RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7968
(91 letters)
>gnl|CDD|99936 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.
Length = 115
Score = 90.5 bits (225), Expect = 2e-25
Identities = 34/64 (53%), Positives = 41/64 (64%)
Query: 20 VPDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKEDSEIYEPTIKL 79
VPDY+ II KPMD GTIK KLNM +Y+ E L D LVF NCF YN E + +Y+ +L
Sbjct: 42 VPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHTSVYKAGTRL 101
Query: 80 NTFL 83
F
Sbjct: 102 QRFF 105
>gnl|CDD|197636 smart00297, BROMO, bromo domain.
Length = 107
Score = 76.5 bits (189), Expect = 5e-20
Identities = 27/55 (49%), Positives = 34/55 (61%)
Query: 20 VPDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKEDSEIYE 74
PDY+ II KPMD TIK KL +Y + E + D NL+F N YN DSE+Y+
Sbjct: 37 APDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYNGPDSEVYK 91
>gnl|CDD|99922 cd04369, Bromodomain, Bromodomain. Bromodomains are found in many
chromatin-associated proteins and in nuclear histone
acetyltransferases. They interact specifically with
acetylated lysine.
Length = 99
Score = 75.9 bits (187), Expect = 9e-20
Identities = 25/64 (39%), Positives = 32/64 (50%)
Query: 20 VPDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKEDSEIYEPTIKL 79
PDY+ +I PMD TIK KL +Y++ E D L+F N YN S IY+ KL
Sbjct: 32 APDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGPGSPIYKDAKKL 91
Query: 80 NTFL 83
Sbjct: 92 EKLF 95
>gnl|CDD|99941 cd05509, Bromo_gcn5_like, Bromodomain; Gcn5_like subfamily. Gcn5p
is a histone acetyltransferase (HAT) which mediates
acetylation of histones at lysine residues; such
acetylation is generally correlated with the activation
of transcription. Bromodomains are 110 amino acid long
domains, that are found in many chromatin associated
proteins. Bromodomains can interact specifically with
acetylated lysine.
Length = 101
Score = 68.0 bits (167), Expect = 1e-16
Identities = 28/67 (41%), Positives = 36/67 (53%)
Query: 16 SVEPVPDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKEDSEIYEP 75
E PDY+ +I KPMD T++ KL Y E + D L+FDNC YN D+E Y+
Sbjct: 27 DKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEYYKC 86
Query: 76 TIKLNTF 82
KL F
Sbjct: 87 ANKLEKF 93
>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
Score = 67.3 bits (165), Expect = 2e-16
Identities = 25/60 (41%), Positives = 33/60 (55%)
Query: 20 VPDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKEDSEIYEPTIKL 79
+ DYH II PMD TIK KL+ +Y + E D L+F NC+ YN D ++ KL
Sbjct: 35 LHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKL 94
>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 = 66.3 bits (162), Expect = 7e-16
Identities = 25/54 (46%), Positives = 34/54 (62%)
Query: 20 VPDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKEDSEIY 73
+PDYH+II PMD GTIK +L Y + SE + D N +F NC+ YNK ++
Sbjct: 37 LPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKPGDDVV 90
>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
Score = 65.8 bits (161), Expect = 9e-16
Identities = 25/68 (36%), Positives = 34/68 (50%), Gaps = 4/68 (5%)
Query: 17 VEPV----PDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKEDSEI 72
V+ V PDY II KPMD GT+K KL +Y + E D L F N YN +++
Sbjct: 25 VDVVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDV 84
Query: 73 YEPTIKLN 80
+ +L
Sbjct: 85 HTMAKELL 92
>gnl|CDD|99935 cd05503, Bromo_BAZ2A_B_like, 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.
Length = 97
Score = 65.5 bits (160), Expect = 1e-15
Identities = 28/53 (52%), Positives = 35/53 (66%)
Query: 20 VPDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKEDSEI 72
VP Y +II KPMDF TI+ KL QY+ E D LVFDNC +N++DSE+
Sbjct: 30 VPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSEV 82
>gnl|CDD|215921 pfam00439, Bromodomain, Bromodomain. 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 = 64.3 bits (157), Expect = 3e-15
Identities = 25/55 (45%), Positives = 36/55 (65%)
Query: 20 VPDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKEDSEIYE 74
PDY+ +I +PMD TI+ KL +Y++ +E L D L+F N YN EDS+IY+
Sbjct: 26 YPDYYEVIKEPMDLSTIRQKLKSGKYKSLAEFLKDVELIFSNAITYNGEDSDIYK 80
>gnl|CDD|99932 cd05500, Bromo_BDF1_2_I, 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.
