RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5115
(171 letters)
>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 = 145 bits (367), Expect = 9e-46
Identities = 48/98 (48%), Positives = 71/98 (72%)
Query: 64 DFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSE 123
+ L+K++ ++ HKSAWPF+EPVD EAPDYY+V+K+PMDL T+E ++ Y L E
Sbjct: 2 LYTQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEE 61
Query: 124 FIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
F+ D+ IFDNCR YN ++ ++K A++LE FF +K+K
Sbjct: 62 FVADLKLIFDNCRLYNGPDTEYYKCANKLEKFFWKKLK 99
>gnl|CDD|197636 smart00297, BROMO, bromo domain.
Length = 107
Score = 107 bits (269), Expect = 8e-31
Identities = 40/98 (40%), Positives = 66/98 (67%)
Query: 66 ESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFI 125
E L+ ++ ++ +H +WPF++PV EAPDYY+++K+PMDLKTI+ ++ +Y + EF+
Sbjct: 10 ELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFV 69
Query: 126 GDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKIL 163
D +F N R YN +S +K A +LE FF +K++ L
Sbjct: 70 ADFNLMFSNARTYNGPDSEVYKDAKKLEKFFEKKLREL 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 = 103 bits (259), Expect = 2e-29
Identities = 42/97 (43%), Positives = 58/97 (59%), Gaps = 2/97 (2%)
Query: 66 ESLRKLMKQIQAH--KSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSE 123
+ LR L+ ++ + PF+EPVDP EAPDYY V+K PMDL TI+ ++ YK L E
Sbjct: 3 KKLRSLLDALKKLKRDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEE 62
Query: 124 FIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKV 160
F D+ IF N + YN SP +K A +LE F + +
Sbjct: 63 FEADVRLIFSNAKTYNGPGSPIYKDAKKLEKLFEKLL 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 = 94.0 bits (234), Expect = 2e-25
Identities = 38/96 (39%), Positives = 61/96 (63%)
Query: 68 LRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGD 127
L +L+ +I HK +WPF+ PV E PDYY+++K+PMDL TI+ ++ YK EF+ D
Sbjct: 17 LEQLLVEIVKHKDSWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSD 76
Query: 128 MTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKIL 163
+ +F NC YNP + +K +L+ FF+++ + L
Sbjct: 77 IQLVFSNCFLYNPEHTSVYKAGTRLQRFFIKRCRKL 112
>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 = 88.6 bits (220), Expect = 1e-23
Identities = 33/93 (35%), Positives = 53/93 (56%)
Query: 64 DFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSE 123
D ++ +++AH+ AWPF+EPV+ P Y ++K+PMD TI ++ +YK L E
Sbjct: 1 DLALCETILDEMEAHEDAWPFLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEE 60
Query: 124 FIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFF 156
F D+ +FDNC +N +S + H + FF
Sbjct: 61 FAEDVRLVFDNCETFNEDDSEVGRAGHNMRKFF 93
>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 = 85.4 bits (212), Expect = 3e-22
Identities = 33/90 (36%), Positives = 53/90 (58%)
Query: 81 AWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNP 140
+WPF PV+ + PDYY ++K PMDL+TI +I++ +Y+ EF+ D+ I DN YN
Sbjct: 18 SWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNG 77
Query: 141 RESPFFKHAHQLEMFFVQKVKILREKLVEL 170
+S + K A ++ + + EKL +L
Sbjct: 78 PDSVYTKKAKEMLELAEELLAEREEKLTQL 107
>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 = 84.8 bits (210), Expect = 3e-22
Identities = 37/84 (44%), Positives = 53/84 (63%)
Query: 68 LRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGD 127
++++ + H A PF+EPVDP E PDYY V+KEPMDL TI ++ +YK L+EF+ D
Sbjct: 1 CLEILEDLMEHPLAEPFLEPVDPEEYPDYYEVIKEPMDLSTIRQKLKSGKYKSLAEFLKD 60
Query: 128 MTKIFDNCRYYNPRESPFFKHAHQ 151
+ IF N YN +S +K A +
Sbjct: 61 VELIFSNAITYNGEDSDIYKDAKK 84
>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 = 83.5 bits (207), Expect = 1e-21
Identities = 34/92 (36%), Positives = 49/92 (53%), Gaps = 7/92 (7%)
Query: 67 SLRKLMKQIQAHKSAWPFMEPVDPH--EAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEF 124
LRKLMK HK W F PVD PDY++++K+PMDL T++ ++ + Y EF
Sbjct: 8 LLRKLMK----HKWGWVFNAPVDVVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEF 63
Query: 125 IGDMTKIFDNCRYYNPRESPFFKHAHQL-EMF 155
D+ F N YNP + A +L ++F
Sbjct: 64 AADVRLTFANAMRYNPPGNDVHTMAKELLKIF 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 = 81.6 bits (202), Expect = 8e-21
