RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16435
(277 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 = 136 bits (346), Expect = 4e-41
Identities = 48/98 (48%), Positives = 66/98 (67%)
Query: 108 DLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFG 167
L + KV++ LK+H+ AWPF +PVD+ AP+YY+ IK+PMDL+ MEEKL+ G Y T
Sbjct: 1 PLYTQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLE 60
Query: 168 QFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAV 205
+F AD +LI DNCR YNG D EY +L++ F +
Sbjct: 61 EFVADLKLIFDNCRLYNGPDTEYYKCANKLEKFFWKKL 98
>gnl|CDD|197636 smart00297, BROMO, bromo domain.
Length = 107
Score = 105 bits (263), Expect = 1e-28
Identities = 37/89 (41%), Positives = 58/89 (65%)
Query: 113 MHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRAD 172
+ V+++L SH +WPF PV AP+YY+ IK+PMDL +++KL+ G+Y + +F AD
Sbjct: 12 LKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVAD 71
Query: 173 FQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
F L+ N R YNG D+E ++L++ F
Sbjct: 72 FNLMFSNARTYNGPDSEVYKDAKKLEKFF 100
>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 = 99.8 bits (249), Expect = 1e-26
Identities = 34/91 (37%), Positives = 55/91 (60%), Gaps = 2/91 (2%)
Query: 115 KVMNRLKSH--EDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRAD 172
+++ LK + + PF +PVD AP+YYE IK PMDL+ +++KL G YK+ +F AD
Sbjct: 7 SLLDALKKLKRDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEAD 66
Query: 173 FQLIVDNCRKYNGLDNEYTDMVRRLQQIFRD 203
+LI N + YNG + ++L+++F
Sbjct: 67 VRLIFSNAKTYNGPGSPIYKDAKKLEKLFEK 97
>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 = 92.0 bits (229), Expect = 1e-23
Identities = 37/91 (40%), Positives = 53/91 (58%), Gaps = 2/91 (2%)
Query: 113 MHKVMNRLKSHEDAWPFCDPVD--EATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFR 170
+ + LK +DA PF PVD + P+Y IK+PMDL +E KL + Y + +F
Sbjct: 9 LLSSIRSLKRLKDARPFLVPVDPVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFT 68
Query: 171 ADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
ADF L+VDNC +NG ++ + M +RLQ F
Sbjct: 69 ADFNLMVDNCLTFNGPEHPVSQMGKRLQAAF 99
>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 = 90.4 bits (225), Expect = 4e-23
Identities = 32/85 (37%), Positives = 47/85 (55%), Gaps = 2/85 (2%)
Query: 121 KSHEDAWPFCDPVDEAT--APNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVD 178
K WPF DPVD PNY+ IK+PMDL + +KL G+Y++ +F D +LI
Sbjct: 16 KHSAYNWPFLDPVDPVALNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFK 75
Query: 179 NCRKYNGLDNEYTDMVRRLQQIFRD 203
NC +N + M +L+++F D
Sbjct: 76 NCYTFNPEGTDVYMMGHQLEEVFND 100
>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 = 88.5 bits (220), Expect = 2e-22
Identities = 38/95 (40%), Positives = 54/95 (56%), Gaps = 7/95 (7%)
Query: 115 KVMNRLKS--HED-AWPFCDPVDEATA---PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQ 168
++ L S H+ AWPF PVD A +Y++ IK PMDL+ +++KLD Y +
Sbjct: 7 GILKELFSKKHKAYAWPFYKPVD-PEALGLHDYHDIIKHPMDLSTIKKKLDNREYADAQE 65
Query: 169 FRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRD 203
F AD +L+ NC KYN D+ M R+LQ +F D
Sbjct: 66 FAADVRLMFSNCYKYNPPDHPVHAMARKLQDVFED 100
>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 = 86.5 bits (215), Expect = 2e-21
Identities = 34/83 (40%), Positives = 54/83 (65%)
Query: 115 KVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQ 174
+++N LK+ D+WPF PV++ P+YY+ IKRPMDL + +K+ +Y++ +F D +
Sbjct: 7 EIVNELKNLPDSWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIE 66
Query: 175 LIVDNCRKYNGLDNEYTDMVRRL 197
LIVDN YNG D+ YT + +
Sbjct: 67 LIVDNSVLYNGPDSVYTKKAKEM 89
>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 = 84.4 bits (209), Expect = 5e-21
Identities = 32/82 (39%), Positives = 49/82 (59%)
Query: 115 KVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQ 174
+++ L H A PF +PVD P+YYE IK PMDL+ + +KL +G+YK+ +F D +
Sbjct: 3 EILEDLMEHPLAEPFLEPVDPEEYPDYYEVIKEPMDLSTIRQKLKSGKYKSLAEFLKDVE 62
Query: 175 LIVDNCRKYNGLDNEYTDMVRR 196
LI N YNG D++ ++
Sbjct: 63 LIFSNAITYNGEDSDIYKDAKK 84
>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 = 80.5 bits (199), Expect = 2e-19
Identities = 32/79 (40%), Positives = 51/79 (64%)
Query: 109 LRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQ 168
L + + K +++L+ + A F +PVD + P+Y + IK+PMD + M +KL++ RY+T
Sbjct: 2 LEVLLRKTLDQLQEKDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLED 61
Query: 169 FRADFQLIVDNCRKYNGLD 187
F ADF LI++NC YN D
Sbjct: 62 FEADFNLIINNCLAYNAKD 80
>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 = 80.5 bits (199), Expect = 3e-19
Identities = 34/89 (38%), Positives = 52/89 (58%)
Query: 113 MHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRAD 172
+ +++ + H+D+WPF PV + P+YY+ IK+PMDL ++EKL+ G YK +F +D
Sbjct: 17 LEQLLVEIVKHKDSWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSD 76
Query: 173 FQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
QL+ NC YN RLQ+ F
Sbjct: 77 IQLVFSNCFLYNPEHTSVYKAGTRLQRFF 105
>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 = 76.6 bits (189), Expect = 5e-18
Identities = 32/70 (45%), Positives = 49/70 (70%)
Query: 120 LKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDN 179
+++HEDAWPF +PV+ P Y + IK+PMD + + EKL++G+YKT +F D +L+ DN
Sbjct: 12 MEAHEDAWPFLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDN 71
Query: 180 CRKYNGLDNE 189
C +N D+E
Sbjct: 72 CETFNEDDSE 81
>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 = 75.9 bits (187), Expect = 1e-17
Identities = 32/87 (36%), Positives = 48/87 (55%), Gaps = 2/87 (2%)
Query: 115 KVMNRLKSH-EDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADF 173
KV+N LK++ E + PF V + AP+YY+ IK+PMDL M +KL +YK+ +F D
Sbjct: 14 KVLNELKTYTEHSTPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDL 73
Query: 174 QLIVDNCRKYNG-LDNEYTDMVRRLQQ 199
LI NC YN + +++
Sbjct: 74 NLIWKNCLLYNSDPSHPLRRHANFMKK 100
>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 = 71.2 bits (175), Expect = 1e-15
Identities = 39/104 (37%), Positives = 54/104 (51%)
Query: 109 LRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQ 168
LR+ + V+ RL S + F PVDE P+YYE IK+PMDL + +KLD +Y T
Sbjct: 4 LRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKD 63
Query: 169 FRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGE 212
F D LIV N +YN + ++R RD V ++ E
Sbjct: 64 FLKDIDLIVTNALEYNPDRDPADKLIRSRACELRDEVHAMIEAE 107
>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 = 69.7 bits (171), Expect = 3e-15
Identities = 32/90 (35%), Positives = 51/90 (56%), Gaps = 4/90 (4%)
Query: 115 KVMNRLKSHEDAWPFCDPVDEATA---PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRA 171
++ +L H+ W F PVD A P+Y++ IK+PMDL +++KL+ G Y + +F A
Sbjct: 7 TLLRKLMKHKWGWVFNAPVD-VVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAA 65
Query: 172 DFQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
D +L N +YN N+ M + L +IF
Sbjct: 66 DVRLTFANAMRYNPPGNDVHTMAKELLKIF 95
>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 = 67.1 bits (164), Expect = 2e-14
Identities = 26/72 (36%), Positives = 39/72 (54%)
Query: 129 FCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDN 188
F PV + AP Y IK PMD + M+EK+ Y++ +F+ DF+L+ +N KYN D
Sbjct: 22 FAFPVTDFIAPGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDT 81
Query: 189 EYTDMVRRLQQI 200
Y ++L
Sbjct: 82 IYYKAAKKLLHS 93
>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 = 64.5 bits (157), Expect = 2e-13
Identities = 24/88 (27%), Positives = 44/88 (50%)
Query: 116 VMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQL 175
+++++ + +WPF +PV A +Y + I PMDL M+ K G Y + +F D +L
Sbjct: 8 ILSKILKYRFSWPFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKL 67
Query: 176 IVDNCRKYNGLDNEYTDMVRRLQQIFRD 203
+ N KY + +R+ +Q +
Sbjct: 68 VFSNAEKYYENGSYVLSCMRKTEQCCVN 95
>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 = 35/108 (32%), Positives = 56/108 (51%), Gaps = 5/108 (4%)
Query: 105 TEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLD---AG 161
+ D R +++ L HE + PF +PV + PNYY+ IK PMDL+ + +KL
Sbjct: 2 SPIDQRK-CERLLLELYCHELSLPFHEPVSP-SVPNYYKIIKTPMDLSLIRKKLQPKSPQ 59
Query: 162 RYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYL 209
Y + +F AD +L+ NC K+N D+E + L+ F + + L
Sbjct: 60 HYSSPEEFVADVRLMFKNCYKFNEEDSEVAQAGKELELFFEEQLKEIL 107
>gnl|CDD|227408 COG5076, COG5076, Transcription factor involved in chromatin
remodeling, contains bromodomain [Chromatin structure
and dynamics / Transcription].
