD_PRKCBP1 cd15538
PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed ...
913-954 1.45e-07

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: 48.86  E-value: 1.45e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 767904604  913 CAVCQNGGDLLCCEKCPKVFHLTCHVPTllSFPSGDWICTFC 954
Cdd:cd15538     2 CWRCHKEGQVLCCSLCPRVYHKKCLKLT--SEPDEDWVCPEC 41
RING-HC_TRIM45_C-VII cd16588
RING finger, HC subclass, found in tripartite motif-containing protein 45 (TRIM45) and similar ...
125-187 1.68e-07

RING finger, HC subclass, found in tripartite motif-containing protein 45 (TRIM45) and similar proteins; TRIM45, also known as RING finger protein 99 (RNF99), is a novel receptor for activated C-kinase (RACK1)-interacting protein that suppresses transcriptional activities of Elk-1 and AP-1 and downregulates mitogen-activated protein kinase (MAPK) signal transduction through inhibiting RACK1/PKC (protein kinase C) complex formation. It also negatively regulates tumor necrosis factor alpha (TNFalpha)-induced nuclear factor-kappaB (NF-kappa B)-mediated transcription and suppresses cell proliferation. TRIM45 belongs to the C-VII subclass of the TRIM (tripartite motif) family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a filamin-type immunoglobulin (IG-FLMN) domain and NHL repeats positioned C-terminal to the RBCC domain.


Pssm-ID: 438250 [Multi-domain]  Cd Length: 59  Bit Score: 49.06  E-value: 1.68e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767904604  125 CAVCQQSLQsrreaEPKLLPCLHSFCLRCLPEPErQLSVPIPGGSNGDIQQVGVIRCPVCRQE 187
Cdd:cd16588     3 CPVCGKLFQ-----EPRLLPCLHTLCSPCLRQLE-PFSVCGLRGGDRSEKSNYSVLCPVCDSE 59
PHD1_Rco1 cd15535
PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and ...
913-954 2.12e-07

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: 48.18  E-value: 2.12e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 767904604  913 CAVCQNGGDLLCCEKCPKVFHLTCHVPTL--LSFPSGDWICTFC 954
Cdd:cd15535     2 CSACGGYGSFLCCDGCPRSFHFSCLDPPLeeDNLPDDEWFCNEC 45
Bromo_SNF2L2 cd05516
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ...
1006-1063 3.82e-07

Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99947  Cd Length: 107  Bit Score: 49.73  E-value: 3.82e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 767904604 1006 QEPVPASIPNYYKIIKKPMDLstvkKKLQKKHSQH-YQIPDDFVADVRLIFKNCERFNE 1063
Cdd:cd05516    30 QLPSRKELPEYYELIRKPVDF----KKIKERIRNHkYRSLEDLEKDVMLLCQNAQTFNL 84
Bromo_RACK7 cd05508
Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) ...
1005-1062 4.04e-07

Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) was identified as a potential tumor suppressor genes, it shares domain architecture with BS69/ZMYND11; both have been implicated in the regulation of cellular proliferation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99940  Cd Length: 99  Bit Score: 49.30  E-value: 4.04e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 767904604 1005 FQEPVPAS-IPNYYKIIKKPMDLSTVKKKLQKKhsqHYQIPDDFVADVRLIFKNCERFN 1062
Cdd:cd05508    23 FLKPVDLEqFPDYAQYVFKPMDLSTLEKNVRKK---AYGSTDAFLADAKWILHNAIIYN 78
RING-HC_PML_C-V cd16579
RING finger, HC subclass, found in promyelocytic leukemia protein (PML) and similar proteins; ...
124-186 5.16e-07

RING finger, HC subclass, found in promyelocytic leukemia protein (PML) and similar proteins; Protein PML, also known as RING finger protein 71 (RNF71) or tripartite motif-containing protein 19 (TRIM19), is predominantly a nuclear protein with a broad intrinsic antiviral activity. It is the eponymous component of PML nuclear bodies (PML NBs) and has been implicated in a wide variety of cell processes, including DNA damage signaling, apoptosis, and transcription. PML interferes with the replication of many unrelated viruses, including human immunodeficiency virus 1 (HIV-1), human foamy virus (HFV), poliovirus, influenza virus, rabies virus, EMCV, adeno-associated virus (AAV), and vesicular stomatitis virus (VSV). It also selectively interacts with misfolded proteins through distinct substrate recognition sites and conjugates these proteins with the small ubiquitin-like modifiers (SUMOs) through its SUMO ligase activity. PML belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain.


Pssm-ID: 438241 [Multi-domain]  Cd Length: 52  Bit Score: 47.55  E-value: 5.16e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767904604  124 TCAVCQQSLqsrreAEPKLLPCLHSFCLRCLPEPERQLSvpipggsngdiqQVGVIRCPVCRQ 186
Cdd:cd16579     6 RCPGCKAEY-----KCPKLLPCLHTVCSGCLEALAEQAS------------ETTEFQCPICKA 51
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
1014-1077 5.70e-07

Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99948  Cd Length: 103  Bit Score: 48.97  E-value: 5.70e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767904604 1014 PNYYKIIKKPMDLSTVKKKLQkkhSQHYQIPDDFVADVRLIFKNCERFNEMMKvvQVYADTQEI 1077
Cdd:cd05517    37 PDYYAVIKEPIDLKTIAQRIQ---SGYYKSIEDMEKDLDLMVKNAKTFNEPGS--QVYKDANAI 95
PHD_BAZ2A cd15629
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also ...
913-954 5.93e-07

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: 47.15  E-value: 5.93e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 767904604  913 CAVCQNGGD---LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 954
Cdd:cd15629     2 CLVCRKGDNdeyLLLCDGCDRGCHMYCHRPKMLQVPEGDWFCPNC 46
PHD_PHF21B cd15524
PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) ...
912-954 7.69e-07

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: 46.81  E-value: 7.69e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 767904604  912 WCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 954
Cdd:cd15524     1 HCAACKRGGNLQPCGTCPRAYHLDCLDPPLKTAPKGVWVCPKC 43
Bbox1_TRIM19_C-V cd19804
B-box-type 1 zinc finger found in promyelocytic leukemia protein (PML) and similar proteins; ...
214-261 1.06e-06

B-box-type 1 zinc finger found in promyelocytic leukemia protein (PML) and similar proteins; Protein PML, also known as RING finger protein 71 (RNF71) or tripartite motif-containing protein 19 (TRIM19), is predominantly a nuclear protein with a broad intrinsic antiviral activity. It is the eponymous component of PML nuclear bodies (PML NBs) and has been implicated in a wide variety of cellular processes, including DNA damage signaling, apoptosis, and transcription. PML interferes with the replication of many unrelated viruses, including human immunodeficiency virus 1 (HIV-1), human foamy virus (HFV), poliovirus, influenza virus, rabies virus, EMCV, adeno-associated virus (AAV), and vesicular stomatitis virus (VSV). It also selectively interacts with misfolded proteins through distinct substrate recognition sites, and conjugates these proteins with the small ubiquitin-like modifiers (SUMOs) through its SUMO ligase activity. PML belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif.


Pssm-ID: 380862 [Multi-domain]  Cd Length: 47  Bit Score: 46.30  E-value: 1.06e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 767904604  214 EQVCTSCEDNaSAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKED 261
Cdd:cd19804     1 ELMCNRCSES-EAEFWCSECEEFLCRKCFEAHQRFKKRKKHEALRLAE 47
Bbox2_TRIM2-like cd19759
B-box-type 2 zinc finger found in tripartite motif-containing protein TRIM2, TRIM3, and ...
273-314 1.29e-06

B-box-type 2 zinc finger found in tripartite motif-containing protein TRIM2, TRIM3, and similar proteins; TRIM2, also known as RING finger protein 86 (RNF86), is an E3 ubiquitin-protein ligase that ubiquitinates the neurofilament light chain, a component of the intermediate filament in axons. Loss of function of TRIM2 results in early-onset axonal neuropathy. TRIM3, also known as brain-expressed RING finger protein (BERP), RING finger protein 97 (RNF97), or RING finger protein 22 (RNF22), is an E3 ubiquitin-protein ligase involved in the pathogenesis of various cancers. It also plays an important role in the central nervous system (CNS). In addition, TRIM3 may be involved in vesicular trafficking via its association with the cytoskeleton-associated-recycling or transport (CART) complex that is necessary for efficient transferrin receptor recycling, but not for epidermal growth factor receptor (EGFR) degradation. Both TRIM2 and TRIM3 belong to the C-VII subclass of TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380817 [Multi-domain]  Cd Length: 42  Bit Score: 45.90  E-value: 1.29e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 767904604  273 PVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEE 314
Cdd:cd19759     1 PLVCPNHDGETLEFYCESCETAVCRECTAGEHNEHRTVLLKD 42
PHD_BAZ1B cd15628
PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also ...
913-954 1.48e-06

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: 45.89  E-value: 1.48e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 767904604  913 CAVCQNGGD---LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 954
Cdd:cd15628     2 CKVCRKKGEddkLILCDECNQAFHLFCLRPALYEVPDGEWMCPAC 46
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
1014-1076 2.10e-06

Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99954 [Multi-domain]  Cd Length: 113  Bit Score: 47.71  E-value: 2.10e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767904604 1014 PNYYKIIKKPMDLSTVKKKLQkkhSQHYQIPDDFVADVRLIFKNCERF--------NEMMKVVQVYADTQE 1076
Cdd:cd05524    39 PEYYEVVSNPIDLLKIQQKLK---TEEYDDVDDLTADFELLINNAKAYykpdspehKDACKLWELFLSARN 106
PHD_BAZ1A cd15627
PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also ...
913-954 2.62e-06

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: 45.46  E-value: 2.62e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 767904604  913 CAVCQNGGD---LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 954
Cdd:cd15627     2 CRICRRKGDaekMLLCDGCDRGHHMYCLRPPLKKVPEGDWFCPDC 46
PHD_BAZ2A_like cd15545
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B ...
913-954 2.69e-06

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: 45.38  E-value: 2.69e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 767904604  913 CAVCQNGGD---LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 954
Cdd:cd15545     2 CQICRSGDNedqLLLCDGCDRGYHTYCFKPKMTNVPEGDWFCPEC 46
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
1005-1063 2.96e-06

Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99951  Cd Length: 103  Bit Score: 46.95  E-value: 2.96e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 767904604 1005 FQEPVPASIPNYYKIIKKPMDLSTVKKKLQKkhsQHYQIPDDFVADVRLIFKNCERFNE 1063
Cdd:cd05520    28 LKLPSKRKYPDYYQEIKNPISLQQIRTKLKN---GEYETLEELEADLNLMFENAKRYNV 83
CC_brat-like cd20482
coiled-coil (CC) domain of Drosophila brain tumor (brat) and similar proteins; This family ...
319-440 4.89e-06

coiled-coil (CC) domain of Drosophila brain tumor (brat) and similar proteins; This family contains the coiled-coil (CC) region of Drosophila brain tumor (Brat), a translational repressor that belongs to the tripartite motif (TRIM) protein superfamily. TRIM proteins play important roles in various cellular processes and are involved in many diseases which consists of two B-box domains and a coiled-coil (CC) domain at the N-terminal region, and an NHL domain at the C-terminus. Brat localizes at the basal cortex during asymmetric division of Drosophila neuroblasts by directly interacting with the scaffolding protein Miranda (Mira), which it does through the CC-NHL domain tandem, indicating that the function of the Brat CC domain is to assemble Brat-NHL in dimeric form which is necessary for Mira binding. Brat CC forms an elongated antiparallel dimer similar to its other TRIM protein counterparts, but the overall length of Brat CC dimer is shorter than the TRIMs.


