RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4829
(120 letters)
>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 = 83.5 bits (207), Expect = 3e-22
Identities = 25/76 (32%), Positives = 45/76 (59%)
Query: 21 KGYHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYAKTDQEYSDAK 80
Y++ +K PM ++R +L P P+ Y + +F++D+RL+FKN + + + + K
Sbjct: 34 PNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYKFNEEDSEVAQAGK 93
Query: 81 NLEEYFEHMLEKWLPD 96
LE +FE L++ LPD
Sbjct: 94 ELELFFEEQLKEILPD 109
>gnl|CDD|197636 smart00297, BROMO, bromo domain.
Length = 107
Score = 59.6 bits (145), Expect = 7e-13
Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 3/70 (4%)
Query: 23 YHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYAKTDQEYSDAKNL 82
Y++ +K PM ++ +L Y ++ +F++D L+F NA Y + Y DAK L
Sbjct: 40 YYDIIKKPMDLKTIKKKLENGK---YSSVEEFVADFNLMFSNARTYNGPDSEVYKDAKKL 96
Query: 83 EEYFEHMLEK 92
E++FE L +
Sbjct: 97 EKFFEKKLRE 106
>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 = 58.9 bits (143), Expect = 1e-12
Identities = 29/91 (31%), Positives = 42/91 (46%), Gaps = 5/91 (5%)
Query: 1 MKQLIQYHQELRLMRRKCSDKGYHEKVKNPMSFDVVRWRLNPSHPEG-YKTIVQFISDIR 59
K + Y+E +KNPM ++ +L G YK++ +F +D+R
Sbjct: 13 KKLKRDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLK----NGEYKSLEEFEADVR 68
Query: 60 LIFKNAFVYYAKTDQEYSDAKNLEEYFEHML 90
LIF NA Y Y DAK LE+ FE +L
Sbjct: 69 LIFSNAKTYNGPGSPIYKDAKKLEKLFEKLL 99
>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 = 51.6 bits (124), Expect = 5e-10
Identities = 21/64 (32%), Positives = 31/64 (48%), Gaps = 3/64 (4%)
Query: 17 KCSDKGYHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYAKTDQEY 76
Y+E +K PM +R +L YK++ +F+ D+ LIF NA Y + Y
Sbjct: 23 PEEYPDYYEVIKEPMDLSTIRQKLKSGK---YKSLAEFLKDVELIFSNAITYNGEDSDIY 79
Query: 77 SDAK 80
DAK
Sbjct: 80 KDAK 83
>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 = 50.4 bits (121), Expect = 2e-09
Identities = 18/67 (26%), Positives = 35/67 (52%), Gaps = 3/67 (4%)
Query: 23 YHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYAKTDQEYSDAKNL 82
YH+ +K+PM ++ +L+ Y +F +D+RL+F N + Y ++ A+ L
Sbjct: 38 YHDIIKHPMDLSTIKKKLDNRE---YADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKL 94
Query: 83 EEYFEHM 89
++ FE
Sbjct: 95 QDVFEDR 101
>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 = 48.7 bits (117), Expect = 1e-08
Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 3/71 (4%)
Query: 23 YHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYAKTDQEYSDAKNL 82
Y++ +K PM + +L + Y T+ +F++D++LIF N +Y + Y A L
Sbjct: 34 YYDVIKKPMDLSTMEEKLENGY---YVTLEEFVADLKLIFDNCRLYNGPDTEYYKCANKL 90
Query: 83 EEYFEHMLEKW 93
E++F L++
Sbjct: 91 EKFFWKKLKEL 101
>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 = 48.1 bits (115), Expect = 2e-08
Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 6/71 (8%)
Query: 23 YHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYAKTDQEYSDAKNL 82
Y + +K PM V+ +L Y + +F +D+RL F NA Y + ++ AK L
Sbjct: 35 YFDIIKKPMDLGTVKKKLEKGE---YSSPEEFAADVRLTFANAMRYNPPGNDVHTMAKEL 91
Query: 83 EEYFEHMLEKW 93
+ FE +W
Sbjct: 92 LKIFE---TRW 99
>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 = 48.5 bits (116), Expect = 2e-08
Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 3/70 (4%)
Query: 23 YHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYAKTDQEYSDAKNL 82
Y++ +K PM ++ +LN YK +F+SDI+L+F N F+Y + Y L
Sbjct: 45 YYDIIKKPMDLGTIKEKLNMGE---YKLAEEFLSDIQLVFSNCFLYNPEHTSVYKAGTRL 101
Query: 83 EEYFEHMLEK 92
+ +F K
Sbjct: 102 QRFFIKRCRK 111
>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 = 46.5 bits (111), Expect = 7e-08
Identities = 19/66 (28%), Positives = 29/66 (43%), Gaps = 3/66 (4%)
Query: 22 GYHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYAKTDQEYSDAKN 81
Y +K PM + +L Y++ +F D+RLIFKN + + + Y
Sbjct: 37 NYFSIIKKPMDLGTISKKLQNGQ---YQSAKEFERDVRLIFKNCYTFNPEGTDVYMMGHQ 93
Query: 82 LEEYFE 87
LEE F
Sbjct: 94 LEEVFN 99
>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 = 45.8 bits (109), Expect = 2e-07
Identities = 15/68 (22%), Positives = 27/68 (39%), Gaps = 4/68 (5%)
Query: 23 YHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYAKTDQEYSDAKNL 82
Y +K PM + +L + Y ++ +F +D L+ N + K L
Sbjct: 39 YPTIIKKPMDLGTIERKLKSNV---YTSVEEFTADFNLMVDNCLTFNGPEHPVSQMGKRL 95
Query: 83 EEYFE-HM 89
+ FE H+
Sbjct: 96 QAAFEKHL 103
>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 = 45.3 bits (108), Expect = 2e-07
Identities = 22/64 (34%), Positives = 39/64 (60%), Gaps = 3/64 (4%)
Query: 23 YHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYAKTDQEYSDAKNL 82
Y++++ NP+S D ++ ++ YK+ QF++D+ L+F+NA +Y QEY DA L
Sbjct: 40 YYQEISNPISLDDIKKKVKRRK---YKSFDQFLNDLNLMFENAKLYNENDSQEYKDAVLL 96
Query: 83 EEYF 86
E+
Sbjct: 97 EKEA 100
>gnl|CDD|227408 COG5076, COG5076, Transcription factor involved in chromatin
remodeling, contains bromodomain [Chromatin structure
and dynamics / Transcription].
Length = 371
Score = 46.7 bits (111), Expect = 4e-07
Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 3/75 (4%)
Query: 23 YHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYAKTDQEYSDAKNL 82
Y+E +K+PM ++ +L YK+ +F+SD+ L+F N +Y Y DAK L
Sbjct: 181 YYEIIKSPMDLLTIQKKLKNGR---YKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKEL 237
Query: 83 EEYFEHMLEKWLPDY 97
E+YF ++E+ +
Sbjct: 238 EKYFLKLIEEIPEEM 252
>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 = 44.6 bits (106), Expect = 5e-07
Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 4/77 (5%)
Query: 11 LRLMRRKCSDKGYHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYA 70
+R+ +R+ ++ Y+E V NP+ ++ +L E Y + +D L+ NA YY
Sbjct: 30 IRVPKRR-NEPEYYEVVSNPIDLLKIQQKLKT---EEYDDVDDLTADFELLINNAKAYYK 85
Query: 71 KTDQEYSDAKNLEEYFE 87
E+ DA L E F
Sbjct: 86 PDSPEHKDACKLWELFL 102
>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 = 44.0 bits (104), Expect = 7e-07
Identities = 23/65 (35%), Positives = 35/65 (53%), Gaps = 3/65 (4%)
Query: 23 YHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYAKTDQEYSDAKNL 82
Y + VKNPM +R +L+ Y+ Q++ D+ L+F NA++Y KT + Y L
Sbjct: 39 YFDIVKNPMDLSTIRRKLDTGQ---YQDPWQYVDDVWLMFDNAWLYNRKTSRVYKYCTKL 95
Query: 83 EEYFE 87
E FE
Sbjct: 96 AEVFE 100
>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 = 40.8 bits (96), Expect = 1e-05
Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 3/67 (4%)