Length = 371
Score = 69.1 bits (169), Expect = 2e-13
Identities = 30/81 (37%), Positives = 45/81 (55%)
Query: 121 KSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNC 180
+ F + P+YYE IK PMDL +++KL GRYK+F +F +D L+ DNC
Sbjct: 161 DGRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNC 220
Query: 181 RKYNGLDNEYTDMVRRLQQIF 201
+ YNG D+ + L++ F
Sbjct: 221 KLYNGPDSSVYVDAKELEKYF 241
Score = 33.2 bits (76), Expect = 0.14
Identities = 29/71 (40%), Positives = 39/71 (54%)
Query: 120 LKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDN 179
++H AWPF PV + P+YY+ I+ PMDL+ E KL Y+ F D +L DN
Sbjct: 275 SQAHVGAWPFLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVRDAKLFFDN 334
Query: 180 CRKYNGLDNEY 190
C YNG +Y
Sbjct: 335 CVMYNGEVTDY 345
>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 = 62.8 bits (153), Expect = 9e-13
Identities = 30/94 (31%), Positives = 51/94 (54%), Gaps = 4/94 (4%)
Query: 116 VMNRLKSHEDAWPFCDPVDEATA---PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRAD 172
V+ L H+ AWPF PVD A P+Y++ IK PMDL ++++L+ Y + + D
Sbjct: 13 VLKALWKHKFAWPFQQPVD-AVKLNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQD 71
Query: 173 FQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVS 206
F + NC YN ++ M + L+++F ++
Sbjct: 72 FNTMFTNCYIYNKPGDDVVLMAQTLEKLFLQKLA 105
>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 = 60.5 bits (147), Expect = 8e-12
Identities = 31/98 (31%), Positives = 51/98 (52%), Gaps = 3/98 (3%)
Query: 107 EDLRIGMHKVMNRL-KSHEDAWPFCDPVDEAT--APNYYEQIKRPMDLTRMEEKLDAGRY 163
E+LR + + +L K ++ PF PVD P+Y++ +K PMDL+ + KLD G+Y
Sbjct: 2 EELRQALMPTLEKLYKQDPESLPFRQPVDPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQY 61
Query: 164 KTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
+ Q+ D L+ DN YN + +L ++F
Sbjct: 62 QDPWQYVDDVWLMFDNAWLYNRKTSRVYKYCTKLAEVF 99
>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 = 59.3 bits (144), Expect = 2e-11
Identities = 25/86 (29%), Positives = 43/86 (50%), Gaps = 4/86 (4%)
Query: 117 MNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLI 176
M + + PF PVD P+Y + + +PMDL+ +E+ + Y + F AD + I
Sbjct: 15 MKQPGAE----PFLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWI 70
Query: 177 VDNCRKYNGLDNEYTDMVRRLQQIFR 202
+ N YNG D++ T + + +I
Sbjct: 71 LHNAIIYNGGDHKLTQAAKAIVKICE 96
>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 = 58.5 bits (142), Expect = 3e-11
Identities = 22/68 (32%), Positives = 41/68 (60%), Gaps = 10/68 (14%)
Query: 139 PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQ 198
P+YY+ IK+P+D+ ++ K++ +Y++ +DF L+ DN KYN D+
Sbjct: 37 PDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYNEPDS---------- 86
Query: 199 QIFRDAVS 206
QI++DA++
Sbjct: 87 QIYKDALT 94
>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 = 58.5 bits (142), Expect = 4e-11
Identities = 27/106 (25%), Positives = 52/106 (49%), Gaps = 8/106 (7%)
Query: 114 HKVMNRLKSH--EDAWPFCDPVDEA----TAPNYYEQIKRPMDLTRMEEKLDAGRYKTFG 167
++ + ++++ ED C+ P YYE + P+DL ++++KL Y
Sbjct: 8 QELYDTIRNYKSEDGRILCESFIRVPKRRNEPEYYEVVSNPIDLLKIQQKLKTEEYDDVD 67
Query: 168 QFRADFQLIVDNCRKYNGLDN-EYTDMVRRLQQIFRDAVSRYLDGE 212
ADF+L+++N + Y D+ E+ D +L ++F A + L G
Sbjct: 68 DLTADFELLINNAKAYYKPDSPEHKDAC-KLWELFLSARNEVLSGG 112
>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 = 55.8 bits (135), Expect = 3e-10
Identities = 27/85 (31%), Positives = 44/85 (51%)
Query: 115 KVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQ 174
V L SH A F PV E AP Y+ + RPMDL+ +++ ++ G ++ +F+ D
Sbjct: 10 LVYRTLASHRYASVFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVL 69
Query: 175 LIVDNCRKYNGLDNEYTDMVRRLQQ 199
L+ N YN D++ M +Q+
Sbjct: 70 LMFQNAIMYNSSDHDVYLMAVEMQR 94
>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 = 55.2 bits (133), Expect = 7e-10
Identities = 25/70 (35%), Positives = 37/70 (52%)
Query: 115 KVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQ 174
+++N + ED+ PF PVD P+Y + I PMDL ++E L G Y +F D +
Sbjct: 12 ELVNLMWDCEDSEPFRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVR 71
Query: 175 LIVDNCRKYN 184
LI N + Y
Sbjct: 72 LIFSNSKSYT 81
>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 = 51.6 bits (124), Expect = 2e-08
Identities = 27/96 (28%), Positives = 46/96 (47%), Gaps = 2/96 (2%)
Query: 107 EDLRIGMHKVMNRLKSHEDAWPFCDPVDE-ATAPNYYEQIKRPMDLTRMEEKLDAGRYKT 165
E L G+ K++ L+ F PVD A P+Y+ ++ PMDL + +L+ Y++
Sbjct: 27 ERLISGLDKLLLSLQLEIAE-YFEYPVDLRAWYPDYWNRVPVPMDLETIRSRLENRYYRS 85
Query: 166 FGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
R D +LI+ N +N ++E +RL
Sbjct: 86 LEALRHDVRLILSNAETFNEPNSEIAKKAKRLSDWL 121
>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 = 50.3 bits (121), Expect = 3e-08
Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 10/72 (13%)
Query: 134 DEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDM 193
D+A P YY++I P+ L +++K+ +YK+F QF D L+ +N + YN D
Sbjct: 33 DKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNEND------ 86
Query: 194 VRRLQQIFRDAV 205
Q ++DAV
Sbjct: 87 ----SQEYKDAV 94
>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 = 50.1 bits (120), Expect = 3e-08
Identities = 23/66 (34%), Positives = 37/66 (56%)
Query: 139 PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQ 198
P+YYE+I P+DL+ +E+++ G YKT F +D + N KY G + V RL+
Sbjct: 39 PDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYYGRKSPIGRDVCRLR 98
Query: 199 QIFRDA 204
+ + A
Sbjct: 99 KAYYQA 104
>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 = 50.1 bits (120), Expect = 4e-08
Identities = 22/101 (21%), Positives = 48/101 (47%), Gaps = 6/101 (5%)
Query: 113 MHKVMNRLKSHED------AWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTF 166
M+K+++ + ++D A F P YYE I++P+D +++E++ +Y++
Sbjct: 6 MNKIVDVVIKYKDSDGRQLAEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSL 65
Query: 167 GQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSR 207
D L+ N + +N + + LQ +F+ A +
Sbjct: 66 EDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFKSARQK 106
>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 = 48.1 bits (115), Expect = 2e-07
Identities = 20/64 (31%), Positives = 38/64 (59%)
Query: 139 PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQ 198
P+YY++IK P+ L ++ KL G Y+T + AD L+ +N ++YN ++ +LQ
Sbjct: 37 PDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPNSRIYKDAEKLQ 96
Query: 199 QIFR 202
++ +
Sbjct: 97 KLMQ 100
>gnl|CDD|99950 cd05519, Bromo_SNF2, Bromodomain, SNF2-like subfamily, specific to
fungi. SNF2 is a yeast protein involved in
transcriptional activation, it is the catalytic
component of the SWI/SNF ATP-dependent chromatin
remodeling complex. The protein is essential for the
regulation of gene expression (both positive and
negative) of a large number of genes. The SWI/SNF
complex changes chromatin structure by altering
DNA-histone contacts within the nucleosome, which
results in a re-positioning of the nucleosome and
facilitates or represses the binding of gene-specific
transcription factors. Bromodomains are 110 amino acid
long domains, that are found in many chromatin
associated proteins. Bromodomains can interact
specifically with acetylated lysine.