Pssm-ID: 467844 [Multi-domain]  Cd Length: 122  Bit Score: 46.76  E-value: 4.89e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604  319 QKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKL-LQ 397
Cdd:cd20482     1 HKESLQQLLEEARAKIPELRDALKNVEHALSRLQMQYHKAQNEINETFQFYRSMLEERKDELLKELESIYNAKQLSLnEQ 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 767904604  398 QQNDITGLSRqVKHVMNFTNWAIASGSSTALLYSKRLITFQLR 440
Cdd:cd20482    81 QQKLQETIEK-IQQGCEFTERLLKHGSETEVLLFKKLLEARLQ 122
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
603-763 5.65e-06

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 50.69  E-value: 5.65e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604   603 PRHSGPQYS---MMQPHLQRQHSNPGHAGPFPVVSVhnTTINPTSPTTATMANANrGPTSPSVTAIELIPSVTNPE---N 676
Cdd:pfam05109  494 PRDNGTESKapdMTSPTSAVTTPTPNATSPTPAVTT--PTPNATSPTLGKTSPTS-AVTTPTPNATSPTPAVTTPTpnaT 570
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604   677 LPSLPDIPPIQANVVPMMHSWY----EFGAREKTQDQNLEDAGSSSL-----DNLLSRYISGSH-LPPQPTSTMN--PSP 744
Cdd:pfam05109  571 IPTLGKTSPTSAVTTPTPNATSptvgETSPQANTTNHTLGGTSSTPVvtsppKNATSAVTTGQHnITSSSTSSMSlrPSS 650
                          170
                   ....*....|....*....
gi 767904604   745 GPSALSPGSSGLSNSHTPV 763
Cdd:pfam05109  651 ISETLSPSTSDNSTSHMPL 669
BBOX smart00336
B-Box-type zinc finger;
212-248 8.44e-06

B-Box-type zinc finger;


Pssm-ID: 197662 [Multi-domain]  Cd Length: 42  Bit Score: 43.87  E-value: 8.44e-06
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|.
gi 767904604    212 KSEQVCTSCEDNAsAVGFCVECGEWLCKTCIEA----HQRV 248
Cdd:smart00336    1 QRAPKCDSHGDEP-AEFFCEECGALLCRTCDEAehrgHTVV 40
RING-HC_TRIM65_C-IV cd16609
RING finger, HC subclass, found in tripartite motif-containing protein TRIM65 and similar ...
124-187 9.96e-06

RING finger, HC subclass, found in tripartite motif-containing protein TRIM65 and similar proteins; TRIM65 is an E3 ubiquitin-protein ligase that interacts with the innate immune receptor MDA5, enhancing its ability to stimulate interferon-beta signaling. It functions as a potential oncogenic protein that negatively regulates p53 through ubiquitination, providing insight into the development of novel approaches targeting TRIM65 for non-small cell lung carcinoma (NSCLC) treatment, and also overcoming chemotherapy resistance. Moreover, TRIM65 negatively regulates microRNA-driven suppression of mRNA translation by targeting TNRC6 proteins for ubiquitination and degradation. TRIM65 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438271 [Multi-domain]  Cd Length: 58  Bit Score: 43.90  E-value: 9.96e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767904604  124 TCAVCQQSLQsrreaEPKLLPCLHSFCLRCLPEPERQLSvpipggsngdiqqVGVIRCPVCRQE 187
Cdd:cd16609     5 TCSICLGLYQ-----DPVTLPCQHSFCRACIEDHWRQKD-------------EGSFSCPECRAP 50
Bromo_SNF2 cd05519
Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in ...
1014-1077 1.02e-05

Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99950  Cd Length: 103  Bit Score: 45.41  E-value: 1.02e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767904604 1014 PNYYKIIKKPMDLSTVKKKLQkkhSQHYQIPDDFVADVRLIFKNCERFNEMMKVvqVYADTQEI 1077
Cdd:cd05519    37 PDYYVIIKRPIALDQIKRRIE---GRAYKSLEEFLEDFHLMFANARTYNQEGSI--VYEDAVEM 95
Bbox2_TRIM14 cd19768
B-box-type 2 zinc finger found in tripartite motif-containing protein 14 (TRIM14) and similar ...
276-315 1.25e-05

B-box-type 2 zinc finger found in tripartite motif-containing protein 14 (TRIM14) and similar proteins; TRIM14 is a mitochondrial adaptor that facilitates innate immune signaling. It also plays a critical role in tumor development. TRIM14 belongs to an unclassified TRIM (tripartite motif) family of proteins that do not have RING fingers and thus lack the characteristic tripartite (RING (R), B-box, and coiled coil (CC)) RBCC motif. It contains a Bbox2 zinc finger as well as a C-terminal SPRY/B30.2 domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380826 [Multi-domain]  Cd Length: 44  Bit Score: 43.18  E-value: 1.25e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 767904604  276 CPVHKQEQLKLFCETCDRLTCRDCQLL-EHKEHRYQFLEEA 315
Cdd:cd19768     3 CPEHKDRPLELFCKTCKRCVCALCPILgQHRGHDVRLIDEE 43
Bbox1_TRIM45_C-X cd19809
B-box-type 1 zinc finger found in tripartite motif-containing protein 45 (TRIM45) and similar ...
216-257 1.37e-05

B-box-type 1 zinc finger found in tripartite motif-containing protein 45 (TRIM45) and similar proteins; TRIM45, also known as RING finger protein 99 (RNF99), is a novel receptor for activated C-kinase (RACK1)-interacting protein that suppresses transcriptional activities of Elk-1 and AP-1, and downregulates mitogen-activated protein kinase (MAPK) signal transduction by inhibiting RACK1/PKC (protein kinase C) complex formation. It also negatively regulates tumor necrosis factor alpha (TNFalpha)-induced nuclear factor-kappaB (NF-kappa B)-mediated transcription, and suppresses cell proliferation. TRIM45 belongs to the C-X subclass of the TRIM (tripartite motif) family of proteins that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a filamin-type immunoglobulin (IG-FLMN) domain and NHL repeats positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif.


Pssm-ID: 380867  Cd Length: 46  Bit Score: 43.13  E-value: 1.37e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 767904604  216 VCTSC-EDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIR 257
Cdd:cd19809     2 LCDLCtDGNSSAEYRCFDCSENLCEFCKQAHRRQRKTASHRII 44
PHD1_KDM5A_like cd15515
PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar ...
913-954 1.59e-05

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: 43.15  E-value: 1.59e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 767904604  913 CAVCQNGGD---LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 954
Cdd:cd15515     2 CQVCGRGDDedkLLLCDGCDDSYHTFCLIPPLPDIPPGDWRCPKC 46
ADDz_ATRX cd11726
ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked); ADDz_ATRX is a ...
904-936 2.11e-05

ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked); ADDz_ATRX is a PHD-like zinc finger domain of ATRX, which belongs to the SNF2 family of chromatin remodeling proteins. ATRX is a large chromatin-associated nuclear protein with two domains, ADDz_ATRX at the N-terminus, followed by a C-terminal ATPase/helicase domain. The ADDz_ATRX domain recognizes a specific methylated histone, and this interaction is required for heterochromatin localization of the ATRX protein. Missense mutations in either of the two ATRX domains lead to the X-linked alpha-thalassemia and mental retardation syndrome; however the mutations in the ADDz_ATRX domain produce a more severe disease phenotype that may also relate to disturbing unknown functions or interaction sites of this domain. The ADDz domain is also present in chromatin-associated proteins cytosine-5-methyltransferase 3 (Dnmt3); it is a PHD-like zinc finger motif that contains two parts, a C2-C2 and a PHD-like zinc finger. PHD zinc finger domains have been identified in more than 40 proteins that are mainly involved in chromatin mediated transcriptional control; the classical PHD zinc finger has a C4-H-C3 motif that spans about 50-80 amino acids. In ADDz, the conserved histidine residue of the PHD finger is replaced by a cysteine, and an additional zinc finger C2-C2 like motif is located about twenty residues upstream of the C4-C-C3 motif.


Pssm-ID: 277252 [Multi-domain]  Cd Length: 102  Bit Score: 44.60  E-value: 2.11e-05
                          10        20        30
                  ....*....|....*....|....*....|...
gi 767904604  904 KDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTC 936
Cdd:cd11726    44 KDEDGSDEYCRWCGQGGDLICCDFCPNVFCKKC 76
PHD1_Lid2p_like cd15519
PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
913-954 2.38e-05

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: 42.45  E-value: 2.38e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 767904604  913 CAVC---QNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 954
Cdd:cd15519     2 CEVCgldDNEGEVLLCDGCDAEYHTSCLDPPLGEIPPGTWFCPSC 46
Bbox2_TRIM3_C-VII cd19825
B-box-type 2 zinc finger found in tripartite motif-containing protein 3 (TRIM3); TRIM3, also ...
272-307 2.52e-05

B-box-type 2 zinc finger found in tripartite motif-containing protein 3 (TRIM3); TRIM3, also known as brain-expressed RING finger protein (BERP), RING finger protein 97 (RNF97), or RING finger protein 22 (RNF22), is an E3 ubiquitin-protein ligase involved in the pathogenesis of various cancers. It functions as a tumor suppressor that regulates asymmetric cell division in neuroblastoma. It binds to the ck inhibitor p21(WAF1/CIP1) and regulates its availability that promotes cyclins D1-cdk4 nuclear accumulation. Moreover, TRIM3 plays an important role in the central nervous system (CNS). It corresponds to gene BERP (brain-expressed RING finger protein), a unique p53-regulated gene that modulates seizure susceptibility and GABAAR cell surface expression. Furthermore, TRIM3 mediates activity-dependent turnover of presynaptic density (PSD) scaffold proteins GKAP/SAPAP1 and is a negative regulator of dendrite spine morphology. In addition, TRIM3 may be involved in vesicular trafficking via its association with the cytoskeleton-associated-recycling or transport (CART) complex that is necessary for efficient transferrin receptor recycling, but not for epidermal growth factor receptor (EGFR) degradation. It also regulates the motility of the kinesin superfamily protein KIF21B. TRIM3 belongs to the C-VII subclass of TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380883 [Multi-domain]  Cd Length: 47  Bit Score: 42.69  E-value: 2.52e-05
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 767904604  272 RPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEH 307
Cdd:cd19825     5 KPLSCPNHEGKTMEFYCESCETAMCRECTEGEHREH 40
PHD_BAZ2B cd15630
PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also ...
912-954 4.48e-05

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: 41.88  E-value: 4.48e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 767904604  912 WCAVCQNGGD---LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 954
Cdd:cd15630     2 YCQICRKGDNeelLLLCDGCDKGCHTYCHRPKITTIPEGDWFCPAC 47
PHD1_KDM5B cd15603
PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
913-954 4.71e-05

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: 41.86  E-value: 4.71e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 767904604  913 CAVCQNGGD---LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 954
Cdd:cd15603     2 CLVCGSGNDedrLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 46
PHD_RSF1 cd15543
PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV ...
913-954 5.06e-05

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: 41.49  E-value: 5.06e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 767904604  913 CAVCQNGGD---LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 954
Cdd:cd15543     2 CRKCGLSDHpewILLCDRCDAGYHTACLRPPLMIIPDGNWFCPPC 46
RING-HC_TRIM7-like_C-IV cd16594
RING finger, HC subclass, found in tripartite motif-containing proteins, TRIM7, TRIM11 and ...
124-196 6.62e-05