Query: 23 YHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYAKTDQEYSDAKNL 82
Y+ +K P++ D ++ R+ YK++ +F+ D L+F NA Y + Y DA +
Sbjct: 39 YYVIIKRPIALDQIKRRIEGRA---YKSLEEFLEDFHLMFANARTYNQEGSIVYEDAVEM 95
Query: 83 EEYFEHM 89
E+ F+
Sbjct: 96 EKAFKKK 102
>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 = 39.2 bits (92), Expect = 6e-05
Identities = 23/82 (28%), Positives = 40/82 (48%), Gaps = 13/82 (15%)
Query: 21 KGYHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVY------YAKTDQ 74
Y++ +K PM +R +++ H Y++ +F+ DI LI N+ +Y Y K +
Sbjct: 31 PDYYKIIKRPMDLQTIRKKIS-KH--KYQSREEFLEDIELIVDNSVLYNGPDSVYTKKAK 87
Query: 75 EYSD--AKNLEEYFEHM--LEK 92
E + + L E E + LEK
Sbjct: 88 EMLELAEELLAEREEKLTQLEK 109
>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 = 38.2 bits (89), Expect = 1e-04
Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 3/64 (4%)
Query: 23 YHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYAKTDQEYSDAKNL 82
YH+ +K PM ++ RL ++ Y + + I D +F N ++Y D A+ L
Sbjct: 40 YHKIIKTPMDLGTIKKRLENNY---YWSASECIQDFNTMFTNCYIYNKPGDDVVLMAQTL 96
Query: 83 EEYF 86
E+ F
Sbjct: 97 EKLF 100
>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 = 37.3 bits (87), Expect = 3e-04
Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 23 YHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYAKTDQEYSDAKNL 82
Y++ +KNP+S + V+ RL Y +F++D+ I NA +Y K Y A L
Sbjct: 40 YYKIIKNPLSLNTVKKRLP-----HYTNAQEFVNDLAQIPWNARLYNTKGSVIYKYALIL 94
Query: 83 EEY 85
E+Y
Sbjct: 95 EKY 97
>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 = 36.7 bits (85), Expect = 4e-04
Identities = 16/68 (23%), Positives = 33/68 (48%), Gaps = 3/68 (4%)
Query: 23 YHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYAKTDQEYSDAKNL 82
Y + + NPM ++ + + Y ++ +F+ D++L+F NA YY S +
Sbjct: 33 YKKVITNPMDLQTMQTKCSCGS---YSSVQEFLDDMKLVFSNAEKYYENGSYVLSCMRKT 89
Query: 83 EEYFEHML 90
E+ ++L
Sbjct: 90 EQCCVNLL 97
>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 = 36.3 bits (84), Expect = 5e-04
Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 8/72 (11%)
Query: 21 KGYHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYAKTDQEYSDAK 80
+ Y + +K PM + V+ RLN Y T+ F+ D+RLIF N ++Y + D
Sbjct: 31 RDYCQGIKEPMWLNKVKERLNE---RVYHTVEGFVRDMRLIFHNHKLFY-----KDDDFG 82
Query: 81 NLEEYFEHMLEK 92
+ E EK
Sbjct: 83 QVGITLEKKFEK 94
>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 = 35.8 bits (83), Expect = 8e-04
Identities = 21/70 (30%), Positives = 39/70 (55%), Gaps = 6/70 (8%)
Query: 23 YHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYAKTDQEYSDAKNL 82
Y++++KNP+S +R +L Y+T+ + +D+ L+F+NA Y + Y DA+ L
Sbjct: 39 YYQEIKNPISLQQIRTKLKN---GEYETLEELEADLNLMFENAKRYNVPNSRIYKDAEKL 95
Query: 83 EEYFEHMLEK 92
+ + M K
Sbjct: 96 Q---KLMQAK 102
>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 = 35.4 bits (82), Expect = 0.001
Identities = 17/43 (39%), Positives = 25/43 (58%), Gaps = 3/43 (6%)
Query: 22 GYHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKN 64
GY + +K PM F +R +L YKT+ +F D+RL+F N
Sbjct: 32 GYRKIIKKPMDFSTIREKLESG---QYKTLEEFAEDVRLVFDN 71
>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 = 35.4 bits (82), Expect = 0.001