Length = 103
Score = 46.6 bits (111), Expect = 6e-07
Identities = 19/56 (33%), Positives = 32/56 (57%)
Query: 129 FCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYN 184
F + + P+YY IKRP+ L +++ +++ YK+ +F DF L+ N R YN
Sbjct: 27 FLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYN 82
>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 = 44.7 bits (106), Expect = 3e-06
Identities = 17/46 (36%), Positives = 26/46 (56%)
Query: 139 PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYN 184
P+YY+ I P+DL +E + +Y T + DF+L+ N R YN
Sbjct: 37 PDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYN 82
>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 = 42.4 bits (100), Expect = 2e-05
Identities = 17/65 (26%), Positives = 36/65 (55%), Gaps = 1/65 (1%)
Query: 134 DEATAPNYYEQIKR-PMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTD 192
+AT ++ +D+ ++EK+++ +Y + +F+AD L++ N ++G D+E D
Sbjct: 31 GKATKLPKRRRLIHTHLDVADIQEKINSEKYTSLEEFKADALLLLHNTAIFHGADSEQYD 90
Query: 193 MVRRL 197
R L
Sbjct: 91 AARWL 95
>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 = 40.1 bits (94), Expect = 1e-04
Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 141 YYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQI 200
Y + IK PM L +++E+L+ Y T F D +LI N + + D+++ + L++
Sbjct: 33 YCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYK-DDDFGQVGITLEKK 91
Query: 201 F 201
F
Sbjct: 92 F 92
>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 = 40.1 bits (94), Expect = 1e-04
Identities = 17/41 (41%), Positives = 24/41 (58%), Gaps = 2/41 (4%)
Query: 116 VMNRLKSHEDAWPFCDPVDEAT--APNYYEQIKRPMDLTRM 154
+ R + +EDAWPF +PV+ AP+Y + IKRPM
Sbjct: 11 ELKRHRRNEDAWPFLEPVNPPRRGAPDYRDVIKRPMSFGTK 51
>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 = 39.3 bits (92), Expect = 2e-04
Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 10/68 (14%)
Query: 139 PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQ 198
P+YY IK P+DL + +++ +G YK+ D L+V N + +N +
Sbjct: 37 PDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFNEPGS---------- 86
Query: 199 QIFRDAVS 206
Q+++DA +
Sbjct: 87 QVYKDANA 94
>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 = 35.4 bits (82), Expect = 0.006
Identities = 18/69 (26%), Positives = 30/69 (43%), Gaps = 2/69 (2%)
Query: 137 TAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRR 196
P+YY+ IK P+ L ++++L Y +F D I N R YN +
Sbjct: 36 DYPDYYKIIKNPLSLNTVKKRLP--HYTNAQEFVNDLAQIPWNARLYNTKGSVIYKYALI 93
Query: 197 LQQIFRDAV 205
L++ D +
Sbjct: 94 LEKYINDVI 102
>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682). The
members of this family are all hypothetical eukaryotic
proteins of unknown function. One member is described as
being an adipocyte-specific protein, but no evidence of
this was found.
Length = 322
Score = 36.8 bits (86), Expect = 0.009
Identities = 14/47 (29%), Positives = 32/47 (68%)
Query: 28 KEIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQRRIENRER 74
++I + +++++EE + +EE+++ E E + K + E QR++E +ER
Sbjct: 270 EKILKAAEEERQEEAQEKKEEKKKEEREAKLAKLSPEEQRKLEEKER 316
Score = 29.1 bits (66), Expect = 2.5
Identities = 16/52 (30%), Positives = 31/52 (59%), Gaps = 5/52 (9%)
Query: 21 IEKLKHSKEIERKLQKQKEEETRRHQEEEERLE----EEWRKHKAARERQRR 68
EK+ + E ER+ + Q+++E ++ +E E +L EE RK +ER+++
Sbjct: 269 EEKILKAAEEERQEEAQEKKEEKKKEEREAKLAKLSPEEQRK-LEEKERKKQ 319
>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 = 31.7 bits (72), Expect = 0.15
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 149 MDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRK 182
MDL +EE+L G Y T F D + IV + +
Sbjct: 65 MDLDTIEERLWNGYYATPKDFLKDIKRIVRDAKT 98
>gnl|CDD|218127 pfam04522, DUF585, Protein of unknown function (DUF585). This
region represents the N terminus of bromovirus 2a
protein, and is always found N terminal to a predicted
RNA-dependent RNA polymerase region (pfam00978).
Length = 248
Score = 32.5 bits (74), Expect = 0.17
Identities = 14/54 (25%), Positives = 24/54 (44%), Gaps = 3/54 (5%)
Query: 95 YQTSTGGYRSTEEDLRIG---MHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQI 145
Y ++ + S E D ++ + V R+ ED P + D T P Y E++
Sbjct: 185 YVVTSEEFASLESDYQVTLNLTNPVEQRVSILEDTLPHFEEDDHPTMPIYRERV 238
>gnl|CDD|218896 pfam06098, Radial_spoke_3, Radial spoke protein 3. This family
consists of several radial spoke protein 3 (RSP3)
sequences. Eukaryotic cilia and flagella present in
diverse types of cells perform motile, sensory, and
developmental functions in organisms from protists to
humans. They are centred by precisely organised,
microtubule-based structures, the axonemes. The axoneme
consists of two central singlet microtubules, called the
central pair, and nine outer doublet microtubules. These
structures are well-conserved during evolution. The
outer doublet microtubules, each composed of A and B
sub-fibres, are connected to each other by nexin links,
while the central pair is held at the centre of the
axoneme by radial spokes. The radial spokes are T-shaped
structures extending from the A-tubule of each outer
doublet microtubule to the centre of the axoneme. Radial
spoke protein 3 (RSP3), is present at the proximal end
of the spoke stalk and helps in anchoring the radial
spoke to the outer doublet. It is thought that radial
spokes regulate the activity of inner arm dynein through
protein phosphorylation and dephosphorylation.
