RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1228
(202 letters)
>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 = 139 bits (351), Expect = 7e-43
Identities = 51/103 (49%), Positives = 74/103 (71%)
Query: 82 LKRRLYTLCKCLMDYRDQDGRQPMLMFMELPSAKIYPEYYKVIKQPIDMCQIESNIQNEK 141
K+R+ L +++YR+ GR+ +FME PS K YP+YYK+I +PID+ IE NI+N+K
Sbjct: 1 RKKRMLALFLYVLEYREGSGRRLCDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDK 60
Query: 142 YRSQDEILSDFRLMFGNCREFNEPGSLIYEDAVNLEKVLLERV 184
Y +++E++ DF+LMF N R +NE GS +YEDA LEKVL E+
Sbjct: 61 YATEEELMDDFKLMFRNARHYNEEGSQVYEDANILEKVLKEKR 103
>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 = 121 bits (306), Expect = 6e-36
Identities = 50/101 (49%), Positives = 73/101 (72%)
Query: 82 LKRRLYTLCKCLMDYRDQDGRQPMLMFMELPSAKIYPEYYKVIKQPIDMCQIESNIQNEK 141
++++L+ L + +Y D GR+ L+FM LPS YP+YY VIK+PIDM +I S I+ +
Sbjct: 1 MQQKLWELYNAVKNYTDGRGRRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQ 60
Query: 142 YRSQDEILSDFRLMFGNCREFNEPGSLIYEDAVNLEKVLLE 182
Y+S D+++SDF LMF N ++NEP S IY+DA+ L+KVLLE
Sbjct: 61 YQSLDDMVSDFVLMFDNACKYNEPDSQIYKDALTLQKVLLE 101
>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 = 107 bits (270), Expect = 1e-30
Identities = 42/101 (41%), Positives = 66/101 (65%)
Query: 82 LKRRLYTLCKCLMDYRDQDGRQPMLMFMELPSAKIYPEYYKVIKQPIDMCQIESNIQNEK 141
LK + + +++ D+ GR+ +F+E PS K+YP+YY +IK+PI + QI+ I+
Sbjct: 1 LKAAMLEIYDAVLNCEDETGRKLSELFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRA 60
Query: 142 YRSQDEILSDFRLMFGNCREFNEPGSLIYEDAVNLEKVLLE 182
Y+S +E L DF LMF N R +N+ GS++YEDAV +EK +
Sbjct: 61 YKSLEEFLEDFHLMFANARTYNQEGSIVYEDAVEMEKAFKK 101
>gnl|CDD|197636 smart00297, BROMO, bromo domain.
Length = 107
Score = 102 bits (257), Expect = 1e-28
Identities = 40/108 (37%), Positives = 64/108 (59%), Gaps = 2/108 (1%)
Query: 80 KPLKRRLYTLCKCLMDYRDQDGRQPMLMFMELPSAKIYPEYYKVIKQPIDMCQIESNIQN 139
L+++L L K ++D D F++ S K P+YY +IK+P+D+ I+ ++N
Sbjct: 2 PKLQKKLQELLKAVLDKLDS--HPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLEN 59
Query: 140 EKYRSQDEILSDFRLMFGNCREFNEPGSLIYEDAVNLEKVLLERVAEL 187
KY S +E ++DF LMF N R +N P S +Y+DA LEK +++ EL
Sbjct: 60 GKYSSVEEFVADFNLMFSNARTYNGPDSEVYKDAKKLEKFFEKKLREL 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 = 96.7 bits (241), Expect = 2e-26
Identities = 36/99 (36%), Positives = 58/99 (58%)
Query: 86 LYTLCKCLMDYRDQDGRQPMLMFMELPSAKIYPEYYKVIKQPIDMCQIESNIQNEKYRSQ 145