Identities = 35/95 (36%), Positives = 54/95 (56%), Gaps = 5/95 (5%)
Query: 68 LRKLMKQIQAHKS-AWPFMEPVDPH--EAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEF 124
L++L + HK+ AWPF +PVDP DY++++K PMDL TI+ ++ + Y EF
Sbjct: 9 LKELFSK--KHKAYAWPFYKPVDPEALGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEF 66
Query: 125 IGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQK 159
D+ +F NC YNP + P A +L+ F +
Sbjct: 67 AADVRLMFSNCYKYNPPDHPVHAMARKLQDVFEDR 101
>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 = 80.5 bits (199), Expect = 2e-20
Identities = 38/96 (39%), Positives = 51/96 (53%), Gaps = 2/96 (2%)
Query: 68 LRKLMKQIQAHKSAWPFMEPVDPH--EAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFI 125
L+ ++K + HK AWPF +PVD PDY+ ++K PMDL TI+ R+ Y SE I
Sbjct: 10 LKVVLKALWKHKFAWPFQQPVDAVKLNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECI 69
Query: 126 GDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
D +F NC YN A LE F+QK+
Sbjct: 70 QDFNTMFTNCYIYNKPGDDVVLMAQTLEKLFLQKLA 105
>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 = 79.3 bits (196), Expect = 6e-20
Identities = 36/93 (38%), Positives = 55/93 (59%), Gaps = 3/93 (3%)
Query: 66 ESLRKLMKQIQAHKSAWPFMEPVDP--HEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSE 123
E L++LMK + WPF++PVDP P+Y++++K+PMDL TI ++ +Y+ E
Sbjct: 7 EVLKELMKP-KHSAYNWPFLDPVDPVALNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKE 65
Query: 124 FIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFF 156
F D+ IF NC +NP + + HQLE F
Sbjct: 66 FERDVRLIFKNCYTFNPEGTDVYMMGHQLEEVF 98
>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 = 76.6 bits (189), Expect = 7e-19
Identities = 30/86 (34%), Positives = 45/86 (52%), Gaps = 2/86 (2%)
Query: 73 KQIQAHKSAWPFMEPVDP--HEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTK 130
+ ++ K A PF+ PVDP P Y ++K+PMDL TIE ++ Y + EF D
Sbjct: 14 RSLKRLKDARPFLVPVDPVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNL 73
Query: 131 IFDNCRYYNPRESPFFKHAHQLEMFF 156
+ DNC +N E P + +L+ F
Sbjct: 74 MVDNCLTFNGPEHPVSQMGKRLQAAF 99
>gnl|CDD|227408 COG5076, COG5076, Transcription factor involved in chromatin
remodeling, contains bromodomain [Chromatin structure
and dynamics / Transcription].
Length = 371
Score = 81.8 bits (202), Expect = 7e-19
Identities = 38/115 (33%), Positives = 64/115 (55%), Gaps = 3/115 (2%)
Query: 59 NLTPRDFESLRKLMKQ---IQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQ 115
L D +++ K KQ + F+ E PDYY ++K PMDL TI+ ++
Sbjct: 141 ELLYADNKAIAKFKKQLFLRDGRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKN 200
Query: 116 QRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVEL 170
RYK EF+ D+ +FDNC+ YN +S + A +LE +F++ ++ + E+++EL
Sbjct: 201 GRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLIEEIPEEMLEL 255
Score = 54.4 bits (131), Expect = 3e-09
Identities = 32/91 (35%), Positives = 43/91 (47%), Gaps = 1/91 (1%)
Query: 50 SSSNLANMKNLTPRDFESLRKLMKQ-IQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKT 108
L + E ++ QAH AWPF+ PV E PDYY +++PMDL T
Sbjct: 249 PEEMLELSIKPGREEREERESVLITNSQAHVGAWPFLRPVSDEEVPDYYKDIRDPMDLST 308
Query: 109 IELRIAQQRYKKLSEFIGDMTKIFDNCRYYN 139
EL++ Y+ F+ D FDNC YN
Sbjct: 309 KELKLRNNYYRPEETFVRDAKLFFDNCVMYN 339
>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 = 76.3 bits (188), Expect = 1e-18
Identities = 34/86 (39%), Positives = 52/86 (60%)
Query: 67 SLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIG 126
LRK + Q+Q +A F EPVD E PDY + +K+PMD T+ ++ QRY+ L +F
Sbjct: 5 LLRKTLDQLQEKDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEA 64
Query: 127 DMTKIFDNCRYYNPRESPFFKHAHQL 152
D I +NC YN +++ F++ A +L
Sbjct: 65 DFNLIINNCLAYNAKDTIFYRAAVRL 90
>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 = 75.2 bits (185), Expect = 2e-18
Identities = 32/84 (38%), Positives = 45/84 (53%), Gaps = 7/84 (8%)
Query: 84 FMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRES 143
FME + PDYY ++ EP+DLKTIE I +Y E + D +F N R+YN S
Sbjct: 27 FMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYNEEGS 86
Query: 144 PFFKHAHQLEMFFVQKVKILREKL 167
