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 1917203834 1181 LSMYDQKKCEKLVLSLCCNNLSLPFHEPVSPLARHYYQIIKRPMDLSIIRRKLQKKDPAHYTTPEEVVSDVRLMFWNCAK 1260
Cdd:cd05502      1 LSPIDQRKCERLLLELYCHELSLPFHEPVSPSVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYK 80

                           90       100
                   ....*....|....*....|....*....
gi 1917203834 1261 FNYPDSEVAEAGRCLEVFFEGWLKEIYPE 1289
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 1917203834 1108 NEDFCAVCLNGGELLCCDRCPKVFHLSCHVPALLSFPGGEWVCTLCRSL 1156
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 1917203834  112 NCSECKEKRAAHILCTYCNRWLCSSCTEEHRHSPVPG 148
Cdd:cd19811      1 SCSECKEKRPAHSLCTTCNKWLCSSCTEEHRHGKSTS 37

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 1917203834 1181 LSMYDQKKCEKLVLSLCCNNLSLPFHEPVSPLARHYYQIIKRPMDLSIIRRKLQKKDPAHYTTPEEVVSDVRLMFWNCAK 1260
Cdd:cd05502      1 LSPIDQRKCERLLLELYCHELSLPFHEPVSPSVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYK 80

                           90       100
                   ....*....|....*....|....*....
gi 1917203834 1261 FNYPDSEVAEAGRCLEVFFEGWLKEIYPE 1289
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 1917203834 1108 NEDFCAVCLNGGELLCCDRCPKVFHLSCHVPALLSFPGGEWVCTLCRSL 1156
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 1917203834  171 LYCPLHTQEVLKLFCETCDMLTCHSCLVVEHKEHRCRHVEEVL 213
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 1917203834 1200 NLSLPFHEPVSP-LARHYYQIIKRPMDLSIIRRKLQKKdpaHYTTPEEVVSDVRLMFWNCAKFNYPDSEVAEAGRCLEVF 1278
Cdd:COG5076    164 FLSSIFLGLPSKrEYPDYYEIIKSPMDLLTIQKKLKNG---RYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKY 240

                           90
                   ....*....|...
gi 1917203834 1279 FEGWLKEIYPEKR 1291
Cdd:COG5076    241 FLKLIEEIPEEML 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 1917203834 1111 FCAVCL---NGGELLCCDRCPKVFHLSCHVPALLS--FPGGEWVCTLCRS 1155
Cdd:pfam00628    1 YCAVCGksdDGGELVQCDGCDDWFHLACLGPPLDPaeIPSGEWLCPECKP 50

B-Box-type zinc finger;

                            10        20        30
                    ....*....|....*....|....*....|....*
gi 1917203834   171 LYCPLHTQEVLKLFCETCDMLTCHSCLVVEHKEHR 205
Cdd:smart00336    4 PKCDSHGDEPAEFFCEECGALLCRTCDEAEHRGHT 38

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 1917203834  208 HVEEVLQnqrmLLEGVTTQVahkkSSLQTSAKQIEDRIFEVKHQHRKVENQIKMAKMVLMNELNKQANGLIEELEGITNE 287
Cdd:cd20482      1 HKESLQQ----LLEEARAKI----PELRDALKNVEHALSRLQMQYHKAQNEINETFQFYRSMLEERKDELLKELESIYNA 72

                           90
                   ....*....|..
gi 1917203834  288 RKRKLEQQLQSI 299
Cdd:cd20482     73 KQLSLNEQQQKL 84

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 1917203834 1181 LSMYDQKKCEKLVLSLCCNNLSLPFHEPVSPLARHYYQIIKRPMDLSIIRRKLQKKDPAHYTTPEEVVSDVRLMFWNCAK 1260
Cdd:cd05502      1 LSPIDQRKCERLLLELYCHELSLPFHEPVSPSVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYK 80

                           90       100
                   ....*....|....*....|....*....
gi 1917203834 1261 FNYPDSEVAEAGRCLEVFFEGWLKEIYPE 1289
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 1917203834 1108 NEDFCAVCLNGGELLCCDRCPKVFHLSCHVPALLSFPGGEWVCTLCRSL 1156
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 1917203834 1185 DQKKCEKLVLSL--CCNNLSLPFHEPVSP-LARHYYQIIKRPMDLSIIRRKLQKKdpaHYTTPEEVVSDVRLMFWNCAKF 1261
Cdd:cd04369      1 LKKKLRSLLDALkkLKRDLSEPFLEPVDPkEAPDYYEVIKNPMDLSTIKKKLKNG---EYKSLEEFEADVRLIFSNAKTY 77

