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 1810975933 1113 LSIYDQKRCEKLVLSLCCNSLSLPFHEPVSPLARHYYQIIKRPMDLSIIRRKLQKKDPAHYTTPEEVVSDVRLMFWNCAK 1192
Cdd:cd05502      1 LSPIDQRKCERLLLELYCHELSLPFHEPVSPSVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYK 80

                           90       100
                   ....*....|....*....|....*....
gi 1810975933 1193 FNYPDSEVAEAGRCLEVFFEGWLKEIYPE 1221
Cdd:cd05502     81 FNEEDSEVAQAGKELELFFEEQLKEILPD 109

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

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1810975933 1040 NEDFCAVCLNGGELLCCDRCPKVYHLSCHLPALLSFPGGDWVCTLCRSL 1088
Cdd:cd15625      1 NEDFCAVCLNGGELLCCDRCPKVFHLSCHVPALLSFPVGEWVCTLCRNL 49

B-box-type 1 zinc finger found in tripartite motif-containing protein 66 (TRIM66) and similar proteins; TRIM66, also termed transcriptional intermediary factor 1 delta (TIF1delta), is a novel heterochromatin protein 1 (HP1)-interacting member of the transcriptional intermediary factor 1 (TIF1) family, and is expressed by elongating spermatids. Like other TIF1 proteins, TRIM66 displays a potent trichostatin A (TSA)-sensitive repression function; TSA is a specific inhibitor of histone deacetylases. Moreover, TRIM66 plays an important role in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. It functions as a negative regulator of postmeiotic genes acting through HP1 isotype gamma (HP1gamma) complex formation and centromere association. TRIM66 belongs to an unclassified TRIM (tripartite motif) family of proteins that do not have RING fingers and thus lack the characteristic tripartite (RING (R), B-box, and coiled coil (CC)) RBCC motif. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif.

                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 1810975933   53 NCSECKEKRAAHILCTYCNRWLCSSCTEEHRHGPAPG 89
Cdd:cd19811      1 SCSECKEKRPAHSLCTTCNKWLCSSCTEEHRHGKSTS 37

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 1810975933  320 QLSRADTPAYGglQGPSSFYQSHQSPVAQQETLSHPSHKFQSPALCSSSVCCSHCSPVSPSLKGQVPPPSIHPAHSFRQP 399
Cdd:pfam03154  106 EISRPNSPSEG--EGESSDGRSVNDEGSSDPKDIDQDNRSTSPSIPSPQDNESDSDSSAQQQILQTQPPVLQAQSGAASP 183

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810975933  400 SEMVPQQLGSLQCSTLLPREKELPCNPHPPkLLQPWLETQPPVEQ----ESTSQRLGQQLTS-----QPVCI-VPPQDVQ 469
Cdd:pfam03154  184 PSPPPPGTTQAATAGPTPSAPSVPPQGSPA-TSQPPNQTQSTAAPhtliQQTPTLHPQRLPSphpplQPMTQpPPPSQVS 262

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810975933  470 PGAHAQPTLQSPsiQVQFGHHQKLKLSHFQQQPQQQLPLPPPPPPPPQQQPAPPLPPSQHLASSQHESPPGPAcsqnvdi 549
Cdd:pfam03154  263 PQPLPQPSLHGQ--MPPMPHSLQTGPSHMQHPVPPQPFPLTPQSSQSQVPPGPSPAAPGQSQQRIHTPPSQSQ------- 333

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810975933  550 mhhkfeleemqkdlellLQAQQPSLQLSQTKSPQHLQQTivgqinyivrQPAPVQSQSQEDTVQATDEPPASEGPKPAlp 629
Cdd:pfam03154  334 -----------------LQSQQPPREQPLPPAPLSMPHI----------KPPPTTPIPQLPNPQSHKHPPHLSGPSPF-- 384

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810975933  630 ldkNTAANLPQASGEETPHSVPSQDNAIQHSSPnvvrkhstsvsimgfsntvemelsstrlaRTLEPQIQSMSSLTAGTP 709
Cdd:pfam03154  385 ---QMNSNLPPPPALKPLSSLSTHHPPSAHPPP-----------------------------LQLMPQSQQLPPPPAQPP 432