Length = 103
Score = 63.5 bits (155), Expect = 8e-15
Identities = 25/61 (40%), Positives = 32/61 (52%), Gaps = 4/61 (6%)
Query: 17 VEPV----PDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKEDSEI 72
V+PV P Y II KPMD GTI+ KL Y + E D NL+ DNC +N + +
Sbjct: 29 VDPVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNGPEHPV 88
Query: 73 Y 73
Sbjct: 89 S 89
>gnl|CDD|99944 cd05512, Bromo_brd1_like, Bromodomain; brd1_like subfamily. BRD1
is a mammalian gene which encodes for a nuclear protein
assumed to be a transcriptional regulator. BRD1 has
been implicated with brain development and
susceptibility to schizophrenia and bipolar affective
disorder. Bromodomains are 110 amino acid long domains
that are found in many chromatin associated proteins.
Bromodomains can interact specifically with acetylated
lysine.
Length = 98
Score = 62.8 bits (153), Expect = 1e-14
Identities = 25/60 (41%), Positives = 36/60 (60%)
Query: 20 VPDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKEDSEIYEPTIKL 79
VPDY I +PMDF T++ KL +YR + D NL+ +NC AYN +D+ Y ++L
Sbjct: 31 VPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKDTIFYRAAVRL 90
>gnl|CDD|99942 cd05510, Bromo_SPT7_like, 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.
Length = 112
Score = 62.8 bits (153), Expect = 2e-14
Identities = 24/54 (44%), Positives = 33/54 (61%)
Query: 20 VPDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKEDSEIY 73
PDY+ II KPMD GT+ KL QY++ +E + D NL++ NC YN + S
Sbjct: 38 APDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYNSDPSHPL 91
>gnl|CDD|99927 cd05495, Bromo_cbp_like, Bromodomain, cbp_like subfamily. Cbp
(CREB binding protein or CREBBP) is an
acetyltransferase acting on histone, which gives a
specific tag for transcriptional activation and also
acetylates non-histone proteins. CREBBP binds
specifically to phosphorylated CREB protein and
augments the activity of phosphorylated CREB to
activate transcription of cAMP-responsive genes.
Bromodomains are 110 amino acid long domains, that are
found in many chromatin associated proteins.
Bromodomains can interact specifically with acetylated
lysine.
Length = 108
Score = 61.7 bits (150), Expect = 4e-14
Identities = 24/60 (40%), Positives = 38/60 (63%)
Query: 20 VPDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKEDSEIYEPTIKL 79
+PDY I+ PMD TI+ KL+ QY++ + + D L+FDN + YN++ S +Y+ KL
Sbjct: 36 IPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYNRKTSRVYKYCTKL 95
>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 = 60.0 bits (146), Expect = 2e-13
Identities = 23/59 (38%), Positives = 38/59 (64%)
Query: 21 PDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKEDSEIYEPTIKL 79
PDY+ +I KP+D I+ K+ QY++ +++ D L+FDN YN+ DS+IY+ + L
Sbjct: 37 PDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYNEPDSQIYKDALTL 95
>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
Score = 59.7 bits (145), Expect = 2e-13
Identities = 22/59 (37%), Positives = 35/59 (59%)
Query: 21 PDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKEDSEIYEPTIKL 79
P+Y+ +I KP+DF IK ++ +YR+ ++ D L+ N +N E S IYE +I L
Sbjct: 38 PEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTFNLEGSLIYEDSIVL 96
>gnl|CDD|99931 cd05499, Bromo_BDF1_2_II, 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.