RING finger, HC subclass, found in tripartite motif-containing proteins, TRIM7, TRIM11 and TRIM27, and similar proteins; TRIM7, TRIM11 and TRIM27, closely related tripartite motif-containing proteins, belong to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. TRIM7, also known as glycogenin-interacting protein (GNIP) or RING finger protein 90 (RNF90), is an E3 ubiquitin-protein ligase that mediates c-Jun/AP-1 activation by Ras signalling. Its phosphorylation and activation by MSK1 in response to direct activation by the Ras-Raf-MEK-ERK pathway can stimulate TRIM7 E3 ubiquitin ligase activity in mediating Lys63-linked ubiquitination of the AP-1 coactivator RACO-1, leading to RACO-1 protein stabilization. Moreover, TRIM7 binds and activates glycogenin, the self-glucosylating initiator of glycogen biosynthesis. TRIM11, also known as protein BIA1, or RING finger protein 92 (RNF92), is an E3 ubiquitin-protein ligase involved in the development of the central nervous system. It is overexpressed in high-grade gliomas and promotes proliferation, invasion, migration and glial tumor growth. TRIM11 acts as a potential therapeutic target for congenital central hypoventilation syndrome (CCHS) by mediating the degradation of CCHS-associated polyalanine-expanded Phox2b. TRIM11 modulates the function of neurogenic transcription factor Pax6 through the ubiquitin-proteosome system, and thus plays an essential role for Pax6-dependent neurogenesis. It also binds to and destabilizes a key component of the activator-mediated cofactor complex (ARC105), humanin, a neuroprotective peptide against Alzheimer's disease-relevant insults, and further regulates ARC105 function in transforming growth factor beta (TGFbeta) signaling. Moreover, TRIM11 negatively regulates retinoic acid-inducible gene-I (RIG-I)-mediated interferon-beta (IFNbeta) production and antiviral activity by targeting TANK-binding kinase-1 (TBK1). It may contribute to the endogenous restriction of retroviruses in cells. It enhances N-tropic murine leukemia virus (N-MLV) entry by interfering with Ref1 restriction. It also suppresses the early steps of human immunodeficiency virus HIV-1 transduction, resulting in decreased reverse transcripts. TRIM27, also known as RING finger protein 76 (RNF76), RET finger protein (RFP), or zinc finger protein RFP, is a nuclear E3 ubiquitin-protein ligase that is highly expressed in testis and in various tumor cell lines. Expression of TRIM27 is associated with prognosis of colon and endometrial cancers. TRIM27 was first identified as a fusion partner of the RET receptor tyrosine kinase. It functions as a transcriptional repressor and associates with several proteins involved in transcriptional activity, such as enhancer of polycomb 1 (Epc1), a member of the Polycomb group proteins, and Mi-2beta, a main component of the nucleosome remodeling and deacetylase (NuRD) complex, and the cell cycle regulator retinoblastoma protein (RB1). It also interacts with HDAC1, leading to downregulation of thioredoxin binding protein 2 (TBP-2), which inhibits the function of thioredoxin. Moreover, TRIM27 mediates Pax7-induced ubiquitination of MyoD in skeletal muscle atrophy. In addition, it inhibits muscle differentiation by modulating serum response factor (SRF) and Epc1. TRIM27 promotes a non-canonical polyubiquitination of PTEN, a lipid phosphatase that catalyzes PtdIns(3,4,5)P3 (PIP3) to PtdIns(4,5)P2 (PIP2). It is an IKKepsilon-interacting protein that regulates IkappaB kinase (IKK) function and negatively regulates signaling involved in the antiviral response and inflammation. TRIM27 also forms a protein complex with MBD4 or MBD2 or MBD3, and thus plays an important role in the enhancement of transcriptional repression through MBD proteins in tumorigenesis, spermatogenesis, and embryogenesis. It is a component of an estrogen receptor 1 (ESR1) regulatory complex that is involved in estrogen receptor-mediated transcription in MCF-7 cells.


Pssm-ID: 438256 [Multi-domain]  Cd Length: 61  Bit Score: 41.90  E-value: 6.62e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767904604  124 TCAVCQQSLQsrreaEPKLLPCLHSFCLRCL----PEPERQLSvpipggsngdiqqvgvirCPVCRQECRQIDLVDN 196
Cdd:cd16594     7 TCPICLDYFT-----DPVTLDCGHSFCRACIarcwEEPETSAS------------------CPQCRETCPQRNLRPN 60
RING-HC_EHV1-like cd23130
RING finger, HC subclass, found in Equid alphaherpesvirus 1 (Equine herpesvirus 1/EHV-1) ...
123-154 8.92e-05

RING finger, HC subclass, found in Equid alphaherpesvirus 1 (Equine herpesvirus 1/EHV-1) regulatory protein and similar proteins; EHV-1 regulatory protein belongs to the Vmw110 (IPC0) protein family. It contains a typical C3HC4-type RING-HC finger and binds zinc stably.


Pssm-ID: 438492 [Multi-domain]  Cd Length: 51  Bit Score: 41.18  E-value: 8.92e-05
                          10        20        30
                  ....*....|....*....|....*....|..
gi 767904604  123 DTCAVCQQSLqsrrEAEPKLLPCLHSFCLRCL 154
Cdd:cd23130     1 DVCPICLDDP----EDEAITLPCLHQFCYTCI 28
RING-HC_TRIM2_like_C-VII cd16586
RING finger, HC subclass, found in tripartite motif-containing protein TRIM2, TRIM3, and ...
125-185 1.03e-04

RING finger, HC subclass, found in tripartite motif-containing protein TRIM2, TRIM3, and similar proteins; TRIM2, also known as RING finger protein 86 (RNF86), is an E3 ubiquitin-protein ligase that ubiquitinates the neurofilament light chain, a component of the intermediate filament in axons. Loss of function of TRIM2 results in early-onset axonal neuropathy. TRIM3, also known as brain-expressed RING finger protein (BERP), RING finger protein 97 (RNF97), or RING finger protein 22 (RNF22), is an E3 ubiquitin-protein ligase involved in the pathogenesis of various cancers. It also plays an important role in the central nervous system (CNS). In addition, TRIM3 may be involved in vesicular trafficking via its association with the cytoskeleton-associated-recycling or transport (CART) complex that is necessary for efficient transferrin receptor recycling, but not for epidermal growth factor receptor (EGFR) degradation. Both TRIM2 and TRIM3 belong to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438248 [Multi-domain]  Cd Length: 45  Bit Score: 40.90  E-value: 1.03e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767904604  125 CAVCQQslqsrREAEPKLLPCLHSFCLRCLPE--PERQLSVPipggsngdiqqvgvirCPVCR 185
Cdd:cd16586     4 CGICLE-----RYKNPKVLPCLHTFCERCLQNyiPAESLSLS----------------CPVCR 45
Bromo_brd8_like cd05507
Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with ...
995-1062 1.17e-04

Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99939  Cd Length: 104  Bit Score: 42.35  E-value: 1.17e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767904604  995 YLYCHELSIEFQEPVPASI-PNYYKIIKKPMDLSTVKKKLQK---KHSQHYQIpddfvaDVRLIFKNCERFN 1062
Cdd:cd05507    14 TLASHRYASVFLKPVTEDIaPGYHSVVYRPMDLSTIKKNIENgtiRSTAEFQR------DVLLMFQNAIMYN 79
RING-HC_RNF183-like cd16556
RING finger, HC subclass, found in RING finger protein RNF183, RNF223, RNF225 and similar ...
140-186 1.23e-04

RING finger, HC subclass, found in RING finger protein RNF183, RNF223, RNF225 and similar proteins; RNF183 is an E3 ubiquitin-protein ligase that is upregulated during intestinal inflammation and is negatively regulated by miR-7. It promotes intestinal inflammation by increasing the ubiquitination and degradation of inhibitor of kappa B, thereby resulting in secondary activation of the Nuclear factor-kappaB (NF-kB) pathway. The interaction between RNF183-mediated ubiquitination and miRNA may be an important novel epigenetic mechanism in the pathogenesis of inflammatory bowel disease (IBD). The biological function of RNF223 and RNF225 remains unclear. Members of this family contain an N-terminal C3HC4-type RING-HC finger.


Pssm-ID: 438218 [Multi-domain]  Cd Length: 57  Bit Score: 40.82  E-value: 1.23e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 767904604  140 PKLLPCLHSFCLRCLPeperQLSVPIPGGSNGdiqqvgvIRCPVCRQ 186
Cdd:cd16556    17 PKLLDCGHTFCLECLA----RLSLASPPQAER-------VPCPLCRQ 52
Bbox2_TRIM11_C-IV cd19766
B-box-type 2 zinc finger found in tripartite motif-containing protein 11 (TRIM11) and similar ...
276-317 1.31e-04

B-box-type 2 zinc finger found in tripartite motif-containing protein 11 (TRIM11) and similar proteins; TRIM11, also known as protein BIA1, or RING finger protein 92 (RNF92), is an E3 ubiquitin-protein ligase involved in the development of the central nervous system. It is overexpressed in high-grade gliomas and promotes proliferation, invasion, migration and glial tumor growth. TRIM11 acts as a potential therapeutic target for congenital central hypoventilation syndrome (CCHS) through mediating the degradation of CCHS-associated polyalanine-expanded Phox2b. Trim11 modulates the function of neurogenic transcription factor Pax6 through the ubiquitin-proteosome system, and thus plays an essential role for Pax6-dependent neurogenesis. It also binds to and destabilizes a key component of the activator-mediated cofactor complex (ARC105), humanin, a neuroprotective peptide against Alzheimer's disease-relevant insults, and further regulates ARC105 function in transforming growth factor beta (TGFbeta) signaling. Moreover, TRIM11 negatively regulates retinoic acid-inducible gene-I (RIG-I)-mediated interferon-beta (IFNbeta) production and antiviral activity by targeting TANK-binding kinase-1 (TBK1). It may contribute to the endogenous restriction of retroviruses in cells. It enhances N-tropic murine leukemia virus (N-MLV) entry by interfering with Ref1 restriction. It also suppresses the early steps of human immunodeficiency virus HIV-1 transduction, resulting in decreased reverse transcripts. TRIM11 belongs to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380824 [Multi-domain]  Cd Length: 44  Bit Score: 40.57  E-value: 1.31e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 767904604  276 CPVHKqEQLKLFCETCDRLTCRDC-QLLEHKEHRYQFLEEAFQ 317
Cdd:cd19766     3 CGKHR-EPLKLFCKDHEALLCVVCeRSREHWGHRVVPAEEAAQ 44
Bbox2_TRIM2_C-VII cd19824
B-box-type 2 zinc finger found in tripartite motif-containing protein 2 (TRIM2) and similar ...
273-307 1.76e-04

B-box-type 2 zinc finger found in tripartite motif-containing protein 2 (TRIM2) and similar proteins; TRIM2, also known as RING finger protein 86 (RNF86), is an E3 ubiquitin-protein ligase that ubiquitinates the neurofilament light chain, a component of the intermediate filament in axons. Loss of function of TRIM2 results in early-onset axonal neuropathy. TRIM2 also plays a role in mediating the p42/p44 Semi-independent ubiquitination of the cell death-promoting protein Bcl-2-interacting mediator of cell death (Aim) in rapid ischemic tolerance. TRIM2 belongs to the C-VII subclass of TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380882 [Multi-domain]  Cd Length: 42  Bit Score: 40.04  E-value: 1.76e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 767904604  273 PVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEH 307
Cdd:cd19824     1 PLSCPNHDGNVMEFYCQSCETAMCQECTEGEHAEH 35
Bromo_ASH1 cd05525
Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the ...
1008-1062 1.87e-04

Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99955 [Multi-domain]  Cd Length: 106  Bit Score: 41.99  E-value: 1.87e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 767904604 1008 PVPASIPNYYKIIKKPMDLSTVKKKLQKKhsqHYQIPDDFVADVRLIFKNCERFN 1062
Cdd:cd05525    33 PSKKKNPDYYERITDPVDLSTIEKQILTG---YYKTPEAFDSDMLKVFRNAEKYY 84
PHD1_MTF2_PHF19_like cd15499
PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ...
913-954 2.48e-04

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: 39.79  E-value: 2.48e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 767904604  913 CAVCQN-----GGDLLCCEKCPKVFHLTCHVPTLLSFP---SGDWICTFC 954
Cdd:cd15499     2 CSICGGaeardGNEILICDKCDKGYHQLCHSPKVRTSPlegDEKWFCSRC 51
RING-HC cd16449
HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type ...
124-184 2.85e-04

HC subclass of RING (RING-HC) finger 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 a different Cys/His pattern. Some lack a single Cys or His residue at typical Zn ligand positions, especially, the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can chelate Zn in a RING finger as well. This family corresponds to the HC subclass of RING (RING-HC) fingers that are characterized by containing C3HC4-type canonical RING-HC fingers or noncanonical RING-HC finger variants, including C4C4-, C3HC3D-, C2H2C4-, and C3HC5-type modified RING-HC fingers. The canonical RING-HC finger has been defined as C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C. It binds two Zn ions in a unique "cross-brace" arrangement, which distinguishes it from tandem zinc fingers and other similar motifs. RING-HC fingers 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 serve as scaffolds 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: 438113 [Multi-domain]  Cd Length: 41  Bit Score: 39.39  E-value: 2.85e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767904604  124 TCAVCQQSLQsrreaEPKLLPCLHSFCLRCLPEperqlsvpipggsngdIQQVGVIRCPVC 184
Cdd:cd16449     2 ECPICLERLK-----DPVLLPCGHVFCRECIRR----------------LLESGSIKCPIC 41
RING-HC_TRIM32_C-VII cd16587
RING finger, HC subclass, found in tripartite motif-containing protein 32 (TRIM32) and similar ...
124-186 3.45e-04

RING finger, HC subclass, found in tripartite motif-containing protein 32 (TRIM32) and similar proteins; TRIM32, also known as 72 kDa Tat-interacting protein, zinc finger protein HT2A, or BBS11, is an E3 ubiquitin-protein ligase that promotes degradation of several targets, including actin, PIASgamma, Abl interactor 2, dysbindin, X-linked inhibitor of apoptosis (XIAP), p73 transcription factor, thin filaments and Z-bands during fasting. It plays important roles in neuronal differentiation of neural progenitor cells, as well as in controlling cell fate in skeletal muscle progenitor cells. It reduces PI3K-Akt-FoxO signaling in muscle atrophy by promoting plakoglobin-PI3K dissociation. It also functions as a pluripotency-reprogramming roadblock that facilitates cellular transition towards differentiation by modulating the levels of Oct4 and cMyc. Moreover, TRIM32 is an intrinsic influenza A virus (IAV) restriction factor which senses and targets the polymerase basic protein 1 (PB1) for ubiquitination and protein degradation. It also plays a significant role in mediating the biological activity of the HIV-1 Tat protein in vivo, binds specifically to the activation domain of HIV-1 Tat, and can also interact with the HIV-2 and EIAV Tat proteins in vivo. Furthermore, TRIM32 regulates myoblast proliferation by controlling turnover of NDRG2 (N-myc downstream-regulated gene). It negatively regulates tumor suppressor p53 to promote tumorigenesis. It also facilitates degradation of MYCN on spindle poles and induces asymmetric cell division in human neuroblastoma cells. In addition, TRIM32 plays important roles in regulation of hyperactivities and positively regulates the development of anxiety and depression disorders induced by chronic stress. It also plays a role in regeneration by affecting satellite cell cycle progression via modulation of the SUMO ligase PIASy (PIAS4). Defects in TRIM32 leads to limb-girdle muscular dystrophy type 2H (LGMD2H), sarcotubular myopathies (STM) and Bardet-Biedl syndrome. TRIM32 belongs to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. The NHL domain mediates the interaction with Argonaute proteins and consequently allows TRIM32 to modulate the activity of certain miRNAs.


Pssm-ID: 438249 [Multi-domain]  Cd Length: 51  Bit Score: 39.31  E-value: 3.45e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767904604  124 TCAVCQQSL--QSRReaePKLLPCLHSFCLRCLPEPERQLSVPipggsngdiqqvgVIRCPVCRQ 186
Cdd:cd16587     2 ECPICLESFdeGQLR---PKLLHCGHTICEQCLEKLLASLSIN-------------GVRCPFCRK 50
PHD2_AIRE cd15540
PHD finger 2 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
913-954 3.53e-04

PHD finger 2 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 second PHD finger that may play a critical role in the activation of gene transcription.


Pssm-ID: 277015  Cd Length: 42  Bit Score: 39.11  E-value: 3.53e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 767904604  913 CAVCQNG-GDLLCCEKCPKVFHLTCHVPTLLSfpSGDWICTFC 954
Cdd:cd15540     2 CGVCRGGrGDLLRCPQCLQAFHWHCHFPSGSS--GGRMRCKSC 42
Bbox2_TRIM56_C-V cd19789
B-box-type 2 zinc finger found in tripartite motif-containing protein 56 (TRIM56) and similar ...
275-315 3.81e-04

B-box-type 2 zinc finger found in tripartite motif-containing protein 56 (TRIM56) and similar proteins; TRIM56, also known as RING finger protein 109 (RNF109), is a virus-inducible E3 ubiquitin ligase that restricts pestivirus infection. It positively regulates the Toll-like receptor 3 (TLR3) antiviral signaling pathway, and possesses antiviral activity against bovine viral diarrhea virus (BVDV), a ruminant pestivirus classified within the family Flaviviridae shared by tick-borne encephalitis virus (TBEV). It also possesses antiviral activity against two classical flaviviruses, yellow fever virus (YFV) and dengue virus (DENV), as well as a human coronavirus, HCoV-OC43, which is responsible for a significant share of common cold cases. It may not act on positive-strand RNA viruses indiscriminately. Moreover, TRIM56 is an interferon-inducible E3 ubiquitin ligase that modulates STING to confer double-stranded DNA-mediated innate immune responses. TRIM56 belongs to the C-V subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380847  Cd Length: 47  Bit Score: 39.06  E-value: 3.81e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 767904604  275 FCPVHKQEQLKLFCETCDRLTCRDCQLLEHKE--HRYQFLEEA 315
Cdd:cd19789     4 MCREHRDERLLLYCTPCEAAVCRECRLRPHLSltHRCLPLAEA 46
PHD2_KMT2C_like cd15510
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
913-954 5.03e-04

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: 5.03e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 767904604  913 CAVCQNGGD---LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 954
Cdd:cd15510     2 CQACRQPGDdtkMLVCETCDKGYHTSCLRPVMSSIPKYGWKCKNC 46
Bbox2_TRIM16-like cd19769
B-box-type 2 zinc finger found in tripartite motif-containing proteins, TRIM16, TRIM29, ...
276-320 5.42e-04

B-box-type 2 zinc finger found in tripartite motif-containing proteins, TRIM16, TRIM29, TRIM47 and similar proteins; This family includes a group of tripartite motif-containing proteins, such as TRIM16, TRIM29 and TRIM47. TRIM16, also termed estrogen-responsive B box protein (EBBP), is a regulator that may play a role in the regulation of keratinocyte differentiation. It may also act as a tumor suppressor through affecting cell proliferation and migration or tumorigenicity in carcinogenesis. TRIM29, also termed ataxia telangiectasia group D-associated protein (ATDC), plays a crucial role in the regulation of macrophage activation in response to viral or bacterial infections within the respiratory tract. TRIM47, also known as gene overexpressed in astrocytoma protein (GOA) or RING finger protein 100 (RNF100), plays an important role in the process of dedifferentiation that is associated with astrocytoma tumorigenesis. TRIM16 and TRIM29 belong to an unclassified TRIM (tripartite motif) family of proteins that do not have RING fingers and thus lack the characteristic tripartite (RING (R), B-box, and coiled coil (CC)) RBCC motif. TRIM47 belongs to the C-IV subclass of TRIM family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380827 [Multi-domain]  Cd Length: 46  Bit Score: 38.85  E-value: 5.42e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 767904604  276 CPVHKQeQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQK 320
Cdd:cd19769     3 CPIHKK-PLELFCRTDQMCICELCAKEEHRGHDVVTVEEEREKKE 46
RING-HC_TRIM13_C-V cd16762
RING finger, HC subclass, found in tripartite motif-containing protein 13 (TRIM13) and similar ...
124-187 6.50e-04

RING finger, HC subclass, found in tripartite motif-containing protein 13 (TRIM13) and similar proteins; TRIM13, also known as B-cell chronic lymphocytic leukemia tumor suppressor Leu5, leukemia-associated protein 5, putative tumor suppressor RFP2, RING finger protein 77 (RNF77), or Ret finger protein 2, is an endoplasmic reticulum (ER) membrane anchored E3 ubiquitin-protein ligase that interacts with proteins localized to the ER, including valosin-containing protein (VCP), a protein indispensable for ER-associated degradation (ERAD). It also targets the known ER proteolytic substrate CD3-delta, but not the N-end rule substrate Ub-R-YFP (yellow fluorescent protein) for degradation. Moreover, TRIM13 regulates ubiquitination and degradation of NEMO to suppress tumor necrosis factor (TNF) induced nuclear factor-kappaB (NF- kappa B) activation. It is also involved in NF-kappaB p65 activation and nuclear factor of activated T-cells (NFAT)-dependent activation of c-Rel upon T-cell receptor engagement. Furthermore, TRIM13 negatively regulates melanoma differentiation-associated gene 5 (MDA5)-mediated type I interferon production. It also regulates caspase-8 ubiquitination, translocation to autophagosomes, and activation during ER stress induced cell death. Meanwhile, TRIM13 enhances ionizing radiation-induced apoptosis by increasing p53 stability and decreasing AKT kinase activity through MDM2 and AKT degradation. TRIM13 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region. In addition, TRIM13 contains a C-terminal transmembrane domain.


Pssm-ID: 438418 [Multi-domain]  Cd Length: 56  Bit Score: 38.74  E-value: 6.50e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767904604  124 TCAVCQQSLQsrreaEPKLLPCLHSFCLRCLPEperqlsvpIPGGSNGDIQQVGVIRCPVCRQE 187
Cdd:cd16762     5 TCPICCCLFD-----DPRVLPCSHNFCKKCLEG--------ILEGNVRTMLWRPPFKCPTCRKE 55
PHD5_NSD3 cd15661
PHD finger 5 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed ...
912-951 6.55e-04

PHD finger 5 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed histone-lysine N-methyltransferase NSD3, or protein whistle, or WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, or Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1-like protein 1, or WHSC1L1), is a lysine methyltransferase encoded by gene NSD3, which is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD3 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, five plant-homeodomain (PHD) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the fifth PHD finger.


Pssm-ID: 277131  Cd Length: 43  Bit Score: 38.41  E-value: 6.55e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 767904604  912 WCAVCQNGGDLLCCEK--CPKVFHLTCHvpTLLSFPSGDWIC 951
Cdd:cd15661     1 YCFQCGDGGELVMCDKkdCPKAYHLLCL--NLTQPPYGKWEC 40
RING-HC_TRIM40-C-V cd16583
RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar ...
123-197 7.55e-04

RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar proteins; TRIM40, also known as probable E3 NEDD8-protein ligase or RING finger protein 35 (RNF35), is highly expressed in the gastrointestinal tract including the stomach, small intestine, and large intestine. It enhances neddylation of inhibitor of nuclear factor kappaB kinase subunit gamma (IKKgamma), inhibits the activity of nuclear factor-kappaB (NF-kappaB)-mediated transcription, and thus prevents inflammation-associated carcinogenesis in the gastrointestinal tract. TRIM40 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain.