L + L+D + R F+E K P+YY+VIK P+D+ I+ ++N +Y+S
Sbjct: 1 LKKKLRSLLDALKKLKRDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSL 60
Query: 146 DEILSDFRLMFGNCREFNEPGSLIYEDAVNLEKVLLERV 184
+E +D RL+F N + +N PGS IY+DA LEK+ + +
Sbjct: 61 EEFEADVRLIFSNAKTYNGPGSPIYKDAKKLEKLFEKLL 99
>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 = 88.3 bits (219), Expect = 6e-23
Identities = 40/98 (40%), Positives = 66/98 (67%)
Query: 82 LKRRLYTLCKCLMDYRDQDGRQPMLMFMELPSAKIYPEYYKVIKQPIDMCQIESNIQNEK 141
L +++ + ++ Y+D DGRQ +F++LPS K PEYY++I++P+D +I+ I+N K
Sbjct: 2 LTKKMNKIVDVVIKYKDSDGRQLAEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHK 61
Query: 142 YRSQDEILSDFRLMFGNCREFNEPGSLIYEDAVNLEKV 179
YRS +++ D L+ N + FN GSLIYED++ L+ V
Sbjct: 62 YRSLEDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSV 99
>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 = 87.9 bits (218), Expect = 7e-23
Identities = 41/98 (41%), Positives = 61/98 (62%)
Query: 82 LKRRLYTLCKCLMDYRDQDGRQPMLMFMELPSAKIYPEYYKVIKQPIDMCQIESNIQNEK 141
LK+ L L + +M D GR +F +LPS +YP+YY VIK+PID+ I IQ+
Sbjct: 1 LKQILEQLLEAVMTATDPSGRLISELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGY 60
Query: 142 YRSQDEILSDFRLMFGNCREFNEPGSLIYEDAVNLEKV 179
Y+S +++ D LM N + FNEPGS +Y+DA ++K+
Sbjct: 61 YKSIEDMEKDLDLMVKNAKTFNEPGSQVYKDANAIKKI 98
>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 = 85.5 bits (212), Expect = 7e-22
Identities = 31/73 (42%), Positives = 51/73 (69%)
Query: 108 FMELPSAKIYPEYYKVIKQPIDMCQIESNIQNEKYRSQDEILSDFRLMFGNCREFNEPGS 167
F++LPS + YP+YY+ IK PI + QI + ++N +Y + +E+ +D LMF N + +N P S
Sbjct: 27 FLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPNS 86
Query: 168 LIYEDAVNLEKVL 180
IY+DA L+K++
Sbjct: 87 RIYKDAEKLQKLM 99
>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 = 83.4 bits (207), Expect = 3e-21
Identities = 40/98 (40%), Positives = 57/98 (58%)
Query: 81 PLKRRLYTLCKCLMDYRDQDGRQPMLMFMELPSAKIYPEYYKVIKQPIDMCQIESNIQNE 140
P + R+ + K L RD++GR L F +LP PEYY+ I PI + I+ ++
Sbjct: 1 PYEARIKNILKGLRKERDENGRLLTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRR 60
Query: 141 KYRSQDEILSDFRLMFGNCREFNEPGSLIYEDAVNLEK 178
KY+S D+ L+D LMF N + +NE S Y+DAV LEK
Sbjct: 61 KYKSFDQFLNDLNLMFENAKLYNENDSQEYKDAVLLEK 98
>gnl|CDD|227408 COG5076, COG5076, Transcription factor involved in chromatin
remodeling, contains bromodomain [Chromatin structure
and dynamics / Transcription].
