Score = 53.9 bits (128), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 30/70 (42%), Positives = 38/70 (54%), Gaps = 2/70 (2%)
Query: 18 ELILNILQRKDTNEIFAEPVDTKEVEDYYEIIKEPMDFGTMRAKLHEGMYTSLEQFEVCS 77
E+IL ++ D F EPV+ + V Y IIK PMDF TMR +L G YTS E+F +
Sbjct: 1803 EIILMEMESHDAAWPFLEPVNPRLVSGYRRIIKNPMDFSTMRERLLRGGYTSSEEFAADA 1862
Query: 78 F--FTLCLKF 85
F C F
Sbjct: 1863 LLVFDNCQTF 1872
Essential component of the NoRC (nucleolar remodeling complex) complex, a complex that mediates silencing of a fraction of rDNA by recruiting histone-modifying enzymes and DNA methyltransferases, leading to heterochromatin formation and transcriptional silencing. In the complex, it plays a central role by being recruited to rDNA and by targeting chromatin modifying enzymes such as HDAC1, leading to repress RNA polymerase I transcription. Recruited to rDNA via its interaction with TTF1 and its ability to recognize and bind histone H4 acetylated on 'Lys-16' (H4K16ac), leading to deacetylation of H4K5ac, H4K8ac, H4K12ac but not H4K16ac. Specifically binds pRNAs, 150-250 nucleotide RNAs that are complementary in sequence to the rDNA promoter; pRNA-binding is required for heterochromatin formation and rDNA silencing.
Score = 53.9 bits (128), Expect = 3e-07, Method: Composition-based stats.
Identities = 23/41 (56%), Positives = 26/41 (63%)
Query: 33 FAEPVDTKEVEDYYEIIKEPMDFGTMRAKLHEGMYTSLEQF 73
F EPVD KE DYY++IKEPMD M KL YT L +F
Sbjct: 2581 FMEPVDPKEAPDYYKVIKEPMDLKRMEIKLESNTYTKLSEF 2621
Histone-binding component of NURF (nucleosome remodeling factor), a complex which catalyzes ATP-dependent nucleosome sliding and facilitates transcription of chromatin. Specifically recognizes H3 tails trimethylated on 'Lys-4' (H3K4me3), which mark transcription start sites of virtually all active genes. Required for homeotic gene expression, proper larval blood cell development, normal male X chromosome morphology, ecdysteroid signaling and metamorphosis.
Drosophila melanogaster (taxid: 7227)
>sp|Q9H8M2|BRD9_HUMAN Bromodomain-containing protein 9 OS=Homo sapiens GN=BRD9 PE=1 SV=2
Score = 53.5 bits (127), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 29/70 (41%), Positives = 38/70 (54%), Gaps = 2/70 (2%)
Query: 18 ELILNILQRKDTNEIFAEPVDTKEVEDYYEIIKEPMDFGTMRAKLHEGMYTSLEQFEVCS 77
E+IL ++ D F EPV+ + V Y +IK PMDF TMR +L G YTS E+F +
Sbjct: 1787 EIILMEMESHDAAWPFLEPVNPRLVSGYRRVIKNPMDFSTMRERLLRGGYTSSEEFAADA 1846
Query: 78 F--FTLCLKF 85
F C F
Sbjct: 1847 LLVFDNCQTF 1856
Essential component of the NoRC (nucleolar remodeling complex) complex, a complex that mediates silencing of a fraction of rDNA by recruiting histone-modifying enzymes and DNA methyltransferases, leading to heterochromatin formation and transcriptional silencing. In the complex, it plays a central role by being recruited to rDNA and by targeting chromatin modifying enzymes such as HDAC1, leading to repress RNA polymerase I transcription. Recruited to rDNA via its interaction with TTF1 and its ability to recognize and bind histone H4 acetylated on 'Lys-16' (H4K16ac), leading to deacetylation of H4K5ac, H4K8ac, H4K12ac but not H4K16ac. Specifically binds pRNAs, 150-250 nucleotide RNAs that are complementary in sequence to the rDNA promoter; pRNA-binding is required for heterochromatin formation and rDNA silencing.