Pssm-ID: 438245 [Multi-domain]  Cd Length: 63  Bit Score: 39.04  E-value: 7.55e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767904604  123 DTCAVCQQSLQsrreaEPKLLPCLHSFCLRCLPEPERQLSVPipggsngdiqqvGVIRCPVCRQECRQIDLVDNY 197
Cdd:cd16583     6 GVCPICQEPLK-----EAVSTDCGHLFCRMCLTQHAKKASAS------------GVFSCPVCRKPCSEGVLGDGY 63
PHD1_Lid_like cd15605
PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar ...
913-954 7.75e-04

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: 38.20  E-value: 7.75e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 767904604  913 CAVCQNGGD---LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 954
Cdd:cd15605     2 CHTCGRGDGeesMLLCDGCDDSYHTFCLLPPLSEVPKGDWRCPKC 46
PHD1_KDM5A cd15602
PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone ...
912-954 8.29e-04

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: 38.39  E-value: 8.29e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 767904604  912 WCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 954
Cdd:cd15602     4 FCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKC 46
PHD_BS69 cd15537
PHD finger found in protein BS69; Protein BS69, also termed zinc finger MYND domain-containing ...
912-954 9.63e-04

PHD finger found in protein BS69; Protein BS69, also termed zinc finger MYND domain-containing protein 11 (ZMYND11 or ZMY11), is a ubiquitously expressed nuclear protein acting as a transcriptional co-repressor in association with various transcription factors. It was originally identified as an adenovirus 5 E1A-binding protein that inhibits E1A transactivation, as well as c-Myb transcription. It also mediates repression, at least in part, through interaction with the co-repressor N-CoR. Moreover, it interacts with Toll-interleukin 1 receptor domain (TIR)-containing adaptor molecule-1 (TICAM-1, also named TRIF) to facilitate NF-kappaB activation and type I IFN induction. It associates with PIAS1, a SUMO E3 enzyme, and Ubc9, a SUMO E2 enzyme, and plays an inhibitory role in muscle and neuronal differentiation. Moreover, BS69 regulates Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1)/C-terminal activation region 2 (CTAR2)-mediated NF-kappaB activation by interfering with the complex formation between TNFR-associated death domain protein (TRADD) and LMP1/CTAR2. It also cooperates with tumor necrosis factor receptor (TNFR)-associated factor 3 (TRAF3) in the regulation of EBV-derived LMP1/CTAR1-induced NF-kappaB activation. Furthermore, BS69 is involved in the p53-p21Cip1-mediated senescence pathway. BS69 contains a plant homeodomain (PHD) finger, a bromodomain, a proline-tryptophan-tryptophan-proline (PWWP) domain, and a Myeloid translocation protein 8, Nervy and DEAF-1 (MYND) domain.


Pssm-ID: 277012  Cd Length: 43  Bit Score: 38.09  E-value: 9.63e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 767904604  912 WCAVCQNGGDLLCCEKCPKVFHLTChVPTLLSFPSGD-WICTFC 954
Cdd:cd15537     1 YCFECHAPGEVLPCSGCFRVYHSDC-LSEDFRPDSTShWTCPVC 43
Bbox2_TRIM68_C-IV cd19795
B-box-type 2 zinc finger found in tripartite motif-containing protein 68 (TRIM68) and similar ...
275-315 1.14e-03

B-box-type 2 zinc finger found in tripartite motif-containing protein 68 (TRIM68) and similar proteins; TRIM68, also known as RING finger protein 137 (RNF137) or SSA protein SS-56 (SS-56), is an E3 ubiquitin-protein ligase that negatively regulates Toll-like receptor (TLR)- and RIG-I-like receptor (RLR)-driven type I interferon production by degrading TRK fused gene (TFG), a novel driver of IFN-beta downstream of anti-viral detection systems. It also functions as a cofactor for androgen receptor-mediated transcription by regulating ligand-dependent transcription of androgen receptor in prostate cancer cells. Moreover, TRIM68 is a cellular target of autoantibody responses in Sjogren's syndrome (SS), as well as systemic lupus erythematosus (SLE). It is also an auto-antigen for T cells in SS and SLE. TRIM68 belongs the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380853 [Multi-domain]  Cd Length: 44  Bit Score: 37.81  E-value: 1.14e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 767904604  275 FCPVHKqEQLKLFCETCDRLTCRDC-QLLEHKEHRYQFLEEA 315
Cdd:cd19795     3 LCERHK-EKLNLFCEEDQELLCVVCeQSPEHKAHTVVPVEEA 43
RING-HC_NHL-1-like cd16524
RING finger, HC subclass, found in Caenorhabditis elegans RING finger protein NHL-1 and ...
122-187 1.39e-03

RING finger, HC subclass, found in Caenorhabditis elegans RING finger protein NHL-1 and similar proteins; NHL-1 functions as an E3 ubiquitin-protein ligase in the presence of both UBC-13 and UBC-1 within the ubiquitin pathway of Caenorhabditis elegans. It acts in chemosensory neurons to promote stress resistance in distal tissues by the transcription factor DAF-16 activation but is dispensable for the activation of heat shock factor 1 (HSF-1). NHL-1 belongs to the TRIM (tripartite motif)-NHL family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as an NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438187 [Multi-domain]  Cd Length: 53  Bit Score: 37.79  E-value: 1.39e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767904604  122 LDTCAVCQQslqsrREAEPKLLPCLHSFCLR-CLpeperqlsvpipggSNGDIQQVGVIRCPVCRQE 187
Cdd:cd16524     5 LLTCPICLD-----RYRRPKLLPCQHTFCLSpCL--------------EGLVDYVTRKLKCPECRAE 52
BAH_plant_2 cd04718
BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH ...
932-993 1.53e-03

BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240069  Cd Length: 148  Bit Score: 40.26  E-value: 1.53e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767904604  932 FHLTCHVPTLLSFPSGDWICTFCrdigkpEVEydcdnlqhsKKGKTAQ-GLSPVDQRKCERLL 993
Cdd:cd04718     2 FHLCCLRPPLKEVPEGDWICPFC------EVE---------KSGQSAMpQLPPTSRSACEKLL 49
PHD2_KMT2C cd15594
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
913-954 1.66e-03

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: 37.61  E-value: 1.66e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 767904604  913 CAVCQNGGD---LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 954
Cdd:cd15594     2 CQTCRQPGDdnkMLVCDTCDKGYHTFCLQPVMTTIPKNGWKCKNC 46
PHD5_NSD1 cd15659
PHD finger 5 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1); NSD1, ...
913-951 1.66e-03

PHD finger 5 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1); NSD1, also termed H3 Lysine-36 and H4 Lysine-20 specific histone-lysine N-methyltransferase, or androgen receptor coactivator 267 kDa protein, or androgen receptor-associated protein of 267 kDa, or H3-K36-HMTase H4-K20-HMTase, or Lysine N-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein, is a lysine methyltransferase that preferentially methylates H3 on Lysine36 (H3-K36) and H4 on Lysine20 (H4-K20), which is primarily associated with active transcription. It plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma and glioblastoma formation. It can alter transcription by interacting with the protein NSD1-interacting zinc finger protein 1 (NIZP1). It also mitigates caspase-1 activation by listeriolysin o (LLO) in macrophages, and requires functional LLO for the regulation of IL-1beta secretion. Moreover, NSD1 regulates RNA polymerase II (RNAP II) recruitment to bone morphogenetic protein 4 (BMP4). NSD1 contains 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). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the fifth PHD finger.


Pssm-ID: 277129  Cd Length: 43  Bit Score: 37.23  E-value: 1.66e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 767904604  913 CAVCQNGGDLLCCEK--CPKVFHLTCHvpTLLSFPSGDWIC 951
Cdd:cd15659     2 CFSCGDGGQLVSCKKpgCPKVYHADCL--NLTKRPAGKWEC 40
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
312-417 1.76e-03

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 42.31  E-value: 1.76e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604   312 LEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVE------QEIKVAIFTLINE----INKKGKSLL 381
Cdd:TIGR04523  237 KQQEINEKTTEISNTQTQLNQLKDEQNKIKKQLSEKQKELEQNNKKIKelekqlNQLKSEISDLNNQkeqdWNKELKSEL 316
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 767904604   382 QQLENVTKERQMKLLQQQNDITGLSRQV----KHVMNFTN 417
Cdd:TIGR04523  317 KNQEKKLEEIQNQISQNNKIISQLNEQIsqlkKELTNSES 356
RING-HC_SHPRH-like cd16569
RING finger, HC subclass, found in SNF2 histone-linker PHD finger RING finger helicase (SHPRH) ...
122-187 1.92e-03

RING finger, HC subclass, found in SNF2 histone-linker PHD finger RING finger helicase (SHPRH) and similar proteins; SHPRH is a yeast RAD5 homolog found in mammals. It functions as an E3 ubiquitin-protein ligase that associates with proliferating cell nuclear antigen (PCNA), RAD18, and the ubiquitin-conjugating enzyme UBC13 (E2), and suppresses genomic instability by proliferating methyl methanesulfonate (MMS)-induced PCNA polyubiquitination. SHPRH contains a SWI/SNF helicase domain that is divided into N- and C-terminal parts by an insertion of a linker histone domain (H15), a PHD-finger, and a C3HC4-type RING-HC finger involved in the poly-ubiquitination of PCNA. This subfamily also includes tripartite motif-containing protein 15 (TRIM15). TRIM15, also known as RING finger protein 93 (RNF93), zinc finger protein 178 (ZNF178), or zinc finger protein B7 (ZNFB7), is a focal adhesion protein that regulates focal adhesion disassembly. It localizes to focal contacts in a myosin-II-independent manner by an interaction between its coiled-coil domain and the LD2 motif of paxillin. TRIM15 can also associate with coronin 1B, cortactin, filamin binding LIM protein1, and vasodilator-stimulated phosphoprotein, which are involved in actin cytoskeleton dynamics. As an additional component of the integrin adhesome, it regulates focal adhesion turnover and cell migration. TRIM15 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438231 [Multi-domain]  Cd Length: 53  Bit Score: 37.32  E-value: 1.92e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767904604  122 LDTCAVCQQSLQSRREaepkLLPCLHSFCLRCLPEPERQLSVpipggsngdiQQVGVIRCPVCRQE 187
Cdd:cd16569     1 PEPCPICARPLGKQWS----VLPCGHCFCLECIAILIDQYAQ----------SRRRSLKCPICRET 52
RING-HC_TRIM13_like_C-V cd16581
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM13, TRIM59 and ...
124-185 1.93e-03

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM13, TRIM59 and similar proteins; TRIM13 and TRIM59, two closely related tripartite motif-containing proteins, belong to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, followed by a C-terminal transmembrane domain. TRIM13, also known as B-cell chronic lymphocytic leukemia tumor suppressor Leu5, leukemia-associated protein 5, putative tumor suppressor RFP2, RING finger protein 77 (RNF77), or Ret finger protein 2, is an endoplasmic reticulum (ER) membrane anchored E3 ubiquitin-protein ligase that interacts with proteins localized to the ER, including valosin-containing protein (VCP), a protein indispensable for ER-associated degradation (ERAD). TRIM59, also known as RING finger protein 104 (RNF104) or tumor suppressor TSBF-1, is a putative E3 ubiquitin-protein ligase that functions as a novel multiple cancer biomarker for immunohistochemical detection of early tumorigenesis.


