RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1225
(256 letters)
>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 = 113 bits (286), Expect = 3e-32
Identities = 53/86 (61%), Positives = 64/86 (74%)
Query: 8 TEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFEN 67
+G L+EPFLKLP+KR PDYY+ IKNP SL I LK+G Y TL EL +LNLMFEN
Sbjct: 18 NQGQLLAEPFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFEN 77
Query: 68 AKKFNPADSRLYRDAVKLQKLMQRKV 93
AK++N +SR+Y+DA KLQKLMQ K
Sbjct: 78 AKRYNVPNSRIYKDAEKLQKLMQAKK 103
Score = 76.6 bits (189), Expect = 5e-18
Identities = 36/59 (61%), Positives = 43/59 (72%)
Query: 96 NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKV 154
NP SL I LK+G Y TL EL +LNLMFENAK++N +SR+Y+DA KLQKLMQ K
Sbjct: 45 NPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPNSRIYKDAEKLQKLMQAKK 103
Score = 57.3 bits (139), Expect = 7e-11
Identities = 30/71 (42%), Positives = 47/71 (66%), Gaps = 2/71 (2%)
Query: 130 KKFNPADSRLYRDAVKLQKLMQR-KVQEF-SLNELTGELSLMFENAKKFNPADLRLYRDA 187
K+ P + ++ + LQ++ + K E+ +L EL +L+LMFENAK++N + R+Y+DA
Sbjct: 33 KRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPNSRIYKDA 92
Query: 188 VKLQKLMQRKV 198
KLQKLMQ K
Sbjct: 93 EKLQKLMQAKK 103
>gnl|CDD|197636 smart00297, BROMO, bromo domain.
Length = 107
Score = 91.2 bits (227), Expect = 1e-23
Identities = 40/83 (48%), Positives = 57/83 (68%)
Query: 13 LSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFN 72
LS PFLK +++ PDYY IIK P L TI K L++G YS++ E + NLMF NA+ +N
Sbjct: 24 LSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYN 83
Query: 73 PADSRLYRDAVKLQKLMQRKVQE 95
DS +Y+DA KL+K ++K++E
Sbjct: 84 GPDSEVYKDAKKLEKFFEKKLRE 106
Score = 61.1 bits (149), Expect = 3e-12
Identities = 27/63 (42%), Positives = 42/63 (66%)
Query: 95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKV 154
+ P L TI K L++G YS++ E + NLMF NA+ +N DS +Y+DA KL+K ++K+
Sbjct: 45 KKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYNGPDSEVYKDAKKLEKFFEKKL 104
Query: 155 QEF 157
+E
Sbjct: 105 REL 107
Score = 42.7 bits (101), Expect = 2e-05
Identities = 19/57 (33%), Positives = 37/57 (64%), Gaps = 3/57 (5%)
Query: 148 KLMQRKVQEF---SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEV 201
K +++K++ S+ E + +LMF NA+ +N D +Y+DA KL+K ++K++E+
Sbjct: 51 KTIKKKLENGKYSSVEEFVADFNLMFSNARTYNGPDSEVYKDAKKLEKFFEKKLREL 107
>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 = 89.4 bits (222), Expect = 6e-23
Identities = 38/81 (46%), Positives = 53/81 (65%)
Query: 13 LSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFN 72
LSEPFL+ + PDYY +IKNP L TI K LK+G Y +L E ++ L+F NAK +N
Sbjct: 19 LSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYN 78
Query: 73 PADSRLYRDAVKLQKLMQRKV 93
S +Y+DA KL+KL ++ +
Sbjct: 79 GPGSPIYKDAKKLEKLFEKLL 99
Score = 61.6 bits (150), Expect = 2e-12
Identities = 27/64 (42%), Positives = 41/64 (64%)
Query: 91 RKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLM 150
+V +NP L TI K LK+G Y +L E ++ L+F NAK +N S +Y+DA KL+KL
Sbjct: 36 YEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGPGSPIYKDAKKLEKLF 95
Query: 151 QRKV 154
++ +
Sbjct: 96 EKLL 99
Score = 39.3 bits (92), Expect = 2e-04
Identities = 19/65 (29%), Positives = 36/65 (55%), Gaps = 6/65 (9%)
Query: 140 YRDAVKLQ---KLMQRKVQEF---SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKL 193
Y + +K +++K++ SL E ++ L+F NAK +N +Y+DA KL+KL
Sbjct: 35 YYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGPGSPIYKDAKKLEKL 94
Query: 194 MQRKV 198
++ +
Sbjct: 95 FEKLL 99
>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 = 87.4 bits (217), Expect = 5e-22
Identities = 36/93 (38%), Positives = 58/93 (62%), Gaps = 2/93 (2%)
Query: 5 KNQTEGGN--LSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELN 62
KN T+G LS F++LP+K PDYY +IK P + I ++ Y +L+++ +
Sbjct: 13 KNYTDGRGRRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFV 72
Query: 63 LMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE 95
LMF+NA K+N DS++Y+DA+ LQK++ +E
Sbjct: 73 LMFDNACKYNEPDSQIYKDALTLQKVLLETKRE 105
Score = 55.8 bits (135), Expect = 2e-10
Identities = 20/62 (32%), Positives = 38/62 (61%)
Query: 95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKV 154
+ P + I ++ Y +L+++ + LMF+NA K+N DS++Y+DA+ LQK++
Sbjct: 44 KKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYNEPDSQIYKDALTLQKVLLETK 103
Query: 155 QE 156
+E
Sbjct: 104 RE 105
Score = 43.4 bits (103), Expect = 6e-06
Identities = 19/54 (35%), Positives = 34/54 (62%), Gaps = 2/54 (3%)
Query: 147 QKLMQRKVQEFSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQE 200
K+ + Q SL+++ + LMF+NA K+N D ++Y+DA+ LQK++ +E
Sbjct: 54 SKIEGNQYQ--SLDDMVSDFVLMFDNACKYNEPDSQIYKDALTLQKVLLETKRE 105
