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 1958647434  980 LSMYDQKKCEKLVLSLCCNSLSLPFHEPVSPLARHYYQIIKRPMDLSIIRRKLQKKDPAHYTTPEEVVSDVRLMFWNCAK 1059
Cdd:cd05502      1 LSPIDQRKCERLLLELYCHELSLPFHEPVSPSVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYK 80

                           90       100
                   ....*....|....*....|....*....
gi 1958647434 1060 FNYPDSEVAEAGRCLEVFFEGWLKEIYPD 1088
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 1958647434  907 NEDFCAVCINGGELLCCDRCPKVYHLSCHVPALLSFPGGEWVCTLCRSL 955
Cdd:cd15625      1 NEDFCAVCLNGGELLCCDRCPKVFHLSCHVPALLSFPVGEWVCTLCRNL 49

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 1958647434  980 LSMYDQKKCEKLVLSLCCNSLSLPFHEPVSPLARHYYQIIKRPMDLSIIRRKLQKKDPAHYTTPEEVVSDVRLMFWNCAK 1059
Cdd:cd05502      1 LSPIDQRKCERLLLELYCHELSLPFHEPVSPSVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYK 80

                           90       100
                   ....*....|....*....|....*....
gi 1958647434 1060 FNYPDSEVAEAGRCLEVFFEGWLKEIYPD 1088
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 1958647434  907 NEDFCAVCINGGELLCCDRCPKVYHLSCHVPALLSFPGGEWVCTLCRSL 955
Cdd:cd15625      1 NEDFCAVCLNGGELLCCDRCPKVFHLSCHVPALLSFPVGEWVCTLCRNL 49

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 1958647434  988 CEKLVLSLCCNSLSLPFHEPVSPLAR-HYYQIIKRPMDLSIIRRKLQKKdpaHYTTPEEVVSDVRLMFWNCAKFNYPDSE 1066
Cdd:pfam00439    1 CLEILDKLMEHPIAAPFLEPVDPDEYpDYYSVIKKPMDLSTIKKKLENG---EYKSLAEFLADVKLIFSNARTYNGPGSV 77

                   ....*.
gi 1958647434 1067 VAEAGR 1072
Cdd:pfam00439   78 IYKAAE 83

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 1958647434  910 FCAVC---INGGELLCCDRCPKVYHLSCHVPALLS--FPGGEWVCTLCRS 954
Cdd:pfam00628    1 YCAVCgksDDGGELVQCDGCDDWFHLACLGPPLDPaeIPSGEWLCPECKP 50

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958647434   11 HVEEVLQnqrmLLESVTTQVahkkSSLQTSAKQIEDRIFEVKHQHRKVENQIKMAKMVLMNELNKQANGLIEELEGITNE 90
Cdd:cd20482      1 HKESLQQ----LLEEARAKI----PELRDALKNVEHALSRLQMQYHKAQNEINETFQFYRSMLEERKDELLKELESIYNA 72

                           90
                   ....*....|..
gi 1958647434   91 RKRKLEQQLQSI 102
Cdd:cd20482     73 KQLSLNEQQQKL 84

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958647434   16 LQNQRMLLESVTTQVAHKKSSLQTSAKQIEDRIFEVKHQHRKV---ENQIKMAKMVLmNELNKQ-ANGLIEELEGITNER 91
Cdd:TIGR04523  241 INEKTTEISNTQTQLNQLKDEQNKIKKQLSEKQKELEQNNKKIkelEKQLNQLKSEI-SDLNNQkEQDWNKELKSELKNQ 319

                           90       100
                   ....*....|....*....|....*.
gi 1958647434   92 KRKLEQ---QL----QSIMVLNRQFE 110
Cdd:TIGR04523  320 EKKLEEiqnQIsqnnKIISQLNEQIS 345

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 1958647434  980 LSMYDQKKCEKLVLSLCCNSLSLPFHEPVSPLARHYYQIIKRPMDLSIIRRKLQKKDPAHYTTPEEVVSDVRLMFWNCAK 1059
Cdd:cd05502      1 LSPIDQRKCERLLLELYCHELSLPFHEPVSPSVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYK 80

                           90       100
                   ....*....|....*....|....*....
gi 1958647434 1060 FNYPDSEVAEAGRCLEVFFEGWLKEIYPD 1088
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 1958647434  907 NEDFCAVCINGGELLCCDRCPKVYHLSCHVPALLSFPGGEWVCTLCRSL 955
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 1958647434  984 DQKKCEKLVLSL--CCNSLSLPFHEPVSP-LARHYYQIIKRPMDLSIIRRKLQKKdpaHYTTPEEVVSDVRLMFWNCAKF 1060
Cdd:cd04369      1 LKKKLRSLLDALkkLKRDLSEPFLEPVDPkEAPDYYEVIKNPMDLSTIKKKLKNG---EYKSLEEFEADVRLIFSNAKTY 77