Pssm-ID: 438243 [Multi-domain]  Cd Length: 50  Bit Score: 37.49  E-value: 1.93e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767904604  124 TCAVCQQSLQsrreaEPKLLPCLHSFCLRCLpEPERQLSVPIPGGSngdiqqvgvIRCPVCR 185
Cdd:cd16581     4 TCSICYNIFD-----DPKILPCSHTFCKNCL-EKLLAASGYYLLAS---------LKCPTCR 50
RING-HC_TRIM3 cd16768
RING finger, HC subclass, found in tripartite motif-containing protein 3 (TRIM3); TRIM3, also ...
125-185 1.97e-03

RING finger, HC subclass, found in tripartite motif-containing protein 3 (TRIM3); TRIM3, also known as brain-expressed RING finger protein (BERP), RING finger protein 97 (RNF97), or RING finger protein 22 (RNF22), is an E3 ubiquitin-protein ligase involved in the pathogenesis of various cancers. It functions as a tumor suppressor that regulates asymmetric cell division in glioblastoma. It binds to the cdk inhibitor p21(WAF1/CIP1) and regulates its availability that promotes cyclin D1-cdk4 nuclear accumulation. Moreover, TRIM3 plays an important role in the central nervous system (CNS). It is encoded by the gene BERP (brain-expressed RING finger protein), a unique p53-regulated gene that modulates seizure susceptibility and GABAAR cell surface expression. Furthermore, TRIM3 mediates activity-dependent turnover of postsynaptic density (PSD) scaffold proteins GKAP/SAPAP1 and is a negative regulator of dendritic spine morphology. In addition, TRIM3 may be involved in vesicular trafficking via its association with the cytoskeleton-associated-recycling or transport (CART) complex that is necessary for efficient transferrin receptor recycling, but not for epidermal growth factor receptor (EGFR) degradation. It also regulates the motility of the kinesin superfamily protein KIF21B. TRIM3 belongs to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438424 [Multi-domain]  Cd Length: 48  Bit Score: 37.29  E-value: 1.97e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767904604  125 CAVCQQSLQSrreaePKLLPCLHSFCLRCLpeperQLSVPipggsngdiQQVGVIRCPVCR 185
Cdd:cd16768     7 CSICLDRYHN-----PKVLPCLHTFCERCL-----QNYIP---------PQSLTLSCPVCR 48
PHD1_KDM5C_5D cd15604
PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family ...
913-954 2.53e-03

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: 36.74  E-value: 2.53e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 767904604  913 CAVCQNGGD---LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 954
Cdd:cd15604     2 CRMCSRGDEddkLLLCDGCDDNYHTFCLLPPLPEPPKGIWRCPKC 46
Bbox2_xNF7-like cd19800
B-box-type 2 zinc finger found in Xenopus laevis nuclear factor 7 (xNF7) and similar proteins; ...
275-310 2.57e-03

B-box-type 2 zinc finger found in Xenopus laevis nuclear factor 7 (xNF7) and similar proteins; xNF7 is a maternally expressed novel zinc finger nuclear phosphoprotein. It acts as a transcription factor that determines dorsal-ventral body axis. xNF7 harbors a B-box motif that shows high sequence similarity with B-Box-type zinc finger 2 found in tripartite motif-containing proteins (TRIMs). The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380858 [Multi-domain]  Cd Length: 39  Bit Score: 36.61  E-value: 2.57e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 767904604  275 FCPVHKqEQLKLFCETCDRLTCRDCQ-LLEHKEHRYQ 310
Cdd:cd19800     2 VCSEHD-EPLKLFCKDDKRLICVICRdSRKHRGHRFL 37
Bbox2_TRIM36_C-I cd19778
B-box-type 2 zinc finger found in tripartite motif-containing protein 36 (TRIM36) and similar ...
276-316 2.59e-03

B-box-type 2 zinc finger found in tripartite motif-containing protein 36 (TRIM36) and similar proteins; TRIM36, human ortholog of mouse Haprin, also known as RING finger protein 98 (RNF98) or zinc-binding protein Rbcc728, is an E3 ubiquitin-protein ligase expressed in the germ plasm. It has been implicated in acrosome reaction, fertilization, and embryogenesis, as well as in carcinogenesis. TRIM36 functions upstream of Wnt/beta-catenin activation, and plays a role in controlling the stability of proteins regulating microtubule polymerization during cortical rotation, and subsequently dorsal axis formation. It is also potentially associated with chromosome segregation through interacting with the kinetochore protein centromere protein-H (CENP-H), and colocalizing with the microtubule protein alpha-tubulin. Its overexpression may cause chromosomal instability and carcinogenesis. It is, thus, a novel regulator affecting cell cycle progression. Moreover, TRIM36 plays a critical role in the arrangement of somites during embryogenesis. TRIM36 belongs to the C-I subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380836  Cd Length: 45  Bit Score: 36.74  E-value: 2.59e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 767904604  276 CPVHKQEQLKLFCETCDRLTCRDCQLL-EHKEHRYQFLEEAF 316
Cdd:cd19778     3 CPEHEMEKVNMYCEACRRPVCHLCKLGgSHANHRVTSMSSAY 44
PHD_PRHA_like cd15504
PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and ...
913-954 2.81e-03

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


Pssm-ID: 276979  Cd Length: 53  Bit Score: 37.03  E-value: 2.81e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 767904604  913 CAVCQ-----NGGDLLCCE-KCPKVFHLTCHVPTLLSF----PSGDWICTFC 954
Cdd:cd15504     2 CAKCQsgeasPDNDILLCDgGCNRAYHQKCLEPPLLTEdippEDEGWLCPLC 53
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
312-412 2.86e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 41.97  E-value: 2.86e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604  312 LEEAFQNQKGAIENLLAKLLEKKNYVHfAATQVQNRIKEVNETNKRVEQEikvaiftlINEINKKGKSLLQQLENVTKER 391
Cdd:PRK03918  160 YENAYKNLGEVIKEIKRRIERLEKFIK-RTENIEELIKEKEKELEEVLRE--------INEISSELPELREELEKLEKEV 230
                          90       100
                  ....*....|....*....|.
gi 767904604  392 QmKLLQQQNDITGLSRQVKHV 412
Cdd:PRK03918  231 K-ELEELKEEIEELEKELESL 250
RING-HC_TRIM58_C-IV cd16606
RING finger, HC subclass, found in tripartite motif-containing protein TRIM58 and similar ...
125-185 2.88e-03

RING finger, HC subclass, found in tripartite motif-containing protein TRIM58 and similar proteins; TRIM58, also known as protein BIA2, is an erythroid E3 ubiquitin-protein ligase induced during late erythropoiesis. It binds and ubiquitinates the intermediate chain of the microtubule motor dynein (DYNC1LI1/DYNC1LI2), stimulating the degradation of the dynein holoprotein complex. It may participate in the erythroblast enucleation process through regulation of nuclear polarization. TRIM58 belongs to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438268 [Multi-domain]  Cd Length: 53  Bit Score: 37.15  E-value: 2.88e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767904604  125 CAVCQQSLQsrreaEPKLLPCLHSFCLRCLPE-PERqlsvpipggsnGDIQQVGVIRCPVCR 185
Cdd:cd16606     5 CPVCLDFLQ-----EPVSVDCGHSFCLRCISEfCEK-----------SDSAQGGVYACPQCR 50
Bbox1_RNF207-like cd19814
B-box-type 1 zinc finger found in RING finger protein 207 (RNF207) and similar proteins; ...
217-252 2.90e-03

B-box-type 1 zinc finger found in RING finger protein 207 (RNF207) and similar proteins; RNF207 is a cardiac-specific E3 ubiquitin-protein ligase that plays an important role in the regulation of cardiac repolarization. It regulates action potential duration, likely via effects on human ether-a-go-go-related gene (HERG) trafficking and localization, in a heat shock protein-dependent manner. RNF207 contains a RING finger, a B-box motif and Bbox C-terminal (BBC) domain, as well as a C-terminal non-homologous region (CNHR). The B-box motif shows high sequence similarity with B-Box-type 1 zinc finger found in tripartite motif-containing proteins (TRIMs). The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif.


Pssm-ID: 380872  Cd Length: 49  Bit Score: 36.95  E-value: 2.90e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 767904604  217 CTSCEDNASAVGFCVECGEWLCKTCIE-AHQRVKFTK 252
Cdd:cd19814     2 CANCDSECLAMFYCNTCGQPLCDDCREeTHRAKMFSK 38
RING-HC_SH3RF1 cd16748
RING finger, HC subclass, found in SH3 domain-containing RING finger protein 1 (SH3RF1) and ...
125-185 2.90e-03

RING finger, HC subclass, found in SH3 domain-containing RING finger protein 1 (SH3RF1) and similar proteins; SH3RF1, also known as plenty of SH3s (POSH), RING finger protein 142 (RNF142), or SH3 multiple domains protein 2 (SH3MD2), is a trans-Golgi network-associated pro-apoptotic scaffold protein with E3 ubiquitin-protein ligase activity. It also plays a role in calcium homeostasis through the control of the ubiquitin domain protein Herp. It may also have a role in regulating death receptor mediated and c-Jun N-terminal kinase (JNK) mediated apoptosis, linking Rac1 to downstream components. SH3RF1 also enhances the ubiquitination of ROMK1 potassium channel resulting in its increased endocytosis. Moreover, SH3RF1 assembles an inhibitory complex with the actomyosin regulatory protein Shroom3, which links to the actin-myosin network to regulate neuronal process outgrowth. It also forms a complex with apoptosis-linked gene-2 (ALG-2) and ALG-2-interacting protein (ALIX/AIP1) in a calcium-dependent manner to play a role in the regulation of the JNK pathway. Furthermore, direct interaction of SH3RF1 and another molecular scaffold JNK-interacting protein (JIP) is required for apoptotic activation of JNKs. Interaction of SH3RF1 and E3 ubiquitin-protein isopeptide ligases, Siah proteins, further promotes JNK activation and apoptosis. In addition, SH3RF1 binds to and degrades TAK1, a crucial activator of both the JNK and the Relish signaling pathways. SH3RF1 contains an N-terminal C3HC4-type RING-HC finger responsible for the E3 ligase activity and four Src Homology 3 (SH3) domains, which are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs.


Pssm-ID: 438406 [Multi-domain]  Cd Length: 48  Bit Score: 36.91  E-value: 2.90e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767904604  125 CAVCQQslqsRREAEPKLLPCLHSFCLRCLpeperqlsvpipggsNGDIQQVGVIRCPVCR 185
Cdd:cd16748     5 CPVCLE----RLDATAKVLPCQHTFCRRCL---------------LGIVGSRSELRCPECR 46
RING-HC_MID2 cd16754
RING finger, HC subclass, found in midline-2 (MID2) and similar proteins; MID2, also known as ...
124-185 2.94e-03

RING finger, HC subclass, found in midline-2 (MID2) and similar proteins; MID2, also known as midin-2, midline defect 2, RING finger protein 60 (RNF60), or tripartite motif-containing protein 1 (TRIM1), is a probable E3 ubiquitin-protein ligase and is highly related to MID1 that associates with cytoplasmic microtubules along their length and throughout the cell cycle. Like MID1, MID2 associates with the microtubule network and may at least partially compensate for the loss of MID1. Both MID1 and MID2 interacts with Alpha 4, which is a regulatory subunit of PP2-type phosphatases, such as PP2A, and an integral component of the rapamycin-sensitive signaling pathway. MID2 can also substitute for MID1 to control exocytosis of lytic granules in cytotoxic T cells. Loss-of-function mutations in MID2 lead to the human X-linked intellectual disability (XLID). MID2 belongs to the C-I subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxy-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. MID2 hetero-dimerizes in vitro with its paralog MID1.