>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 = 85.3 bits (212), Expect = 2e-21
Identities = 32/80 (40%), Positives = 50/80 (62%)
Query: 16 PFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPAD 75
PFL+ K PDYY +IK P L T+ + L++G+Y TL E +L L+F+N + +N D
Sbjct: 21 PFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPD 80
Query: 76 SRLYRDAVKLQKLMQRKVQE 95
+ Y+ A KL+K +K++E
Sbjct: 81 TEYYKCANKLEKFFWKKLKE 100
Score = 63.3 bits (155), Expect = 4e-13
Identities = 22/61 (36%), Positives = 38/61 (62%)
Query: 97 PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE 156
P L T+ + L++G+Y TL E +L L+F+N + +N D+ Y+ A KL+K +K++E
Sbjct: 41 PMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEYYKCANKLEKFFWKKLKE 100
Query: 157 F 157
Sbjct: 101 L 101
Score = 43.7 bits (104), Expect = 5e-06
Identities = 17/55 (30%), Positives = 32/55 (58%), Gaps = 3/55 (5%)
Query: 150 MQRKVQE---FSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEV 201
M+ K++ +L E +L L+F+N + +N D Y+ A KL+K +K++E+
Sbjct: 47 MEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEYYKCANKLEKFFWKKLKEL 101
>gnl|CDD|227408 COG5076, COG5076, Transcription factor involved in chromatin
remodeling, contains bromodomain [Chromatin structure
and dynamics / Transcription].
Length = 371
Score = 87.2 bits (216), Expect = 7e-20
Identities = 52/173 (30%), Positives = 75/173 (43%), Gaps = 12/173 (6%)
Query: 1 MRPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGE 60
+ Q +G LS FL LP+KR PDYY IIK+P LLTI K LK+G Y + E +
Sbjct: 153 FKKQLFLRDGRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSD 212
Query: 61 LNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNEL-- 118
LNLMF+N K +N DS +Y DA +L+K + ++E P +L + +
Sbjct: 213 LNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLIEEIPEEMLELSIKPGREEREERESVLI 272
Query: 119 ------TGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEFSLNELTGE 165
G + D Y ++ + K + N E
Sbjct: 273 TNSQAHVGAWPFL-RPVSDEEVPD---YYKDIRDPMDLSTKELKLRNNYYRPE 321
Score = 58.7 bits (142), Expect = 6e-10
Identities = 29/85 (34%), Positives = 45/85 (52%)
Query: 95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKV 154
++P LLTI K LK+G Y + E +LNLMF+N K +N DS +Y DA +L+K + +
Sbjct: 186 KSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLI 245
Query: 155 QEFSLNELTGELSLMFENAKKFNPA 179
+E L + E ++
Sbjct: 246 EEIPEEMLELSIKPGREEREERESV 270
Score = 36.7 bits (85), Expect = 0.008
Identities = 16/45 (35%), Positives = 27/45 (60%)
Query: 158 SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEVM 202
S E +L+LMF+N K +N D +Y DA +L+K + ++E+
Sbjct: 205 SFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLIEEIP 249
>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 = 80.7 bits (200), Expect = 1e-19
Identities = 38/87 (43%), Positives = 55/87 (63%), Gaps = 1/87 (1%)
Query: 1 MRPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGE 60
+R ++++ G L+ F KLP K P+YY+ I NP SL I K +K Y + ++ +
Sbjct: 13 LRKERDE-NGRLLTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLND 71
Query: 61 LNLMFENAKKFNPADSRLYRDAVKLQK 87
LNLMFENAK +N DS+ Y+DAV L+K
Sbjct: 72 LNLMFENAKLYNENDSQEYKDAVLLEK 98
Score = 53.4 bits (129), Expect = 2e-09
Identities = 26/54 (48%), Positives = 35/54 (64%)
Query: 95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQK 148
NP SL I K +K Y + ++ +LNLMFENAK +N DS+ Y+DAV L+K
Sbjct: 45 SNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYKDAVLLEK 98
Score = 36.4 bits (85), Expect = 0.002
Identities = 20/45 (44%), Positives = 31/45 (68%), Gaps = 2/45 (4%)
Query: 148 KLMQRKVQEFSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQK 192
K+ +RK + F ++ +L+LMFENAK +N D + Y+DAV L+K
Sbjct: 56 KVKRRKYKSF--DQFLNDLNLMFENAKLYNENDSQEYKDAVLLEK 98
>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 = 75.9 bits (187), Expect = 1e-17
Identities = 25/83 (30%), Positives = 51/83 (61%)
Query: 6 NQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMF 65
++G L+E F++LP+++ P+YY +I+ P I + +++ Y +L +L ++ L+
Sbjct: 17 KDSDGRQLAEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLC 76
Query: 66 ENAKKFNPADSRLYRDAVKLQKL 88
+NA+ FN S +Y D++ LQ +
Sbjct: 77 QNAQTFNLEGSLIYEDSIVLQSV 99
Score = 43.6 bits (103), Expect = 6e-06
Identities = 26/109 (23%), Positives = 52/109 (47%), Gaps = 9/109 (8%)
Query: 56 ELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRK-------VQENPRSLLTIGKTLK 108
ELT ++N + + K+ +D R + +L RK + P I + ++
Sbjct: 1 ELTKKMNKIVDVVIKYKDSDGRQLAEV--FIQLPSRKELPEYYELIRKPVDFKKIKERIR 58
Query: 109 SGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEF 157
+ Y +L +L ++ L+ +NA+ FN S +Y D++ LQ + + Q+
Sbjct: 59 NHKYRSLEDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFKSARQKI 107