Length = 371
Score = 86.0 bits (213), Expect = 5e-20
Identities = 46/167 (27%), Positives = 80/167 (47%), Gaps = 1/167 (0%)
Query: 21 TVFYYYIFKVLDREGRNQYDEESDSDEEQEGARVVRARQKVASTSKSPRALTRGKYLDNK 80
Y +R ++DE E + + K+ + ++++
Sbjct: 83 VGGITYSPFEKNRPESLRFDEIVFLAIE-SVTPESGLGSLLMAHLKTSVKKRKTPKIEDE 141
Query: 81 PLKRRLYTLCKCLMDYRDQDGRQPMLMFMELPSAKIYPEYYKVIKQPIDMCQIESNIQNE 140
L + K +DGR +F+ LPS + YP+YY++IK P+D+ I+ ++N
Sbjct: 142 LLYADNKAIAKFKKQLFLRDGRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNG 201
Query: 141 KYRSQDEILSDFRLMFGNCREFNEPGSLIYEDAVNLEKVLLERVAEL 187
+Y+S +E +SD LMF NC+ +N P S +Y DA LEK L+ + E+
Sbjct: 202 RYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLIEEI 248
Score = 34.4 bits (79), Expect = 0.033
Identities = 19/59 (32%), Positives = 32/59 (54%)
Query: 107 MFMELPSAKIYPEYYKVIKQPIDMCQIESNIQNEKYRSQDEILSDFRLMFGNCREFNEP 165
F+ S + P+YYK I+ P+D+ E ++N YR ++ + D +L F NC +N
Sbjct: 283 PFLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVRDAKLFFDNCVMYNGE 341
>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 = 77.4 bits (191), Expect = 5e-19
Identities = 30/82 (36%), Positives = 44/82 (53%)
Query: 92 CLMDYRDQDGRQPMLMFMELPSAKIYPEYYKVIKQPIDMCQIESNIQNEKYRSQDEILSD 151
CL D F+E + YP+YY+VIK+P+D+ I +++ KY+S E L D
Sbjct: 1 CLEILEDLMEHPLAEPFLEPVDPEEYPDYYEVIKEPMDLSTIRQKLKSGKYKSLAEFLKD 60
Query: 152 FRLMFGNCREFNEPGSLIYEDA 173
L+F N +N S IY+DA
Sbjct: 61 VELIFSNAITYNGEDSDIYKDA 82
>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 = 76.1 bits (188), Expect = 2e-18
Identities = 29/80 (36%), Positives = 50/80 (62%)
Query: 108 FMELPSAKIYPEYYKVIKQPIDMCQIESNIQNEKYRSQDEILSDFRLMFGNCREFNEPGS 167
F+E + P+YY VIK+P+D+ +E ++N Y + +E ++D +L+F NCR +N P +
Sbjct: 22 FLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDT 81
Query: 168 LIYEDAVNLEKVLLERVAEL 187
Y+ A LEK +++ EL
Sbjct: 82 EYYKCANKLEKFFWKKLKEL 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 = 75.5 bits (186), Expect = 5e-18
Identities = 27/70 (38%), Positives = 45/70 (64%)
Query: 118 PEYYKVIKQPIDMCQIESNIQNEKYRSQDEILSDFRLMFGNCREFNEPGSLIYEDAVNLE 177
P+Y+K+IK P+D+ I+ ++N Y S E + DF MF NC +N+PG + A LE
Sbjct: 38 PDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKPGDDVVLMAQTLE 97
Query: 178 KVLLERVAEL 187
K+ L+++A++
Sbjct: 98 KLFLQKLAQM 107
>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 = 74.3 bits (183), Expect = 2e-17
Identities = 32/104 (30%), Positives = 59/104 (56%), Gaps = 4/104 (3%)
Query: 89 LCKCLMD----YRDQDGRQPMLMFMELPSAKIYPEYYKVIKQPIDMCQIESNIQNEKYRS 144
+C+ L D Y+ +DGR F+ +P + PEYY+V+ PID+ +I+ ++ E+Y
Sbjct: 6 VCQELYDTIRNYKSEDGRILCESFIRVPKRRNEPEYYEVVSNPIDLLKIQQKLKTEEYDD 65
Query: 145 QDEILSDFRLMFGNCREFNEPGSLIYEDAVNLEKVLLERVAELG 188
D++ +DF L+ N + + +P S ++DA L ++ L E+
Sbjct: 66 VDDLTADFELLINNAKAYYKPDSPEHKDACKLWELFLSARNEVL 109
>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 = 70.4 bits (173), Expect = 4e-16
Identities = 25/62 (40%), Positives = 37/62 (59%)
Query: 118 PEYYKVIKQPIDMCQIESNIQNEKYRSQDEILSDFRLMFGNCREFNEPGSLIYEDAVNLE 177
P Y+ +IK+P+D+ I +QN +Y+S E D RL+F NC FN G+ +Y LE
Sbjct: 36 PNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTDVYMMGHQLE 95
