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 119637830  971 LSPVDQRKCERLLLYLYCHELSIEFQEPVPVSIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCER 1050
Cdd:cd05502     1 LSPIDQRKCERLLLELYCHELSLPFHEPVSPSVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYK 80

                          90       100
                  ....*....|....*....|....*....
gi 119637830 1051 FNEGDSEVAKAGKAVALYFEDKLSEIYSD 1079
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 119637830  135 LLDTCAVCQQSLQSRReAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDVQQVGVIRCPVCRQEC 202
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 119637830  224 DEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVS 277
Cdd:cd19847     1 DEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHMIRKKEDVS 54

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119637830   600 QAHQMRLAQNAARIPgIPRHSAPQYSMMQPHLQRQHSNPGHAGPFPVVSAHNPiNPTSPTTATMA---NAN---RGPTSP 673
Cdd:pfam05109  502 KAPDMTSPTSAVTTP-TPNATSPTPAVTTPTPNATSPTLGKTSPTSAVTTPTP-NATSPTPAVTTptpNATiptLGKTSP 579

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119637830   674 SVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSL-------DNLLSRYISGSH-LPPQPTSTMN--PSPGPSALSPGS 743
Cdd:pfam05109  580 TSAVTTPTPNATSPTVGETSPQANTTNHTLGGTSSTpvvtsppKNATSAVTTGQHnITSSSTSSMSlrPSSISETLSPST 659

                          170
                   ....*....|
gi 119637830   744 SGLSNSHTPV 753
Cdd:pfam05109  660 SDNSTSHMPL 669

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 119637830  971 LSPVDQRKCERLLLYLYCHELSIEFQEPVPVSIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCER 1050
Cdd:cd05502     1 LSPIDQRKCERLLLELYCHELSLPFHEPVSPSVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYK 80

                          90       100
                  ....*....|....*....|....*....
gi 119637830 1051 FNEGDSEVAKAGKAVALYFEDKLSEIYSD 1079
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 119637830  135 LLDTCAVCQQSLQSRReAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDVQQVGVIRCPVCRQEC 202
Cdd:cd16766     1 LLDTCAVCKQSLQSRD-AEPKLLPCLHSFCRRCLPEPERQLSVPVPGGSNGDIQQVGVIRCPVCRQEC 67

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 119637830  282 TSGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQK 334
Cdd:cd19830     1 ASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQK 53

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 119637830  902 WCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDI 947
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 119637830  957 DNMQHSKKGKTAQGLSPVDQRK-----CERLLLYLYC----HELSIEFQE---------PVPVS---IPNYYKIIKKPMD 1015
Cdd:COG5076   111 SVTPESGLGSLLMAHLKTSVKKrktpkIEDELLYADNkaiaKFKKQLFLRdgrflssifLGLPSkreYPDYYEIIKSPMD 190

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119637830 1016 LSTVKKKLQkkhSQHYQIPDDFVADVRLIFKNCERFNEGDSEVAKAGKAVALYFEDKLSEI---YSDRTFTPLPEFEQDE 1092
Cdd:COG5076   191 LLTIQKKLK---NGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLIEEIpeeMLELSIKPGREEREER 267

                  ....*....
gi 119637830 1093 DDGEVTEDS 1101
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 119637830   902 WCAVCQ---NGGDLLCCEKCPKVFHLTCHVPTLLS--FPSGDWICTFCR 945
Cdd:pfam00628    1 YCAVCGksdDGGELVQCDGCDDWFHLACLGPPLDPaeIPSGEWLCPECK 49

B-box zinc finger;

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 119637830   285 QRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFL 326
Cdd:pfam00643    1 SKERLCPEHEEEPLTLYCNDCQELLCEECSVGEHRGHTVVPL 42

B-Box-type zinc finger;

                            10        20        30        40
                    ....*....|....*....|....*....|....*....|.
gi 119637830    226 KSEQVCTSCEDNAsAVGFCVECGEWLCKTCIEA----HQRV 262
Cdd:smart00336    1 QRAPKCDSHGDEP-AEFFCEECGALLCRTCDEAehrgHTVV 40

large tegument protein UL36; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119637830  611 ARIPGIPRHSAPQYSmmqphlqRQHSNPGHAGPFPVVSAHNPINPTSPTTATMANANRGPTSPS------------VTAI 678
Cdd:PHA03247 2714 ALVSATPLPPGPAAA-------RQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAppaapaagpprrLTRP 2786

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119637830  679 ELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGshLPPQPTSTMNPSPGPSALSPGSSGLSNSHTP-----V 753
Cdd:PHA03247 2787 AVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGP--LPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPggdvrR 2864