Mus musculus (taxid: 10090)
Close Homologs in the Non-Redundant Database Detected by BLAST
>gi|255582032|ref|XP_002531813.1| bromodomain-containing protein [Ricinus communis] gi|223528547|gb|EEF30570.1| bromodomain-containing protein [Ricinus communis]
>gi|255584388|ref|XP_002532927.1| bromodomain-containing protein [Ricinus communis] gi|223527303|gb|EEF29454.1| bromodomain-containing protein [Ricinus communis]
Score = 87.8 bits (218), Expect = 2e-24
Identities = 34/59 (57%), Positives = 40/59 (67%)
Query: 16 VLELILNILQRKDTNEIFAEPVDTKEVEDYYEIIKEPMDFGTMRAKLHEGMYTSLEQFE 74
+L L+ LQ KDT EIF+EPVD EV DY + IK+PMDF TMR KL Y +LE FE
Sbjct: 5 LLRKTLDQLQEKDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFE 63
BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 98
Score = 74.3 bits (183), Expect = 4e-19
Identities = 32/64 (50%), Positives = 42/64 (65%), Gaps = 2/64 (3%)
Query: 13 EKRVLELILNILQRK--DTNEIFAEPVDTKEVEDYYEIIKEPMDFGTMRAKLHEGMYTSL 70
K+ L +L+ L++ D +E F EPVD KE DYYE+IK PMD T++ KL G Y SL
Sbjct: 1 LKKKLRSLLDALKKLKRDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSL 60
Query: 71 EQFE 74
E+FE
Sbjct: 61 EEFE 64
Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine. Length = 99
Score = 74.5 bits (184), Expect = 5e-19
Identities = 27/62 (43%), Positives = 38/62 (61%)
Query: 12 PEKRVLELILNILQRKDTNEIFAEPVDTKEVEDYYEIIKEPMDFGTMRAKLHEGMYTSLE 71
P L+ +L+ L+ + F EPVD +E DYY++IK+PMD TM KL G Y +LE
Sbjct: 1 PLYTQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLE 60
Query: 72 QF 73
+F
Sbjct: 61 EF 62
Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 101
Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 84
Score = 62.8 bits (153), Expect = 2e-14
Identities = 29/71 (40%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 12 PEKRVLELILNILQRKDTNEIFAEPVDTKEVEDYYEIIKEPMDFGTMRAKLHEGMYTSLE 71
P ++ LE ++ LQRKD + FA PV Y IIK PMDF TM+ K+ Y S+E
Sbjct: 1 PLQKALEQLIRQLQRKDPHGFFAFPVTDFIAPGYSSIIKHPMDFSTMKEKIKNNDYQSIE 60
Query: 72 QFEVCSFFTLC 82
+F+ F +C
Sbjct: 61 EFKD-DFKLMC 70
The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 98
Score = 61.2 bits (149), Expect = 5e-14
Identities = 27/61 (44%), Positives = 39/61 (63%)
Query: 13 EKRVLELILNILQRKDTNEIFAEPVDTKEVEDYYEIIKEPMDFGTMRAKLHEGMYTSLEQ 72
+ + E IL+ ++ + F EPV+TK V Y +IIK+PMDF T+R KL G Y +LE+
Sbjct: 1 DLALCETILDEMEAHEDAWPFLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEE 60
Query: 73 F 73
F
Sbjct: 61 F 61
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. Length = 97
Score = 60.4 bits (147), Expect = 1e-13
Identities = 25/60 (41%), Positives = 33/60 (55%), Gaps = 4/60 (6%)
Query: 30 NEIFAEPVDTK--EVEDYYEIIKEPMDFGTMRAKLHEGMYTSLEQFE--VCSFFTLCLKF 85
N F +PVD + +Y+ IIK+PMD GT+ KL G Y S ++FE V F C F
Sbjct: 21 NWPFLDPVDPVALNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTF 80
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. Length = 102
>gnl|CDD|99936 cd05504, Bromo_Acf1_like, Bromodomain; Acf1_like or BAZ1A_like subfamily
Score = 58.6 bits (142), Expect = 9e-13
Identities = 26/56 (46%), Positives = 38/56 (67%), Gaps = 1/56 (1%)
Query: 18 ELILNILQRKDTNEIFAEPVDTKEVEDYYEIIKEPMDFGTMRAKLHEGMYTSLEQF 73
+L++ I++ KD+ F PV EV DYY+IIK+PMD GT++ KL+ G Y E+F
Sbjct: 19 QLLVEIVKHKDSWP-FLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEF 73
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. Length = 115
>gnl|CDD|99930 cd05498, Bromo_Brdt_II_like, Bromodomain, Brdt_like subfamily, repeat II
Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 102
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. Length = 112
>gnl|CDD|99938 cd05506, Bromo_plant1, 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. Length = 99
>gnl|CDD|99957 cd05528, Bromo_AAA, Bromodomain; sub-family co-occurring with AAA domains
Score = 55.4 bits (134), Expect = 2e-11