Query: 178 KV 179
+V
Sbjct: 96 EV 97
>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 = 69.7 bits (171), Expect = 7e-16
Identities = 29/96 (30%), Positives = 52/96 (54%), Gaps = 2/96 (2%)
Query: 88 TLCKCLMDYRDQDGRQPMLMFMELPSAKIYPEYYKVIKQPIDMCQIESNIQNEKYRSQDE 147
LC+ ++D + + + F+E + K+ P Y K+IK+P+D I +++ +Y++ +E
Sbjct: 3 ALCETILD--EMEAHEDAWPFLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEE 60
Query: 148 ILSDFRLMFGNCREFNEPGSLIYEDAVNLEKVLLER 183
D RL+F NC FNE S + N+ K +R
Sbjct: 61 FAEDVRLVFDNCETFNEDDSEVGRAGHNMRKFFEKR 96
>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 = 69.0 bits (169), Expect = 2e-15
Identities = 25/82 (30%), Positives = 47/82 (57%)
Query: 108 FMELPSAKIYPEYYKVIKQPIDMCQIESNIQNEKYRSQDEILSDFRLMFGNCREFNEPGS 167
F+ S P+YY +IK+P+D+ I+ + +Y+ +E LSD +L+F NC +N +
Sbjct: 33 FLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHT 92
Query: 168 LIYEDAVNLEKVLLERVAELGP 189
+Y+ L++ ++R +LG
Sbjct: 93 SVYKAGTRLQRFFIKRCRKLGL 114
>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 = 65.4 bits (160), Expect = 3e-14
Identities = 21/62 (33%), Positives = 33/62 (53%)
Query: 118 PEYYKVIKQPIDMCQIESNIQNEKYRSQDEILSDFRLMFGNCREFNEPGSLIYEDAVNLE 177
P Y +IK+P+D+ IE +++ Y S +E +DF LM NC FN P + + L+
Sbjct: 37 PHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNGPEHPVSQMGKRLQ 96
Query: 178 KV 179
Sbjct: 97 AA 98
>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 = 63.9 bits (156), Expect = 1e-13
Identities = 30/105 (28%), Positives = 58/105 (55%), Gaps = 2/105 (1%)
Query: 81 PLKRRLYTLCKCLMDYRDQDGRQPMLMFMELPSAKIYPEYYKVIKQPIDMCQIESNIQNE 140
L ++L L + ++++G + +F LP K YP+YYK+IK P+ + ++ + +
Sbjct: 1 KLSKKLKPLYDGIYTLKEENGIEIHPIFNVLPLRKDYPDYYKIIKNPLSLNTVKKRLPH- 59
Query: 141 KYRSQDEILSDFRLMFGNCREFNEPGSLIYEDAVNLEKVLLERVA 185
Y + E ++D + N R +N GS+IY+ A+ LEK + + +
Sbjct: 60 -YTNAQEFVNDLAQIPWNARLYNTKGSVIYKYALILEKYINDVII 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 = 63.1 bits (154), Expect = 3e-13
Identities = 30/81 (37%), Positives = 45/81 (55%), Gaps = 3/81 (3%)
Query: 112 PSAKIYPEYYKVIKQPIDMCQIESNIQNE---KYRSQDEILSDFRLMFGNCREFNEPGSL 168
P + P YYK+IK P+D+ I +Q + Y S +E ++D RLMF NC +FNE S
Sbjct: 28 PVSPSVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYKFNEEDSE 87
Query: 169 IYEDAVNLEKVLLERVAELGP 189
+ + LE E++ E+ P
Sbjct: 88 VAQAGKELELFFEEQLKEILP 108
>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 = 61.5 bits (150), Expect = 8e-13
Identities = 22/66 (33%), Positives = 37/66 (56%)
Query: 118 PEYYKVIKQPIDMCQIESNIQNEKYRSQDEILSDFRLMFGNCREFNEPGSLIYEDAVNLE 177
+Y+ +IK P+D+ I+ + N +Y E +D RLMF NC ++N P ++ A L+
Sbjct: 36 HDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKLQ 95
Query: 178 KVLLER 183
V +R
Sbjct: 96 DVFEDR 101
>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 = 60.7 bits (148), Expect = 2e-12
Identities = 30/87 (34%), Positives = 47/87 (54%), Gaps = 4/87 (4%)
Query: 108 FMELPSAKIYPEYYKVIKQPIDMCQIESNIQNEKYRSQDEILSDFRLMFGNCREFNEPGS 167
F + K P+YYK+IK+P+D+ I I KY+S++E L D L+ N +N P S
Sbjct: 21 FHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDS 80
Query: 168 LIYEDAVNL----EKVLLERVAELGPL 190