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810975933  710 QVVPSllSGPPPTVSSLTSHNQAMSSLTASHLPTMPSLVRGTPQSMPSLISDPSQAITSLASDHSQARPSLVSGPTQAVP 789
Cdd:pfam03154  433 VLTQS--QSLPPPAASHPPTSGLHQVPSQSPFPQHPFVPGGPPPITPPSGPPTSTSSAMPGIQPPSSASVSSSGPVPAAV 510

                          490       500
                   ....*....|....*....|..
gi 1810975933  790 GCPLQSL-----PPASDVQPET 806
Cdd:pfam03154  511 SCPLPPVqikeeALDEAEEPES 532

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 1810975933 1113 LSIYDQKRCEKLVLSLCCNSLSLPFHEPVSPLARHYYQIIKRPMDLSIIRRKLQKKDPAHYTTPEEVVSDVRLMFWNCAK 1192
Cdd:cd05502      1 LSPIDQRKCERLLLELYCHELSLPFHEPVSPSVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYK 80

                           90       100
                   ....*....|....*....|....*....
gi 1810975933 1193 FNYPDSEVAEAGRCLEVFFEGWLKEIYPE 1221
Cdd:cd05502     81 FNEEDSEVAQAGKELELFFEEQLKEILPD 109

PHD finger found in transcriptional intermediary factor 1 delta (TIF1delta); TIF1delta, also termed tripartite motif-containing protein 66 (TRIM66), is a novel heterochromatin protein 1 (HP1)-interacting member of the transcriptional intermediary factor1 (TIF1) family expressed by elongating spermatids. Like other TIF1 proteins, TIF1delta displays a potent trichostatin A (TSA)-sensitive repression function; TSA is a specific inhibitor of histone deacetylases. Moreover, TIF1delta plays an important role in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. It functions as a negative regulator of postmeiotic genes acting through HP1 isotype gamma (HP1gamma) complex formation and centromere association. TIF1delta contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1810975933 1040 NEDFCAVCLNGGELLCCDRCPKVYHLSCHLPALLSFPGGDWVCTLCRSL 1088
Cdd:cd15625      1 NEDFCAVCLNGGELLCCDRCPKVFHLSCHVPALLSFPVGEWVCTLCRNL 49

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

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1810975933  112 LYCPLHTQEVLKLFCETCDVLTCHSCLMVEHKEHRCRHLEEVL 154
Cdd:cd19794      1 LMCPLHNQEPLKLFCETCDVLVCRSCLLSEHKEHRFKHLDEAL 43

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810975933 1133 LSLPFHEPVSP-LARHYYQIIKRPMDLSIIRRKLQKKdpaHYTTPEEVVSDVRLMFWNCAKFNYPDSEVAEAGRCLEVFF 1211
Cdd:COG5076    165 LSSIFLGLPSKrEYPDYYEIIKSPMDLLTIQKKLKNG---RYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYF 241

                           90
                   ....*....|..
gi 1810975933 1212 EGWLKEIYPEKR 1223
Cdd:COG5076    242 LKLIEEIPEEML 253

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        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1810975933 1043 FCAVCL---NGGELLCCDRCPKVYHLSCHLPALLS--FPGGDWVCTLCRS 1087
Cdd:pfam00628    1 YCAVCGksdDGGELVQCDGCDDWFHLACLGPPLDPaeIPSGEWLCPECKP 50

B-Box-type zinc finger;

                            10        20        30
                    ....*....|....*....|....*....|....*.
gi 1810975933   111 ALYCPLHTQEVLKLFCETCDVLTCHSCLMVEHKEHR 146
Cdd:smart00336    3 APKCDSHGDEPAEFFCEECGALLCRTCDEAEHRGHT 38

large tegument protein UL36; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810975933  598 RQPAPVQSQSQEDTVQATDEPPASEGPKPALP----LDKNTAANLPQAS--GEETPHSVPSQDNAIQHSSPNVVRKHSTS 671
Cdd:PHA03247  2588 RPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPdthaPDPPPPSPSPAANepDPHPPPTVPPPERPRDDPAPGRVSRPRRA 2667

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810975933  672 VSIMGFSNTVEMELSSTRlaRTLEPQIQSMSSLtAGTPQVVPSLLSGPPPTVSsltshnqamssltASHLPTMPSLVRGT 751
Cdd:PHA03247  2668 RRLGRAAQASSPPQRPRR--RAARPTVGSLTSL-ADPPPPPPTPEPAPHALVS-------------ATPLPPGPAAARQA 2731