Identities = 24/57 (42%), Positives = 31/57 (54%)
Query: 17 LELILNILQRKDTNEIFAEPVDTKEVEDYYEIIKEPMDFGTMRAKLHEGMYTSLEQF 73
L +L L F +PVD +EV DYYEIIK+PMD T+ KL Y + + F
Sbjct: 8 LRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDF 64
Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver. Length = 112
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. Length = 103
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. Length = 109
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. Length = 112
>gnl|CDD|227408 COG5076, COG5076, Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription]
Score = 47.5 bits (113), Expect = 2e-08
Identities = 22/60 (36%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 14 KRVLELILNILQRKDTNEIFAEPVDTKEVEDYYEIIKEPMDFGTMRAKLHEGMYTSLEQF 73
K+ EL+ + +D+ E F +PVD + DY +II PMD GT++ L G Y +F
Sbjct: 8 KQCKELVNLMWDCEDS-EPFRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEF 66
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. Length = 119
>gnl|CDD|99937 cd05505, Bromo_WSTF_like, Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like)
Score = 46.8 bits (111), Expect = 3e-08
Identities = 19/41 (46%), Positives = 26/41 (63%)
Query: 33 FAEPVDTKEVEDYYEIIKEPMDFGTMRAKLHEGMYTSLEQF 73
F EPV E EDY ++I PMD TM+ K G Y+S+++F
Sbjct: 21 FREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEF 61
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. Length = 97
Score = 45.1 bits (107), Expect = 1e-07
Identities = 19/43 (44%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 33 FAEPVDTK--EVEDYYEIIKEPMDFGTMRAKLHEGMYTSLEQF 73
F +PVD K + DY++I+K PMD T+R KL G Y Q+
Sbjct: 25 FRQPVDPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQY 67
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. Length = 108
>gnl|CDD|99947 cd05516, Bromo_SNF2L2, Bromodomain, SNF2L2-like subfamily, specific to animals
SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 107
>gnl|CDD|99929 cd05497, Bromo_Brdt_I_like, 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. Length = 107
Score = 39.7 bits (93), Expect = 2e-05
Identities = 20/48 (41%), Positives = 25/48 (52%), Gaps = 5/48 (10%)
Query: 17 LELILNILQRKDTNEI---FAEPVDTKE--VEDYYEIIKEPMDFGTMR 59
LE +L L+R NE F EPV+ DY ++IK PM FGT
Sbjct: 5 LERVLRELKRHRRNEDAWPFLEPVNPPRRGAPDYRDVIKRPMSFGTKV 52
Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine. Length = 114
>gnl|CDD|99946 cd05515, Bromo_polybromo_V, 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. Length = 105
Score = 37.7 bits (88), Expect = 9e-05
Identities = 14/46 (30%), Positives = 24/46 (52%)
Query: 29 TNEIFAEPVDTKEVEDYYEIIKEPMDFGTMRAKLHEGMYTSLEQFE 74
E F +PVD ++ DY + + +PMD T+ + + Y S + F
Sbjct: 19 GAEPFLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFL 64
RACK7 (also called human protein kinase C-binding protein) was identified as a potential tumor suppressor genes, it shares domain architecture with BS69/ZMYND11; both have been implicated in the regulation of cellular proliferation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 99
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. Length = 102
>gnl|CDD|99949 cd05518, Bromo_polybromo_IV, Bromodomain, polybromo repeat IV
Score = 35.5 bits (82), Expect = 6e-04
Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 5/63 (7%)
Query: 14 KRVLELILNILQRKDTN-----EIFAEPVDTKEVEDYYEIIKEPMDFGTMRAKLHEGMYT 68
KR+L L L +L+ ++ + ++F E K+ DYY+II EP+D T+ + Y
Sbjct: 3 KRMLALFLYVLEYREGSGRRLCDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYA 62
Query: 69 SLE 71
+ E
Sbjct: 63 TEE 65
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. Length = 103
>gnl|CDD|99950 cd05519, Bromo_SNF2, Bromodomain, SNF2-like subfamily, specific to fungi
SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 103