Score = 30.5 bits (69), Expect = 0.27
Identities = 12/36 (33%), Positives = 22/36 (61%)
Query: 158 SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKL 193
SL +L ++ L+ +NA+ FN +Y D++ LQ +
Sbjct: 64 SLEDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSV 99
>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 = 75.5 bits (186), Expect = 1e-17
Identities = 34/84 (40%), Positives = 52/84 (61%)
Query: 9 EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
G LSE FL+ P+K+ PDYY IIK P +L I + ++ Y +L E + +LMF NA
Sbjct: 19 TGRKLSELFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANA 78
Query: 69 KKFNPADSRLYRDAVKLQKLMQRK 92
+ +N S +Y DAV+++K ++K
Sbjct: 79 RTYNQEGSIVYEDAVEMEKAFKKK 102
Score = 45.0 bits (107), Expect = 2e-06
Identities = 19/59 (32%), Positives = 35/59 (59%)
Query: 95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRK 153
+ P +L I + ++ Y +L E + +LMF NA+ +N S +Y DAV+++K ++K
Sbjct: 44 KRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYNQEGSIVYEDAVEMEKAFKKK 102
Score = 33.5 bits (77), Expect = 0.025
Identities = 15/40 (37%), Positives = 24/40 (60%)
Query: 158 SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRK 197
SL E + LMF NA+ +N +Y DAV+++K ++K
Sbjct: 63 SLEEFLEDFHLMFANARTYNQEGSIVYEDAVEMEKAFKKK 102
>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 = 75.2 bits (185), Expect = 2e-17
Identities = 34/80 (42%), Positives = 54/80 (67%)
Query: 13 LSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFN 72
+SE F KLP+K PDYY +IK P L TI + ++SG+Y ++ ++ +L+LM +NAK FN
Sbjct: 23 ISELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFN 82
Query: 73 PADSRLYRDAVKLQKLMQRK 92
S++Y+DA ++K+ K
Sbjct: 83 EPGSQVYKDANAIKKIFTAK 102
Score = 49.4 bits (118), Expect = 6e-08
Identities = 22/61 (36%), Positives = 40/61 (65%)
Query: 93 VQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQR 152
V + P L TI + ++SG+Y ++ ++ +L+LM +NAK FN S++Y+DA ++K+
Sbjct: 42 VIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFNEPGSQVYKDANAIKKIFTA 101
Query: 153 K 153
K
Sbjct: 102 K 102
Score = 31.6 bits (72), Expect = 0.11
Identities = 16/53 (30%), Positives = 31/53 (58%), Gaps = 3/53 (5%)
Query: 148 KLMQRKVQEF---SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRK 197
K + +++Q S+ ++ +L LM +NAK FN ++Y+DA ++K+ K
Sbjct: 50 KTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFNEPGSQVYKDANAIKKIFTAK 102
>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 = 73.5 bits (181), Expect = 9e-17
Identities = 33/95 (34%), Positives = 54/95 (56%), Gaps = 1/95 (1%)
Query: 1 MRPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGE 60
+R K+ +G L E F+++P +R P+YY ++ NP LL I + LK+ Y +++LT +
Sbjct: 14 IRNYKS-EDGRILCESFIRVPKRRNEPEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTAD 72
Query: 61 LNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE 95
L+ NAK + DS ++DA KL +L E
Sbjct: 73 FELLINNAKAYYKPDSPEHKDACKLWELFLSARNE 107
Score = 48.5 bits (116), Expect = 1e-07
Identities = 23/65 (35%), Positives = 34/65 (52%)
Query: 93 VQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQR 152
V NP LL I + LK+ Y +++LT + L+ NAK + DS ++DA KL +L
Sbjct: 44 VVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYKPDSPEHKDACKLWELFLS 103
Query: 153 KVQEF 157
E
Sbjct: 104 ARNEV 108
Score = 36.5 bits (85), Expect = 0.002
Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 6/69 (8%)
Query: 140 YRDAVK----LQKLMQR-KVQEF-SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKL 193
Y + V L K+ Q+ K +E+ +++LT + L+ NAK + D ++DA KL +L
Sbjct: 41 YYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYKPDSPEHKDACKLWEL 100
Query: 194 MQRKVQEVM 202
EV+
Sbjct: 101 FLSARNEVL 109
>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 = 72.4 bits (178), Expect = 1e-16
Identities = 33/72 (45%), Positives = 44/72 (61%)
Query: 13 LSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFN 72
L+EPFL+ PDYY +IK P L TI + LKSG Y +L E ++ L+F NA +N
Sbjct: 13 LAEPFLEPVDPEEYPDYYEVIKEPMDLSTIRQKLKSGKYKSLAEFLKDVELIFSNAITYN 72
Query: 73 PADSRLYRDAVK 84
DS +Y+DA K
Sbjct: 73 GEDSDIYKDAKK 84
Score = 50.9 bits (122), Expect = 1e-08
Identities = 22/51 (43%), Positives = 31/51 (60%)
Query: 95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVK 145
+ P L TI + LKSG Y +L E ++ L+F NA +N DS +Y+DA K
Sbjct: 34 KEPMDLSTIRQKLKSGKYKSLAEFLKDVELIFSNAITYNGEDSDIYKDAKK 84
Score = 31.6 bits (72), Expect = 0.065
Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 6/56 (10%)
Query: 140 YRDAVKLQ---KLMQRKVQEF---SLNELTGELSLMFENAKKFNPADLRLYRDAVK 189
Y + +K +++K++ SL E ++ L+F NA +N D +Y+DA K
Sbjct: 29 YYEVIKEPMDLSTIRQKLKSGKYKSLAEFLKDVELIFSNAITYNGEDSDIYKDAKK 84