Length = 102
Score = 59.6 bits (145), Expect = 3e-13
Identities = 24/55 (43%), Positives = 34/55 (61%)
Query: 20 VPDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKEDSEIYE 74
+P+Y II KPMD GTI KL QY++ E D L+F NC+ +N E +++Y
Sbjct: 35 IPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTDVYM 89
>gnl|CDD|227408 COG5076, COG5076, Transcription factor involved in chromatin
remodeling, contains bromodomain [Chromatin structure
and dynamics / Transcription].
Length = 371
Score = 62.5 bits (152), Expect = 4e-13
Identities = 27/64 (42%), Positives = 37/64 (57%)
Query: 21 PDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKEDSEIYEPTIKLN 80
PDY+ II PMD TI+ KL +Y++ E + D NL+FDNC YN DS +Y +L
Sbjct: 179 PDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELE 238
Query: 81 TFLS 84
+
Sbjct: 239 KYFL 242
Score = 28.2 bits (63), Expect = 0.47
Identities = 23/82 (28%), Positives = 30/82 (36%), Gaps = 8/82 (9%)
Query: 1 MQTFAGEETASSATFSVEP----VPDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCN 56
+ + + F VPDY++ I PMD T + KL YR + D
Sbjct: 270 VLITNSQAHVGAWPFLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVRDAK 329
Query: 57 LVFDNCFAYNKEDSEIYEPTIK 78
L FDNC YN K
Sbjct: 330 LFFDNCVMYN----GEVTDYYK 347
>gnl|CDD|99934 cd05502, Bromo_tif1_like, 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.
Length = 109
Score = 59.2 bits (144), Expect = 4e-13
Identities = 25/66 (37%), Positives = 38/66 (57%), Gaps = 3/66 (4%)
Query: 20 VPDYHRIIGKPMDFGTIKHKLNM---FQYRNNSEVLFDCNLVFDNCFAYNKEDSEIYEPT 76
VP+Y++II PMD I+ KL Y + E + D L+F NC+ +N+EDSE+ +
Sbjct: 33 VPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYKFNEEDSEVAQAG 92
Query: 77 IKLNTF 82
+L F
Sbjct: 93 KELELF 98
>gnl|CDD|99943 cd05511, Bromo_TFIID, 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.
Length = 112
Score = 57.3 bits (139), Expect = 3e-12
Identities = 24/58 (41%), Positives = 34/58 (58%), Gaps = 2/58 (3%)
Query: 15 FSVEP--VPDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKEDS 70
V VPDY++II +PMD TI+ K++ +Y++ E L D L+ DN YN DS
Sbjct: 23 TPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDS 80
>gnl|CDD|99949 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.
Length = 103
Score = 56.7 bits (137), Expect = 4e-12
Identities = 22/54 (40%), Positives = 35/54 (64%)
Query: 21 PDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKEDSEIYE 74
PDY++II +P+D TI+H + +Y E++ D L+F N YN+E S++YE
Sbjct: 37 PDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYNEEGSQVYE 90
>gnl|CDD|99928 cd05496, Bromo_WDR9_II, 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.
Length = 119
Score = 54.0 bits (130), Expect = 6e-11
Identities = 26/71 (36%), Positives = 35/71 (49%), Gaps = 6/71 (8%)
Query: 18 EPV-----PDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYN-KEDSE 71
+PV PDY II PMD GT+K L Y + E D L+F N +Y + S
Sbjct: 28 QPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYTPNKRSR 87
Query: 72 IYEPTIKLNTF 82
IY T++L+
Sbjct: 88 IYSMTLRLSAL 98
>gnl|CDD|99945 cd05513, Bromo_brd7_like, Bromodomain, brd7_like subgroup. 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 = 50.9 bits (122), Expect = 6e-10
Identities = 23/59 (38%), Positives = 31/59 (52%)
Query: 21 PDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKEDSEIYEPTIKL 79
P Y II PMDF T+K K+ Y++ E D L+ +N YNK D+ Y+ KL
Sbjct: 32 PGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDTIYYKAAKKL 90
>gnl|CDD|99951 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.