+ + A + E++L ER +L L
Sbjct: 81 VYTKKAKEMLELAEELLAEREEKLTQL 107
>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 = 54.0 bits (130), Expect = 5e-10
Identities = 22/61 (36%), Positives = 36/61 (59%)
Query: 116 IYPEYYKVIKQPIDMCQIESNIQNEKYRSQDEILSDFRLMFGNCREFNEPGSLIYEDAVN 175
I P Y +IK P+D ++ I+N Y+S +E DF+LM N ++N+P ++ Y+ A
Sbjct: 30 IAPGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDTIYYKAAKK 89
Query: 176 L 176
L
Sbjct: 90 L 90
>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 = 53.5 bits (129), Expect = 1e-09
Identities = 28/91 (30%), Positives = 46/91 (50%)
Query: 89 LCKCLMDYRDQDGRQPMLMFMELPSAKIYPEYYKVIKQPIDMCQIESNIQNEKYRSQDEI 148
+C ++ Y+D +G+ + F+ LPS K P+YY+ I P+D+ IE I Y++ +
Sbjct: 10 ICDAIITYKDSNGQSLAIPFINLPSKKKNPDYYERITDPVDLSTIEKQILTGYYKTPEAF 69
Query: 149 LSDFRLMFGNCREFNEPGSLIYEDAVNLEKV 179
SD +F N ++ S I D L K
Sbjct: 70 DSDMLKVFRNAEKYYGRKSPIGRDVCRLRKA 100
>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 = 53.1 bits (128), Expect = 1e-09
Identities = 21/66 (31%), Positives = 39/66 (59%)
Query: 118 PEYYKVIKQPIDMCQIESNIQNEKYRSQDEILSDFRLMFGNCREFNEPGSLIYEDAVNLE 177
P+Y+ +IK+P+D+ ++ ++ +Y S +E +D RL F N +N PG+ ++ A L
Sbjct: 33 PDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVHTMAKELL 92
Query: 178 KVLLER 183
K+ R
Sbjct: 93 KIFETR 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 = 53.5 bits (129), Expect = 2e-09
Identities = 25/65 (38%), Positives = 36/65 (55%)
Query: 117 YPEYYKVIKQPIDMCQIESNIQNEKYRSQDEILSDFRLMFGNCREFNEPGSLIYEDAVNL 176
YP+Y+ + P+D+ I S ++N YRS + + D RL+ N FNEP S I + A L
Sbjct: 58 YPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEPNSEIAKKAKRL 117
Query: 177 EKVLL 181
LL
Sbjct: 118 SDWLL 122
>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 = 49.1 bits (117), Expect = 4e-08
Identities = 20/62 (32%), Positives = 32/62 (51%)
Query: 108 FMELPSAKIYPEYYKVIKQPIDMCQIESNIQNEKYRSQDEILSDFRLMFGNCREFNEPGS 167
F E +A +Y KVI P+D+ +++ Y S E L D +L+F N ++ E GS
Sbjct: 21 FREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGS 80
Query: 168 LI 169
+
Sbjct: 81 YV 82
>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 = 48.5 bits (116), Expect = 5e-08
Identities = 21/75 (28%), Positives = 39/75 (52%)
Query: 102 RQPMLMFMELPSAKIYPEYYKVIKQPIDMCQIESNIQNEKYRSQDEILSDFRLMFGNCRE 161
+ +F E P+Y IKQP+D + +++++YR+ ++ +DF L+ NC
Sbjct: 16 KDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLA 75
Query: 162 FNEPGSLIYEDAVNL 176
+N ++ Y AV L
Sbjct: 76 YNAKDTIFYRAAVRL 90
>gnl|CDD|99942 cd05510, Bromo_SPT7_like, Bromodomain; SPT7_like subfamily. SPT7 is
a yeast protein that functions as a component of the
transcription regulatory histone acetylation (HAT)
complexes SAGA, SALSA, and SLIK. SAGA is involved in the
RNA polymerase II-dependent transcriptional regulation
of about 10% of all yeast genes. The SPT7 bromodomain
has been shown to weakly interact with acetylated
histone H3, but not H4. The human representative of this
subfamily is cat eye syndrome critical region protein 2
(CECR2). Bromodomains are 110 amino acid long domains,
that are found in many chromatin associated proteins.