>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 = 68.6 bits (168), Expect = 5e-15
Identities = 32/84 (38%), Positives = 51/84 (60%)
Query: 10 GGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAK 69
G L + F++ P+K+ PDYY+II P L TI +++ Y+T EL + LMF NA+
Sbjct: 20 GRRLCDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNAR 79
Query: 70 KFNPADSRLYRDAVKLQKLMQRKV 93
+N S++Y DA L+K+++ K
Sbjct: 80 HYNEEGSQVYEDANILEKVLKEKR 103
Score = 47.4 bits (113), Expect = 3e-07
Identities = 22/63 (34%), Positives = 36/63 (57%)
Query: 92 KVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQ 151
K+ P L TI +++ Y+T EL + LMF NA+ +N S++Y DA L+K+++
Sbjct: 41 KIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYNEEGSQVYEDANILEKVLK 100
Query: 152 RKV 154
K
Sbjct: 101 EKR 103
Score = 32.0 bits (73), Expect = 0.066
Identities = 14/40 (35%), Positives = 23/40 (57%)
Query: 159 LNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKV 198
EL + LMF NA+ +N ++Y DA L+K+++ K
Sbjct: 64 EEELMDDFKLMFRNARHYNEEGSQVYEDANILEKVLKEKR 103
>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 = 67.4 bits (165), Expect = 2e-14
Identities = 30/79 (37%), Positives = 47/79 (59%)
Query: 10 GGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAK 69
G +L+ PF+ LP+K+ NPDYY I +P L TI K + +G+Y T ++ +F NA+
Sbjct: 22 GQSLAIPFINLPSKKKNPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAE 81
Query: 70 KFNPADSRLYRDAVKLQKL 88
K+ S + RD +L+K
Sbjct: 82 KYYGRKSPIGRDVCRLRKA 100
Score = 39.7 bits (93), Expect = 2e-04
Identities = 17/54 (31%), Positives = 29/54 (53%)
Query: 96 NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKL 149
+P L TI K + +G+Y T ++ +F NA+K+ S + RD +L+K
Sbjct: 47 DPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYYGRKSPIGRDVCRLRKA 100
>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 = 64.6 bits (158), Expect = 2e-13
Identities = 31/87 (35%), Positives = 47/87 (54%), Gaps = 4/87 (4%)
Query: 12 NLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLK---SGHYSTLNELTGELNLMFENA 68
LS PF + P P+YY+IIK P L I K L+ HYS+ E ++ LMF+N
Sbjct: 20 ELSLPFHE-PVSPSVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNC 78
Query: 69 KKFNPADSRLYRDAVKLQKLMQRKVQE 95
KFN DS + + +L+ + +++E
Sbjct: 79 YKFNEEDSEVAQAGKELELFFEEQLKE 105
Score = 46.1 bits (110), Expect = 9e-07
Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 3/65 (4%)
Query: 96 NPRSLLTIGKTLK---SGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQR 152
P L I K L+ HYS+ E ++ LMF+N KFN DS + + +L+ +
Sbjct: 42 TPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYKFNEEDSEVAQAGKELELFFEE 101
Query: 153 KVQEF 157
+++E
Sbjct: 102 QLKEI 106
Score = 33.4 bits (77), Expect = 0.029
Identities = 15/60 (25%), Positives = 31/60 (51%), Gaps = 6/60 (10%)
Query: 148 KLMQRKVQE------FSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEV 201
L+++K+Q S E ++ LMF+N KFN D + + +L+ + +++E+
Sbjct: 47 SLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYKFNEEDSEVAQAGKELELFFEEQLKEI 106
>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 = 63.4 bits (155), Expect = 5e-13
Identities = 27/87 (31%), Positives = 43/87 (49%)
Query: 14 SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
S PF K+ PDYY+IIK P L TI K + Y + E ++ L+ +N+ +N
Sbjct: 18 SWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNG 77
Query: 74 ADSRLYRDAVKLQKLMQRKVQENPRSL 100
DS + A ++ +L + + E L
Sbjct: 78 PDSVYTKKAKEMLELAEELLAEREEKL 104
Score = 39.9 bits (94), Expect = 2e-04
Identities = 16/66 (24%), Positives = 32/66 (48%)
Query: 92 KVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQ 151
K+ + P L TI K + Y + E ++ L+ +N+ +N DS + A ++ +L +
Sbjct: 35 KIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSVYTKKAKEMLELAE 94
Query: 152 RKVQEF 157
+ E
Sbjct: 95 ELLAER 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 = 62.7 bits (153), Expect = 8e-13
Identities = 30/85 (35%), Positives = 46/85 (54%), Gaps = 2/85 (2%)
Query: 9 EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
G + F LP ++ PDYY+IIKNP SL T+ K L HY+ E +L + NA
Sbjct: 20 NGIEIHPIFNVLPLRKDYPDYYKIIKNPLSLNTVKKRLP--HYTNAQEFVNDLAQIPWNA 77
Query: 69 KKFNPADSRLYRDAVKLQKLMQRKV 93
+ +N S +Y+ A+ L+K + +
Sbjct: 78 RLYNTKGSVIYKYALILEKYINDVI 102
Score = 38.8 bits (91), Expect = 3e-04
Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 2/63 (3%)
Query: 92 KVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQ 151
K+ +NP SL T+ K L HY+ E +L + NA+ +N S +Y+ A+ L+K +
Sbjct: 42 KIIKNPLSLNTVKKRLP--HYTNAQEFVNDLAQIPWNARLYNTKGSVIYKYALILEKYIN 99
Query: 152 RKV 154
+
Sbjct: 100 DVI 102
>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 = 9e-13
Identities = 28/70 (40%), Positives = 37/70 (52%)