Pssm-ID: 438412 [Multi-domain]  Cd Length: 70  Bit Score: 37.66  E-value: 2.94e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767904604  124 TCAVCQQSLQsrreaEPKLLPCLHSFCLRClpePERQLSVPIpgGSNGDIQQVGVIRCPVCR 185
Cdd:cd16754     9 TCPICLELFE-----DPLLLPCAHSLCFSC---AHRILTSGC--ASGESIEPPSAFQCPTCR 60
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
913-954 4.12e-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: 36.30  E-value: 4.12e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 767904604  913 CAVCQNGGD---LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 954
Cdd:cd15513     2 CEGCGKASDesrLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 46
RING-HC_TRIM25_C-IV cd16597
RING finger, HC subclass, found in tripartite motif-containing protein TRIM25 and similar ...
124-187 4.25e-03

RING finger, HC subclass, found in tripartite motif-containing protein TRIM25 and similar proteins; TRIM25, also known as estrogen-responsive finger protein (EFP), RING finger protein 147 (RNF147), or RING-type E3 ubiquitin transferase, is an E3 ubiquitin/ISG15 ligase that is induced by estrogen and is therefore particularly abundant in placenta and uterus. TRIM25 regulates various cellular processes through E3 ubiquitin ligase activity, transferring ubiquitin and ISG15 to target proteins. It mediates K63-linked polyubiquitination of retinoic acid inducible gene I (RIG-I) that is crucial for downstream antiviral interferon signaling. It is also required for melanoma differentiation-associated gene 5 (MDA5) and mitochondrial antiviral signaling (MAVS, also known as IPS-1, VISA, Cardiff) mediated activation of nuclear factor-kappaB (NF-kappaB) and interferon production. Upon UV irradiation, TRIM25 interacts with mono-ubiquitinated PCNA and promotes its ISG15 modification (ISGylation), suggesting a crucial role in termination of error-prone translesion DNA synthesis. TRIM25 also functions as a novel regulator of p53 and Mdm2. It enhances p53 and Mdm2 abundance by inhibiting their ubiquitination and degradation in 26S proteasomes. Meanwhile, it inhibits p53's transcriptional activity and dampens the response to DNA damage, and is essential for medaka development and this dependence is rescued by silencing of p53. Moreover, TRIM25 is involved in the host cellular innate immune response against retroviral infection. It interferes with the late stage of feline leukemia virus (FeLV) replication. Furthermore, TRIM25 acts as an oncogene in gastric cancer. Its blockade by RNA interference inhibits migration and invasion of gastric cancer cells through transforming growth factor-beta (TGF-beta) signaling, suggesting it presents a novel target for the detection and treatment of gastric cancer. In addition, TRIM25 acts as an RNA-specific activator for Lin28a/TuT4-mediated uridylation. TRIM25 belongs to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438259 [Multi-domain]  Cd Length: 71  Bit Score: 36.90  E-value: 4.25e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767904604  124 TCAVCQQSLQsrreaEPKLLPCLHSFCLRCLpeperqlsvpipgGSNGDIQQVGVIRCPVCRQE 187
Cdd:cd16597     7 TCSICLELFK-----DPVTLPCGHNFCGVCI-------------EKTWDSQHGSEYSCPQCRAT 52
RING-HC_TRIM2 cd16767
RING finger, HC subclass, found in tripartite motif-containing protein 2 (TRIM2); TRIM2, also ...
125-186 4.27e-03

RING finger, HC subclass, found in tripartite motif-containing protein 2 (TRIM2); TRIM2, also known as RING finger protein 86 (RNF86), is an E3 ubiquitin-protein ligase that ubiquitinates the neurofilament light chain, a component of the intermediate filament in axons. Loss of function of TRIM2 results in early-onset axonal neuropathy. TRIM2 also plays a role in mediating the p42/p44 MAPK-dependent ubiquitination of the cell death-promoting protein Bcl-2-interacting mediator of cell death (Bim) in rapid ischemic tolerance. TRIM2 belongs to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438423 [Multi-domain]  Cd Length: 51  Bit Score: 36.53  E-value: 4.27e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767904604  125 CAVCQQslqsrREAEPKLLPCLHSFCLRCLPE--PERQLSvpipggsngdiqqvgvIRCPVCRQ 186
Cdd:cd16767     9 CSICLD-----RYKNPKVLPCLHTFCERCLQNyiPAHSLT----------------LSCPVCRQ 51
RING-HC_RNF222 cd16564
RING finger, HC subclass, found in RING finger protein 222 (RNF222) and similar proteins; ...
124-187 4.28e-03

RING finger, HC subclass, found in RING finger protein 222 (RNF222) and similar proteins; RNF222 is an uncharacterized C3HC4-type RING-HC finger-containing protein. It may function as an E3 ubiquitin-protein ligase.


Pssm-ID: 438226 [Multi-domain]  Cd Length: 50  Bit Score: 36.23  E-value: 4.28e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767904604  124 TCAVCQQSLQSRreaePKLLPCLHSFCLRCLPeperqlsvpipggsngDIQQVGVIRCPVCRQE 187
Cdd:cd16564     2 ECPVCYEDFDDA----PRILSCGHSFCEDCLV----------------KQLVSMTISCPICRRV 45
Bbox1_TRIM8-like cd19802
B-box-type 1 zinc finger found in tripartite motif-containing proteins, TRIM8, TRIM16, TRIM25, ...
217-255 4.54e-03

B-box-type 1 zinc finger found in tripartite motif-containing proteins, TRIM8, TRIM16, TRIM25, TRIM29, TRIM44, TRIM47 and similar proteins; This family includes a group of tripartite motif-containing proteins, including TRIM8, TRIM16, TRIM25, TRIM29, TRIM44 and TRIM47. TRIM8, also known as glioblastoma-expressed RING finger protein (GERP) or RING finger protein 27 (RNF27), is a probable E3 ubiquitin-protein ligase that may promote proteasomal degradation of suppressor of cytokine signaling 1 (SOCS1) and further regulate interferon-gamma signaling. It functions as a new p53 modulator that stabilizes p53, impairing its association with MDM2 and inducing the reduction of cell proliferation. TRIM16, also termed estrogen-responsive B box protein (EBBP), may play a role in the regulation of keratinocyte differentiation. It may also act as a tumor suppressor by affecting cell proliferation and migration or tumorigenicity in carcinogenesis. TRIM25, also termed estrogen-responsive finger protein (EFP), or ubiquitin/ISG15-conjugating enzyme TRIM25, or zinc finger protein 147 (ZNF147), or E3 ubiquitin/ISG15 ligase TRIM25, is induced by estrogen and is particularly abundant in placenta and uterus. It has been implicated in cell proliferation, protein modification, and the retinoic acid inducible gene I (RIG-I)-mediated antiviral signaling pathway. It functions as an E3-ubiquitin ligase able to transfer ubiquitin and ISG15 to target proteins. TRIM29, also termed ataxia telangiectasia group D-associated protein (ATDC), plays a crucial role in the regulation of macrophage activation in response to viral or bacterial infections within the respiratory tract. TRIM44, also termed protein DIPB, functions as a critical regulator in tumor metastasis and progression. TRIM47, also known as gene overexpressed in astrocytoma protein (GOA) or RING finger protein 100 (RNF100), plays an important role in the process of dedifferentiation that is associated with astrocytoma tumorigenesis. The TRIM (tripartite motif) family of proteins are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif.


Pssm-ID: 380860  Cd Length: 46  Bit Score: 36.25  E-value: 4.54e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 767904604  217 CTSCEDNAS--AVGFCVECGEWLCKTCIEAHQRVKFTKDHL 255
Cdd:cd19802     2 CDFCDPGKAlkAVKSCLTCEASLCEIHLRPHLESPALKSHQ 42
PHD_JADE1 cd15679
PHD finger found in protein Jade-1 and similar proteins; Jade-1, also termed PHD finger ...
913-954 4.64e-03

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: 36.21  E-value: 4.64e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 767904604  913 CAVCQ-----NGGDLLCCEKCPKVFHLTCHvpTLLSFPSGDWICTFC 954
Cdd:cd15679     2 CDVCQspdgeDGNEMVFCDKCNICVHQACY--GILKVPEGSWLCRTC 46
RING-HC_TRIM47-like_C-IV cd16604
RING finger, HC subclass, found in tripartite motif-containing protein 47 (TRIM47) and similar ...
125-186 4.92e-03

RING finger, HC subclass, found in tripartite motif-containing protein 47 (TRIM47) and similar proteins; TRIM47, also known as gene overexpressed in astrocytoma protein (GOA) or RING finger protein 100 (RNF100), belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, a B-box, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. It plays an important role in the process of dedifferentiation that is associated with astrocytoma tumorigenesis. This subfamily also includes RING finger protein 135 (RNF135). RNF135, also known as RIG-I E3 ubiquitin ligase (REUL) or Riplet, is a widely expressed E3 ubiquitin-protein ligase that consists of an N-terminal C3HC4-type RING-HC finger and C-terminal B30.2/SPRY and PRY motifs, but lacks the B-box and coiled-coil domains that are also typically present in TRIM proteins. RNF135 serves as a specific retinoic acid-inducible gene-I (RIG-I)-interacting protein that ubiquitinates RIG-I and specifically stimulates RIG-I-mediated innate antiviral activity to produce antiviral type-I interferon (IFN) during the early phase of viral infection. It also has been identified as a bio-marker and therapy target of glioblastoma. It associates with the ERK signal transduction pathway and plays a role in glioblastoma cell proliferation, migration and cell cycle.


Pssm-ID: 438266 [Multi-domain]  Cd Length: 49  Bit Score: 36.24  E-value: 4.92e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767904604  125 CAVCQQSLQsrreaEPKLLPCLHSFCLRCLpeperqlsvpipgGSNGDIQQVGVIRCPVCRQ 186
Cdd:cd16604     3 CPICLDLLK-----DPVTLPCGHSFCMGCL-------------GALWGAGRGGRASCPLCRQ 46
RING-HC_MID1 cd16753
RING finger, HC subclass, found in midline-1 (MID1) and similar proteins; MID1, also known as ...
124-185 5.01e-03

RING finger, HC subclass, found in midline-1 (MID1) and similar proteins; MID1, also known as midin, midline 1 RING finger protein, putative transcription factor XPRF, RING finger protein 59 (RNF59), or tripartite motif-containing protein 18 (TRIM18), is a microtubule-associated E3 ubiquitin-protein ligase implicated in epithelial-mesenchymal differentiation, cell migration and adhesion, and programmed cell death along specific regions of the ventral midline during embryogenesis. It monoubiquinates the alpha4 subunit of protein phosphatase 2A (PP2A), promoting proteosomal degradation of the catalytic subunit of PP2A (PP2Ac) and preventing the A and B subunits from forming an active complex. It promotes allergen and rhinovirus-induced asthma through the inhibition of PP2A activity. It is strongly upregulated in cytotoxic lymphocytes (CTLs) and directs lytic granule exocytosis and cytotoxicity of killer T cells. Loss-of-function mutations in MID1 lead to the human X-linked Opitz G/BBB (XLOS) syndrome characterized by defective midline development during embryogenesis. MID1 belongs to the C-I subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. MID1 hetero-dimerizes in vitro with its paralog MID2.