Bromodomains can interact specifically with acetylated
lysine.
Length = 112
Score = 47.8 bits (114), Expect = 1e-07
Identities = 16/46 (34%), Positives = 31/46 (67%)
Query: 118 PEYYKVIKQPIDMCQIESNIQNEKYRSQDEILSDFRLMFGNCREFN 163
P+YY +IK+P+D+ + ++N +Y+S+ E + D L++ NC +N
Sbjct: 39 PDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYN 84
>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 = 47.4 bits (113), Expect = 2e-07
Identities = 17/67 (25%), Positives = 34/67 (50%)
Query: 118 PEYYKVIKQPIDMCQIESNIQNEKYRSQDEILSDFRLMFGNCREFNEPGSLIYEDAVNLE 177
P+Y+ ++K P+D+ I + +Y+ + + D LMF N +N S +Y+ L
Sbjct: 37 PDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYNRKTSRVYKYCTKLA 96
Query: 178 KVLLERV 184
+V + +
Sbjct: 97 EVFEQEI 103
>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 = 43.5 bits (103), Expect = 6e-06
Identities = 16/46 (34%), Positives = 27/46 (58%)
Query: 118 PEYYKVIKQPIDMCQIESNIQNEKYRSQDEILSDFRLMFGNCREFN 163
P+YY++IKQP+D+ I + +Y + + L D L+ N E+N
Sbjct: 34 PDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYN 79
>gnl|CDD|99939 cd05507, Bromo_brd8_like, Bromodomain, brd8_like subgroup. In
mammals, brd8 (bromodomain containing 8) interacts with
the thyroid hormone receptor in a ligand-dependent
fashion and enhances thyroid hormone-dependent
activation from thyroid response elements. Brd8 is
thought to be a nuclear receptor coactivator.
Bromodomains are 110 amino acid long domains, that are
found in many chromatin associated proteins.
Bromodomains can interact specifically with acetylated
lysine.
Length = 104
Score = 42.0 bits (99), Expect = 2e-05
Identities = 23/69 (33%), Positives = 36/69 (52%)
Query: 108 FMELPSAKIYPEYYKVIKQPIDMCQIESNIQNEKYRSQDEILSDFRLMFGNCREFNEPGS 167
F++ + I P Y+ V+ +P+D+ I+ NI+N RS E D LMF N +N
Sbjct: 24 FLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNSSDH 83
Query: 168 LIYEDAVNL 176
+Y AV +
Sbjct: 84 DVYLMAVEM 92
>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 = 40.8 bits (96), Expect = 3e-05
Identities = 13/47 (27%), Positives = 28/47 (59%)
Query: 117 YPEYYKVIKQPIDMCQIESNIQNEKYRSQDEILSDFRLMFGNCREFN 163
+P+Y + + +P+D+ +E N++ + Y S D L+D + + N +N
Sbjct: 32 FPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYN 78
>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 = 40.4 bits (95), Expect = 5e-05
Identities = 28/93 (30%), Positives = 45/93 (48%), Gaps = 2/93 (2%)
Query: 86 LYTLCKCLMDYRDQDGRQPMLMFMELPSAKIYPEYYKVIKQPIDMCQIESNIQNEKYRSQ 145
L TL +M+++D++GR ELP + K I P+ + I+ N+ +YR
Sbjct: 8 LATLFVSVMNHQDEEGRCYSDSLAELPELAVDGVGPKKI--PLTLDIIKRNVDKGRYRRL 65
Query: 146 DEILSDFRLMFGNCREFNEPGSLIYEDAVNLEK 178
D+ D + R + S IYEDAV L++