++ A+ LE K+L+EK
Sbjct: 87 QVYEDANILE-------KVLKEKR 103
>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 = 75.2 bits (185), Expect = 3e-18
Identities = 33/91 (36%), Positives = 59/91 (64%), Gaps = 2/91 (2%)
Query: 65 FESLRKLMKQIQAH-KSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSE 123
+ESL K++ +++ + + + PF+ V EAPDYY+++K+PMDL T+ ++ +YK +E
Sbjct: 9 YESLDKVLNELKTYTEHSTPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAE 68
Query: 124 FIGDMTKIFDNCRYYNPRES-PFFKHAHQLE 153
F+ D+ I+ NC YN S P +HA+ ++
Sbjct: 69 FVDDLNLIWKNCLLYNSDPSHPLRRHANFMK 99
>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 = 68.6 bits (168), Expect = 9e-16
Identities = 34/95 (35%), Positives = 54/95 (56%), Gaps = 5/95 (5%)
Query: 68 LRKLMKQIQAHKSAWPFMEPVDPH--EAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFI 125
L KL KQ + PF +PVDP PDY+++VK PMDL TI ++ +Y+ +++
Sbjct: 12 LEKLYKQ---DPESLPFRQPVDPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYV 68
Query: 126 GDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKV 160
D+ +FDN YN + S +K+ +L F Q++
Sbjct: 69 DDVWLMFDNAWLYNRKTSRVYKYCTKLAEVFEQEI 103
>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 = 67.7 bits (166), Expect = 2e-15
Identities = 35/105 (33%), Positives = 59/105 (56%), Gaps = 4/105 (3%)
Query: 60 LTPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRI---AQQ 116
L+P D +L+ ++ H+ + PF EPV P P+YY ++K PMDL I ++ + Q
Sbjct: 1 LSPIDQRKCERLLLELYCHELSLPFHEPVSP-SVPNYYKIIKTPMDLSLIRKKLQPKSPQ 59
Query: 117 RYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
Y EF+ D+ +F NC +N +S + +LE+FF +++K
Sbjct: 60 HYSSPEEFVADVRLMFKNCYKFNEEDSEVAQAGKELELFFEEQLK 104
>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 = 67.6 bits (165), Expect = 2e-15
Identities = 26/80 (32%), Positives = 44/80 (55%)
Query: 64 DFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSE 123
+ + +++ +I ++ +WPF EPV EA DY V+ PMDL+T++ + + Y + E
Sbjct: 1 ELQKCEEILSKILKYRFSWPFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQE 60
Query: 124 FIGDMTKIFDNCRYYNPRES 143
F+ DM +F N Y S
Sbjct: 61 FLDDMKLVFSNAEKYYENGS 80
>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 = 64.7 bits (158), Expect = 3e-14
Identities = 29/77 (37%), Positives = 45/77 (58%)
Query: 68 LRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGD 127
LR ++K++ + K F +PVD E PDYY ++K+PMDL+TI ++ +Y +F+ D
Sbjct: 8 LRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKD 67
Query: 128 MTKIFDNCRYYNPRESP 144
+ I N YNP P
Sbjct: 68 IDLIVTNALEYNPDRDP 84
>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 = 62.3 bits (152), Expect = 2e-13
Identities = 25/82 (30%), Positives = 44/82 (53%)
Query: 78 HKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRY 137
+ + FM E PDYY+V+K+P+D++ I +I +Y+ L + + D +FDN
Sbjct: 21 RRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACK 80
Query: 138 YNPRESPFFKHAHQLEMFFVQK 159
YN +S +K A L+ ++
Sbjct: 81 YNEPDSQIYKDALTLQKVLLET 102
>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 = 57.3 bits (139), Expect = 3e-11
Identities = 31/94 (32%), Positives = 42/94 (44%), Gaps = 2/94 (2%)
Query: 61 TPRDFESLRKLMKQIQAHKSAWPFMEPVD-PHEAPDYYNVVKEPMDLKTIELRIAQQRYK 119
R L KL+ +Q + F PVD PDY+N V PMDL+TI R+ + Y+
Sbjct: 26 RERLISGLDKLLLSLQLEIAE-YFEYPVDLRAWYPDYWNRVPVPMDLETIRSRLENRYYR 84
Query: 120 KLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLE 153
L D+ I N +N S K A +L
Sbjct: 85 SLEALRHDVRLILSNAETFNEPNSEIAKKAKRLS 118
>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 = 2e-10
Identities = 27/94 (28%), Positives = 48/94 (51%), Gaps = 1/94 (1%)
Query: 69 RKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDM 128
++L+ + + + PF +PVD + PDY +++ PMDL T++ + Y EF D+
Sbjct: 11 KELVNLMWDCEDSEPFRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDV 70
Query: 129 TKIFDNCRYYNP-RESPFFKHAHQLEMFFVQKVK 161
IF N + Y P + S + +L F + +K
Sbjct: 71 RLIFSNSKSYTPNKRSRIYSMTLRLSALFEEHIK 104
>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 = 53.9 bits (130), Expect = 4e-10
Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 2/69 (2%)
Query: 92 EAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQ 151