                  ...
gi 119637830  754 RPP 756
Cdd:PHA03247 2865 RPP 2867

DNA double-strand break repair ATPase Rad50;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119637830  326 LEEAFQNQKGAIENLLAKLLEKKNYVHfAATQVQNRIKEVNETNKRVEQEikvaiftlINEINKKGKSLLQQLENVTKER 405
Cdd:PRK03918  160 YENAYKNLGEVIKEIKRRIERLEKFIK-RTENIEELIKEKEKELEEVLRE--------INEISSELPELREELEKLEKEV 230

                          90       100
                  ....*....|....*....|.
gi 119637830  406 QmKLLQQQNDITGLSRQVKHV 426
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 119637830  971 LSPVDQRKCERLLLYLYCHELSIEFQEPVPVSIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCER 1050
Cdd:cd05502     1 LSPIDQRKCERLLLELYCHELSLPFHEPVSPSVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYK 80

                          90       100
                  ....*....|....*....|....*....
gi 119637830 1051 FNEGDSEVAKAGKAVALYFEDKLSEIYSD 1079
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 119637830  135 LLDTCAVCQQSLQSRReAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDVQQVGVIRCPVCRQEC 202
Cdd:cd16766     1 LLDTCAVCKQSLQSRD-AEPKLLPCLHSFCRRCLPEPERQLSVPVPGGSNGDIQQVGVIRCPVCRQEC 67

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 119637830  282 TSGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQK 334
Cdd:cd19830     1 ASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQK 53

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 119637830  224 DEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVS 277
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 119637830  902 WCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDI 947
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 119637830  975 DQRKCERLLLYLYCHELSIEFQEPVPVS-IPNYYKIIKKPMDLSTVKKKLQKKHsqhYQIPDDFVADVRLIFKNCERFNE 1053
Cdd:cd05509     2 LYTQLKKVLDSLKNHKSAWPFLEPVDKEeAPDYYDVIKKPMDLSTMEEKLENGY---YVTLEEFVADLKLIFDNCRLYNG 78

                          90       100
                  ....*....|....*....|...
gi 119637830 1054 GDSEVAKAGKAVALYFEDKLSEI 1076
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 119637830  229 QVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKK 273
Cdd:cd19845     1 QVCTSCEDNAEANGFCVECVEWLCKTCIEAHQRVKFTKDHTVRQK 45

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 119637830  136 LDTCAVCQQSLQSRreaEPKLLPCLHSFCLRCLPEPERQLSVPIPggSNGDVQQVGVIRCPVCRQEC 202
Cdd:cd16585     1 LDTCAVCKQSFQSR---EPKLLPCLHSFCKRCLPPADRAAANPSP--SGGAAGQVGVIRCPVCKQEC 62

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 119637830  230 VCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKK 273
Cdd:cd19805     1 VCTSCEDNAPATSFCVECSEWLCDTCVQAHQRVKVTKDHTIRSK 44

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119637830  977 RKCERLLLYLYCHELSIEFQEPVPVS---IPNYYKIIKKPMDLSTVKKKLQKKhsqHYQIPDDFVADVRLIFKNCERFNE 1053
Cdd:cd05506     3 KQCGTLLRKLMKHKWGWVFNAPVDVValgLPDYFDIIKKPMDLGTVKKKLEKG---EYSSPEEFAADVRLTFANAMRYNP 79

                          90
                  ....*....|....*....
gi 119637830 1054 GDSEVAKAGKAVALYFEDK 1072
Cdd:cd05506    80 PGNDVHTMAKELLKIFETR 98

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119637830  995 FQEPV-PVS--IPNYYKIIKKPMDLSTVKKKLQKKHsqhYQIPDDFVADVRLIFKNCERFNEGDSEVAKAGKAVALYFED 1071
Cdd:cd05498    24 FYKPVdPEAlgLHDYHDIIKHPMDLSTIKKKLDNRE---YADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKLQDVFED 100

                  .
gi 119637830 1072 K 1072
Cdd:cd05498   101 R 101

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 119637830  287 PVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEA 329
Cdd:cd19829     1 TVYCSIHKQEPLKLFCETCDTLTCRDCQLNAHKDHQYQFLEDA 43

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 119637830  227 SEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKK 273
Cdd:cd19846     2 TIQCCTSCEDNAPATSYCVECSEPLCETCVEAHQRVKYTKDHTVRVK 48

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119637830  979 CERLLLYLYCHELSIEFQEPVPVS-IPNYYKIIKKPMDLSTVKKKLQKkhsQHYQIPDDFVADVRLIFKNCERFNEGDSE 1057
Cdd:cd05504    17 LEQLLVEIVKHKDSWPFLRPVSKIeVPDYYDIIKKPMDLGTIKEKLNM---GEYKLAEEFLSDIQLVFSNCFLYNPEHTS 93