Sbjct: 66 DKFQEDMFEVLERARRLSRTDSEIYEDAVELQQ 98
>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 = 37.8 bits (88), Expect = 7e-04
Identities = 18/72 (25%), Positives = 33/72 (45%), Gaps = 1/72 (1%)
Query: 117 YPEYYKVIKQPIDMCQIESNIQNEKYRSQDEILSDFRLMFGNCREFN-EPGSLIYEDAVN 175
YP+Y +I P+D+ ++ + Y E D RL+F N + + S IY +
Sbjct: 35 YPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYTPNKRSRIYSMTLR 94
Query: 176 LEKVLLERVAEL 187
L + E + ++
Sbjct: 95 LSALFEEHIKKI 106
>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 = 35.9 bits (83), Expect = 0.003
Identities = 11/45 (24%), Positives = 25/45 (55%)
Query: 119 EYYKVIKQPIDMCQIESNIQNEKYRSQDEILSDFRLMFGNCREFN 163
+Y + IK+P+ + +++ + Y + + + D RL+F N + F
Sbjct: 32 DYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFY 76
>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 = 31.6 bits (72), Expect = 0.074
Identities = 17/56 (30%), Positives = 29/56 (51%)
Query: 118 PEYYKVIKQPIDMCQIESNIQNEKYRSQDEILSDFRLMFGNCREFNEPGSLIYEDA 173
P+ ++I +D+ I+ I +EKY S +E +D L+ N F+ S Y+ A
Sbjct: 37 PKRRRLIHTHLDVADIQEKINSEKYTSLEEFKADALLLLHNTAIFHGADSEQYDAA 92
>gnl|CDD|221876 pfam12969, DUF3857, Domain of Unknown Function with PDB structure
(DUF3857). This family is based on the first domain of
the PDB structure PDB:3KD4(residues 1-228). It is
structurally similar to domains in other hydrolases,
eg. M1 family aminopeptidase (3ebi, Z=10, rmsd 3.6A for
152 CA, seq id 12%), despite lack of any significant
sequence similarity.
Length = 177
Score = 29.2 bits (66), Expect = 0.92
Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 6/54 (11%)
Query: 20 QTVFYYYIFKVLDREGRNQYDEES---DSDEEQ---EGARVVRARQKVASTSKS 67
T + Y+ K+L G +Y + S D D E ARV+R K+ +
Sbjct: 8 VTRYVRYVVKILTEAGVEEYSQISLSYDPDYETLEVHKARVIRPDGKIIELDPA 61
>gnl|CDD|227651 COG5347, COG5347, GTPase-activating protein that regulates ARFs
(ADP-ribosylation factors), involved in ARF-mediated
vesicular transport [Intracellular trafficking and
secretion].
Length = 319
Score = 29.7 bits (67), Expect = 1.1
Identities = 25/130 (19%), Positives = 39/130 (30%), Gaps = 13/130 (10%)
Query: 27 IFKVLDREGRNQYDEESDSDEEQEGARVVRARQKVASTSKSPRALTRGKYLDNKPLKRRL 86
+ LD E +++ S + + + ST PR+LT K + L L
Sbjct: 146 VDDRLDSESQSRSSSASLGNSNRP--DDELNVESFQSTGSKPRSLTSTKSNKDNLLNSEL 203
Query: 87 YTLCKCLMDYRDQDGRQPMLMFMELPSAKIYPEY----YKVIKQPIDMCQIESNIQNEKY 142
TL L + + S V P++ S K
Sbjct: 204 LTLNSLLSSNSEVG------SGTKSRSDAQEKSSTKATESVKPGPVNTSSTSSLPPAIK- 256
Query: 143 RSQDEILSDF 152
RS + L F
Sbjct: 257 RSPVQQLESF 266
>gnl|CDD|238570 cd01164, FruK_PfkB_like, 1-phosphofructokinase (FruK), minor
6-phosphofructokinase (pfkB) and related sugar kinases.