>gnl|CDD|99948 cd05517, Bromo_polybromo_II, Bromodomain, polybromo repeat II
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. Length = 103
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. Length = 104
>gnl|CDD|99951 cd05520, Bromo_polybromo_III, Bromodomain, polybromo repeat III
Score = 33.9 bits (78), Expect = 0.002
Identities = 14/31 (45%), Positives = 19/31 (61%)
Query: 44 DYYEIIKEPMDFGTMRAKLHEGMYTSLEQFE 74
DYY+ IK P+ +R KL G Y +LE+ E
Sbjct: 38 DYYQEIKNPISLQQIRTKLKNGEYETLEELE 68
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. Length = 103
The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
>cd05505 Bromo_WSTF_like 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.
RACK7 (also called human protein kinase C-binding protein) was identified as a potential tumor suppressor genes, it shares domain architecture with BS69/ZMYND11; both have been implicated in the regulation of cellular proliferation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
>cd05497 Bromo_Brdt_I_like 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.
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.
BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
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.
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.
>cd05504 Bromo_Acf1_like 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.
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.
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.
Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
>cd05528 Bromo_AAA Bromodomain; sub-family co-occurring with AAA domains
Probab=99.95 E-value=3.9e-28 Score=151.81 Aligned_cols=79 Identities=32% Similarity=0.415 Sum_probs=76.1
Q ss_pred hHHHHHHHHHHHHhcCCCCccCcCCCCccccccHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHhh--hhhhhcCCC
Q 036733 12 PEKRVLELILNILQRKDTNEIFAEPVDTKEVEDYYEIIKEPMDFGTMRAKLHEGMYTSLEQFEVCSFFT--LCLKFWSIG 89 (96)
Q Consensus 12 ~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~~I~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li--N~~~yN~~~ 89 (96)
.++.+|..+++.|++++.+++|.+||+++.+|||+++|++||||+||++||+++.|.|+++|.+|++|| ||+.||+++
T Consensus 3 ~lr~~L~~il~~l~~~~~~~~F~~pv~~~~~pdY~~vI~~PmdL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yN~~~ 82 (112)
T cd05528 3 ELRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPDR 82 (112)
T ss_pred HHHHHHHHHHHHHHhCCCchhhcCCCCccccCcHHHHHcCCCCHHHHHHHHcCCCcCCHHHHHHHHHHHHHHHHHHCCCC
Confidence 367789999999999999999999999999999999999999999999999999999999999999999 999999997
Q ss_pred C
Q 036733 90 I 90 (96)
Q Consensus 90 s 90 (96)
|
T Consensus 83 s 83 (112)
T cd05528 83 D 83 (112)
T ss_pred C
Confidence 5
Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver
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.
>cd05506 Bromo_plant1 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.
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.
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.
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.
>KOG1474 consensus Transcription initiation factor TFIID, subunit BDF1 and related bromodomain proteins [Transcription]
SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
>cd05498 Bromo_Brdt_II_like Bromodomain, Brdt_like subfamily, repeat II
Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
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.
>cd05519 Bromo_SNF2 Bromodomain, SNF2-like subfamily, specific to fungi
SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
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.
>cd05517 Bromo_polybromo_II Bromodomain, polybromo repeat II
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.
>cd05515 Bromo_polybromo_V 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.