Length = 288
Score = 32.7 bits (75), Expect = 0.18
Identities = 12/52 (23%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 22 EKLKHSKEIERKLQKQKEEETRRHQEEEERL-EEEWRKHKAARERQRRIENR 72
+ + + E ++ EE RR +EE+ER +++ + + +E +I R
Sbjct: 162 RQFEQRRNAELAETQRLEEAERRRREEKERRKKQDKERKQREKETAEKIAAR 213
>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family. Atrophin-1 is the
protein product of the dentatorubral-pallidoluysian
atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive
neurodegenerative disorder. It is caused by the
expansion of a CAG repeat in the DRPLA gene on
chromosome 12p. This results in an extended
polyglutamine region in atrophin-1, that is thought to
confer toxicity to the protein, possibly through
altering its interactions with other proteins. The
expansion of a CAG repeat is also the underlying defect
in six other neurodegenerative disorders, including
Huntington's disease. One interaction of expanded
polyglutamine repeats that is thought to be pathogenic
is that with the short glutamine repeat in the
transcriptional coactivator CREB binding protein, CBP.
This interaction draws CBP away from its usual nuclear
location to the expanded polyglutamine repeat protein
aggregates that are characteristic of the polyglutamine
neurodegenerative disorders. This interferes with
CBP-mediated transcription and causes cytotoxicity.
Length = 979
Score = 32.7 bits (74), Expect = 0.23
Identities = 20/59 (33%), Positives = 35/59 (59%), Gaps = 2/59 (3%)
Query: 25 KHSKEIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQRRIENRERGSRSNSEDR 83
K +K+ E ++K K E ++ +EE ER +E+ ++ + RER+R E + S S+ E R
Sbjct: 576 KLAKKREEAVEKAKREAEQKAREEREREKEKEKERE--REREREAERAAKASSSSHESR 632
>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase
component YidC; Validated.
Length = 429
Score = 32.1 bits (73), Expect = 0.33
Identities = 21/88 (23%), Positives = 38/88 (43%), Gaps = 5/88 (5%)
Query: 17 QSTRIEKLKHSKEIERKLQKQKEEETRRHQEEE-ERLEEEWRKHKAARERQRRIENRER- 74
++ I+K + +++ E K +K++ + RR E E R + R AR R RR + +
Sbjct: 328 ENAEIKKTRTAEKNEAKARKKEIAQKRRAAEREINREARQERAAAMARARARRAAVKAKK 387
Query: 75 ---GSRSNSEDRWTTEDTSSLCSYQTST 99
S +ED + + S Q
Sbjct: 388 KGLIDASPNEDTPSENEESKGSPPQVEA 415
>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional.
Length = 651
Score = 31.9 bits (73), Expect = 0.35
Identities = 9/36 (25%), Positives = 21/36 (58%), Gaps = 3/36 (8%)
Query: 28 KEIERKLQKQKEEETRRHQEEEERLE---EEWRKHK 60
+E E K ++++ R+ +++EE+ + E+ K K
Sbjct: 555 REKEEKEALKEQKRLRKLKKQEEKKKKELEKLEKAK 590
>gnl|CDD|227822 COG5535, RAD4, DNA repair protein RAD4 [DNA replication,
recombination, and repair].
Length = 650
Score = 31.7 bits (72), Expect = 0.40
Identities = 11/110 (10%), Positives = 31/110 (28%), Gaps = 1/110 (0%)
Query: 38 KEEETRRHQEEEERLEEEWRKHKAARERQRRIENRERGSRSNSEDRWTTEDTSSLCSYQT 97
K + + ++ R + K + + + +++ + E E
Sbjct: 2 KRDLENSYNDQARRKNSKIEKKNVSFKEEEEVDSSFDSFYQDEEKDIDEEPVELDGDLTV 61
Query: 98 STGGYRSTEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKR 147
+ R + +L+S + P + N + +R
Sbjct: 62 TVNNIRRDRSKVSKYSDDHNEKLQSSQLHL-IMIPFMLLKSRNKWIDDER 110
>gnl|CDD|216270 pfam01057, Parvo_NS1, Parvovirus non-structural protein NS1. This
family also contains the NS2 protein. Parvoviruses
encode two non-structural proteins, NS1 and NS2. The
mRNA for NS2 contains the coding sequence for the first
87 amino acids of NS1, then by an alternative splicing
mechanism mRNA from a different reading frame, encoding
the last 78 amino acids, makes up the full length of the
NS2 mRNA. NS1, is the major non-structural protein. It
is essential for DNA replication. It is an 83-kDa
nuclear phosphoprotein. It has DNA helicase and ATPase
activity.
Length = 271
Score = 31.5 bits (72), Expect = 0.42
Identities = 11/47 (23%), Positives = 17/47 (36%), Gaps = 1/47 (2%)
Query: 79 NSEDRWTTEDTSSLCSYQTSTGGYRSTEEDLRIGMHKVMNRLKSHED 125
+E+ W D S S G R + L++ M K+ D
Sbjct: 21 VTEEDWIAIDPDSYLRLSASPAGRRQIKNALQM-AIIRMFSTKTALD 66
>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell
envelope biogenesis, outer membrane].
Length = 387
Score = 31.5 bits (71), Expect = 0.46
Identities = 15/58 (25%), Positives = 33/58 (56%)
Query: 17 QSTRIEKLKHSKEIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQRRIENRER 74
QS + K ++ ++K ++ EE + E+ERL++ ++ A+E+Q++ E E+
Sbjct: 68 QSQQSSAKKGEQQRKKKEEQVAEELKPKQAAEQERLKQLEKERLKAQEQQKQAEEAEK 125
Score = 30.7 bits (69), Expect = 0.89
Identities = 17/52 (32%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 23 KLKHSKEIERKLQKQKEEETRRHQEEEERLEE-EWRKHKAARERQRRIENRE 73
K K + E KQ E+ R Q E+ERL+ E +K E+Q ++E ++
Sbjct: 82 KKKEEQVAEELKPKQAAEQERLKQLEKERLKAQEQQKQAEEAEKQAQLEQKQ 133
Score = 29.1 bits (65), Expect = 2.5
Identities = 17/54 (31%), Positives = 35/54 (64%), Gaps = 2/54 (3%)
Query: 17 QSTRIEKLKHSKEIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQRRIE 70
+ R+++L+ + ++ QKQ EE ++ Q E+++ EE+ R KAA E++++ E
Sbjct: 99 EQERLKQLEKERLKAQEQQKQAEEAEKQAQLEQKQQEEQAR--KAAAEQKKKAE 150
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 31.2 bits (71), Expect = 0.57
Identities = 13/69 (18%), Positives = 21/69 (30%), Gaps = 6/69 (8%)
Query: 19 TRIEKLKHSKEIERKLQK-QKEEETRRHQEEE-----ERLEEEWRKHKAARERQRRIENR 72
E+ K ++ +L QK+ E R E E K + A R
Sbjct: 204 LLEERKKTLAQLNSELSADQKKLEELRANESRLKNEIASAEAAAAKAREAAAAAEAAAAR 263
Query: 73 ERGSRSNSE 81
R + +
Sbjct: 264 ARAAEAKRT 272
>gnl|CDD|218517 pfam05236, TAF4, Transcription initiation factor TFIID component
TAF4 family. This region of similarity is found in
Transcription initiation factor TFIID component TAF4.