Length = 103
Score = 50.8 bits (122), Expect = 8e-10
Identities = 22/59 (37%), Positives = 32/59 (54%)
Query: 21 PDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKEDSEIYEPTIKL 79
PDY++ I P+ I+ KL +Y E+ D NL+F+N YN +S IY+ KL
Sbjct: 37 PDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPNSRIYKDAEKL 95
>gnl|CDD|99957 cd05528, Bromo_AAA, Bromodomain; sub-family co-occurring with AAA
domains. 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
Score = 49.7 bits (119), Expect = 2e-09
Identities = 22/49 (44%), Positives = 28/49 (57%)
Query: 18 EPVPDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYN 66
E VPDY+ II +PMD TI KL+ QY + L D +L+ N YN
Sbjct: 31 EEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYN 79
>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
Score = 46.9 bits (112), Expect = 2e-08
Identities = 21/59 (35%), Positives = 35/59 (59%)
Query: 21 PDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKEDSEIYEPTIKL 79
PDY+ II +P+ IK ++ Y++ E L D +L+F N YN+E S +YE +++
Sbjct: 37 PDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYNQEGSIVYEDAVEM 95
>gnl|CDD|99953 cd05522, Bromo_Rsc1_2_II, 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.
Length = 104
Score = 45.7 bits (109), Expect = 6e-08
Identities = 19/54 (35%), Positives = 33/54 (61%)
Query: 21 PDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKEDSEIYE 74
P+Y++ I P+ IK K+ +Y++ + L D NL+F+N YN+ DS+ Y+
Sbjct: 38 PEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYK 91
>gnl|CDD|99937 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.
Length = 97
Score = 45.2 bits (107), Expect = 8e-08
Identities = 18/58 (31%), Positives = 28/58 (48%)
Query: 15 FSVEPVPDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKEDSEI 72
+ + DY ++I PMD T++ K + Y + E L D LVF N Y + S +
Sbjct: 25 VTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGSYV 82
>gnl|CDD|99954 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.
Length = 113
Score = 43.1 bits (102), Expect = 7e-07
Identities = 18/59 (30%), Positives = 32/59 (54%)
Query: 21 PDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKEDSEIYEPTIKL 79
P+Y+ ++ P+D I+ KL +Y + ++ D L+ +N AY K DS ++ KL
Sbjct: 39 PEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYKPDSPEHKDACKL 97
>gnl|CDD|99952 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.
Length = 106
Score = 43.1 bits (102), Expect = 7e-07
Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 6/76 (7%)
Query: 12 SATFSVEPV----PDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNK 67
F+V P+ PDY++II P+ T+K +L Y N E + D + N YN
Sbjct: 25 HPIFNVLPLRKDYPDYYKIIKNPLSLNTVKKRLP--HYTNAQEFVNDLAQIPWNARLYNT 82
Query: 68 EDSEIYEPTIKLNTFL 83
+ S IY+ + L ++
Sbjct: 83 KGSVIYKYALILEKYI 98
>gnl|CDD|99939 cd05507, Bromo_brd8_like, 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.
Length = 104
Score = 42.4 bits (100), Expect = 1e-06
Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 18 EPVPD-----YHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKEDSEI 72
+PV + YH ++ +PMD TIK + R+ +E D L+F N YN D ++
Sbjct: 26 KPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNSSDHDV 85
Query: 73 Y 73
Y
Sbjct: 86 Y 86
>gnl|CDD|99958 cd05529, Bromo_WDR9_I_like, 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.
Length = 128
Score = 37.7 bits (88), Expect = 1e-04
Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 2/54 (3%)
Query: 20 VPDYHRIIGKPMDFGTIKHKL-NMFQYRNNSEVLFDCNLVFDNCFAYNKEDSEI 72
PDY + PMD TI+ +L N + YR+ + D L+ N +N+ +SEI
Sbjct: 58 YPDYWNRVPVPMDLETIRSRLENRY-YRSLEALRHDVRLILSNAETFNEPNSEI 110
>gnl|CDD|99926 cd05494, Bromodomain_1, Bromodomain; uncharacterized subfamily.
Bromodomains are found in many chromatin-associated
proteins and in nuclear histone acetyltransferases.
They interact specifically with acetylated lysine.