+ PDYY ++K P+ L T++ R+ Y EF+ D+ +I N R YN + S +K+A
Sbjct: 36 DYPDYYKIIKNPLSLNTVKKRL--PHYTNAQEFVNDLAQIPWNARLYNTKGSVIYKYALI 93
Query: 152 LEMFFVQKV 160
LE + +
Sbjct: 94 LEKYINDVI 102
>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 = 53.5 bits (129), Expect = 6e-10
Identities = 24/73 (32%), Positives = 40/73 (54%)
Query: 67 SLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIG 126
++ + + + +H+ A F++PV AP Y++VV PMDL TI+ I + +EF
Sbjct: 7 AILLVYRTLASHRYASVFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQR 66
Query: 127 DMTKIFDNCRYYN 139
D+ +F N YN
Sbjct: 67 DVLLMFQNAIMYN 79
>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 = 52.6 bits (127), Expect = 1e-09
Identities = 20/65 (30%), Positives = 37/65 (56%)
Query: 89 DPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKH 148
D P+YY + P+ L I+ ++ +++YK +F+ D+ +F+N + YN +S +K
Sbjct: 33 DKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYKD 92
Query: 149 AHQLE 153
A LE
Sbjct: 93 AVLLE 97
>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 = 52.4 bits (126), Expect = 1e-09
Identities = 22/98 (22%), Positives = 48/98 (48%), Gaps = 6/98 (6%)
Query: 66 ESLRKLMKQIQAHKS------AWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYK 119
+ + K++ + +K A F++ E P+YY ++++P+D K I+ RI +Y+
Sbjct: 4 KKMNKIVDVVIKYKDSDGRQLAEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYR 63
Query: 120 KLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFV 157
L + D+ + N + +N S ++ + L+ F
Sbjct: 64 SLEDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFK 101
>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 = 52.4 bits (126), Expect = 1e-09
Identities = 26/87 (29%), Positives = 47/87 (54%)
Query: 66 ESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFI 125
++L +L++Q+Q F PV AP Y +++K PMD T++ +I Y+ + EF
Sbjct: 4 KALEQLIRQLQRKDPHGFFAFPVTDFIAPGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFK 63
Query: 126 GDMTKIFDNCRYYNPRESPFFKHAHQL 152
D + +N YN ++ ++K A +L
Sbjct: 64 DDFKLMCENAMKYNKPDTIYYKAAKKL 90
>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 = 50.8 bits (122), Expect = 6e-09
Identities = 28/76 (36%), Positives = 41/76 (53%)
Query: 84 FMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRES 143
F+E PDYY ++K P+ L I+ RI + YK L EF+ D +F N R YN S
Sbjct: 27 FLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYNQEGS 86
Query: 144 PFFKHAHQLEMFFVQK 159
++ A ++E F +K
Sbjct: 87 IVYEDAVEMEKAFKKK 102
>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 = 49.3 bits (118), Expect = 2e-08
Identities = 22/71 (30%), Positives = 38/71 (53%)
Query: 83 PFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRE 142
PF++ + PDYY +K P+ L+ I ++ Y+ L E D+ +F+N + YN
Sbjct: 26 PFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPN 85
Query: 143 SPFFKHAHQLE 153
S +K A +L+
Sbjct: 86 SRIYKDAEKLQ 96
>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 = 48.6 bits (116), Expect = 3e-08
Identities = 25/66 (37%), Positives = 37/66 (56%)
Query: 94 PDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLE 153
PDYY V+KEP+DLKTI RI YK + + D+ + N + +N S +K A+ ++
Sbjct: 37 PDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFNEPGSQVYKDANAIK 96
Query: 154 MFFVQK 159
F K
Sbjct: 97 KIFTAK 102
>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 = 47.8 bits (114), Expect = 8e-08
Identities = 25/65 (38%), Positives = 34/65 (52%)
Query: 94 PDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLE 153
PDYY + +P+DL TIE +I YK F DM K+F N Y R+SP + +L
Sbjct: 39 PDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYYGRKSPIGRDVCRLR 98
Query: 154 MFFVQ 158
+ Q
Sbjct: 99 KAYYQ 103
>gnl|CDD|214584 smart00249, PHD, PHD zinc finger. The plant homeodomain (PHD)
finger is a C4HC3 zinc-finger-like motif found in
nuclear proteins thought to be involved in epigenetics
and chromatin-mediated transcriptional regulation. The
PHD finger binds two zinc ions using the so-called
'cross-brace' motif and is thus structurally related to
the RING finger and the FYVE finger. It is not yet
known if PHD fingers have a common molecular function.