Identities = 24/77 (31%), Positives = 33/77 (42%), Gaps = 7/77 (9%)
Query: 23 YHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYAKTDQE----YSD 78
Y+E +K PM + +L+ +H Y T F+ DI LI NA Y D S
Sbjct: 36 YYEIIKQPMDLQTILQKLD-THQ--YLTAKDFLKDIDLIVTNALEYNPDRDPADKLIRSR 92
Query: 79 AKNLEEYFEHMLEKWLP 95
A L + M+E L
Sbjct: 93 ACELRDEVHAMIEAELD 109
>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 = 33.6 bits (77), Expect = 0.007
Identities = 22/76 (28%), Positives = 35/76 (46%), Gaps = 4/76 (5%)
Query: 23 YHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYA-KTDQEYSDAKN 81
Y + + PM V+ L + Y ++F D+RLIF N+ Y K + YS
Sbjct: 38 YRDIIDTPMDLGTVKETLFGGN---YDDPMEFAKDVRLIFSNSKSYTPNKRSRIYSMTLR 94
Query: 82 LEEYFEHMLEKWLPDY 97
L FE ++K + D+
Sbjct: 95 LSALFEEHIKKIISDW 110
>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 = 32.4 bits (74), Expect = 0.016
Identities = 18/70 (25%), Positives = 35/70 (50%), Gaps = 4/70 (5%)
Query: 23 YHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYAKTDQEYSDAKN- 81
Y++ +K PM + +L YK+ +F+ D+ LI+KN +Y + N
Sbjct: 41 YYDIIKKPMDLGTMLKKLKNLQ---YKSKAEFVDDLNLIWKNCLLYNSDPSHPLRRHANF 97
Query: 82 LEEYFEHMLE 91
+++ EH+L+
Sbjct: 98 MKKKAEHLLK 107
>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 = 31.9 bits (73), Expect = 0.022
Identities = 17/61 (27%), Positives = 31/61 (50%), Gaps = 3/61 (4%)
Query: 23 YHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYAKTDQEYSDAKNL 82
Y++ +K P+ + +R ++ Y+++ +SD L+F NA Y Q Y DA L
Sbjct: 39 YYDVIKKPIDMEKIRSKIEG---NQYQSLDDMVSDFVLMFDNACKYNEPDSQIYKDALTL 95
Query: 83 E 83
+
Sbjct: 96 Q 96
>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 = 32.3 bits (74), Expect = 0.025
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 23 YHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYAKTDQEYSD-AKN 81
Y +V PM + +R RL + Y+++ D+RLI NA + + + E + AK
Sbjct: 61 YWNRVPVPMDLETIRSRLENRY---YRSLEALRHDVRLILSNAETFN-EPNSEIAKKAKR 116
Query: 82 LEEYFEHMLE 91
L ++ +L
Sbjct: 117 LSDWLLRILS 126
>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 = 30.8 bits (70), Expect = 0.050
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 3/49 (6%)
Query: 23 YHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYAK 71
Y + +K PM F +R +L + Y+T+ F +D LI N Y AK
Sbjct: 34 YLDHIKQPMDFSTMRKKLE---SQRYRTLEDFEADFNLIINNCLAYNAK 79
>gnl|CDD|107324 cd06329, PBP1_SBP_like_3, Periplasmic solute-binding domain of
active transport proteins. Periplasmic solute-binding
domain of active transport proteins found in bacteria
and Archaea. Members of this group are initial receptors
in the process of active transport across cellular
membrane, but their substrate specificities are not
known in detail. However, they closely resemble the
group of AmiC and active transport systems for
short-chain amides and urea (FmdDEF), and thus are
likely to exhibit a ligand-binding mode similar to that
of the amide sensor protein AmiC from Pseudomonas
aeruginosa. Moreover, this binding domain has high
sequence identity to the family of hydrophobic amino
acid transporters (HAAT), and thus it may also be
involved in transport of amino acids.