Length = 255
Score = 30.8 bits (70), Expect = 0.65
Identities = 19/79 (24%), Positives = 29/79 (36%), Gaps = 11/79 (13%)
Query: 12 SISSCQSTRIEKLKH--------SKEIERKLQKQKEEETRRHQEEEERL---EEEWRKHK 60
+ S K +++ QKQKEEE RR + E E+ R +
Sbjct: 89 IVLSRHRRDGIKSDPNYEIRSDVRRQLRFLAQKQKEEEERRVERRRELGLEDPEQLRLKQ 148
Query: 61 AARERQRRIENRERGSRSN 79
A+E Q+ R +N
Sbjct: 149 KAKEEQKAESEETRHRAAN 167
>gnl|CDD|173965 cd08045, TAF4, TATA Binding Protein (TBP) Associated Factor 4
(TAF4) is one of several TAFs that bind TBP and is
involved in forming Transcription Factor IID (TFIID)
complex. The TATA Binding Protein (TBP) Associated
Factor 4 (TAF4) is one of several TAFs that bind TBP and
are involved in forming the Transcription Factor IID
(TFIID) complex. TFIID is one of seven General
Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE,
TFIIF, and TFIID) that are involved in accurate
initiation of transcription by RNA polymerase II in
eukaryote. TFIID plays an important role in the
recognition of promoter DNA and assembly of the
pre-initiation complex. TFIID complex is composed of the
TBP and at least 13 TAFs. TAFs from various species were
originally named by their predicted molecular weight or
their electrophoretic mobility in polyacrylamide gels. A
new, unified nomenclature for the pol II TAFs has been
suggested to show the relationship between TAF orthologs
and paralogs. Several hypotheses are proposed for TAFs
functions such as serving as activator-binding sites,
core-promoter recognition or a role in essential
catalytic activity. Each TAF, with the help of a
specific activator, is required only for the expression
of subset of genes and is not universally involved for
transcription as are GTFs. In yeast and human cells,
TAFs have been found as components of other complexes
besides TFIID. Several TAFs interact via histone-fold
(HFD) motifs; HFD is the interaction motif involved in
heterodimerization of the core histones and their
assembly into nucleosome octamers. The minimal HFD
contains three alpha-helices linked by two loops and is
found in core histones, TAFS and many other
transcription factors. TFIID has a histone octamer-like
substructure. TAF4 domain interacts with TAF12 and makes
a novel histone-like heterodimer that binds DNA and has
a core promoter function of a subset of genes.
Length = 212
Score = 30.4 bits (69), Expect = 0.74
Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 3/57 (5%)
Query: 26 HSKEIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQRRIENRERGSRSNSED 82
K++ Q ++EEE +R +EE ERL K+ E+ R + + + E+
Sbjct: 112 VRKQLRFLEQLEREEEEKRDEEERERLLRAA---KSRSEQSRLKQKAKEMQKEEDEE 165
>gnl|CDD|227084 COG4741, COG4741, Predicted secreted endonuclease distantly
related to archaeal Holliday junction resolvase
[Nucleotide transport and metabolism].
Length = 175
Score = 30.1 bits (68), Expect = 0.80
Identities = 17/56 (30%), Positives = 23/56 (41%), Gaps = 3/56 (5%)
Query: 27 SKEIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQRRIENRERGSRSNSED 82
SK E + QK E R E + R EEEW K +++IE + S
Sbjct: 33 SKARELEETLQKAERERLVNEAQARKEEEW---KLKEWIEKKIEEAREDAVRKSRA 85
>gnl|CDD|181362 PRK08296, PRK08296, hypothetical protein; Provisional.
Length = 603
Score = 30.8 bits (70), Expect = 0.81
Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 8/46 (17%)
Query: 21 IEKLKHSKEIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQ 66
I +L+ + IER T + E +R+ EE+R ER+
Sbjct: 318 IGRLRRGETIER--------PTEALRAERDRIVEEYRDLLDGDERK 355
>gnl|CDD|220897 pfam10883, DUF2681, Protein of unknown function (DUF2681). This
family of proteins is found in bacteria. Proteins in
this family are typically between 81 and 117 amino
acids in length.
Length = 87
Score = 28.9 bits (65), Expect = 0.82
Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 7/61 (11%)
Query: 23 KLKHSKEIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQRRIENRERGSRSNSED 82
KLK ++ RKLQ + E+ E + K A+ RQ+ EN R SR + ++
Sbjct: 24 KLKKAQRENRKLQAENEQLATEKAVAETEV-------KNAKVRQKNEENTRRLSRDDVDE 76
Query: 83 R 83
+
Sbjct: 77 Q 77
>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein
TolA; Provisional.
Length = 387
Score = 30.5 bits (69), Expect = 0.90
Identities = 11/43 (25%), Positives = 25/43 (58%)
Query: 20 RIEKLKHSKEIERKLQKQKEEETRRHQEEEERLEEEWRKHKAA 62
R+++L+ + ++ +KQ EE ++ ++++ EE K AA
Sbjct: 102 RLKQLEKERLAAQEQKKQAEEAAKQAALKQKQAEEAAAKAAAA 144
Score = 29.4 bits (66), Expect = 2.2
Identities = 13/47 (27%), Positives = 31/47 (65%)
Query: 28 KEIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQRRIENRER 74
++ ++K Q+Q EE ++ E+ERL++ ++ AA+E++++ E +
Sbjct: 79 EQRKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQAEEAAK 125
Score = 29.0 bits (65), Expect = 2.7
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 3/53 (5%)
Query: 18 STRIEKLKHSKE---IERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQR 67
+ R E+ + KE E QKQ E+ R Q E+ERL + +K +A ++
Sbjct: 74 AKRAEEQRKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQAEEAAKQ 126
>gnl|CDD|222581 pfam14181, YqfQ, YqfQ-like protein. The YqfQ-like protein family
includes the B. subtilis YqfQ protein, also known as
VrrA, which is functionally uncharacterized. This family
of proteins is found in bacteria. Proteins in this
family are typically between 146 and 237 amino acids in
length. There are two conserved sequence motifs: QYGP
and PKLY.
Length = 155
Score = 29.7 bits (67), Expect = 0.93
Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 5/83 (6%)
Query: 189 EYTDMVRRLQQIFRDAVSRYLDGERSSGSEDEEEMAVEFQEELPPKPKG-KRGRKKKIVL 247
+Y +VR L +++ + R L E EEE E ++E PP+ K + +KK+ V
Sbjct: 73 QYGPLVRNLPAMWK--IFRELSSSDDEEEETEEESTDETEQEDPPETKTESKEKKKREV- 129
Query: 248 SPRSLTPTDEEEDKENEEKSGTP 270
P+ T ++ + + + K P
Sbjct: 130 -PKPKTEKEKPKTEPKKPKPSKP 151
>gnl|CDD|233467 TIGR01554, major_cap_HK97, phage major capsid protein, HK97
family. This model family represents the major capsid
protein component of the heads (capsids) of
bacteriophage HK97, phi-105, P27, and related phage.
This model represents one of several analogous families
lacking detectable sequence similarity. The gene
encoding this component is typically located in an
operon encoding the small and large terminase subunits,
the portal protein and the prohead or maturation
protease [Mobile and extrachromosomal element
functions, Prophage functions].
Length = 384
Score = 30.4 bits (69), Expect = 0.96
Identities = 13/61 (21%), Positives = 26/61 (42%), Gaps = 2/61 (3%)
Query: 20 RIEKLKHSKEIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQRRIENRERGSRSN 79
+ +L KE+ + + +K E + E + L+EE K A +R + + +
Sbjct: 7 ALAELA--KELRKLTEDEKLAEAEEEKAEYDALKEEIDKLDAEIDRLEELLDELEAKPAA 64
Query: 80 S 80
S
Sbjct: 65 S 65
>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain. This is a family of proteins of
approximately 300 residues, found in plants and
vertebrates. They contain a highly conserved DDRGK
motif.
Length = 189
Score = 30.1 bits (68), Expect = 0.99
Identities = 19/46 (41%), Positives = 27/46 (58%)
Query: 29 EIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQRRIENRER 74
E ER+ +K+ EE+ ++EEE LEEE K K ER+ R E +
Sbjct: 25 EEEREERKKLEEKREGERKEEEELEEEREKKKEEEERKEREEQARK 70
Score = 29.7 bits (67), Expect = 1.1
Identities = 18/46 (39%), Positives = 29/46 (63%)
Query: 22 EKLKHSKEIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQR 67
+KL+ +E ERK +++ EEE + +EEEER E E + K E ++
Sbjct: 32 KKLEEKREGERKEEEELEEEREKKKEEEERKEREEQARKEQEEYEK 77
>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein. TolA couples the inner
membrane complex of itself with TolQ and TolR to the
outer membrane complex of TolB and OprL (also called
Pal). Most of the length of the protein consists of
low-complexity sequence that may differ in both length
and composition from one species to another,
complicating efforts to discriminate TolA (the most
divergent gene in the tol-pal system) from paralogs such
as TonB. Selection of members of the seed alignment and
criteria for setting scoring cutoffs are based largely
conserved operon struction. //The Tol-Pal complex is
required for maintaining outer membrane integrity. Also
involved in transport (uptake) of colicins and
filamentous DNA, and implicated in pathogenesis.