Query: 14 SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
S PFL +KR PDYY IIK P L T+ K LK+ Y + E +LNL+++N +N
Sbjct: 26 STPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYNS 85
Query: 74 ADSRLYRDAV 83
S R
Sbjct: 86 DPSHPLRRHA 95
Score = 37.0 bits (86), Expect = 0.002
Identities = 19/76 (25%), Positives = 31/76 (40%), Gaps = 11/76 (14%)
Query: 69 KKFNPADSRLYRDAVKLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFEN 128
K + ++ Y D +K P L T+ K LK+ Y + E +LNL+++N
Sbjct: 31 TKVSKREAPDYYDIIK-----------KPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKN 79
Query: 129 AKKFNPADSRLYRDAV 144
+N S R
Sbjct: 80 CLLYNSDPSHPLRRHA 95
>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 = 61.9 bits (151), Expect = 1e-12
Identities = 25/66 (37%), Positives = 37/66 (56%)
Query: 27 PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ 86
DY+ IIK+P L TI K L + Y+ E ++ LMF N K+NP D ++ A KLQ
Sbjct: 36 HDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKLQ 95
Query: 87 KLMQRK 92
+ + +
Sbjct: 96 DVFEDR 101
Score = 46.5 bits (111), Expect = 5e-07
Identities = 20/62 (32%), Positives = 33/62 (53%)
Query: 92 KVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQ 151
+ ++P L TI K L + Y+ E ++ LMF N K+NP D ++ A KLQ + +
Sbjct: 40 DIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKLQDVFE 99
Query: 152 RK 153
+
Sbjct: 100 DR 101
Score = 29.9 bits (68), Expect = 0.36
Identities = 13/40 (32%), Positives = 21/40 (52%)
Query: 158 SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRK 197
E ++ LMF N K+NP D ++ A KLQ + + +
Sbjct: 62 DAQEFAADVRLMFSNCYKYNPPDHPVHAMARKLQDVFEDR 101
>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 = 62.4 bits (152), Expect = 1e-12
Identities = 28/82 (34%), Positives = 44/82 (53%)
Query: 14 SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
S PFL+ +K PDYY IIK P L TI + L G Y E ++ L+F N +NP
Sbjct: 30 SWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNP 89
Query: 74 ADSRLYRDAVKLQKLMQRKVQE 95
+ +Y+ +LQ+ ++ ++
Sbjct: 90 EHTSVYKAGTRLQRFFIKRCRK 111
Score = 40.5 bits (95), Expect = 9e-05
Identities = 17/65 (26%), Positives = 31/65 (47%)
Query: 96 NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQ 155
P L TI + L G Y E ++ L+F N +NP + +Y+ +LQ+ ++ +
Sbjct: 51 KPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHTSVYKAGTRLQRFFIKRCR 110
Query: 156 EFSLN 160
+ L
Sbjct: 111 KLGLP 115
Score = 26.6 bits (59), Expect = 6.3
Identities = 9/43 (20%), Positives = 21/43 (48%)
Query: 158 SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQE 200
E ++ L+F N +NP +Y+ +LQ+ ++ ++
Sbjct: 69 LAEEFLSDIQLVFSNCFLYNPEHTSVYKAGTRLQRFFIKRCRK 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 = 59.6 bits (145), Expect = 1e-11
Identities = 27/83 (32%), Positives = 43/83 (51%), Gaps = 2/83 (2%)
Query: 12 NLSEPFLKLP-AKRYN-PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAK 69
+ PFL N P+Y+ IIK P L TI K L++G Y + E ++ L+F+N
Sbjct: 19 AYNWPFLDPVDPVALNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCY 78
Query: 70 KFNPADSRLYRDAVKLQKLMQRK 92
FNP + +Y +L+++ K
Sbjct: 79 TFNPEGTDVYMMGHQLEEVFNDK 101
Score = 44.2 bits (105), Expect = 4e-06
Identities = 18/62 (29%), Positives = 33/62 (53%)
Query: 92 KVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQ 151
+ + P L TI K L++G Y + E ++ L+F+N FNP + +Y +L+++
Sbjct: 40 SIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTDVYMMGHQLEEVFN 99
Query: 152 RK 153
K
Sbjct: 100 DK 101
Score = 30.3 bits (69), Expect = 0.32
Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 148 KLMQRKVQEFSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRK 197
KL + Q S E ++ L+F+N FNP +Y +L+++ K
Sbjct: 54 KLQNGQYQ--SAKEFERDVRLIFKNCYTFNPEGTDVYMMGHQLEEVFNDK 101
>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 = 58.5 bits (142), Expect = 2e-11
Identities = 28/81 (34%), Positives = 41/81 (50%), Gaps = 2/81 (2%)
Query: 14 SEPFLKL--PAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKF 71
+ PFL P K P Y IIK P L TI + LKS Y+++ E T + NLM +N F
Sbjct: 22 ARPFLVPVDPVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTF 81
Query: 72 NPADSRLYRDAVKLQKLMQRK 92
N + + + +LQ ++
Sbjct: 82 NGPEHPVSQMGKRLQAAFEKH 102
Score = 45.8 bits (109), Expect = 1e-06
Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 3/82 (3%)
Query: 75 DSRLYR---DAVKLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKK 131
D+R + D VKL + + P L TI + LKS Y+++ E T + NLM +N
Sbjct: 21 DARPFLVPVDPVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLT 80
Query: 132 FNPADSRLYRDAVKLQKLMQRK 153
FN + + + +LQ ++
Sbjct: 81 FNGPEHPVSQMGKRLQAAFEKH 102
Score = 26.5 bits (59), Expect = 5.5
Identities = 12/51 (23%), Positives = 26/51 (50%), Gaps = 3/51 (5%)