Length = 114
Score = 33.2 bits (76), Expect = 0.005
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 18 EPVPDYHRIIGKPMDFGTI 36
PDY +I +PM FGT
Sbjct: 33 RGAPDYRDVIKRPMSFGTK 51
>gnl|CDD|99940 cd05508, Bromo_RACK7, Bromodomain, RACK7_like subfamily. 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
Score = 32.7 bits (75), Expect = 0.006
Identities = 16/58 (27%), Positives = 26/58 (44%)
Query: 15 FSVEPVPDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKEDSEI 72
+E PDY + + KPMD T++ + Y + L D + N YN D ++
Sbjct: 27 VDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYNGGDHKL 84
>gnl|CDD|99933 cd05501, Bromo_SP100C_like, 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.
Length = 102
Score = 32.4 bits (74), Expect = 0.007
Identities = 15/48 (31%), Positives = 23/48 (47%)
Query: 22 DYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKED 69
DY + I +PM +K +LN Y + D L+F N + K+D
Sbjct: 32 DYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKDD 79
>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
Score = 31.6 bits (72), Expect = 0.014
Identities = 15/55 (27%), Positives = 32/55 (58%)
Query: 21 PDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKEDSEIYEP 75
PDY+ +I +P+D TI ++ Y++ ++ D +L+ N +N+ S++Y+
Sbjct: 37 PDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFNEPGSQVYKD 91
>gnl|CDD|99955 cd05525, Bromo_ASH1, Bromodomain; ASH1_like sub-family. 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.
Length = 106
Score = 31.2 bits (71), Expect = 0.027
Identities = 17/60 (28%), Positives = 24/60 (40%)
Query: 20 VPDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKEDSEIYEPTIKL 79
PDY+ I P+D TI+ ++ Y+ D VF N Y S I +L
Sbjct: 38 NPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYYGRKSPIGRDVCRL 97
>gnl|CDD|99924 cd05492, Bromo_ZMYND11, Bromodomain; ZMYND11_like sub-family.
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.
Length = 109
Score = 30.4 bits (69), Expect = 0.049
Identities = 16/54 (29%), Positives = 26/54 (48%)
Query: 21 PDYHRIIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCFAYNKEDSEIYE 74
P R+I +D I+ K+N +Y + E D L+ N ++ DSE Y+
Sbjct: 37 PKRRRLIHTHLDVADIQEKINSEKYTSLEEFKADALLLLHNTAIFHGADSEQYD 90
>gnl|CDD|99956 cd05526, Bromo_polybromo_VI, Bromodomain, polybromo repeat VI.
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 = 110
Score = 27.3 bits (61), Expect = 0.76
Identities = 18/79 (22%), Positives = 31/79 (39%), Gaps = 20/79 (25%)
Query: 16 SVEPVPDYHRII----GKPMDFGTIK--------HKLNMFQYRNNSEVLFDCNLVFDNCF 63
S+ +P+ P+ IK +L+ FQ E +F+ +
Sbjct: 29 SLAELPELAVDGVGPKKIPLTLDIIKRNVDKGRYRRLDKFQ-----EDMFEV---LERAR 80
Query: 64 AYNKEDSEIYEPTIKLNTF 82
++ DSEIYE ++L F
Sbjct: 81 RLSRTDSEIYEDAVELQQF 99
>gnl|CDD|223690 COG0617, PcnB, tRNA nucleotidyltransferase/poly(A) polymerase
[Translation, ribosomal structure and biogenesis].
Length = 412
Score = 26.6 bits (59), Expect = 1.7
Identities = 18/75 (24%), Positives = 24/75 (32%), Gaps = 23/75 (30%)
Query: 23 YHRIIGKPMDFGTIKHKLN-------------MFQYRNNSEVLFDCNLVFD--------N 61
R +G+ FGT+ N V+F L D N
Sbjct: 61 NTRPVGR--KFGTVTVPFNGEIIEVTTFRKEGYGYNGRPLPVVFPGTLEEDLKRRDFTIN 118
Query: 62 CFAYNKEDSEIYEPT 76
AY+ ED EI +P
Sbjct: 119 ALAYDPEDGEIIDPF 133
>gnl|CDD|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed.
Length = 565
Score = 26.3 bits (59), Expect = 2.3
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 4/33 (12%)
Query: 16 SVEPVPDYHRIIGKPMDFGTIKHKLNMFQYRNN 48
V PV D + GK ++F IK + + RNN
Sbjct: 147 DVRPVRDTDPLEGKELEFKVIK----LDKKRNN 175
>gnl|CDD|224875 COG1964, COG1964, Predicted Fe-S oxidoreductases [General
function prediction only].