Transport is energized by the proton motive force. TolA
is an inner membrane protein that interacts with
periplasmic TolB and with outer membrane porins ompC,
phoE and lamB [Transport and binding proteins, Other,
Cellular processes, Pathogenesis].
Length = 346
Score = 30.2 bits (68), Expect = 1.2
Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 3/57 (5%)
Query: 17 QSTRIEKLKHSKEIERKLQKQ---KEEETRRHQEEEERLEEEWRKHKAARERQRRIE 70
+ R + KE+E++ + K+ E Q EE++ + E K K A E + + E
Sbjct: 81 EKQRAAEQARQKELEQRAAAEKAAKQAEQAAKQAEEKQKQAEEAKAKQAAEAKAKAE 137
Score = 28.3 bits (63), Expect = 5.3
Identities = 11/47 (23%), Positives = 20/47 (42%)
Query: 20 RIEKLKHSKEIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQ 66
+ + K+ E KQ E + + E E+ +E K +A E +
Sbjct: 111 AKQAEEKQKQAEEAKAKQAAEAKAKAEAEAEKKAKEEAKKQAEEEAK 157
Score = 27.9 bits (62), Expect = 6.2
Identities = 12/52 (23%), Positives = 25/52 (48%)
Query: 21 IEKLKHSKEIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQRRIENR 72
E+ K ++ + +KQ+ E R +E E+R E +A + ++ E +
Sbjct: 67 QERQKKLEQQAEEAEKQRAAEQARQKELEQRAAAEKAAKQAEQAAKQAEEKQ 118
Score = 27.5 bits (61), Expect = 8.4
Identities = 15/48 (31%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 21 IEKLKHSKEIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQRR 68
E+ K + E K + + E E ++ +EE ++ EE K KAA E +++
Sbjct: 121 AEEAKAKQAAEAKAKAEAEAE-KKAKEEAKKQAEEEAKAKAAAEAKKK 167
>gnl|CDD|223853 COG0782, COG0782, Uncharacterized conserved protein, YhbC family
[Function unknown].
Length = 151
Score = 28.8 bits (65), Expect = 1.8
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 5/53 (9%)
Query: 22 EKLKHSKEIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQRRIENRER 74
E+L++ K +ER ++ + R + E E +AA+E Q IE R R
Sbjct: 11 EELEYLKPVERPEIVEEIADARELGDLSENAEY-----RAAKEEQAFIERRIR 58
>gnl|CDD|215180 PLN02316, PLN02316, synthase/transferase.
Length = 1036
Score = 29.8 bits (67), Expect = 2.0
Identities = 18/48 (37%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 28 KEIERKLQK-QKEEETRRHQEEEERLEEEWRKHKAARERQRRIENRER 74
+E R+L+K KEE R Q EE+R EE + A Q + E +R
Sbjct: 252 EEKRRELEKLAKEEAERERQAEEQRRREEEKAAMEADRAQAKAEVEKR 299
>gnl|CDD|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome
biogenesis [Translation, ribosomal structure and
biogenesis].
Length = 1077
Score = 29.3 bits (65), Expect = 2.6
Identities = 19/61 (31%), Positives = 31/61 (50%)
Query: 22 EKLKHSKEIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQRRIENRERGSRSNSE 81
+ E ER+ +K+EE R + E EER + E + E +R+IE + + +RS E
Sbjct: 633 SADEVDYETEREENARKKEELRGNFELEERGDPEKKDVDWYTEEKRKIEEQLKINRSEFE 692
Query: 82 D 82
Sbjct: 693 T 693
Score = 28.6 bits (63), Expect = 4.2
Identities = 14/54 (25%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 21 IEKLKHSKEIERK--LQKQKEEETRRHQEEEERLEEEWRKHKAARERQRRIENR 72
E++K +E ER LQ+ KEEE + ++E E+ + ++R++ +
Sbjct: 1023 KERIKDQEEKERMESLQRAKEEEIGKKEKEREQRIRKTIHDNYKEMAKKRLKKK 1076
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 29.0 bits (66), Expect = 2.9
Identities = 18/53 (33%), Positives = 31/53 (58%), Gaps = 2/53 (3%)
Query: 22 EKLKHSKEIERKLQKQKEEETRRHQEEEERLEEEW-RKHKAARERQRRIENRE 73
E+ +++E++L QKEE R E E+ EEE +K K ++Q+ +E +E
Sbjct: 79 ERRNELQKLEKRLL-QKEENLDRKLELLEKREEELEKKEKELEQKQQELEKKE 130
>gnl|CDD|236380 PRK09107, PRK09107, acetolactate synthase 3 catalytic subunit;
Validated.
Length = 595
Score = 28.9 bits (65), Expect = 3.0
Identities = 14/35 (40%), Positives = 18/35 (51%), Gaps = 8/35 (22%)
Query: 186 LDNEYTDMVRRLQQIFRDAVSRYLDGERSSGSEDE 220
L+N+Y MVR+ QQ+ L G R S S E
Sbjct: 482 LNNQYMGMVRQWQQL--------LHGNRLSHSYTE 508
>gnl|CDD|225688 COG3146, COG3146, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 387
Score = 28.9 bits (65), Expect = 3.1
Identities = 12/32 (37%), Positives = 15/32 (46%), Gaps = 4/32 (12%)
Query: 201 FRDAVSRYLDGERSSGSEDEEEMAVEFQEELP 232
R AV+ YLD ER + E E +E P
Sbjct: 355 LRQAVADYLDRER----AEVEAYEEELEEHSP 382
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 28.8 bits (65), Expect = 3.8
Identities = 11/42 (26%), Positives = 23/42 (54%)
Query: 17 QSTRIEKLKHSKEIERKLQKQKEEETRRHQEEEERLEEEWRK 58
+ T+++ L+ K + +++ E E R + E +RL EE +
Sbjct: 26 EDTKLKLLEKEKRLLLLEEQRLEAEGLRLKREVDRLREEIER 67
Score = 28.4 bits (64), Expect = 4.0
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 4/61 (6%)
Query: 11 DSISSCQSTRIEKLKHSK-EIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQRRI 69
D S + KL+ +K ++ K ++ E +R + E RL+ E + RE R+
Sbjct: 12 DLESYEPQEYLNKLEDTKLKLLEKEKRLLLLEEQRLEAEGLRLKREVDR---LREEIERL 68
Query: 70 E 70
+
Sbjct: 69 K 69
>gnl|CDD|106979 PHA00671, PHA00671, hypothetical protein.
Length = 135
Score = 27.7 bits (60), Expect = 3.9
Identities = 14/67 (20%), Positives = 36/67 (53%)
Query: 25 KHSKEIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQRRIENRERGSRSNSEDRW 84
K + +++ Q+Q +++ + + E +RL +E++K A ++Q +I ++ S +R
Sbjct: 28 KAQRSAQQQAQQQAQQQADQAKAESDRLTQEYQKQTEAYQQQAKIMQQQLLDSQQSFNRA 87
Query: 85 TTEDTSS 91
+ +S
Sbjct: 88 NQKQPNS 94
>gnl|CDD|99956 cd05526, Bromo_polybromo_VI, Bromodomain, polybromo repeat VI.
Polybromo is a nuclear protein of unknown function,
which contains 6 bromodomains. The human ortholog BAF180
is part of a SWI/SNF chromatin-remodeling complex, and
it may carry out the functions of Yeast Rsc-1 and Rsc-2.
It was shown that polybromo bromodomains bind to histone
H3 at specific acetyl-lysine positions. Bromodomains are
found in many chromatin-associated proteins and in
nuclear histone acetyltransferases. They interact
specifically with acetylated lysine, but not all the
bromodomains in polybromo may bind to acetyl-lysine.