                           90
                   ....*....|....*....
gi 1958647434 1061 NYPDSEVAEAGRCLEVFFE 1079
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 1958647434 1001 SLPFHEPVSPLAR---HYYQIIKRPMDLSIIRRKLQKKDpahYTTPEEVVSDVRLMFWNCAKFNYPDSEVAEAGRCLEVF 1077
Cdd:cd05500     22 ARPFLVPVDPVKLnipHYPTIIKKPMDLGTIERKLKSNV---YTSVEEFTADFNLMVDNCLTFNGPEHPVSQMGKRLQAA 98

                   ..
gi 1958647434 1078 FE 1079
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 1958647434  988 CEKLVLSLCCNSLSLPFHEPVSP-LARHYYQIIKRPMDLSIIRRKLQKKdpaHYTTPEEVVSDVRLMFWNCAKFNYPDSE 1066
Cdd:cd05503      5 CETILDEMEAHEDAWPFLEPVNTkLVPGYRKIIKKPMDFSTIREKLESG---QYKTLEEFAEDVRLVFDNCETFNEDDSE 81

                           90
                   ....*....|...
gi 1958647434 1067 VAEAGRCLEVFFE 1079
Cdd:cd05503     82 VGRAGHNMRKFFE 94

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 1958647434  910 FCAVCINGGELLCCDRCPKVYHLSCHVPALLSFPGGEWVCTLCRSL 955
Cdd:cd15624      1 WCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDI 46

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958647434  999 SLSLPFHEPVSPLAR---HYYQIIKRPMDLSIIRRKLQKKDpahYTTPEEVVSDVRLMFWNCAKFNYPDSEVAEAGRCLE 1075
Cdd:cd05499     19 AYNWPFLDPVDPVALnipNYFSIIKKPMDLGTISKKLQNGQ---YQSAKEFERDVRLIFKNCYTFNPEGTDVYMMGHQLE 95

                   ....*
gi 1958647434 1076 VFFEG 1080
Cdd:cd05499     96 EVFND 100

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 1958647434  988 CEKLVLSLCCNSLSLPFHEPVSPLAR-HYYQIIKRPMDLSIIRRKLQKKdpaHYTTPEEVVSDVRLMFWNCAKFNYPDSE 1066
Cdd:pfam00439    1 CLEILDKLMEHPIAAPFLEPVDPDEYpDYYSVIKKPMDLSTIKKKLENG---EYKSLAEFLADVKLIFSNARTYNGPGSV 77

                   ....*.
gi 1958647434 1067 VAEAGR 1072
Cdd:pfam00439   78 IYKAAE 83

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 1958647434  986 KKCEKLVLSLCCNSLSLPFHEPVSPLA---RHYYQIIKRPMDLSIIRRKLQKKdpaHYTTPEEVVSDVRLMFWNCAKFNY 1062
Cdd:cd05506      3 KQCGTLLRKLMKHKWGWVFNAPVDVVAlglPDYFDIIKKPMDLGTVKKKLEKG---EYSSPEEFAADVRLTFANAMRYNP 79

                           90       100
                   ....*....|....*....|
gi 1958647434 1063 PDSEV-AEAGRCLEVFFEGW 1081
Cdd:cd05506     80 PGNDVhTMAKELLKIFETRW 99

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 1958647434  910 FCAVCINGGELLCCDRCPKVYHLSCHVPALLSFPGGEWVCTLC 952
Cdd:cd15532      1 FCRVCKDGGELLCCDGCPSSYHLHCLNPPLAEIPDGDWFCPRC 43

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 1958647434 1001 SLPFHEPVSP-LARHYYQIIKRPMDLSIIRRKLQKKDpahYTTPEEVVSDVRLMFWNCAKFNYPDS 1065
Cdd:cd05511     18 SWPFHTPVNKkKVPDYYKIIKRPMDLQTIRKKISKHK---YQSREEFLEDIELIVDNSVLYNGPDS 80

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 1958647434 1001 SLPFHEPVSPLARH---YYQIIKRPMDLSIIRRKLQKKdpaHYTTPEEVVSDVRLMFWNCAKFNYPDSEVAEAGRCLEVF 1077
Cdd:cd05497     23 AWPFQQPVDAVKLNlpdYHKIIKTPMDLGTIKKRLENN---YYWSASECIQDFNTMFTNCYIYNKPGDDVVLMAQTLEKL 99