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810975933  752 PQSMPSLISDPSQAITSL--ASDHSQARPSLVSGPTQAVPGCPLQSLPPASDVQPeTGSSCSPGSGRAAASLCPGDGADP 829
Cdd:PHA03247  2732 SPALPAAPAPPAVPAGPAtpGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRP-AVASLSESRESLPSPWDPADPPAA 2810

                   ....*
gi 1810975933  830 SLGNA 834
Cdd:PHA03247  2811 VLAPA 2815

Hamartin protein; This family includes the hamartin protein which is thought to function as a tumour suppressor. The hamartin protein interacts with the tuberin protein pfam03542. Tuberous sclerosis complex (TSC) is an autosomal dominant disorder and is characterized by the presence of hamartomas in many organs, such as brain, skin, heart, lung, and kidney. It is caused by mutation either TSC1 or TSC2 tumour suppressor gene. TSC1 encodes a protein, hamartin, containing two coiled-coil regions, which have been shown to mediate binding to tuberin. The TSC2 gene codes for tuberin pfam03542. These two proteins function within the same pathway(s) regulating cell cycle, cell growth, adhesion, and vesicular trafficking.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810975933  641 ASGEETPHSVPsqdnAIQHSSPNVVRKHSTSVSIMGFSNTVEMELSSTRLARtlePQIQSMSS---LTAGTPQVVPSLLS 717
Cdd:pfam04388  263 ASCEEGYSSSA----ADPTASPYTDQQSSYGSSTSTPSSTPRLQLSSSSGTS---PPYLSPPSirlKTDSFPLWSPSSVC 335

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810975933  718 G--PPPTVSSLTSHNQAMSSLTASHL-----PTMPSLVRGTPQSMPSLISDPSQAITSLASDHSQArpslvsgptqAVPG 790
Cdd:pfam04388  336 GmtTPPTSPGMVPTTPSELSPSSSHLssrgsSPPEAAGEATPETTPAKDSPYLKQPPPLSDSHVHR----------ALPA 405

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810975933  791 CPLQSLPPASDVQPETGSSCspgsgraAASLCPGDGADPSLGNALCKMENEDSTRFTDSLGQGPTAAGLDASKDLAIPSE 870
Cdd:pfam04388  406 SSQPSSPPRKDGRSQSSFPP-------LSKQAPTNPNSRGLLEPPGDKSSVTLSELPDFIKDLALSSEDSVEGAEEEAAI 478

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810975933  871 LEEPINLSV-KKPALVPVGN----TSVALQQY----RSPKEYETYEQGALGLDTKGNQSIRPFNSEPKIPYvRLERLKIC 941
Cdd:pfam04388  479 SQELSEITTeKNETDCSRGGldmpFSRTMESLagsqRSRNRIASYCSSTSQSDSHGPATTPESKPSALAED-GLRRTKSC 557

                   ....*....
gi 1810975933  942 AASSGEMPV 950
Cdd:pfam04388  558 SFKQSFTPI 566

Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only];

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810975933  144 EHRCRHLEEVLQNQRMLLESVTTQVAHKK---SSLQTSAKQIEDRIFEVKHQHRKVENQIKMAKmvlmNelNKQANGLIE 220
Cdd:COG1579     23 EHRLKELPAELAELEDELAALEARLEAAKtelEDLEKEIKRLELEIEEVEARIKKYEEQLGNVR----N--NKEYEALQK 96

                           90       100
                   ....*....|....*....|.
gi 1810975933  221 ELEGITnERKQKLEQQLQSIM 241
Cdd:COG1579     97 EIESLK-RRISDLEDEILELM 116

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 1810975933 1113 LSIYDQKRCEKLVLSLCCNSLSLPFHEPVSPLARHYYQIIKRPMDLSIIRRKLQKKDPAHYTTPEEVVSDVRLMFWNCAK 1192
Cdd:cd05502      1 LSPIDQRKCERLLLELYCHELSLPFHEPVSPSVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYK 80

                           90       100
                   ....*....|....*....|....*....
gi 1810975933 1193 FNYPDSEVAEAGRCLEVFFEGWLKEIYPE 1221
Cdd:cd05502     81 FNEEDSEVAQAGKELELFFEEQLKEILPD 109