Length = 342
Score = 31.9 bits (73), Expect = 0.056
Identities = 12/65 (18%), Positives = 23/65 (35%), Gaps = 7/65 (10%)
Query: 37 RW--RLNPSHPEGYKTIVQFISDIRLIFKNAFVYYAKTDQEYSDAKNLEEYFEHMLEKWL 94
W R + + + + +I K + Q+YS +++ F+ ML
Sbjct: 117 FWHFRTDANTDMKMEALASYIKKQPDGKKVYLIN-----QDYSWGQDVAAAFKAMLAAKR 171
Query: 95 PDYAY 99
PD
Sbjct: 172 PDIQI 176
>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 = 29.3 bits (66), Expect = 0.19
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 3/61 (4%)
Query: 22 GYHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYAKTDQEYSDAKN 81
GY +K+PM F ++ ++ Y++I +F D +L+ +NA Y Y AK
Sbjct: 33 GYSSIIKHPMDFSTMKEKIKN---NDYQSIEEFKDDFKLMCENAMKYNKPDTIYYKAAKK 89
Query: 82 L 82
L
Sbjct: 90 L 90
>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 = 29.3 bits (66), Expect = 0.23
Identities = 16/70 (22%), Positives = 36/70 (51%), Gaps = 3/70 (4%)
Query: 23 YHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYAKTDQEYSDAKNL 82
Y+E ++ P+ F ++ R+ +H Y+++ D+ L+ +NA + + Y D+ L
Sbjct: 40 YYELIRKPVDFKKIKERIR-NHK--YRSLEDLEKDVMLLCQNAQTFNLEGSLIYEDSIVL 96
Query: 83 EEYFEHMLEK 92
+ F+ +K
Sbjct: 97 QSVFKSARQK 106
>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 = 28.9 bits (65), Expect = 0.33
Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 3/64 (4%)
Query: 23 YHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYAKTDQEYSDAKNL 82
Y+ +K P+ + R+ + YK+I D+ L+ KNA + Q Y DA +
Sbjct: 39 YYAVIKEPIDLKTIAQRIQSGY---YKSIEDMEKDLDLMVKNAKTFNEPGSQVYKDANAI 95
Query: 83 EEYF 86
++ F
Sbjct: 96 KKIF 99
>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 = 28.1 bits (63), Expect = 0.65
Identities = 17/71 (23%), Positives = 33/71 (46%), Gaps = 3/71 (4%)
Query: 17 KCSDKGYHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYAKTDQEY 76
K + Y+E++ +P+ + ++ + YKT F SD+ +F+NA YY +
Sbjct: 35 KKKNPDYYERITDPVDLSTIEKQILTGY---YKTPEAFDSDMLKVFRNAEKYYGRKSPIG 91
Query: 77 SDAKNLEEYFE 87
D L + +
Sbjct: 92 RDVCRLRKAYY 102
>gnl|CDD|183957 PRK13294, PRK13294, F420-0--gamma-glutamyl ligase; Provisional.
Length = 448
Score = 28.4 bits (64), Expect = 0.95
Identities = 11/31 (35%), Positives = 14/31 (45%), Gaps = 4/31 (12%)
Query: 89 MLEKWLPDYAYDDSLDGELSEPSAKRLRRGQ 119
M + W D D G E A+R+RRG
Sbjct: 313 MRDAWRADLRAD----GLSEESIARRVRRGD 339
>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 = 27.4 bits (61), Expect = 1.1
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 8/51 (15%)
Query: 46 EGYKTIVQFISDIRLIFKNAFVYYAKTDQEYSDAKNLEEYFEHMLEKWLPD 96
+ Y T + + D +L+F+NA Y + Q Y DA ++LEK L +
Sbjct: 59 DKYATEEELMDDFKLMFRNARHYNEEGSQVYEDA--------NILEKVLKE 101
>gnl|CDD|238375 cd00733, GlyRS_alpha_core, Class II Glycyl-tRNA synthetase (GlyRS)
alpha subunit core catalytic domain. GlyRS functions as
a homodimer in eukaryotes, archaea and some bacteria and
as a heterotetramer in the remainder of prokaryotes and
in arabidopsis. It is responsible for the attachment of
glycine to the 3' OH group of ribose of the appropriate
tRNA. This domain is primarily responsible for the
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. This alignment contains only
sequences from the GlyRS form which heterotetramerizes.
The homodimer form of GlyRS is in a different family of
class II aaRS. Class II assignment is based upon
structure and the presence of three characteristic
sequence motifs.
Length = 279
Score = 27.7 bits (62), Expect = 1.2
Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 7/47 (14%)
Query: 61 IFKNAFVYYAKTDQEYSDAKNLEEYFE-------HMLEKWLPDYAYD 100
+F + + + EY++ L + FE +LE LP AYD
Sbjct: 187 VFLQNEIEQSVYNFEYANVDMLFQLFEDYEKEAKRLLELGLPLPAYD 233
>gnl|CDD|233781 TIGR02212, lolCE, lipoprotein releasing system, transmembrane
protein, LolC/E family. This model describes the LolC
protein, and its paralog LolE found in some species.