Length = 475
Score = 26.2 bits (58), Expect = 2.5
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 62 CFAYNKEDSEIYEPTI 77
CFAY +E IYEPT+
Sbjct: 78 CFAYAEEAGYIYEPTL 93
>gnl|CDD|215284 PLN02519, PLN02519, isovaleryl-CoA dehydrogenase.
Length = 404
Score = 26.0 bits (57), Expect = 3.1
Identities = 14/38 (36%), Positives = 18/38 (47%), Gaps = 4/38 (10%)
Query: 26 IIGKPMDFGTIKHKLNMFQYRNNSEVLFDCNLVFDNCF 63
II K M + KL+ R + C LVF+NCF
Sbjct: 208 IIEKGMPGFSTAQKLDKLGMRGSDT----CELVFENCF 241
>gnl|CDD|221320 pfam11927, DUF3445, Protein of unknown function (DUF3445). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria and eukaryotes.
Proteins in this family are typically between 264 to 418
amino acids in length. This protein has a conserved RLP
sequence motif. This protein has two completely
conserved R residues that may be functionally important.
Length = 245
Score = 25.2 bits (56), Expect = 4.9
Identities = 6/15 (40%), Positives = 8/15 (53%)
Query: 18 EPVPDYHRIIGKPMD 32
PVP Y + + MD
Sbjct: 146 GPVPGYKEKLARSMD 160
>gnl|CDD|234430 TIGR03986, TIGR03986, CRISPR-associated protein. Members of this
protein family, part of the larger RAMP family, are
found exclusively in species with CRISPR systems, in
local contexts containing other RAMP (Repeat-Associated
Mystery Proteins).
Length = 562
Score = 25.0 bits (55), Expect = 6.7
Identities = 9/16 (56%), Positives = 14/16 (87%), Gaps = 1/16 (6%)
Query: 23 YHRI-IGKPMDFGTIK 37
YH+I +GKP+ FG++K
Sbjct: 484 YHKIGMGKPLGFGSVK 499
>gnl|CDD|220230 pfam09419, PGP_phosphatase, Mitochondrial PGP phosphatase. This
is a family of proteins that acts as a mitochondrial
phosphatase in cardiolipin biosynthesis. Cardiolipin is
a unique dimeric phosphoglycerolipid predominantly
present in mitochondrial membranes. The inverted
phosphatase motif includes the highly conserved DKD
triad.
Length = 166
Score = 24.6 bits (54), Expect = 8.2
Identities = 7/21 (33%), Positives = 11/21 (52%), Gaps = 3/21 (14%)
Query: 57 LVFD--NCFAYNKEDSEIYEP 75
+V D NC +D +I+ P
Sbjct: 42 VVLDKDNCLTLPHDD-KIWPP 61
>gnl|CDD|193538 cd05662, M28_like_2, M28 Zn-Peptidases. Peptidase family M28 (also
called aminopeptidase Y family), uncharacterized
subfamily. The M28 family contains aminopeptidases as
well as carboxypeptidases. They have co-catalytic zinc
ions; each zinc ion is tetrahedrally co-ordinated, with
three amino acid ligands plus activated water; one
aspartate residue binds both metal ions. This subfamily
is composed of uncharacterized proteins that do not
contain a protease-associated (PA) domain.
Length = 267
Score = 24.5 bits (54), Expect = 8.3
Identities = 11/23 (47%), Positives = 11/23 (47%), Gaps = 5/23 (21%)
Query: 15 FSVEPVPDYHRIIGKPMD-FGTI 36
F VE PDYH P D F I
Sbjct: 229 FGVEDHPDYH----TPTDTFEKI 247
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.323 0.137 0.430
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,325,885
Number of extensions: 334597
Number of successful extensions: 265
Number of sequences better than 10.0: 1
Number of HSP's gapped: 262
Number of HSP's successfully gapped: 50
Length of query: 91
Length of database: 10,937,602
Length adjustment: 58
Effective length of query: 33
Effective length of database: 8,365,070
Effective search space: 276047310
Effective search space used: 276047310
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.2 bits)