                   .
gi 1958647434 1078 F 1078
Cdd:cd05497    100 F 100

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 1958647434  985 QKKCEKLVLSLCCNSLSlPFHEPVSPLARHYYQIIKRPMDLSIIRRKLQKKDpahYTTPEEVVSDVRLMFWNCAKFnYPD 1064
Cdd:cd05501      4 LLKCEFLLLKVYCMSKS-GFFISKPYYIRDYCQGIKEPMWLNKVKERLNERV---YHTVEGFVRDMRLIFHNHKLF-YKD 78

                           90       100
                   ....*....|....*....|..
gi 1958647434 1065 SEVAEAGRCLEVFFEGWLKEIY 1086
Cdd:cd05501     79 DDFGQVGITLEKKFEKNFKEVF 100

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 1958647434  910 FCAVC---INGGELLCCDRCPKVYHLSCHVPALLS--FPGGEWVCTLCRS 954
Cdd:pfam00628    1 YCAVCgksDDGGELVQCDGCDDWFHLACLGPPLDPaeIPSGEWLCPECKP 50

PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also termed Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), or KRAB-interacting protein 1 (KRIP-1), or nuclear co-repressor KAP-1, or RING finger protein 96, or tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, acts as a nuclear co-repressor that plays a role in transcription and in DNA damage response. Upon DNA damage, the phosphorylation of KAP-1 on serine 824 by the ataxia telangiectasia-mutated (ATM) kinase enhances cell survival and facilitates chromatin relaxation and heterochromatic DNA repair. It also regulates CHD3 nucleosome remodeling during DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. In addition, KAP-1 is a co-activator of the orphan nuclear receptor NGFI-B (or Nur77) and is involved in NGFI-B-dependent transcription. It is also a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase. TIF1-beta contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), which can interact with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and mediates homo- and heterodimerization, a plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region, which interact with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1958647434  911 CAVCINGGELLCCDRCPKVYHLSCHVPALLSFPGGEWVCTLC 952
Cdd:cd15623      2 CRVCQKAGALVMCDQCEFCFHLDCHLPALQEVPGEDWKCLLC 43

PHD finger 5 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the fifth PHD finger.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1958647434  910 FCAVCINGGELLCCDR--CPKVYHLSChvPALLSFPGGEWVC 949
Cdd:cd15568      1 ECFRCGDGGDLVLCDFkgCPKVYHLSC--LGLEKPPGGKWIC 40

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

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958647434  999 SLSLPFhEPVSPLARH--YYQIIKRPMDLSIIRRKLQKKdpaHYTTPEEVVSDVRLMFWNCAKFNYPDSEVAEAGRCLE 1075
Cdd:cd05522     23 LLTLHF-EKLPDKAREpeYYQEISNPISLDDIKKKVKRR---KYKSFDQFLNDLNLMFENAKLYNENDSQEYKDAVLLE 97

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

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958647434 1000 LSLPFHE-PVSPLARHYYQIIKRPMDLSIIRRKLQKKDpahYTTPEEVVSDVRLMFWNCAKFNYPDSEV 1067
Cdd:cd05520     23 LAEPFLKlPSKRKYPDYYQEIKNPISLQQIRTKLKNGE---YETLEELEADLNLMFENAKRYNVPNSRI 88

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

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958647434 1015 YYQIIKRPMDLSIIRRKLQKKdpaHYTTPEEVVSDVRLMFWNCAKFNYPDSEVAEAGRCLE 1075
Cdd:cd05518     39 YYKIILEPIDLKTIEHNIRND---KYATEEELMDDFKLMFRNARHYNEEGSQVYEDANILE 96

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958647434  984 DQKKCEKLVLSLCCNSLSLPFHEPVSPL-ARHYYQIIKRPMDLSIIRRKLQKKDpahYTTPEEVVSDVRLMFWNCAKFNY 1062
Cdd:cd05505      1 ELQKCEEILSKILKYRFSWPFREPVTADeAEDYKKVITNPMDLQTMQTKCSCGS---YSSVQEFLDDMKLVFSNAEKYYE 77

                   ....*
gi 1958647434 1063 PDSEV 1067
Cdd:cd05505     78 NGSYV 82

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 1958647434  986 KKCEKLVLSLCCNSLSLPFHEPVSPLAR-HYYQIIKRPMDLSIIRRKLqkkDPAHYTTPEEVVSDVRLMFWNCAKFNyPD 1064
Cdd:cd05496      8 KQCKELVNLMWDCEDSEPFRQPVDLLKYpDYRDIIDTPMDLGTVKETL---FGGNYDDPMEFAKDVRLIFSNSKSYT-PN 83