Query: 150 MQRKVQEF---SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRK 197
++RK++ S+ E T + +LM +N FN + + + +LQ ++
Sbjct: 52 IERKLKSNVYTSVEEFTADFNLMVDNCLTFNGPEHPVSQMGKRLQAAFEKH 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 = 57.0 bits (138), Expect = 8e-11
Identities = 27/77 (35%), Positives = 43/77 (55%)
Query: 16 PFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPAD 75
PFL+ + P Y +IIK P TI + L+SG Y TL E ++ L+F+N + FN D
Sbjct: 20 PFLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDD 79
Query: 76 SRLYRDAVKLQKLMQRK 92
S + R ++K +++
Sbjct: 80 SEVGRAGHNMRKFFEKR 96
Score = 45.1 bits (107), Expect = 1e-06
Identities = 21/63 (33%), Positives = 36/63 (57%)
Query: 91 RKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLM 150
RK+ + P TI + L+SG Y TL E ++ L+F+N + FN DS + R ++K
Sbjct: 34 RKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSEVGRAGHNMRKFF 93
Query: 151 QRK 153
+++
Sbjct: 94 EKR 96
>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 = 54.8 bits (132), Expect = 6e-10
Identities = 28/82 (34%), Positives = 47/82 (57%), Gaps = 2/82 (2%)
Query: 14 SEPFLK-LPAKRYN-PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKF 71
S PF + + K PDY+ I+KNP L TI + L +G Y + ++ LMF+NA +
Sbjct: 22 SLPFRQPVDPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLY 81
Query: 72 NPADSRLYRDAVKLQKLMQRKV 93
N SR+Y+ KL ++ ++++
Sbjct: 82 NRKTSRVYKYCTKLAEVFEQEI 103
Score = 39.3 bits (92), Expect = 2e-04
Identities = 21/74 (28%), Positives = 38/74 (51%)
Query: 81 DAVKLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLY 140
D L + +NP L TI + L +G Y + ++ LMF+NA +N SR+Y
Sbjct: 30 DPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYNRKTSRVY 89
Query: 141 RDAVKLQKLMQRKV 154
+ KL ++ ++++
Sbjct: 90 KYCTKLAEVFEQEI 103
Score = 29.3 bits (66), Expect = 0.69
Identities = 12/35 (34%), Positives = 22/35 (62%)
Query: 168 LMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEVM 202
LMF+NA +N R+Y+ KL ++ ++++ VM
Sbjct: 73 LMFDNAWLYNRKTSRVYKYCTKLAEVFEQEIDPVM 107
>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 = 54.8 bits (132), Expect = 9e-10
Identities = 27/81 (33%), Positives = 41/81 (50%), Gaps = 1/81 (1%)
Query: 14 SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
SEPF + PDY II P L T+ +TL G+Y E ++ L+F N+K + P
Sbjct: 23 SEPFRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYTP 82
Query: 74 -ADSRLYRDAVKLQKLMQRKV 93
SR+Y ++L L + +
Sbjct: 83 NKRSRIYSMTLRLSALFEEHI 103
Score = 44.8 bits (106), Expect = 4e-06
Identities = 28/98 (28%), Positives = 48/98 (48%), Gaps = 12/98 (12%)
Query: 61 LNLMF--ENAKKF-NPADSRLYRDAVKLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNE 117
+NLM+ E+++ F P D Y D R + + P L T+ +TL G+Y E
Sbjct: 14 VNLMWDCEDSEPFRQPVDLLKYPD--------YRDIIDTPMDLGTVKETLFGGNYDDPME 65
Query: 118 LTGELNLMFENAKKFNP-ADSRLYRDAVKLQKLMQRKV 154
++ L+F N+K + P SR+Y ++L L + +
Sbjct: 66 FAKDVRLIFSNSKSYTPNKRSRIYSMTLRLSALFEEHI 103
>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 = 54.3 bits (131), Expect = 1e-09
Identities = 24/62 (38%), Positives = 37/62 (59%)
Query: 27 PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ 86
PDY+ IIK P L T+ K L+ G YS+ E ++ L F NA ++NP + ++ A +L
Sbjct: 33 PDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVHTMAKELL 92
Query: 87 KL 88
K+
Sbjct: 93 KI 94
Score = 40.8 bits (96), Expect = 5e-05
Identities = 21/69 (30%), Positives = 35/69 (50%)
Query: 81 DAVKLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLY 140
D V L + + P L T+ K L+ G YS+ E ++ L F NA ++NP + ++
Sbjct: 26 DVVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVH 85
Query: 141 RDAVKLQKL 149
A +L K+
Sbjct: 86 TMAKELLKI 94
>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 = 52.8 bits (127), Expect = 3e-09
Identities = 23/60 (38%), Positives = 32/60 (53%)
Query: 27 PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ 86
PDY IK P T+ K L+S Y TL + + NL+ N +N D+ YR AV+L+
Sbjct: 32 PDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKDTIFYRAAVRLR 91
Score = 41.6 bits (98), Expect = 3e-05
Identities = 18/51 (35%), Positives = 27/51 (52%)
Query: 97 PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ 147
P T+ K L+S Y TL + + NL+ N +N D+ YR AV+L+
Sbjct: 41 PMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKDTIFYRAAVRLR 91
Score = 30.1 bits (68), Expect = 0.29
Identities = 12/45 (26%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 150 MQRKVQEF---SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQ 191
M++K++ +L + + +L+ N +N D YR AV+L+
Sbjct: 47 MRKKLESQRYRTLEDFEADFNLIINNCLAYNAKDTIFYRAAVRLR 91
>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 = 52.8 bits (127), Expect = 4e-09