                          90
                  ....*....|....*....
gi 119637830 1058 VAKAGKAVALYFEDKLSEI 1076
Cdd:cd05504    94 VYKAGTRLQRFFIKRCRKL 112

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 119637830  979 CERLLLYLYCH-ELSIEFQEPV-PVSIPNYYKIIKKPMDLSTVKKKLQKKhsqHYQIPDDFVADVRLIFKNCERFN 1052
Cdd:cd05510    12 LDKVLNELKTYtEHSTPFLTKVsKREAPDYYDIIKKPMDLGTMLKKLKNL---QYKSKAEFVDDLNLIWKNCLLYN 84

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119637830  992 SIEFQEPV-PV--SIPNYYKIIKKPMDLSTVKKKLQkkhSQHYQIPDDFVADVRLIFKNCERFNEGDSEVAKAGKAVALY 1068
Cdd:cd05495    22 SLPFRQPVdPKllGIPDYFDIVKNPMDLSTIRRKLD---TGQYQDPWQYVDDVWLMFDNAWLYNRKTSRVYKYCTKLAEV 98

                  ....*...
gi 119637830 1069 FEdklSEI 1076
Cdd:cd05495    99 FE---QEI 103

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 119637830  287 PVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEA 329
Cdd:cd19785     1 PVLCPFHPAEELRLFCETCDKPVCRDCVLVEHRGHQCDFTSDV 43

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119637830  986 LYCHELSIEFQEPV---PVSIPNYYKIIKKPMDLSTVKKKLQKKhsqHYQIPDDFVADVRLIFKNCERFNEGDSEVAKAG 1062
Cdd:cd05497    17 LWKHKFAWPFQQPVdavKLNLPDYHKIIKTPMDLGTIKKRLENN---YYWSASECIQDFNTMFTNCYIYNKPGDDVVLMA 93

                          90
                  ....*....|...
gi 119637830 1063 KAVALYFEDKLSE 1075
Cdd:cd05497    94 QTLEKLFLQKLAQ 106

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 119637830  989 HELSIEFQE-PVPVSIPNYYKIIKKPMDLSTVKKKLQkkhSQHYQIPDDFVADVRLIFKNCERFNEGDSEVAK 1060
Cdd:cd05515    21 RRLSLIFMRlPSKSEYPDYYDVIKKPIDMEKIRSKIE---GNQYQSLDDMVSDFVLMFDNACKYNEPDSQIYK 90

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 119637830  903 CAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 944
Cdd:cd15532     2 CRVCKDGGELLCCDGCPSSYHLHCLNPPLAEIPDGDWFCPRC 43

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119637830  977 RKCERLLLYLYCHELSIEFQEPVP-VSIPNYYKIIKKPMDLSTVKKKLQkkhSQHYQIPDDFVADVRLIFKNCERFNEGD 1055
Cdd:cd05496     8 KQCKELVNLMWDCEDSEPFRQPVDlLKYPDYRDIIDTPMDLGTVKETLF---GGNYDDPMEFAKDVRLIFSNSKSYTPNK 84

                          90       100
                  ....*....|....*....|....*
gi 119637830 1056 -SEVAKAGKAVALYFEDKLSEIYSD 1079
Cdd:cd05496    85 rSRIYSMTLRLSALFEEHIKKIISD 109

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 119637830  995 FQEPVPVS-IPNYYKIIKKPMDLSTVKKKLQkkhSQHYQIPDDFVADVRLIFKNCERFNEGDSEVAKAG 1062
Cdd:cd05512    22 FSEPVDLSeVPDYLDHIKQPMDFSTMRKKLE---SQRYRTLEDFEADFNLIINNCLAYNAKDTIFYRAA 87

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119637830  136 LDTCAVCQQSLQSRREaePKLLPCLHSFCLRCLPeperqLSVPIPGGSNGDVQQVG---VIRCPVCRQEC 202
Cdd:cd16765     1 LEHCGVCRERLRPERE--PRLLPCLHSVCSACLG-----PAAPAAANSSGDGGAAGdgtVVDCPVCKQQC 63

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 119637830  903 CAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 944
Cdd:cd15559     2 CRVCHKLGDLLCCETCSAVYHLECVDPPLEEVPEEDWQCEVC 43

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119637830  994 EFQEPVPV--SIPNYYKIIKKPMDLSTVKKKLQkkhSQHYQIPDDFVADVRLIFKNCERFNEGDSEVAKAGKAValyfED 1071
Cdd:cd05529    47 YFEYPVDLraWYPDYWNRVPVPMDLETIRSRLE---NRYYRSLEALRHDVRLILSNAETFNEPNSEIAKKAKRL----SD 119