PHD finger found in transcriptional intermediary factor 1 delta (TIF1delta); TIF1delta, also termed tripartite motif-containing protein 66 (TRIM66), is a novel heterochromatin protein 1 (HP1)-interacting member of the transcriptional intermediary factor1 (TIF1) family expressed by elongating spermatids. Like other TIF1 proteins, TIF1delta displays a potent trichostatin A (TSA)-sensitive repression function; TSA is a specific inhibitor of histone deacetylases. Moreover, TIF1delta plays an important role in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. It functions as a negative regulator of postmeiotic genes acting through HP1 isotype gamma (HP1gamma) complex formation and centromere association. TIF1delta contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1810975933 1040 NEDFCAVCLNGGELLCCDRCPKVYHLSCHLPALLSFPGGDWVCTLCRSL 1088
Cdd:cd15625      1 NEDFCAVCLNGGELLCCDRCPKVFHLSCHVPALLSFPVGEWVCTLCRNL 49

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810975933 1117 DQKRCEKLVLSL--CCNSLSLPFHEPVSP-LARHYYQIIKRPMDLSIIRRKLQKKdpaHYTTPEEVVSDVRLMFWNCAKF 1193
Cdd:cd04369      1 LKKKLRSLLDALkkLKRDLSEPFLEPVDPkEAPDYYEVIKNPMDLSTIKKKLKNG---EYKSLEEFEADVRLIFSNAKTY 77

                           90
                   ....*....|....*....
gi 1810975933 1194 NYPDSEVAEAGRCLEVFFE 1212
Cdd:cd04369     78 NGPGSPIYKDAKKLEKLFE 96

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810975933 1134 SLPFHEPVSPLAR---HYYQIIKRPMDLSIIRRKLQKKDpahYTTPEEVVSDVRLMFWNCAKFNYPDSEVAEAGRCLEVF 1210
Cdd:cd05500     22 ARPFLVPVDPVKLnipHYPTIIKKPMDLGTIERKLKSNV---YTSVEEFTADFNLMVDNCLTFNGPEHPVSQMGKRLQAA 98

                   ..
gi 1810975933 1211 FE 1212
Cdd:cd05500     99 FE 100

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810975933 1121 CEKLVLSLCCNSLSLPFHEPVSP-LARHYYQIIKRPMDLSIIRRKLQKKdpaHYTTPEEVVSDVRLMFWNCAKFNYPDSE 1199
Cdd:cd05503      5 CETILDEMEAHEDAWPFLEPVNTkLVPGYRKIIKKPMDFSTIREKLESG---QYKTLEEFAEDVRLVFDNCETFNEDDSE 81

                           90
                   ....*....|...
gi 1810975933 1200 VAEAGRCLEVFFE 1212
Cdd:cd05503     82 VGRAGHNMRKFFE 94

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

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1810975933  112 LYCPLHTQEVLKLFCETCDVLTCHSCLMVEHKEHRCRHLEEVL 154
Cdd:cd19794      1 LMCPLHNQEPLKLFCETCDVLVCRSCLLSEHKEHRFKHLDEAL 43

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 1810975933 1043 FCAVCLNGGELLCCDRCPKVYHLSCHLPALLSFPGGDWVCTLCRSL 1088
Cdd:cd15624      1 WCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDI 46

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 1810975933 1043 FCAVCLNGGELLCCDRCPKVYHLSCHLPALLSFPGGDWVCTLC 1085
Cdd:cd15622      1 WCAVCQNGGELLCCEKCPKVFHLSCHVPTLMNFPSGEWICTFC 43

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810975933 1133 LSLPFHEPVSP-LARHYYQIIKRPMDLSIIRRKLQKKdpaHYTTPEEVVSDVRLMFWNCAKFNYPDSEVAEAGRCLEVFF 1211
Cdd:COG5076    165 LSSIFLGLPSKrEYPDYYEIIKSPMDLLTIQKKLKNG---RYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYF 241

                           90
                   ....*....|..
gi 1810975933 1212 EGWLKEIYPEKR 1223
Cdd:COG5076    242 LKLIEEIPEEML 253

B-box-type 1 zinc finger found in tripartite motif-containing protein 66 (TRIM66) and similar proteins; TRIM66, also termed transcriptional intermediary factor 1 delta (TIF1delta), is a novel heterochromatin protein 1 (HP1)-interacting member of the transcriptional intermediary factor 1 (TIF1) family, and is expressed by elongating spermatids. Like other TIF1 proteins, TRIM66 displays a potent trichostatin A (TSA)-sensitive repression function; TSA is a specific inhibitor of histone deacetylases. Moreover, TRIM66 plays an important role in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. It functions as a negative regulator of postmeiotic genes acting through HP1 isotype gamma (HP1gamma) complex formation and centromere association. TRIM66 belongs to an unclassified TRIM (tripartite motif) family of proteins that do not have RING fingers and thus lack the characteristic tripartite (RING (R), B-box, and coiled coil (CC)) RBCC motif. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif.