Several reports suggest that it can function as a
protein-protein interacton domain and it was recently
demonstrated that the PHD finger of p300 can cooperate
with the adjacent BROMO domain in nucleosome binding in
vitro. Other reports suggesting that the PHD finger is
a ubiquitin ligase have been refuted as these domains
were RING fingers misidentified as PHD fingers.
Length = 47
Score = 45.7 bits (108), Expect = 2e-07
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 15 ICCDTCQDWFHGRCVGILQSEADNIDEYICPNC 47
+ CD C W+H C+G E + ++ CP C
Sbjct: 15 LQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
>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 = 46.2 bits (110), Expect = 3e-07
Identities = 26/68 (38%), Positives = 35/68 (51%), Gaps = 4/68 (5%)
Query: 72 MKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKI 131
MKQ A PF++PVD + PDY V +PMDL T+E + ++ Y F+ D I
Sbjct: 15 MKQPGAE----PFLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWI 70
Query: 132 FDNCRYYN 139
N YN
Sbjct: 71 LHNAIIYN 78
>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 = 46.2 bits (110), Expect = 3e-07
Identities = 21/71 (29%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 94 PDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQL- 152
P+YY VV P+DL I+ ++ + Y + + D + +N + Y +SP K A +L
Sbjct: 39 PEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYKPDSPEHKDACKLW 98
Query: 153 EMFFVQKVKIL 163
E+F + ++L
Sbjct: 99 ELFLSARNEVL 109
>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 = 45.5 bits (108), Expect = 8e-07
Identities = 18/41 (43%), Positives = 27/41 (65%), Gaps = 2/41 (4%)
Query: 71 LMKQIQAHKSAWPFMEPVDPHE--APDYYNVVKEPMDLKTI 109
+K+ + ++ AWPF+EPV+P APDY +V+K PM T
Sbjct: 11 ELKRHRRNEDAWPFLEPVNPPRRGAPDYRDVIKRPMSFGTK 51
>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 = 42.8 bits (101), Expect = 6e-06
Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 89 DPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKH 148
P+ DY +KEPM L ++ R+ ++ Y + F+ DM IF N + + ++ F +
Sbjct: 26 KPYYIRDYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFY-KDDDFGQV 84
Query: 149 AHQLEMFF 156
LE F
Sbjct: 85 GITLEKKF 92
>gnl|CDD|201356 pfam00628, PHD, PHD-finger. PHD folds into an interleaved type
of Zn-finger chelating 2 Zn ions in a similar manner to
that of the RING and FYVE domains. Several PHD fingers
have been identified as binding modules of methylated
histone H3.
Length = 51
Score = 40.9 bits (96), Expect = 9e-06
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 10 EPKFYICCDTCQDWFHGRCVGI-LQSEADNIDEYICPNC 47
+ + CD C WFH C+G L+ E E+ CP C
Sbjct: 10 DDGELLLCDGCDRWFHLACLGPPLEPEEIPEGEWYCPEC 48
>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 = 36.2 bits (84), Expect = 0.001
Identities = 19/70 (27%), Positives = 37/70 (52%)
Query: 90 PHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHA 149
P A D K P+ L I+ + + RY++L +F DM ++ + R + +S ++ A
Sbjct: 34 PELAVDGVGPKKIPLTLDIIKRNVDKGRYRRLDKFQEDMFEVLERARRLSRTDSEIYEDA 93
Query: 150 HQLEMFFVQK 159
+L+ FF++
Sbjct: 94 VELQQFFIKI 103
>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 = 29.3 bits (66), Expect = 0.47
Identities = 9/35 (25%), Positives = 17/35 (48%)
Query: 100 VKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDN 134
+ +D+ I+ +I ++Y L EF D + N
Sbjct: 43 IHTHLDVADIQEKINSEKYTSLEEFKADALLLLHN 77
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 28.9 bits (66), Expect = 1.3
Identities = 12/40 (30%), Positives = 21/40 (52%), Gaps = 10/40 (25%)
Query: 103 PMDLKTIELRIAQQRYKKLSEFIGDMT------KIFDN-C 135
P++L +LR+A + L E G++T +IF + C
Sbjct: 410 PLELLAEDLRLALEA---LGEITGEVTSEDLLDRIFSSFC 446
>gnl|CDD|240432 PTZ00477, PTZ00477, rhoptry-associated protein; Provisional.