                           90
                   ....*....|....*....
gi 1917203834 1262 NYPDSEVAEAGRCLEVFFE 1280
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 1917203834 1202 SLPFHEPVSPLAR---HYYQIIKRPMDLSIIRRKLQKKDpahYTTPEEVVSDVRLMFWNCAKFNYPDSEVAEAGRCLEVF 1278
Cdd:cd05500     22 ARPFLVPVDPVKLnipHYPTIIKKPMDLGTIERKLKSNV---YTSVEEFTADFNLMVDNCLTFNGPEHPVSQMGKRLQAA 98

                   ..
gi 1917203834 1279 FE 1280
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 1917203834 1202 SLPFHEPVSP-LARHYYQIIKRPMDLSIIRRKLQKKdpaHYTTPEEVVSDVRLMFWNCAKFNYPDSEVAEAGRCLEVFFE 1280
Cdd:cd05503     18 AWPFLEPVNTkLVPGYRKIIKKPMDFSTIREKLESG---QYKTLEEFAEDVRLVFDNCETFNEDDSEVGRAGHNMRKFFE 94

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 1917203834 1200 NLSLPFHEPVSPLAR---HYYQIIKRPMDLSIIRRKLQKKDpahYTTPEEVVSDVRLMFWNCAKFNYPDSEVAEAGRCLE 1276
Cdd:cd05499     19 AYNWPFLDPVDPVALnipNYFSIIKKPMDLGTISKKLQNGQ---YQSAKEFERDVRLIFKNCYTFNPEGTDVYMMGHQLE 95

                   ....*
gi 1917203834 1277 VFFEG 1281
Cdd:cd05499     96 EVFND 100

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 1917203834  171 LYCPLHTQEVLKLFCETCDMLTCHSCLVVEHKEHRCRHVEEVL 213
Cdd:cd19794      1 LMCPLHNQEPLKLFCETCDVLVCRSCLLSEHKEHRFKHLDEAL 43

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 1917203834 1189 CEKLVLSLCCNNLSLPFHEPVS----PlarHYYQIIKRPMDLSIIRRKLQKKDpahYTTPEEVVSDVRLMFWNCAKFNYP 1264
Cdd:cd05504     17 LEQLLVEIVKHKDSWPFLRPVSkievP---DYYDIIKKPMDLGTIKEKLNMGE---YKLAEEFLSDIQLVFSNCFLYNPE 90

                           90       100
                   ....*....|....*....|....*
gi 1917203834 1265 DSEVAEAGRCLEVFFEGWLKEIYPE 1289
Cdd:cd05504     91 HTSVYKAGTRLQRFFIKRCRKLGLP 115

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1917203834 1200 NLSLPFHEPVSP-LARHYYQIIKRPMDLSIIRRKLQKKdpaHYTTPEEVVSDVRLMFWNCAKFNYPDSEVAEAGRCLEVF 1278
Cdd:COG5076    164 FLSSIFLGLPSKrEYPDYYEIIKSPMDLLTIQKKLKNG---RYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKY 240

                           90
                   ....*....|...
gi 1917203834 1279 FEGWLKEIYPEKR 1291
Cdd:COG5076    241 FLKLIEEIPEEML 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 1917203834  112 NCSECKEKRAAHILCTYCNRWLCSSCTEEHRHSPVPG 148
Cdd:cd19811      1 SCSECKEKRPAHSLCTTCNKWLCSSCTEEHRHGKSTS 37

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 1917203834  167 GDFTLYCPLHTQEVLKLFCETCDMLTCHSCLVVEHKEHRCRHVEEVLQNQR 217
Cdd:cd19830      3 GQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQK 53

PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED) protein, functions as a regulator of gene transcription in the thymus. It is essential for prevention of autoimmunity. AIRE plays a critical role in the induction of central tolerance. It promotes self-tolerance through tissue-specific antigen (TSA) expression. It also acts as an active regulator of chondrocyte differentiation. AIRE contains a homogeneously-staining region (HSR) or caspase-recruitment domain (CARD), a nuclear localization signal (NLS), a SAND (for Sp100, AIRE, nuclear phosphoprotein 41/75 or NucP41/75, and deformed epidermal auto regulatory factor 1 or Deaf1) domain, two plant homeodomain (PHD) fingers, and four LXXLL (where L stands for leucine) motifs. This model corresponds to the first PHD finger that recognizes the unmethylated tail of histone H3 and targets AIRE-dependent genes.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1917203834 1112 CAVCLNGGELLCCDRCPKVFHLSCHVPALLSFPGGEWVCTLC 1153
Cdd:cd15539      2 CAVCGDGGELLCCDGCPRAFHLACLVPPLTLIPSGTWRCSSC 43

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1917203834 1183 MYDQkkCEKLVLSL-CCNNLSLPFHEPVSPL-ARHYYQIIKRPMDLSIIRRKLQKKdpaHYTTPEEVVSDVRLMFWNCAK 1260
Cdd:cd05510      8 FYES--LDKVLNELkTYTEHSTPFLTKVSKReAPDYYDIIKKPMDLGTMLKKLKNL---QYKSKAEFVDDLNLIWKNCLL 82

                   ..
gi 1917203834 1261 FN 1262
Cdd:cd05510     83 YN 84

B-box-type 2 zinc finger found in transcription intermediary factor 1 (TIF1) family; This family corresponds to the TIF1 family of transcriptional cofactors including TIF1-alpha (TRIM24), TIF1-beta (TRIM28), and TIF1-gamma (TRIM33), which belong to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TIF1 proteins couple chromatin modifications to transcriptional regulation, signaling, and tumor suppression. They exert a deacetylase-dependent silencing effect when tethered to a promoter region. TIF1alpha and TIF1beta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. They bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. TIF1gamma is structurally closely related to TIF1alpha and TIF1beta, but has very little functional features in common with them. It does not interact with the KRAB silencing domain of KOX1 or the heterochromatinic proteins HP1alpha, beta and gamma. It cannot bind to nuclear receptors (NRs).

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1917203834  170 TLYCPLHTQEVLKLFCETCDMLTCHSCLVVEHKEHRCRHVEE 211
Cdd:cd19775      1 PLFCPVHPQEPLKLFCETCDKLTCRDCQLLEHKDHKYQFAEE 42

PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is a plant homeodomain (PHD) zinc finger-containing protein that bridges the transducin-like enhancer of split (TLE) corepressor to the mSin3A-histone deacetylase (HDAC)-complex, and further represses transcription at targeted genes. PHF12 also interacts with MRG15 (mortality factor-related genes on chromosome 15), a member of the mortality factor (MORF) family of proteins implicated in regulating cellular senescence. PHF12 contains two plant-homeodomain (PHD) zinc fingers followed by a polybasic region. The PHD fingers function downstream of phosphoinositide signaling triggered by the interaction between polybasic regions and phosphoinositides. This model corresponds to the first PHD finger.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1917203834 1112 CAVCLNGGELLCCDRCPKVFHLSCHVPAL--LSFPGGEWVCTLC 1153
Cdd:cd15533      2 CDSCGEGGDLLCCDRCPASFHLQCCNPPLdeEDLPPGEWLCHRC 45

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 1917203834 1216 YYQIIKRPMDLSIIRRKLQKKdpaHYTTPEEVVSDVRLMFWNCAKFNYPDSEV 1268
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.

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                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1917203834 1186 QKKCEKLVLSLCCNNLSlPFHEPVSPLARHYYQIIKRPMDLSIIRRKLQKKDpahYTTPEEVVSDVRLMFWNCAKFnYPD 1265
Cdd:cd05501      4 LLKCEFLLLKVYCMSKS-GFFISKPYYIRDYCQGIKEPMWLNKVKERLNERV---YHTVEGFVRDMRLIFHNHKLF-YKD 78

                           90       100
                   ....*....|....*....|..
gi 1917203834 1266 SEVAEAGRCLEVFFEGWLKEIY 1287
Cdd:cd05501     79 DDFGQVGITLEKKFEKNFKEVF 100

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.