FruK plays an important role in the predominant pathway
for fructose utilisation.This group also contains
tagatose-6-phophate kinase, an enzyme of the tagatose
6-phosphate pathway, which responsible for breakdown of
the galactose moiety during lactose metabolism by
bacteria such as L. lactis.
Length = 289
Score = 28.3 bits (64), Expect = 2.3
Identities = 18/52 (34%), Positives = 23/52 (44%), Gaps = 15/52 (28%)
Query: 161 EFNEPGSLIYEDAVNLEKVLLERVAEL----------GPLPSG--EDFFILL 200
E NEPG I E+ + LLE++ L G LP G DF+ L
Sbjct: 102 EINEPGPEISEEELEA---LLEKLKALLKKGDIVVLSGSLPPGVPADFYAEL 150
>gnl|CDD|220388 pfam09766, FimP, Fms-interacting protein. This entry carries part
of the crucial 144 N-terminal residues of the FmiP
protein, which is essential for the binding of the
protein to the cytoplasmic domain of activated
Fms-molecules in M-CSF induced haematopoietic
differentiation of macrophages. The C-terminus contains
a putative nuclear localisation sequence and a leucine
zipper which suggest further, as yet unknown, nuclear
functions. The level of FMIP expression might form a
threshold that determines whether cells differentiate
into macrophages or into granulocytes.
Length = 352
Score = 28.5 bits (64), Expect = 2.7
Identities = 22/103 (21%), Positives = 38/103 (36%), Gaps = 17/103 (16%)
Query: 34 EGRNQYDEESDSDEEQEGARVVRARQKVASTSKSPRALTRGKYLDNKPLKRRLYTLCKCL 93
E D +SD +EEQ+ + R+ + K + K + PL L
Sbjct: 213 EQSQDDDSDSDEEEEQKRQKKRRSTDQEKLDDKRLK---NSKLYEVHPLSVEL------- 262
Query: 94 MDYRDQDGRQPMLMFMELPSAKIYPEYYKVIKQPIDMCQIESN 136
D + +D ++ L F L I V +P I+++
Sbjct: 263 -DIKCKDKKKLSLQFYYLTKLNI------VTVKPSLSDDIDAS 298
>gnl|CDD|234133 TIGR03168, 1-PFK, hexose kinase, 1-phosphofructokinase family.
This family consists largely of 1-phosphofructokinases,
but also includes tagatose-6-kinases and
6-phosphofructokinases.
Length = 303
Score = 27.9 bits (63), Expect = 3.7
Identities = 19/52 (36%), Positives = 24/52 (46%), Gaps = 15/52 (28%)
Query: 161 EFNEPGSLIYEDAVNLEKVLLERVAEL----------GPLPSG--EDFFILL 200
E NEPG I E+ + LLE++ EL G LP G DF+ L
Sbjct: 101 ELNEPGPEISEEELEQ---LLEKLRELLASGDIVVISGSLPPGVPPDFYAQL 149
>gnl|CDD|188409 TIGR03894, chp_P_marinus_1, conserved hypothetical protein,
TIGR03894 family. This protein family is restricted to
the Prochlorococcus and Synechococcus lineages of the
Cyanobacteria, and is sporadic in those lineages.
Members average 100 amino acids in length, including a
30-residue, highly polar, low complexity region
sandwiched between an N-terminal region of about 60
residues and a C-terminal [KR]VVR[KR]RS motif, both
well-conserved. The function is unknown [Hypothetical
proteins, Conserved].
Length = 95
Score = 25.9 bits (57), Expect = 7.7
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 32 DREGRNQYDEESDSDEEQEGARVVRAR 58
+ + D ES+S+ +EG RVVR R
Sbjct: 68 GEDSETKEDSESESESSREGPRVVRKR 94
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
0.321 0.138 0.403
Gapped
Lambda K H
0.267 0.0745 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,405,106
Number of extensions: 956411
Number of successful extensions: 848
Number of sequences better than 10.0: 1
Number of HSP's gapped: 846
Number of HSP's successfully gapped: 57
Length of query: 202
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 110
Effective length of database: 6,857,034
Effective search space: 754273740
Effective search space used: 754273740
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (25.3 bits)