Length = 524
Score = 28.6 bits (64), Expect = 1.5
Identities = 13/93 (13%), Positives = 34/93 (36%), Gaps = 7/93 (7%)
Query: 66 ESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFI 125
+ L L+ + +++A + H+ D+Y+ + I+ + + L F
Sbjct: 114 DRLGVLLPHLAQYETALYVFKNSGAHQGSDFYDR------FRKIKNKYRMSTERTLRSFT 167
Query: 126 GDMTKI-FDNCRYYNPRESPFFKHAHQLEMFFV 157
+ K D N + + + L +++
Sbjct: 168 NQILKRNLDAMNVENETMAVLNEVLYALTLYYQ 200
>gnl|CDD|99923 cd05491, Bromo_TBP7_like, Bromodomain; TBP7_like subfamily, limited
to fungi. TBP7, or TAT-binding protein homolog 7, is a
yeast protein of unknown function that contains
AAA-superfamily ATP-ase domains and a bromodomain.
Bromodomains are found in many chromatin-associated
proteins and in nuclear histone acetyltransferases. They
interact specifically with acetylated lysine.
Length = 119
Score = 27.8 bits (62), Expect = 1.6
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 5/41 (12%)
Query: 96 YYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCR 136
+YN MDL TIE R+ Y +F+ D+ +I + +
Sbjct: 62 FYN-----MDLDTIEERLWNGYYATPKDFLKDIKRIVRDAK 97
>gnl|CDD|234944 PRK01345, PRK01345, heat shock protein HtpX; Provisional.
Length = 317
Score = 28.4 bits (64), Expect = 1.9
Identities = 6/15 (40%), Positives = 10/15 (66%)
Query: 88 VDPHEAPDYYNVVKE 102
VD AP+ Y +V++
Sbjct: 61 VDERSAPELYRMVRD 75
>gnl|CDD|204989 pfam12631, GTPase_Cys_C, Catalytic cysteine-containing C-terminus
of GTPase, MnmE. This short C-terminal region contains
the only cysteine present in these proteins. It is
proposed that MnmE is a tRNA-modifying enzyme and that
Cys-451 functions as a catalytic residue in the
modification reaction.
Length = 73
Score = 26.7 bits (60), Expect = 2.0
Identities = 13/41 (31%), Positives = 20/41 (48%), Gaps = 10/41 (24%)
Query: 102 EPMDLKTIELRIAQQRYKKLSEFIGDMT------KIFDN-C 135
P+DL +LR+A + L E G++ +IF N C
Sbjct: 36 LPLDLVAEDLRLALEA---LGEITGEVDSEDLLDEIFSNFC 73
>gnl|CDD|238269 cd00483, HPPK, 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase
(HPPK). Folate derivatives are essential cofactors in
the biosynthesis of purines, pyrimidines, and amino
acids as well as formyl-tRNA. Mammalian cells are able
to utilize pre-formed folates after uptake by a
carrier-mediated active transport system. Most microbes
and plants lack this system and must synthesize folates
de novo from guanosine triphosphate. One enzyme from
this pathway is HPPK which catalyzes pyrophosphoryl
transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin
(HP). The functional enzyme is a monomer. Mammals lack
many of the enzymes in the folate pathway including,
HPPK.
Length = 128
Score = 27.1 bits (61), Expect = 2.7
Identities = 24/80 (30%), Positives = 35/80 (43%), Gaps = 18/80 (22%)
Query: 52 SNLAN-MKNLTPRDFESLRKLMKQIQAHKSAW-PFME--PVDPHEAPDYYN-VVK----- 101
SNL + + NL +LR L A P E PV + PD+ N VV+
Sbjct: 7 SNLGDRLANLR----AALRALAALPGIEILAVSPLYETAPVGFTDQPDFLNAVVELETSL 62
Query: 102 EPMDL----KTIELRIAQQR 117
P++L + IE R+ + R
Sbjct: 63 SPLELLDALQAIEQRLGRVR 82
>gnl|CDD|216414 pfam01288, HPPK,
7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase
(HPPK).
