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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1919048149  970 LSPMDQRKCERLLLYLYCHELSIEFQEPVPVSIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCER 1049
Cdd:cd05502      1 LSPIDQRKCERLLLELYCHELSLPFHEPVSPSVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYK 80

                           90       100
                   ....*....|....*....|....*....
gi 1919048149 1050 FNEADSEVAQAGKSVALYFEDKLTEIYSD 1078
Cdd:cd05502     81 FNEEDSEVAQAGKELELFFEEQLKEILPD 109

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.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1919048149  134 LLDTCAVCQQSLQSRReAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPICRQEC 201
Cdd:cd16766      1 LLDTCAVCKQSLQSRD-AEPKLLPCLHSFCRRCLPEPERQLSVPVPGGSNGDIQQVGVIRCPVCRQEC 67

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.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1919048149  223 DEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVS 276
Cdd:cd19847      1 DEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHMIRKKEDVS 54

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1919048149  552 PPAGAATTTTPPQQHPRQAAPQMLQQQ-----PPRLISVQT-MQRGNMNCGAFQAHQMRMAQNAARIPGIPR----HSGP 621
Cdd:pfam03154  207 PPQGSPATSQPPNQTQSTAAPHTLIQQtptlhPQRLPSPHPpLQPMTQPPPPSQVSPQPLPQPSLHGQMPPMphslQTGP 286

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1919048149  622 qysmmqPHLQrqhsNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLP----SLPDIP 697
Cdd:pfam03154  287 ------SHMQ----HPVPPQPFPLTPQSSQSQVPPGPSPAAPGQSQQRIHTPPSQSQLQSQQPPREQPLPpaplSMPHIK 356

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1919048149  698 PIQLEDAgsSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSgLSNSHTP-VRPP 756
Cdd:pfam03154  357 PPPTTPI--PQLPNPQSHKHPPHLSGPSPFQMNSNLPPPPALKPLSS-LSTHHPPsAHPP 413

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1919048149  970 LSPMDQRKCERLLLYLYCHELSIEFQEPVPVSIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCER 1049
Cdd:cd05502      1 LSPIDQRKCERLLLELYCHELSLPFHEPVSPSVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYK 80

                           90       100
                   ....*....|....*....|....*....
gi 1919048149 1050 FNEADSEVAQAGKSVALYFEDKLTEIYSD 1078
Cdd:cd05502     81 FNEEDSEVAQAGKELELFFEEQLKEILPD 109

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.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1919048149  134 LLDTCAVCQQSLQSRReAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPICRQEC 201
Cdd:cd16766      1 LLDTCAVCKQSLQSRD-AEPKLLPCLHSFCRRCLPEPERQLSVPVPGGSNGDIQQVGVIRCPVCRQEC 67

bromo domain;

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1919048149   971 SPMDQRKCERLLLYLYC----HELSIEFQEPVPVS-IPNYYKIIKKPMDLSTVKKKLQKkhsQHYQIPDDFVADVRLIFK 1045
Cdd:smart00297    1 DPKLQKKLQELLKAVLDkldsHPLSWPFLKPVSRKeAPDYYDIIKKPMDLKTIKKKLEN---GKYSSVEEFVADFNLMFS 77

                            90       100       110
                    ....*....|....*....|....*....|
gi 1919048149  1046 NCERFNEADSEVAQAGKSVALYFEDKLTEI 1075
Cdd:smart00297   78 NARTYNGPDSEVYKDAKKLEKFFEKKLREL 107

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.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1919048149  901 WCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDL 946
Cdd:cd15624      1 WCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDI 46

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1919048149  956 DNLQHSKKGKTAQGLSPMDQRK-----CERLLLYLYC----HELSIEFQE---------PVPVS---IPNYYKIIKKPMD 1014
Cdd:COG5076    111 SVTPESGLGSLLMAHLKTSVKKrktpkIEDELLYADNkaiaKFKKQLFLRdgrflssifLGLPSkreYPDYYEIIKSPMD 190

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1919048149 1015 LSTVKKKLQkkhSQHYQIPDDFVADVRLIFKNCERFNEADSEVAQAGKSVALYFEDKL---TEIYSDRTFPPLPEFEQEE 1091
Cdd:COG5076    191 LLTIQKKLK---NGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLIeeiPEEMLELSIKPGREEREER 267

                   ....*....
gi 1919048149 1092 DDGEITEDS 1100
Cdd:COG5076    268 ESVLITNSQ 276

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.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1919048149  901 WCAVCQ---NGGDLLCCEKCPKVFHLTCHVPTLLS--FPSGDWICTFCR 944
Cdd:pfam00628    1 YCAVCGksdDGGELVQCDGCDDWFHLACLGPPLDPaeIPSGEWLCPECK 49

B-box zinc finger;

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1919048149  284 QRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFL 325
Cdd:pfam00643    1 SKERLCPEHEEEPLTLYCNDCQELLCEECSVGEHRGHTVVPL 42