Length = 110
Score = 27.3 bits (61), Expect = 4.1
Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 3/65 (4%)
Query: 146 KRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF---R 202
K P+ L ++ +D GRY+ +F+ D +++ R+ + D+E + LQQ F R
Sbjct: 45 KIPLTLDIIKRNVDKGRYRRLDKFQEDMFEVLERARRLSRTDSEIYEDAVELQQFFIKIR 104
Query: 203 DAVSR 207
D + +
Sbjct: 105 DELCK 109
>gnl|CDD|213755 TIGR02977, phageshock_pspA, phage shock protein A. Members of this
family are the phage shock protein PspA, from the phage
shock operon. This is a narrower family than the set of
PspA and its homologs, sometimes several in a genome, as
described by pfam04012. PspA appears to maintain the
protonmotive force under stress conditions that include
overexpression of certain phage secretins, heat shock,
ethanol, and protein export defects [Cellular processes,
Adaptations to atypical conditions].
Length = 219
Score = 28.0 bits (63), Expect = 4.3
Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 5/60 (8%)
Query: 21 IEKLKHSKEIERKLQKQK--EEETRRHQEEEERLEEEWRKHKAARERQRRIENRERGSRS 78
IEK K + E ++ EE + QE+ +L+ K AR RQ+ + R + + S
Sbjct: 92 IEKQKAQELAEALERELAAVEETLAKLQEDIAKLQA---KLAEARARQKALAIRHQAASS 148
>gnl|CDD|176888 cd08879, RHO_alpha_C_AntDO-like, C-terminal catalytic domain of the
oxygenase alpha subunit of Pseudomonas resinovorans
strain CA10 anthranilate 1,2-dioxygenase and related
aromatic ring hydroxylating dioxygenases. C-terminal
catalytic domain of the oxygenase alpha subunit of
anthranilate 1,2-dioxygenase (AntDO) and related
Rieske-type non-heme iron aromatic ring-hydroxylating
oxygenases (RHOs, also known as aromatic ring
hydroxylating dioxygenases). RHOs utilize non-heme
Fe(II) to catalyze the addition of hydroxyl groups to
the aromatic ring, an initial step in the oxidative
degradation of aromatic compounds. RHOs are composed of
either two or three protein components, and are
comprised of an electron transport chain (ETC) and an
oxygenase. The ETC transfers reducing equivalents from
the electron donor to the oxygenase component, which in
turn transfers electrons to the oxygen molecules. The
oxygenase components are oligomers, either (alpha)n or
(alpha)n(beta)n. The alpha subunits are the catalytic
components and have an N-terminal domain, which binds a
Rieske-like 2Fe-2S cluster, and the C-terminal catalytic
domain which binds the non-heme Fe(II). The Fe(II) is
co-ordinated by conserved His and Asp residues.
Oxygenases belonging to this subgroup include the alpha
subunits of AntDO, aniline dioxygenase, Acinetobacter
calcoaceticus benzoate 1,2-dioxygenase, 2-halobenzoate
1,2-dioxygenase from Pseudomonas cepacia 2CBS,
2,4,5-trichlorophenoxyacetic acid oxygenase from
Pseudomonas cepacia AC1100, 2,4-dichlorophenoxyacetic
acid oxygenase from Bradyrhizobium sp. strain HW13,
p-cumate 2,3-dioxygenase, 2-halobenzoate 1,2-dioxygenase
form Pseudomonas cepacia 2CBS, and Pseudomonas putida
IacC, which may be involved in the catabolism of the
plant hormone indole 3-acetic acid. This subfamily
belongs to the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket.
Length = 237
Score = 28.1 bits (63), Expect = 4.4
Identities = 12/49 (24%), Positives = 20/49 (40%), Gaps = 1/49 (2%)
Query: 101 GYRSTEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPM 149
G + E+ + + + + R K+ ED DE N + KR M
Sbjct: 189 GLAARGEE-WVDLSRGLGREKADEDGVVTGAVTDELPMRNQWRAWKRLM 236
>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown].
Length = 434
Score = 28.6 bits (64), Expect = 4.5
Identities = 13/56 (23%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 28 KEIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQRRIENRERGSRSNSEDR 83
++ +KL + K +ET +E E + +EE K + ++Q+ + ++ R E +
Sbjct: 379 QDYTKKLGEVK-DETDASEEAEAKAKEEKLKQEENEKKQKEQADEDKEKRQKDERK 433
>gnl|CDD|239652 cd03680, MM_CoA_mutase_ICM_like, Coenzyme
B12-dependent-methylmalonyl coenzyme A (CoA) mutase
(MCM) family, isobutyryl-CoA mutase (ICM)-like
subfamily; contains archaeal and bacterial proteins
similar to the large subunit of Streptomyces
cinnamonensis coenzyme B12-dependent ICM. ICM from S.
cinnamonensis is comprised of a large and a small
subunit. The holoenzyme appears to be an alpha2beta2
heterotetramer with up to 2 molecules of coenzyme B12
bound. The small subunit binds coenzyme B12. ICM
catalyzes the reversible rearrangement of n-butyryl-CoA
to isobutyryl-CoA, intermediates in fatty acid and
valine catabolism, which in S. cinnamonensis can be
converted to methylmalonyl-CoA and used in polyketide
synthesis.
Length = 538
Score = 28.4 bits (64), Expect = 4.6
Identities = 14/54 (25%), Positives = 18/54 (33%), Gaps = 6/54 (11%)
Query: 33 KLQKQKEEETR------RHQEEEERLEEEWRKHKAARERQRRIENRERGSRSNS 80
K QK+ E R + EEE + ERQ R R N+
Sbjct: 440 KYQKEIESGERIVVGVNKFVVEEEPPIILLKVDDEVEERQIERLKEVRAERDNA 493
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 28.6 bits (65), Expect = 4.7
Identities = 12/57 (21%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 22 EKLKHSKEIERKLQKQKEEETRRHQEEEERLEEEWRKH-KAARERQRRIENRERGSR 77
LK +++++ +L+++KE+ + E E+E ++ K A++ I R +
Sbjct: 541 ALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQQAIKEAKKEADEIIKELRQLQ 597
Score = 27.9 bits (63), Expect = 7.6
Identities = 9/52 (17%), Positives = 22/52 (42%), Gaps = 1/52 (1%)
Query: 30 IERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQRRIENRERGSRSNSE 81
I + ++E E + + E E E + + E++ +++ E +E
Sbjct: 522 IASLEELERELEQKAEEAEALLKEAE-KLKEELEEKKEKLQEEEDKLLEEAE 572
Score = 27.5 bits (62), Expect = 9.6
Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 4/48 (8%)
Query: 21 IEKLKHSKEIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQRR 68
I L E + +QK EE +E E+L+EE + K + +
Sbjct: 522 IASL----EELERELEQKAEEAEALLKEAEKLKEELEEKKEKLQEEED 565
>gnl|CDD|149343 pfam08229, SHR3_chaperone, ER membrane protein SH3. This family of
proteins are membrane localised chaperones that are
required for correct plasma membrane localisation of
amino acid permeases (AAPs). SH3 prevents AAPs proteins
from aggregating and assists in their correct folding.
In the absence of SH3, AAPs are retained in the ER.
Length = 196
Score = 28.1 bits (63), Expect = 4.7
Identities = 9/38 (23%), Positives = 15/38 (39%)
Query: 207 RYLDGERSSGSEDEEEMAVEFQEELPPKPKGKRGRKKK 244
+ +E E A +EE + + K +KKK
Sbjct: 159 WKDAKLLEEFAAEEAEAAAAAKEEESAEGEKKESKKKK 196
>gnl|CDD|178635 PLN03086, PLN03086, PRLI-interacting factor K; Provisional.
Length = 567
Score = 28.3 bits (63), Expect = 5.4
Identities = 14/49 (28%), Positives = 26/49 (53%)
Query: 29 EIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQRRIENRERGSR 77
E+ R +K + E+ R Q + +LE E + + A +++ IE +R R
Sbjct: 4 ELRRAREKLEREQRERKQRAKLKLERERKAKEEAAKQREAIEAAQRSRR 52
>gnl|CDD|183610 PRK12585, PRK12585, putative monovalent cation/H+ antiporter
subunit G; Reviewed.