Identities = 24/69 (34%), Positives = 38/69 (55%)
Query: 27 PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ 86
PDY++IIK P L TI K L++ +Y + +E + N MF N +N + A L+
Sbjct: 38 PDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKPGDDVVLMAQTLE 97
Query: 87 KLMQRKVQE 95
KL +K+ +
Sbjct: 98 KLFLQKLAQ 106
Score = 43.2 bits (102), Expect = 1e-05
Identities = 24/76 (31%), Positives = 38/76 (50%)
Query: 81 DAVKLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLY 140
DAVKL K+ + P L TI K L++ +Y + +E + N MF N +N +
Sbjct: 31 DAVKLNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKPGDDVV 90
Query: 141 RDAVKLQKLMQRKVQE 156
A L+KL +K+ +
Sbjct: 91 LMAQTLEKLFLQKLAQ 106
>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 = 47.1 bits (112), Expect = 3e-07
Identities = 20/63 (31%), Positives = 31/63 (49%)
Query: 14 SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
S PF + DY ++I NP L T+ G YS++ E ++ L+F NA+K+
Sbjct: 18 SWPFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYE 77
Query: 74 ADS 76
S
Sbjct: 78 NGS 80
Score = 32.5 bits (74), Expect = 0.051
Identities = 16/47 (34%), Positives = 25/47 (53%)
Query: 91 RKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADS 137
+KV NP L T+ G YS++ E ++ L+F NA+K+ S
Sbjct: 34 KKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGS 80
>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 = 46.6 bits (111), Expect = 5e-07
Identities = 22/59 (37%), Positives = 33/59 (55%)
Query: 27 PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKL 85
P Y IIK+P T+ + +K+ Y ++ E + LM ENA K+N D+ Y+ A KL
Sbjct: 32 PGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDTIYYKAAKKL 90
Score = 34.7 bits (80), Expect = 0.007
Identities = 17/51 (33%), Positives = 28/51 (54%)
Query: 96 NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKL 146
+P T+ + +K+ Y ++ E + LM ENA K+N D+ Y+ A KL
Sbjct: 40 HPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDTIYYKAAKKL 90
Score = 29.3 bits (66), Expect = 0.64
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 3/44 (6%)
Query: 150 MQRKVQEF---SLNELTGELSLMFENAKKFNPADLRLYRDAVKL 190
M+ K++ S+ E + LM ENA K+N D Y+ A KL
Sbjct: 47 MKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDTIYYKAAKKL 90
>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 = 45.0 bits (107), Expect = 3e-06
Identities = 19/49 (38%), Positives = 28/49 (57%)
Query: 27 PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPAD 75
PDYY IIK P L TI + L + Y T + +++L+ NA ++NP
Sbjct: 34 PDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPDR 82
Score = 30.4 bits (69), Expect = 0.31
Identities = 12/46 (26%), Positives = 24/46 (52%)
Query: 91 RKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPAD 136
++ + P L TI + L + Y T + +++L+ NA ++NP
Sbjct: 37 YEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPDR 82
>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 = 41.2 bits (97), Expect = 4e-05
Identities = 23/73 (31%), Positives = 40/73 (54%)
Query: 14 SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
+ FLK + P Y+ ++ P L TI K +++G + E ++ LMF+NA +N
Sbjct: 21 ASVFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNS 80
Query: 74 ADSRLYRDAVKLQ 86
+D +Y AV++Q
Sbjct: 81 SDHDVYLMAVEMQ 93
Score = 31.6 bits (72), Expect = 0.097
Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 6/66 (9%)
Query: 97 PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKV-- 154
P L TI K +++G + E ++ LMF+NA +N +D +Y A MQR+V
Sbjct: 43 PMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNSSDHDVYLMA----VEMQREVMS 98
Query: 155 QEFSLN 160
Q L
Sbjct: 99 QIQQLL 104
>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 = 38.1 bits (89), Expect = 7e-04
Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 2/79 (2%)
Query: 9 EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
EG S+ +LP + + I P +L I + + G Y L++ ++ + E A
Sbjct: 22 EGRCYSDSLAELPELAVDGVGPKKI--PLTLDIIKRNVDKGRYRRLDKFQEDMFEVLERA 79
Query: 69 KKFNPADSRLYRDAVKLQK 87
++ + DS +Y DAV+LQ+
Sbjct: 80 RRLSRTDSEIYEDAVELQQ 98
Score = 36.2 bits (84), Expect = 0.003
Identities = 16/55 (29%), Positives = 32/55 (58%)
Query: 94 QENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQK 148
++ P +L I + + G Y L++ ++ + E A++ + DS +Y DAV+LQ+
Sbjct: 44 KKIPLTLDIIKRNVDKGRYRRLDKFQEDMFEVLERARRLSRTDSEIYEDAVELQQ 98
Score = 26.2 bits (58), Expect = 9.2
Identities = 9/23 (39%), Positives = 15/23 (65%)
Query: 170 FENAKKFNPADLRLYRDAVKLQK 192
E A++ + D +Y DAV+LQ+
Sbjct: 76 LERARRLSRTDSEIYEDAVELQQ 98
>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 = 36.9 bits (86), Expect = 0.002
Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 2/77 (2%)
Query: 15 EPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPA 74