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1958647434 1065 --SEVAEAGRCLEVFFEGWLKEIYPDKCFAQPQQE 1097
Cdd:cd05496     84 krSRIYSMTLRLSALFEEHIKKIISDWKSALKRNE 118

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
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958647434 1014 HYYQIIKRPMDLSIIRRKLQKKdpaHYTTPEEVVSDVRLMFWNCAKFNYPDSEVAEAGRCLEVffegWLKEIYPD 1088
Cdd:cd05529     60 DYWNRVPVPMDLETIRSRLENR---YYRSLEALRHDVRLILSNAETFNEPNSEIAKKAKRLSD----WLLRILSS 127

PHD finger found in the Sp100/Sp140 family of nuclear body components; The Sp100/Sp140 family includes nuclear body proteins SP100, SP140, and similar proteins. Sp110, also termed interferon-induced protein 41/75, or speckled 110 kDa, or transcriptional coactivator Sp110, is a leukocyte-specific component of the nuclear body. It may function as a nuclear hormone receptor transcriptional coactivator that may play a role in inducing differentiation of myeloid cells. It is also involved in resisting intracellular pathogens and functions as an important drug target for preventing intracellular pathogen diseases, such as tuberculosis, hepatic veno-occlusive disease, and intracellular cancers. Sp110 gene polymorphisms may be associated with susceptibility to tuberculosis in Chinese population. Sp110 contains a Sp100-like domain, a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD). SP140, also termed lymphoid-restricted homolog of Sp100 (LYSp100), or nuclear autoantigen Sp-140, or speckled 140 kDa, is an interferon inducible nuclear leukocyte-specific protein involved in primary biliary cirrhosis and a risk factor in chronic lymphocytic leukemia. It is also implicated in innate immune response to human immunodeficiency virus type 1 (HIV-1) by binding to the virus's viral infectivity factor (Vif) protein. Sp140 contains a nuclear localization signal, a dimerization domain (HSR or CARD domain), a SAND domain, a PHD finger, and a BRD.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1958647434  911 CAVCINGGELLCCDRCPKVYHLSCHVPAlLSFPGGEWVCTLC 952
Cdd:cd15626      2 CEVCGQEGKLFCCCTCSRVFHEDCHIPP-VEAQRSPWSCTFC 42

PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. BAZ1B contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1958647434  911 CAVCINGGE---LLCCDRCPKVYHLSCHVPALLSFPGGEWVCTLC 952
Cdd:cd15628      2 CKVCRKKGEddkLILCDECNQAFHLFCLRPALYEVPDGEWMCPAC 46

PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar proteins; Lid2p is a trimethyl H3K4 (H3K4me3) demethylase responsible for H3K4 hypomethylation in heterochromatin. It interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, and mediates H3K9 methylation and small RNA production. It also acts cooperatively with the histone modification enzymes Set1 and Lsd1 and plays an essential role in cross-talk between H3K4 and H3K9 methylation in euchromatin. Lid2p contains a JmjC domain, three PHD fingers and a JmjN domain. This model corresponds to the first PHD finger.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1958647434  911 CAVC---INGGELLCCDRCPKVYHLSCHVPALLSFPGGEWVCTLC 952
Cdd:cd15519      2 CEVCgldDNEGEVLLCDGCDAEYHTSCLDPPLGEIPPGTWFCPSC 46

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

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1958647434  910 FCAVCINGGELLCCDRCPKVYHLSChvpALLSFPGGEWVCTLCR 953
Cdd:cd15657      1 WCFVCSKGGSLLCCESCPAAFHPDC---LNIEMPDGSWFCNDCR 41

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

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958647434 1003 PFHEPVS-PLARHYYQIIKRPMDLSIIRRKLqkkDPAHYTTPEEVVSDVRLMFWNCAKFNYPDSEVAEA 1070
Cdd:cd05507     23 VFLKPVTeDIAPGYHSVVYRPMDLSTIKKNI---ENGTIRSTAEFQRDVLLMFQNAIMYNSSDHDVYLM 88

PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. Both BAZ1A and BAZ1B contain a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1958647434  911 CAVCINGGE---LLCCDRCPKVYHLSCHVPALLSFPGGEWVCTLC 952
Cdd:cd15544      2 CKVCRKKGDpdnMILCDGCDKAFHLYCLRPALREVPSGDWFCPAC 46