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                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1917203834 1201 LSLPFhEPVSPLARH--YYQIIKRPMDLSIIRRKLQKKdpaHYTTPEEVVSDVRLMFWNCAKFNYPDSEVAEAGRCLE 1276
Cdd:cd05522     24 LTLHF-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        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1917203834 1200 NLSLPFHE-PVSPLARHYYQIIKRPMDLSIIRRKLQKKDpahYTTPEEVVSDVRLMFWNCAKFNYPDSEV 1268
Cdd:cd05520     22 LLAEPFLKlPSKRKYPDYYQEIKNPISLQQIRTKLKNGE---YETLEELEADLNLMFENAKRYNVPNSRI 88

PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC complex protein BHC80) along with HDAC1/2, CtBP1, CoREST, and BRAF35, is associated with LSD1, a lysine (K)-specific histone demethylase. It inhibits LSD1-mediated histone demethylation in vitro. PHF21A is predominantly present in the central nervous system and spermatogenic cells and is one of the six components of BRAF-HDAC complex (BHC) involved in REST-dependent transcriptional repression of neuron-specific genes in non-neuronal cells. It acts as a scaffold protein in BHC in neuronal as well as non-neuronal cells and also plays a role in spermatogenesis. PHF21A contains a C-terminal plant homeodomain (PHD) finger that is responsible for the binding directly to each of five other components of BHC, and of organizing BHC mediating transcriptional repression.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1917203834 1111 FCAVCLNGGELLCCDRCPKVFHLSCHVPALLSFPGGEWVCTLC 1153
Cdd:cd15523      1 FCSVCRKSGELLMCDTCSLVYHLDCLDPPLKTIPKGMWICPKC 43

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

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                    ....*....|....*....|....*....|....*....|....*..
gi 1917203834  1111 FCAVC---LNGGELLCCDRCPKVFHLSCHVPALLSF-PGGEWVCTLC 1153
Cdd:smart00249    1 YCSVCgkpDDGGELLQCDGCDRWYHQTCLGPPLLEEePDGKWYCPKC 47

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

                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 1917203834  172 YCPLHTQEVLKLFCETCDMLTCHSCLV-VEHKEHRCR 207
Cdd:cd19756      1 LCPEHPEEPLKLFCETCQELVCVLCLLsGEHRGHKVV 37

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 1917203834  171 LYCPLHTQEVLKLFCETCDMLTCHSCLVVEHK--EHRCRHV 209
Cdd:cd19798      4 VFCPKHPNEVLKFFCKTCNIPICKDCTLLDHNkgLHDYEYL 44

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 1917203834 1111 FCAVCLNGGELLCCDR--CPKVFHLSChvPALLSFPGGEWVC 1150
Cdd:cd15568      1 ECFRCGDGGDLVLCDFkgCPKVYHLSC--LGLEKPPGGKWIC 40

PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and similar proteins; Rco1 is a component of the Rpd3S histone deacetylase complex that plays an important role at actively transcribed genes. Rco1 contains two plant homeodomain (PHD) fingers, which are required for the methylation of histone H3 lysine 36 (H3K36) nucleosome recognition by Rpd3S. This model corresponds to the first PHD finger.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1917203834 1111 FCAVCLNGGELLCCDRCPKVFHLSCHVPAL--LSFPGGEWVCTLC 1153
Cdd:cd15535      1 FCSACGGYGSFLCCDGCPRSFHFSCLDPPLeeDNLPDDEWFCNEC 45

PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the first PHD finger.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1917203834 1111 FCAVCLNGGELLCCDRCPKVFHLSCHVPALLSFPGGEWVCTLC 1153
Cdd:cd15531      1 YCEVCQQGGEIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 43

B-Box-type zinc finger;

                            10        20        30
                    ....*....|....*....|....*....|....*
gi 1917203834   171 LYCPLHTQEVLKLFCETCDMLTCHSCLVVEHKEHR 205
Cdd:smart00336    4 PKCDSHGDEPAEFFCEECGALLCRTCDEAEHRGHT 38

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 1917203834 1111 FCAVCLNGG----ELLCCDRCPKVFHLSCHVPALLSF-PGGEWVCTLC 1153
Cdd:cd15489      1 SCIVCGKGGdlggELLQCDGCGKWFHADCLGPPLSSFvPNGKWICPVC 48