>PF00439 Bromodomain: Bromodomain; InterPro: IPR001487 Bromodomains are found in a variety of mammalian, invertebrate and yeast DNA-binding proteins []
Bromodomains can interact with acetylated lysine []. In some proteins, the classical bromodomain has diverged to such an extent that parts of the region are either missing or contain an insertion (e.g., mammalian protein HRX, Caenorhabditis elegans hypothetical protein ZK783.4, yeast protein YTA7). The bromodomain may occur as a single copy, or in duplicate. The precise function of the domain is unclear, but it may be involved in protein-protein interactions and may play a role in assembly or activity of multi-component complexes involved in transcriptional activation [].; GO: 0005515 protein binding; PDB: 3P1C_A 4A9K_B 3SVH_A 3P1E_B 3P1F_A 1JSP_B 2L85_A 3P1D_B 3DWY_B 2D82_A ....
ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
>cd05524 Bromo_polybromo_I Bromodomain, polybromo repeat I
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.
>cd05518 Bromo_polybromo_IV 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.
>cd05520 Bromo_polybromo_III 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.
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.
Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
>cd05521 Bromo_Rsc1_2_I Bromodomain, repeat I 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.
ZMYND11 or BS69 is a ubiquitously expressed nuclear protein that has been shown to associate with chromatin. It interacts with chromatin remodeling factors and might play a role in chromatin remodeling and gene expression. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
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.
>COG5076 Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription]
Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
TBP7, or TAT-binding protein homolog 7, is a yeast protein of unknown function that contains AAA-superfamily ATP-ase domains and a bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
ALL-1 is a vertebrate homologue of Drosophila trithorax and is often affected in chromosomal rearrangements that are linked to acute leukemias, such as acute lymphocytic leukemia (ALL). Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
>COG5076 Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription]
This bacterial protein family has a very similar seed alignment to that of Pfam model pfam03693 but is a more stringent model with higher cutoff scores. Proteins that score above the trusted cutoff to this model almost invariably are found adjacent to a ParE family protein (pfam05016), where ParE is the killing partner of an addiction module for plasmid stabilization. Members of this family, therefore, are putative addiction module antidote proteins. Some are encoded on plasmids or in prophage regions, but others appear chromosomal. A genome may contain several identical copies, such as the four in Magnetococcus sp. MC-1. This family is named for one member, CC2985 of Caulobacter crescentus CB15.
>PF03693 RHH_2: Uncharacterised protein family (UPF0156); InterPro: IPR022789 This family of proteins are about 80 amino acids in length and their function is unknown
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/61 (45%), Positives = 37/61 (60%), Gaps = 1/61 (1%)
Query: 13 EKRVLELILNILQRKDTNEIFAEPVDTKEVEDYYEIIKEPMDFGTMRAKLHEGMYTSLEQ 72
+K+ EL+ I Q +D+ E F +PVD E DY +II PMDFGT+R L G Y S +
Sbjct: 12 KKQCKELVNLIFQCEDS-EPFRQPVDLVEYPDYRDIIDTPMDFGTVRETLDAGNYDSPLE 70
Query: 73 F 73
F
Sbjct: 71 F 71
Score = 46.2 bits (108), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 32/82 (39%), Positives = 44/82 (53%), Gaps = 5/82 (6%)
Query: 9 PQMPEKRVLELILNILQRKDTNEI---FAEPVDTKEVEDYYEIIKEPMDFGTMRAKLHEG 65
P+ + + L L IL +T+E F PV+ K V Y ++IK+PMDF T+R KL G
Sbjct: 7 PKRDDSKDLALCSMILTEMETHEDAWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLSSG 66
Query: 66 MYTSLEQF--EVCSFFTLCLKF 85
Y +LE F +V F C F
Sbjct: 67 QYPNLETFALDVRLVFDNCETF 88
>pdb|3UVD|A Chain A, Crystal Structure Of The Bromodomain Of Human Transcription Activator Brg1 (Smarca4) In Complex With N-Methyl-2-Pyrrolidone Length = 124
>pdb|2DAT|A Chain A, Solution Structure Of The Bromodomain Of Human SwiSNF Related Matrix Associated Actin Dependent Regulator Of Cromatin Subfamily A Member 2 Length = 123
>2d9e_A Peregrin; four-helix bundle, transcription activator, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