These proteins are homologous to permease proteins of
ABC transporters. In some species, two paralogs occur,
designated LolC and LolE. In others, a single form is
found and tends to be designated LolC [Protein fate,
Protein and peptide secretion and trafficking].
Length = 411
Score = 28.0 bits (63), Expect = 1.3
Identities = 10/65 (15%), Positives = 21/65 (32%), Gaps = 8/65 (12%)
Query: 4 LIQYHQELRLMRRKCSDKGYHEKVKNPMSFDVVRWRLNPSHPEGYKTIV-------QFIS 56
L+ R +R G K+ +P D + ++ P + + S
Sbjct: 202 LMPLEDAQRFLRYGDQVTGLRLKLDDPFQADALAQQVEP-ELGPELYVRDWTDQNGELFS 260
Query: 57 DIRLI 61
I++
Sbjct: 261 AIQME 265
>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 = 26.9 bits (60), Expect = 1.5
Identities = 15/63 (23%), Positives = 28/63 (44%), Gaps = 3/63 (4%)
Query: 22 GYHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYAKTDQEYSDAKN 81
GYH V PM ++ + ++ +F D+ L+F+NA +Y + Y A
Sbjct: 35 GYHSVVYRPMDLSTIKKNIENGT---IRSTAEFQRDVLLMFQNAIMYNSSDHDVYLMAVE 91
Query: 82 LEE 84
++
Sbjct: 92 MQR 94
>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 = 26.6 bits (59), Expect = 2.3
Identities = 10/56 (17%), Positives = 27/56 (48%), Gaps = 3/56 (5%)
Query: 27 VKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYAKTDQEYSDAKNL 82
+ + ++ ++N E Y ++ +F +D L+ N +++ ++Y A+ L
Sbjct: 43 IHTHLDVADIQEKINS---EKYTSLEEFKADALLLLHNTAIFHGADSEQYDAARWL 95
>gnl|CDD|222172 pfam13490, zf-HC2, Putative zinc-finger. This is a putative
zinc-finger found in some anti-sigma factor proteins.
Length = 36
Score = 24.9 bits (55), Expect = 2.7
Identities = 11/27 (40%), Positives = 12/27 (44%), Gaps = 5/27 (18%)
Query: 91 EKWLPDYAYDDSLDGELSEPSAKRLRR 117
+ L Y LDGELSE RL
Sbjct: 5 RELLSAY-----LDGELSEEERARLEA 26
>gnl|CDD|227148 COG4811, COG4811, Predicted membrane protein [Function unknown].
Length = 152
Score = 25.8 bits (57), Expect = 4.4
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 2/33 (6%)
Query: 54 FISDIRLIFKNAFVYYAKTDQEYSDAK--NLEE 84
FI ++IFK ++A EY+ K NL E
Sbjct: 86 FIRVPKIIFKEKGFFFANVFIEYARIKAMNLSE 118
>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 = 25.4 bits (56), Expect = 5.4
Identities = 11/48 (22%), Positives = 19/48 (39%), Gaps = 3/48 (6%)
Query: 23 YHEKVKNPMSFDVVRWRLNPSHPEGYKTIVQFISDIRLIFKNAFVYYA 70
Y + V PM + + Y + F++D + I NA +Y
Sbjct: 35 YAQYVFKPMDLSTLEKNVRKKA---YGSTDAFLADAKWILHNAIIYNG 79
>gnl|CDD|217759 pfam03845, Spore_permease, Spore germination protein.
Length = 320
Score = 25.3 bits (56), Expect = 8.7
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 60 LIFKNAFVYYAKTDQEYSDAKNLEEYFEHMLEKWL 94
LI + Y K +++ + K L EY + +L KWL
Sbjct: 43 LIGLLLVLLYYKLLKKFPE-KTLIEYMKKILGKWL 76
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
0.319 0.136 0.410
Gapped
Lambda K H
0.267 0.0803 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,396,233
Number of extensions: 561757
Number of successful extensions: 657
Number of sequences better than 10.0: 1
Number of HSP's gapped: 633
Number of HSP's successfully gapped: 63
Length of query: 120
Length of database: 10,937,602
Length adjustment: 83
Effective length of query: 37
Effective length of database: 7,256,220
Effective search space: 268480140
Effective search space used: 268480140
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.1 bits)