Length = 127
Score = 26.3 bits (59), Expect = 5.1
Identities = 19/79 (24%), Positives = 33/79 (41%), Gaps = 18/79 (22%)
Query: 59 NLTPRDFESLRKLMKQIQAHKSAW-----PFME--PVDPHEAPDYYN-VVK-----EPMD 105
NL R +LR ++ + A E PV + PD+ N VV+ P +
Sbjct: 7 NLGDR-EANLRAALEALAALPGIEILRVSSLYETAPVGFTDQPDFLNAVVELETTLSPEE 65
Query: 106 L----KTIELRIAQQRYKK 120
L + IE ++ + R ++
Sbjct: 66 LLALLQAIEAKLGRVRNER 84
>gnl|CDD|237050 PRK12305, thrS, threonyl-tRNA synthetase; Reviewed.
Length = 575
Score = 27.1 bits (61), Expect = 5.2
Identities = 19/85 (22%), Positives = 30/85 (35%), Gaps = 25/85 (29%)
Query: 60 LTPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYK 119
TP D + + K MK+I K PF +E + + A + YK
Sbjct: 50 FTPEDLKKIEKKMKKII--KRGLPF---------------EREEVSREEAREEFANEPYK 92
Query: 120 K--LSEFIGDMTKIFDN------CR 136
+ + + I+DN CR
Sbjct: 93 LELIDDIPEEGITIYDNGDFEDLCR 117
>gnl|CDD|218613 pfam05502, Dynactin_p62, Dynactin p62 family. Dynactin is a
multi-subunit complex and a required cofactor for most,
or all, of the cellular processes powered by the
microtubule-based motor cytoplasmic dynein. p62 binds
directly to the Arp1 subunit of dynactin.
Length = 456
Score = 27.2 bits (60), Expect = 5.3
Identities = 15/45 (33%), Positives = 19/45 (42%), Gaps = 8/45 (17%)
Query: 17 CDTCQDWFHGRCVGILQSEADNIDEYICPNC--NNSSSNLANMKN 59
C+ C RCV + I Y CPNC SS + + KN
Sbjct: 8 CEDCHQIRCPRCV------TEEIVCYYCPNCLFEVPSSEVRSEKN 46
>gnl|CDD|236424 PRK09238, PRK09238, bifunctional aconitate hydratase
2/2-methylisocitrate dehydratase; Validated.
Length = 835
Score = 27.1 bits (61), Expect = 5.5
Identities = 27/131 (20%), Positives = 44/131 (33%), Gaps = 52/131 (39%)
Query: 30 GILQSEADNIDEYICPNCNNSSSNLANMKNLTPRDFESLRKLMKQIQAHKSAW----PFM 85
++ + I EY+ SN+ +K + + R L ++I A + W +
Sbjct: 596 CTIKLSKEPIIEYL-------RSNIVLLKWMIAEGYGDARTLERRIAAME-EWLANPELL 647
Query: 86 EPVDPHEAPDYY-------NVVKEPM--------DLKTIELRIAQQRYKKLSE------- 123
E D +Y +KEP+ D++ LSE
Sbjct: 648 EA-DAD--AEYAAVIEIDLAEIKEPILACPNDPDDVRL------------LSEVAGTKID 692
Query: 124 --FIGD-MTKI 131
FIG MT I
Sbjct: 693 EVFIGSCMTNI 703
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 26.8 bits (60), Expect = 6.5
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 9/38 (23%)
Query: 103 PMDLKTIELRIAQQRYKKLSEFIGDMT------KIFDN 134
P+DL +LR+AQ+ L E G+ +IF N
Sbjct: 415 PLDLLAEDLRLAQEA---LGEITGEFVSEDLLDEIFSN 449
>gnl|CDD|221822 pfam12872, OST-HTH, OST-HTH/LOTUS domain. A predicted RNA-binding
domain found in insect Oskar and vertebrate TDRD5/TDRD7
proteins that nucleate or organize structurally related
ribonucleoprotein (RNP) complexes, the polar granule and
nuage, is poorly understood. The domain adopts the
winged helix-turn- helix fold and bind RNA with a
potential specificity for dsRNA.In eukaryotes this
domain is often combined in the same polypeptide with
protein-protein- or lipid- interaction domains that
might play a role in anchoring these proteins to
specific cytoskeletal structures. Thus, proteins with
this domain might have a key role in the recognition and
localization of dsRNA, including miRNAs, rasiRNAs and
piRNAs hybridized to their targets. In other cases, this
domain is fused to ubiquitin-binding, E3 ligase and
ubiquitin-like domains indicating a previously
under-appreciated role for ubiquitination in regulating
the assembly and stability of nuage-like RNP complexes.