Pssm-ID: 438411 [Multi-domain]  Cd Length: 72  Bit Score: 36.94  E-value: 5.01e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767904604  124 TCAVCQQSLQsrreaEPKLLPCLHSFCLRClpePERQLSVPIpgGSNGDIQQVGVIRCPVCR 185
Cdd:cd16753     7 TCPICLELFE-----DPLLLPCAHSLCFNC---AHRILVSHC--ASNESVESITAFQCPTCR 58
PHD2_KMT2D cd15595
PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
913-954 5.15e-03

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: 36.13  E-value: 5.15e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 767904604  913 CAVCQNGGD---LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 954
Cdd:cd15595     2 CQTCRKPGEdskMLVCEACDKGYHTFCLKPAMESLPTDSWKCKAC 46
PHD3_NSD cd15566
PHD finger 3 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
913-952 5.37e-03

PHD finger 3 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 third PHD finger.


Pssm-ID: 277041  Cd Length: 48  Bit Score: 35.87  E-value: 5.37e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 767904604  913 CAVCQNGGD-----LLCCEKCPKVFHLTCHVPTLLSFPSGDWICT 952
Cdd:cd15566     2 CATCEASGDgssgkLVRCIRCPRAYHAGCIPAGSKLLNKKLIICP 46
PHD2_d4 cd15530
PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three ...
913-954 5.38e-03

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: 35.82  E-value: 5.38e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 767904604  913 CAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 954
Cdd:cd15530     5 CGTSENDDQLLFCDDCDRGYHMYCLSPPMSEPPEGSWSCHLC 46
Bbox2_MID cd19758
B-box-type 2 zinc finger found in midline (MID) family; The MID family includes MID1 and MID2. ...
274-307 5.39e-03

B-box-type 2 zinc finger found in midline (MID) family; The MID family includes MID1 and MID2. MID1, also known as midin, midline 1 RING finger protein, putative transcription factor XPRF, RING finger protein 59 (RNF59), or tripartite motif-containing protein 18 (TRIM18), is a microtubule-associated E3 ubiquitin-protein ligase implicated in epithelial-mesenchymal differentiation, cell migration and adhesion, and programmed cell death along specific regions of the ventral midline during embryogenesis. MID2, also known as midin-2, midline defect 2, RING finger protein 60 (RNF60), or tripartite motif-containing protein 1 (TRIM1), is highly related to MID1. It associates with the microtubule network and may at least partially compensate for the loss of MID1. Both MID1 and MID2 interacts with Alpha 4, which is a regulatory subunit of PP2-type phosphatases, such as PP2A, and an integral component of the rapamycin-sensitive signaling pathway. They also play a central role in the regulation of granule exocytosis, and functional redundancy exists between MID1 and MID2 in cytotoxic lymphocytes (CTL). Both MID1 and MID2 belong to the C-I subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380816  Cd Length: 40  Bit Score: 35.91  E-value: 5.39e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 767904604  274 VFCPVHKQEQLKLFCETCDRLTCRDCQLL-EHKEH 307
Cdd:cd19758     1 LMCSEHEEEKVNMYCLTDDQLICSLCKLVgKHKDH 35
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
125-184 5.42e-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: 35.95  E-value: 5.42e-03
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904604    125 CAVCQQslqsRREAEPKLLPCLHSFCLRCLPEperqlsvpipggsngdIQQVGVIRCPVC 184
Cdd:smart00184    1 CPICLE----EYLKDPVILPCGHTFCRSCIRK----------------WLESGNNTCPIC 40
PHD1_NSD1_2 cd15648
PHD finger 1 found in nuclear receptor-binding SET domain-containing protein NSD1 and NSD2; ...
913-955 6.84e-03

PHD finger 1 found in nuclear receptor-binding SET domain-containing protein NSD1 and NSD2; NSD1, also termed H3 Lysine-36 and H4 Lysine-20 specific histone-lysine N-methyltransferase, or androgen receptor coactivator 267 kDa protein, or androgen receptor-associated protein of 267 kDa, or H3-K36-HMTase H4-K20-HMTase, or Lysine N-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein, is a lysine methyltransferase that preferentially methylates H3 on Lysine36 (H3-K36) and H4 on Lysine20 (H4-K20), which is primarily associated with active transcription. It plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. It can alter transcription by interacting with the protein NSD1-interacting zinc finger protein 1 (NIZP1). It also mitigates caspase-1 activation by listeriolysin o (LLO) in macrophages, and requires functional LLO for the regulation of IL-1beta secretion. Moreover, NSD1 regulates RNA polymerase II (RNAP II) recruitment to bone morphogenetic protein 4 (BMP4). NSD2, also termed histone-lysine N-methyltransferase NSD2, or multiple myeloma SET domain-containing protein (MMSET), or protein trithorax-5 Wolf-Hirschhorn syndrome candidate 1 protein (WHSC1), is overexpressed frequently in the t(4;14) translocation in 15% to 20% of multiple myeloma. It plays important roles in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. It also enhances androgen receptor (AR)-mediated transcription. The principal chromatin-regulatory activity of NSD2 is dimethylation of histone H3 at lysine 36 (H3K36me2). Both NSD1 and NSD2 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). In addition, NSD2 harbors a high mobility group (HMG) box. The SET domain is responsible for histone methyltransferase activity. The PWWP, HMG, and PHD fingers mediate chromatin interaction and recognition of histone marks. This model corresponds to the first PHD finger.


Pssm-ID: 277118  Cd Length: 43  Bit Score: 35.53  E-value: 6.84e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 767904604  913 CAVCQNGGDLLCCE-KCPKVFHLTChvPTLLSFPSGDWICTFCR 955
Cdd:cd15648     2 CQVCEKPGELLLCEgQCCGAFHLDC--IGLSEMPSGKFICDECI 43
RING-HC_TRIM71_C-VII cd16589
RING finger, HC subclass, found in tripartite motif-containing protein 71 (TRIM71) and similar ...
140-187 7.12e-03

RING finger, HC subclass, found in tripartite motif-containing protein 71 (TRIM71) and similar proteins; TRIM71, also known as protein lineage variant 41 (lin-41), is an E3 ubiquitin-protein ligase that may play essential roles in embryonic stem cells, cellular reprogramming and the timing of embryonic neurogenesis. It was first identified in the nematode Caenorhabditis elegans as a target of the differentiation-associated microRNA (miRNA) let-7 (lethal 7) and is therefore part of a heterochronic gene network that controls larval development. In humans, it regulates let-7 microRNA biogenesis via modulation of Lin28B protein polyubiquitination. TRIM71 localizes to cytoplasmic P-bodies and directly interacts with the miRNA pathway proteins Argonaute 2 (AGO2) and DICER. It represses miRNA activity by promoting degradative ubiquitination of AGO2. Moreover, TRIM71 associates with SHCBP1, a novel component of the fibroblast growth factor (FGF) signaling pathway, and regulates its non-degradative polyubiquitination. It is also involved in the post-transcriptional regulation of the CDKN1A, RBL1 and RBL2 or EGR1 mRNAs by mediating RNA-binding in embryonic stem cells. TRIM71 belongs to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438251 [Multi-domain]  Cd Length: 91  Bit Score: 37.00  E-value: 7.12e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 767904604  140 PKLLPCLHSFCLRCLpEPERqlsvpiPGGSNGDIQqvgvIRCPVCRQE 187
Cdd:cd16589    50 LHVLPCLHAFCRQCL-EAQR------SPGAGPALK----LRCPVCDQK 86
Bbox2_GefO-like cd20207
B-box-type 2 zinc finger found in Ras guanine nucleotide exchange factor O (GefO) and similar ...
274-309 7.98e-03

B-box-type 2 zinc finger found in Ras guanine nucleotide exchange factor O (GefO) and similar proteins; Ras guanine-nucleotide exchange factors (RasGEFs) activate Ras by catalyzing the replacement of GDP with GTP, and thus lie near the top of many signaling pathways. They are important for signaling in development and chemotaxis in many organisms. Ras guanine nucleotide exchange factor O (GefO), also known as RasGEF domain-containing protein O, is faintly expressed during development of Dictyostelium discoideum. It contains a C3HC4-type RING finger, a B-box motif that shows high sequence similarity with B-Box-type zinc finger 2 found in tripartite motif-containing proteins (TRIMs), a REM (Ras exchanger motif) domain, and a # RasGEF domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380908  Cd Length: 40  Bit Score: 35.20  E-value: 7.98e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 767904604  274 VFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRY 309
Cdd:cd20207     1 VVCSKHNEHMLDKFCKDCSAPVCENCVLTTHAGHNV 36
RING-HC_RNF39 cd16592
RING finger, HC subclass, found in RING finger protein 39 (RNF39) and similar proteins; RNF39, ...
124-188 8.12e-03

RING finger, HC subclass, found in RING finger protein 39 (RNF39) and similar proteins; RNF39, also called protein HZFw, may play a role in prolonged long term-potentiation (LTP) maintenance. It is involved in the etiology of Behcet's disease (BD). It may also be involved in HIV-1 replication. RNF39 acts as an E3 ubiquitin ligase that inhibits retinoic acid-inducible gene-I (RIG-I)-like receptor (RLR) pathways by mediating K48-linked ubiquitination and proteasomal degradation of DDX3X (DEAD-box RNA helicase 3, X-linked). RNF39 contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438254 [Multi-domain]  Cd Length: 58  Bit Score: 35.89  E-value: 8.12e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767904604  124 TCAVCQQSLQsrreaEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSngdiqqvgVIRCPVCRQEC 188
Cdd:cd16592     6 TCPICLGYFK-----DPVILDCEHSFCRACIARHWGQEAMEGNGAE--------GVFCPQCGEPC 57
Bbox2_TRIM46_C-I cd19786
B-box-type 2 zinc finger found in tripartite motif-containing protein 46 (TRIM46) and similar ...
276-317 9.16e-03

B-box-type 2 zinc finger found in tripartite motif-containing protein 46 (TRIM46) and similar proteins; TRIM46, also known as gene Y protein (GeneY) or tripartite, fibronectin type-III and C-terminal SPRY motif protein (TRIFIC), is a microtubule-associated protein that specifically localizes to the proximal axon, partly overlaps with the axon initial segment (AIS) at later stages, and organizes uniform microtubule orientation in axons. It controls neuronal polarity and axon specification by driving the formation of parallel microtubule arrays. TRIM46 belongs to the C-I subclass of TRIM (tripartite motif) family of proteins, which are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380844 [Multi-domain]  Cd Length: 46  Bit Score: 35.28  E-value: 9.16e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 767904604  276 CPVHKqEQLKLFCETCDRLTCRDCQLLE-HKEHRYQFLEEAFQ 317
Cdd:cd19786     5 CPEHK-EEVTHYCKTCQRLVCQLCRVRRtHAGHKITPVLSAYQ 46
RING-HC_LONFs_rpt1 cd16513
first RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger ...
124-187 9.61e-03

first RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger protein family; The LON peptidase N-terminal domain and RING finger protein family includes LONRF1 (also known as RING finger protein 191 or RNF191), LONRF2 (also known as RING finger protein 192, RNF192, or neuroblastoma apoptosis-related protease), LONRF3 (also known as RING finger protein 127 or RNF127), which are characterized by containing two C3HC4-type RING-HC fingers, four tetratricopeptide (TPR) repeats, and an ATP-dependent protease La (LON) substrate-binding domain at the C-terminus. Their biological functions remain unclear. This model corresponds to the first RING-HC finger.


Pssm-ID: 438176 [Multi-domain]  Cd Length: 47  Bit Score: 35.36  E-value: 9.61e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767904604  124 TCAVCQQSLqsrreAEPKLLPCLHSFCLRCLpepERQLSVpipggsngdiqqvgviRCPVCRQE 187
Cdd:cd16513     4 SCPLCRGLL-----FEPVTLPCGHTFCKRCL---ERDPSS----------------RCRLCRLK 43
 
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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