E + L A PDY+ + P L TI L++ +Y +L L ++ L+ NA+ FN
Sbjct: 49 EYPVDLRAW--YPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEP 106
Query: 75 DSRLYRDAVKLQKLMQR 91
+S + + A +L + R
Sbjct: 107 NSEIAKKAKRLSDWLLR 123
Score = 28.1 bits (63), Expect = 2.7
Identities = 17/58 (29%), Positives = 30/58 (51%)
Query: 95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQR 152
P L TI L++ +Y +L L ++ L+ NA+ FN +S + + A +L + R
Sbjct: 66 PVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEPNSEIAKKAKRLSDWLLR 123
>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 = 35.1 bits (81), Expect = 0.005
Identities = 18/65 (27%), Positives = 30/65 (46%)
Query: 14 SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
+EPFLK PDY + + P L T+ K ++ Y + + + + NA +N
Sbjct: 20 AEPFLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYNG 79
Query: 74 ADSRL 78
D +L
Sbjct: 80 GDHKL 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 = 34.7 bits (80), Expect = 0.010
Identities = 20/79 (25%), Positives = 36/79 (45%), Gaps = 5/79 (6%)
Query: 25 YNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVK 84
Y DY + IK P L + + L Y T+ ++ L+F N K F D D +
Sbjct: 29 YIRDYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKDD-----DFGQ 83
Query: 85 LQKLMQRKVQENPRSLLTI 103
+ +++K ++N + + I
Sbjct: 84 VGITLEKKFEKNFKEVFAI 102
>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 = 32.8 bits (75), Expect = 0.054
Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 2/46 (4%)
Query: 14 SEPFLKL--PAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNEL 57
+ PFL+ P +R PDY +IK P S T + L +L
Sbjct: 21 AWPFLEPVNPPRRGAPDYRDVIKRPMSFGTKVNNIVETGARDLEDL 66
>gnl|CDD|212688 cd11738, HSPA4L_NBD, Nucleotide-binding domain of HSPA4L. Human
HSPA4L (also known as 70-kDa heat shock protein 4-like,
APG-1, HSPH3, and OSP94; the human HSPA4L gene maps to
4q28) is expressed ubiquitously and predominantly in the
testis. It is required for normal spermatogenesis and
plays a role in osmotolerance. HSPA4L belongs to the
105/110 kDa heat shock protein (HSP105/110) subfamily of
the HSP70-like family. HSP105/110s are believed to
function generally as co-chaperones of HSP70 chaperones,
acting as nucleotide exchange factors (NEFs), to remove
ADP from their HSP70 chaperone partners during the ATP
hydrolysis cycle. HSP70 chaperones assist in protein
folding and assembly, and can direct incompetent
"client" proteins towards degradation. Like HSP70
chaperones, HSP105/110s have an N-terminal
nucleotide-binding domain (NBD) and a C-terminal
substrate-binding domain (SBD). For HSP70 chaperones,
the nucleotide sits in a deep cleft formed between the
two lobes of the NBD. The two subdomains of each lobe
change conformation between ATP-bound, ADP-bound, and
nucleotide-free states. ATP binding opens up the
substrate-binding site; substrate-binding increases the
rate of ATP hydrolysis. Hsp70 chaperone activity is also
regulated by J-domain proteins.
Length = 383
Score = 28.5 bits (63), Expect = 3.7
Identities = 16/37 (43%), Positives = 24/37 (64%), Gaps = 1/37 (2%)
Query: 172 NAKKFNPADLRLYRDAVKLQKLMQRKVQEVMILDIEC 208
N K+ + A LRLY++ KL+KLM + + L+IEC
Sbjct: 254 NVKENSRALLRLYQECEKLKKLMSANASD-LPLNIEC 289
>gnl|CDD|234635 PRK00104, scpA, segregation and condensation protein A; Reviewed.
Length = 242
Score = 27.9 bits (63), Expect = 5.0
Identities = 10/49 (20%), Positives = 21/49 (42%)
Query: 113 STLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEFSLNE 161
TL +L + + E K P +++ RD K++ M ++ +
Sbjct: 142 VTLLDLFLAFSKLMERKKANKPRHTKIERDEYKIEDRMLYILELLESKK 190
>gnl|CDD|237869 PRK14962, PRK14962, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 472
Score = 27.4 bits (61), Expect = 8.4
Identities = 15/66 (22%), Positives = 27/66 (40%), Gaps = 1/66 (1%)
Query: 88 LMQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFEN-AKKFNPADSRLYRDAVKL 146
L +V+E+ + + K+ HY + E EL +F K + RL
Sbjct: 398 LSLSEVEEDGDKVKISFDSSKAMHYELMKEKLPELENLFSRKLGKNVEVELRLMGKEETE 457
Query: 147 QKLMQR 152
K++Q+
Sbjct: 458 DKVLQK 463
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
0.316 0.133 0.370
Gapped
Lambda K H
0.267 0.0710 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,827,898
Number of extensions: 1202852
Number of successful extensions: 1166
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1159
Number of HSP's successfully gapped: 117
Length of query: 256
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 161
Effective length of database: 6,723,972
Effective search space: 1082559492
Effective search space used: 1082559492
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (26.2 bits)