Both bacteria and eukaryotes encode a conserved family
of proteins that combines this predicted RNA-binding
domain with a previously uncharacterized RNAse domain
belonging to the superfamily that includes the 5'->3'
nucleases, PIN and NYN domains.
Length = 74
Score = 25.3 bits (56), Expect = 7.6
Identities = 13/74 (17%), Positives = 28/74 (37%), Gaps = 18/74 (24%)
Query: 66 ESLRKLMKQIQ------AHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYK 119
+SL+KL K ++ + + W + + Y + D + Y
Sbjct: 1 KSLKKLKKLLRKALESSSDEDGWASLSEL-----GSEYRKLFPDFDPRNYG-------YS 48
Query: 120 KLSEFIGDMTKIFD 133
KLS+ + + +F+
Sbjct: 49 KLSDLLEAIPDLFE 62
>gnl|CDD|153339 cd07655, F-BAR_PACSIN, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Protein kinase C and
Casein kinase Substrate in Neurons (PACSIN) proteins.
F-BAR domains are dimerization modules that bind and
bend membranes and are found in proteins involved in
membrane dynamics and actin reorganization. Protein
kinase C and Casein kinase Substrate in Neurons (PACSIN)
proteins, also called Synaptic dynamin-associated
proteins (Syndapins), act as regulators of cytoskeletal
and membrane dynamics. They bind both dynamin and
Wiskott-Aldrich syndrome protein (WASP), and may provide
direct links between the actin cytoskeletal machinery
through WASP and dynamin-dependent endocytosis.
Vetebrates harbor three isoforms with distinct
expression patterns and specific functions. PACSINs
contain an N-terminal F-BAR domain and a C-terminal SH3
domain. F-BAR domains form banana-shaped dimers with a
positively-charged concave surface that binds to
negatively-charged lipid membranes. They can induce
membrane deformation in the form of long tubules.
Length = 258
Score = 26.5 bits (59), Expect = 8.2
Identities = 15/67 (22%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 89 DPHEAPDYYNVVKEPMDLKTIELRIAQQRYKK----LSEF----IGDMTKIFDNCRYYNP 140
D +PD +++ ++ E+ + +Y+K L+++ + DM ++FD C+ +
Sbjct: 162 DTSLSPDQVKKLQDKVEKCKQEVSKTKDKYEKALEDLNKYNPRYMEDMEQVFDKCQEFEE 221
Query: 141 RESPFFK 147
+ FFK
Sbjct: 222 KRLDFFK 228
>gnl|CDD|219120 pfam06646, Mycoplasma_p37, High affinity transport system protein
p37. This family consists of several high affinity
transport system protein p37 sequences which are
specific to Mycoplasma species. The p37 gene is part of
an operon encoding two additional proteins which are
highly similar to components of the periplasmic
binding-protein-dependent transport systems of
Gram-negative bacteria.It has been suggested that p37 is
part of a homologous, high-affinity transport system in
M. hyorhinis, a Gram-positive bacterium.
Length = 331
Score = 26.3 bits (58), Expect = 9.0
Identities = 15/55 (27%), Positives = 23/55 (41%), Gaps = 6/55 (10%)
Query: 21 QDWFHGRCVGILQSEADNIDEYICPNC------NNSSSNLANMKNLTPRDFESLR 69
++W R GI E ++ +Y+ P N S LA KN P + +R
Sbjct: 165 KNWDTFRNYGIGHGETNSAGKYLLPELLLKKHFNLSYPTLAEDKNAHPNKYAVVR 219
>gnl|CDD|226727 COG4277, COG4277, Predicted DNA-binding protein with the
Helix-hairpin-helix motif [General function prediction
only].
Length = 404
Score = 26.3 bits (58), Expect = 9.4
Identities = 15/49 (30%), Positives = 20/49 (40%), Gaps = 1/49 (2%)
Query: 17 CDTCQDW-FHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPRD 64
C + GRC+ +L+ N Y C C N SSN TP +
Sbjct: 40 PGICHSYAPDGRCISLLKILLTNFCIYDCAYCINRSSNDTPRARFTPEE 88
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
0.324 0.138 0.435
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,581,882
Number of extensions: 752303
Number of successful extensions: 1163
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1150
Number of HSP's successfully gapped: 80
Length of query: 171
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 81
Effective length of database: 6,945,742
Effective search space: 562605102
Effective search space used: 562605102
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 55 (25.0 bits)