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1919048149  552 PPAGAATTTTPPQQHPRQAAPQMLQQQ-----PPRLISVQT-MQRGNMNCGAFQAHQMRMAQNAARIPGIPR----HSGP 621
Cdd:pfam03154  207 PPQGSPATSQPPNQTQSTAAPHTLIQQtptlhPQRLPSPHPpLQPMTQPPPPSQVSPQPLPQPSLHGQMPPMphslQTGP 286

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1919048149  622 qysmmqPHLQrqhsNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLP----SLPDIP 697
Cdd:pfam03154  287 ------SHMQ----HPVPPQPFPLTPQSSQSQVPPGPSPAAPGQSQQRIHTPPSQSQLQSQQPPREQPLPpaplSMPHIK 356

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1919048149  698 PIQLEDAgsSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSgLSNSHTP-VRPP 756
Cdd:pfam03154  357 PPPTTPI--PQLPNPQSHKHPPHLSGPSPFQMNSNLPPPPALKPLSS-LSTHHPPsAHPP 413

B-Box-type zinc finger;

                            10        20        30        40
                    ....*....|....*....|....*....|....*....|.
gi 1919048149   225 KSEQVCTSCEDNAsAVGFCVECGEWLCKTCIEA----HQRV 261
Cdd:smart00336    1 QRAPKCDSHGDEP-AEFFCEECGALLCRTCDEAehrgHTVV 40

DNA double-strand break repair ATPase Rad50;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1919048149  325 LEEAFQNQKGAIENLLAKLLEKKNYVHfAATQVQNRIKEVNETNKRVEQEikvaiftlINEINKKGKSLLQQLENVTKER 404
Cdd:PRK03918   160 YENAYKNLGEVIKEIKRRIERLEKFIK-RTENIEELIKEKEKELEEVLRE--------INEISSELPELREELEKLEKEV 230

                           90       100
                   ....*....|....*....|.
gi 1919048149  405 QmKLIQQQNDITGLSRQVKHV 425
Cdd:PRK03918   231 K-ELEELKEEIEELEKELESL 250

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1919048149  970 LSPMDQRKCERLLLYLYCHELSIEFQEPVPVSIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCER 1049
Cdd:cd05502      1 LSPIDQRKCERLLLELYCHELSLPFHEPVSPSVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYK 80

                           90       100
                   ....*....|....*....|....*....
gi 1919048149 1050 FNEADSEVAQAGKSVALYFEDKLTEIYSD 1078
Cdd:cd05502     81 FNEEDSEVAQAGKELELFFEEQLKEILPD 109

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.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1919048149  134 LLDTCAVCQQSLQSRReAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPICRQEC 201
Cdd:cd16766      1 LLDTCAVCKQSLQSRD-AEPKLLPCLHSFCRRCLPEPERQLSVPVPGGSNGDIQQVGVIRCPVCRQEC 67

bromo domain;

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1919048149   971 SPMDQRKCERLLLYLYC----HELSIEFQEPVPVS-IPNYYKIIKKPMDLSTVKKKLQKkhsQHYQIPDDFVADVRLIFK 1045
Cdd:smart00297    1 DPKLQKKLQELLKAVLDkldsHPLSWPFLKPVSRKeAPDYYDIIKKPMDLKTIKKKLEN---GKYSSVEEFVADFNLMFS 77

                            90       100       110
                    ....*....|....*....|....*....|
gi 1919048149  1046 NCERFNEADSEVAQAGKSVALYFEDKLTEI 1075
Cdd:smart00297   78 NARTYNGPDSEVYKDAKKLEKFFEKKLREL 107

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.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1919048149  223 DEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVS 276
Cdd:cd19847      1 DEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHMIRKKEDVS 54

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.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1919048149  901 WCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDL 946
Cdd:cd15624      1 WCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDI 46

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1919048149  974 DQRKCERLLLYLYCHELSIEFQEPVPVS-IPNYYKIIKKPMDLSTVKKKLQKKHsqhYQIPDDFVADVRLIFKNCERFNE 1052
Cdd:cd05509      2 LYTQLKKVLDSLKNHKSAWPFLEPVDKEeAPDYYDVIKKPMDLSTMEEKLENGY---YVTLEEFVADLKLIFDNCRLYNG 78

                           90       100
                   ....*....|....*....|...
gi 1919048149 1053 ADSEVAQAGKSVALYFEDKLTEI 1075
Cdd:cd05509     79 PDTEYYKCANKLEKFFWKKLKEL 101

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.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1919048149  228 QVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKK 272
Cdd:cd19845      1 QVCTSCEDNAEANGFCVECVEWLCKTCIEAHQRVKFTKDHTVRQK 45

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1919048149  978 CERLLLYLYCHELSIEFQEPV-PVSIPNYYKIIKKPMDLSTVKKKLqkkHSQHYQIPDDFVADVRLIFKNCERFNEADSE 1056
Cdd:pfam00439    1 CLEILDKLMEHPIAAPFLEPVdPDEYPDYYSVIKKPMDLSTIKKKL---ENGEYKSLAEFLADVKLIFSNARTYNGPGSV 77

                   ....*.
gi 1919048149 1057 VAQAGK 1062
Cdd:pfam00439   78 IYKAAE 83

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.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1919048149  901 WCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 943
Cdd:cd15622      1 WCAVCQNGGELLCCEKCPKVFHLSCHVPTLMNFPSGEWICTFC 43

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).