                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 1810975933   53 NCSECKEKRAAHILCTYCNRWLCSSCTEEHRHGPAPG 89
Cdd:cd19811      1 SCSECKEKRPAHSLCTTCNKWLCSSCTEEHRHGKSTS 37

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 1810975933 1134 SLPFHEPVSPLARH---YYQIIKRPMDLSIIRRKLqkkDPAHYTTPEEVVSDVRLMFWNCAKFNYPDSEVAEAG-RCLEV 1209
Cdd:cd05495     22 SLPFRQPVDPKLLGipdYFDIVKNPMDLSTIRRKL---DTGQYQDPWQYVDDVWLMFDNAWLYNRKTSRVYKYCtKLAEV 98

                           90
                   ....*....|.
gi 1810975933 1210 FfegwLKEIYP 1220
Cdd:cd05495     99 F----EQEIDP 105

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
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1810975933 1134 SLPFHEPVSP-LARHYYQIIKRPMDLSIIRRKLQKKDpahYTTPEEVVSDVRLMFWNCAKFNYPDS 1198
Cdd:cd05511     18 SWPFHTPVNKkKVPDYYKIIKRPMDLQTIRKKISKHK---YQSREEFLEDIELIVDNSVLYNGPDS 80

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

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1810975933  112 LYCPLHTQEVLKLFCETCDVLTCHSCLMVEHKEHRCRHLEEVLQNQRMLLESV 164
Cdd:cd19828      4 VFCPFHKKEQLKLYCETCDKLTCRDCQLLEHKEHRYQFIEEAFQNQKVIIDTL 56

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 1810975933 1134 SLPFHEPVSPLARH---YYQIIKRPMDLSIIRRKLQKKdpaHYTTPEEVVSDVRLMFWNCAKFNYPDSEVAEAGRCLEVF 1210
Cdd:cd05497     23 AWPFQQPVDAVKLNlpdYHKIIKTPMDLGTIKKRLENN---YYWSASECIQDFNTMFTNCYIYNKPGDDVVLMAQTLEKL 99

                   .
gi 1810975933 1211 F 1211
Cdd:cd05497    100 F 100

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 1810975933  111 ALYCPLHTQEVLKLFCETCDVLTCHSCLMVEHKEHRCRHLEE 152
Cdd:cd19829      1 TVYCSIHKQEPLKLFCETCDTLTCRDCQLNAHKDHQYQFLED 42

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
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1810975933 1148 YYQIIKRPMDLSIIRRKLQKKdpaHYTTPEEVVSDVRLMFWNCAKFNYPDSEV 1200
Cdd:cd05515     39 YYDVIKKPIDMEKIRSKIEGN---QYQSLDDMVSDFVLMFDNACKYNEPDSQI 88

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 1810975933 1118 QKRCEKLVLSLCCNSLSlPFHEPVSPLARHYYQIIKRPMDLSIIRRKLQKKDpahYTTPEEVVSDVRLMFWNCAKFnYPD 1197
Cdd:cd05501      4 LLKCEFLLLKVYCMSKS-GFFISKPYYIRDYCQGIKEPMWLNKVKERLNERV---YHTVEGFVRDMRLIFHNHKLF-YKD 78

                           90       100
                   ....*....|....*....|..
gi 1810975933 1198 SEVAEAGRCLEVFFEGWLKEIY 1219
Cdd:cd05501     79 DDFGQVGITLEKKFEKNFKEVF 100

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

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1810975933  112 LYCPLHTQEVLKLFCETCDVLTCHSCLMVEHK--EHRCRHL 150
Cdd:cd19798      4 VFCPKHPNEVLKFFCKTCNIPICKDCTLLDHNkgLHDYEYL 44

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        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1810975933 1043 FCAVCL---NGGELLCCDRCPKVYHLSCHLPALLS--FPGGDWVCTLCRS 1087
Cdd:pfam00628    1 YCAVCGksdDGGELVQCDGCDDWFHLACLGPPLDPaeIPSGEWLCPECKP 50