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1919048149  229 VCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKK 272
Cdd:cd19805      1 VCTSCEDNAPATSFCVECSEWLCDTCVQAHQRVKVTKDHTIRSK 44

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).

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1919048149  901 WCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 943
Cdd:cd15541      1 WCAVCQNGGELLCCDKCPRVFHLDCHIPPIPEFPSGEWSCSLC 43

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.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1919048149  135 LDTCAVCQQSLQSRReaePKLLPCLHSFCLRCLPEPERQLSVPIP-------GGSNGDIQQVGVIRCPICRQEC 201
Cdd:cd16764      1 LDTCGVCKQHIQSRE---PRLLPCLHSFCQRCLPQPERYLMLPAPfspspgpRATSSANRQVGVVRCPVCSQEC 71

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.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1919048149  286 PVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEA 328
Cdd:cd19829      1 TVYCSIHKQEPLKLFCETCDTLTCRDCQLNAHKDHQYQFLEDA 43

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1919048149  978 CERLLLYLYCH-ELSIEFQEPV-PVSIPNYYKIIKKPMDLSTVKKKLQKKhsqHYQIPDDFVADVRLIFKNCERFNEADS 1055
Cdd:cd05510     12 LDKVLNELKTYtEHSTPFLTKVsKREAPDYYDIIKKPMDLGTMLKKLKNL---QYKSKAEFVDDLNLIWKNCLLYNSDPS 88

                   ..
gi 1919048149 1056 EV 1057
Cdd:cd05510     89 HP 90

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1919048149  991 SIEFQEPV-PVSIPNYYKIIKKPMDLSTVKKKLqKKHSqhYQIPDDFVADVRLIFKNCERFNEADSEVAQAGKSVALYFE 1069
Cdd:cd05511     18 SWPFHTPVnKKKVPDYYKIIKRPMDLQTIRKKI-SKHK--YQSREEFLEDIELIVDNSVLYNGPDSVYTKKAKEMLELAE 94

                   ....*
gi 1919048149 1070 DKLTE 1074
Cdd:cd05511     95 ELLAE 99

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.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1919048149  286 PVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEA 328
Cdd:cd19785      1 PVLCPFHPAEELRLFCETCDKPVCRDCVLVEHRGHQCDFTSDV 43

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1919048149  972 PMDQRKCERLLLYLYCHELSIEFQePVPVSIPNYYKIIKKPMDLSTVKKKLqkkHSQHYQIPDDFVADVRLIFKNCERFN 1051
Cdd:cd05501      1 PEELLKCEFLLLKVYCMSKSGFFI-SKPYYIRDYCQGIKEPMWLNKVKERL---NERVYHTVEGFVRDMRLIFHNHKLFY 76

                           90       100
                   ....*....|....*....|....*.
gi 1919048149 1052 EADSEVaQAGKSVALYFEDKLTEIYS 1077
Cdd:cd05501     77 KDDDFG-QVGITLEKKFEKNFKEVFA 101

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.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1919048149  902 CAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 943
Cdd:cd15539      2 CAVCGDGGELLCCDGCPRAFHLACLVPPLTLIPSGTWRCSSC 43

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.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1919048149  230 CTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRK 271
Cdd:cd19812      2 CSSCDEGNAATSRCKDCNEYLCDNCVRAHQRVRLTKDHFIVR 43

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.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1919048149  902 CAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 943
Cdd:cd15532      2 CRVCKDGGELLCCDGCPSSYHLHCLNPPLAEIPDGDWFCPRC 43

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.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1919048149  902 CAVCQNGGDLLCCEKCPKVFHLTCHVPTL--LSFPSGDWICTFC 943
Cdd:cd15533      2 CDSCGEGGDLLCCDRCPASFHLQCCNPPLdeEDLPPGEWLCHRC 45

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.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1919048149  994 FQEPVPVS-IPNYYKIIKKPMDLSTVKKKLQkkhSQHYQIPDDFVADVRLIFKNCERFNEADS 1055
Cdd:cd05512     22 FSEPVDLSeVPDYLDHIKQPMDFSTMRKKLE---SQRYRTLEDFEADFNLIINNCLAYNAKDT 81

B-Box-type zinc finger;

                            10        20        30        40
                    ....*....|....*....|....*....|....*....|..
gi 1919048149   284 QRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFL 325
Cdd:smart00336    1 QRAPKCDSHGDEPAEFFCEECGALLCRTCDEAEHRGHTVVLL 42

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.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1919048149  902 CAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 943
Cdd:cd15559      2 CRVCHKLGDLLCCETCSAVYHLECVDPPLEEVPEEDWQCEVC 43