Length = 197
Score = 27.7 bits (61), Expect = 5.5
Identities = 15/47 (31%), Positives = 25/47 (53%)
Query: 35 QKQKEEETRRHQEEEERLEEEWRKHKAARERQRRIENRERGSRSNSE 81
Q+Q E+ + +E EER+E E R+ K + + RER ++ E
Sbjct: 125 QEQIEKARQEREELEERMEWERREEKIDEREDQEEQEREREEQTIEE 171
>gnl|CDD|218033 pfam04339, DUF482, Protein of unknown function, DUF482. This
family contains several proteins of uncharacterized
function.
Length = 370
Score = 28.2 bits (64), Expect = 5.5
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 4/32 (12%)
Query: 201 FRDAVSRYLDGERSSGSEDEEEMAVEFQEELP 232
FRDA++ +L+ ER E E E LP
Sbjct: 340 FRDAIADFLERER----AAVLEYIEELNEHLP 367
>gnl|CDD|220431 pfam09831, DUF2058, Uncharacterized protein conserved in bacteria
(DUF2058). This domain, found in various prokaryotic
proteins, has no known function.
Length = 177
Score = 27.6 bits (62), Expect = 5.5
Identities = 17/53 (32%), Positives = 30/53 (56%), Gaps = 3/53 (5%)
Query: 22 EKLKHSKEIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQRRIENRER 74
+K K +K+ +RK +KQ + +E ++ EE + KA R+R+ NR+R
Sbjct: 15 KKAKKAKKEKRKQRKQARKGADDGDDELKQAAEEAKAEKAERDREL---NRQR 64
>gnl|CDD|148750 pfam07321, YscO, Type III secretion protein YscO. This family
contains the bacterial type III secretion protein YscO,
which is approximately 150 residues long. YscO has been
shown to be required for high-level expression and
secretion of the anti-host proteins V antigen and Yops
in Yersinia pestis.
Length = 152
Score = 27.4 bits (61), Expect = 5.6
Identities = 14/54 (25%), Positives = 28/54 (51%), Gaps = 4/54 (7%)
Query: 20 RIEKLKHS----KEIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQRRI 69
+EK + +E E L++Q E +R + E +RL + ++ + AR+ Q +
Sbjct: 68 ELEKWQQQVGLLRENEASLEQQLAEAKQRLEAERQRLRQARQQLQEARKAQEKF 121
>gnl|CDD|218698 pfam05695, DUF825, Plant protein of unknown function (DUF825).
This family consists of several plant proteins greater
than 1000 residues in length. The function of this
family is unknown.
Length = 1127
Score = 28.3 bits (63), Expect = 5.7
Identities = 15/78 (19%), Positives = 30/78 (38%), Gaps = 4/78 (5%)
Query: 8 WLVDSISSCQSTRIEKLKHSKEIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQR 67
L+ + S E+ + ++ K + + E+E+ + + E +R
Sbjct: 130 RLIFPLLSFSFLETERTEIESDLSSKCLSEYSPISELFTEDEKYMIN----NLFPEEMER 185
Query: 68 RIENRERGSRSNSEDRWT 85
+ N R RS DRW+
Sbjct: 186 FLGNFTRSIRSFFSDRWS 203
>gnl|CDD|221756 pfam12757, DUF3812, Protein of unknown function (DUF3812). This is
a family of fungal proteins whose function is not known.
Length = 126
Score = 26.9 bits (60), Expect = 5.8
Identities = 13/42 (30%), Positives = 25/42 (59%), Gaps = 6/42 (14%)
Query: 29 EIERK--LQKQKEEETRRHQEEEERLEEEWRKHKAARERQRR 68
EI+ + Q+ ++EE + +EE +R EE + RER+++
Sbjct: 88 EIDERAEAQRARDEEKKLDEEEAKRQHEEAK----EREREKK 125
>gnl|CDD|185616 PTZ00436, PTZ00436, 60S ribosomal protein L19-like protein;
Provisional.
Length = 357
Score = 28.0 bits (61), Expect = 6.1
Identities = 20/61 (32%), Positives = 35/61 (57%), Gaps = 10/61 (16%)
Query: 21 IEKLKHSKEIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQRRIE-NRERGSRSN 79
I K+K+ K+ ER+L +Q + RL++E +HKA ++ R+ E +RER R +
Sbjct: 142 IHKVKNEKKKERQLAEQLAAK---------RLKDEQHRHKARKQELRKREKDRERARRED 192
Query: 80 S 80
+
Sbjct: 193 A 193
>gnl|CDD|99925 cd05493, Bromo_ALL-1, Bromodomain, ALL-1 like proteins. ALL-1 is a
vertebrate homologue of Drosophila trithorax and is
often affected in chromosomal rearrangements that are
linked to acute leukemias, such as acute lymphocytic
leukemia (ALL). Bromodomains are found in many
chromatin-associated proteins and in nuclear histone
acetyltransferases. They interact specifically with
acetylated lysine.
Length = 131
Score = 27.0 bits (60), Expect = 6.3
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 148 PMDLTRMEEKLDAGRYKTFGQFRADFQLIV 177
P+DL + +KL+AG Y + F D I+
Sbjct: 59 PLDLEAVGKKLEAGFYTSVLDFSDDIVKII 88
>gnl|CDD|220735 pfam10408, Ufd2P_core, Ubiquitin elongating factor core. This is
the most conserved part of the core region of Ufd2P
ubiquitin elongating factor or E4, running from helix
alpha-11 to alpha-38. It consists of 31 helices of
variable length connected by loops of variable size
forming a compact unit; the helical packing pattern of
the compact unit consists of five structural repeats
that resemble tandem Armadillo (ARM) repeats. This
domain is involved in ubiquitination as it binds Cdc48p
and escorts ubiquitinated proteins from Cdc48p to the
proteasome for degradation. The core is structurally
similar to the nuclear transporter protein
importin-alpha. The core is associated with the U-box at
the C-terminus, pfam04564, which has ligase activity.
Length = 625
Score = 28.0 bits (63), Expect = 6.3
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 21 IEKLKHSKEIERKLQKQKEEETRRHQEEEERLEE 54
+ LK K+++++LQ + E E+ +E EER E
Sbjct: 453 LSYLKEIKQLQKELQDRAEWESLSQEEREERESE 486
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 27.9 bits (63), Expect = 6.3
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 2/44 (4%)
Query: 219 DEEEMAVEFQEELPPKPKGKRGRKKKIVLSPRSLTPTDEEEDKE 262
DEE M+V +E +PP K+G+ + L P EEE +E
Sbjct: 141 DEETMSVHLKEGVPPM--AKKGKPGEWKLVKIRDEPLTEEELEE 182
>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho;
Provisional.
Length = 672
Score = 27.9 bits (63), Expect = 6.4
Identities = 13/67 (19%), Positives = 27/67 (40%)
Query: 17 QSTRIEKLKHSKEIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQRRIENRERGS 76
R + + ++E ER ++++ + R E E + + + R + RE+G
Sbjct: 154 TEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGD 213
Query: 77 RSNSEDR 83
R R
Sbjct: 214 RREERGR 220
>gnl|CDD|224849 COG1938, COG1938, Archaeal enzymes of ATP-grasp superfamily
[General function prediction only].
Length = 244
Score = 27.7 bits (62), Expect = 7.1
Identities = 11/30 (36%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 24 LKHSKEIERKLQKQKE--EETRRHQEEEER 51
K ++EIE +L+K E E+ E EE
Sbjct: 210 EKEAEEIEEQLEKLAEQLEKEEERVEREEE 239
>gnl|CDD|146486 pfam03879, Cgr1, Cgr1 family. Members of this family are
coiled-coil proteins that are involved in pre-rRNA
processing.
Length = 105
Score = 26.6 bits (59), Expect = 7.3
Identities = 22/54 (40%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 20 RIEKLKHSKEIERKLQKQKEEETRRHQEEEERLEEEWRK-HKAARERQRRIENR 72
R ++LK KE ER+ + Q +E R +EE+ER E+ K H ER +R E R
Sbjct: 46 REKELKDEKEAERQRRIQAIKERRAAKEEKERYEKMAAKMHAKKVERLKRREKR 99
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 27.4 bits (61), Expect = 7.5
Identities = 14/48 (29%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 23 KLKHSKEIERKLQKQKEE-ETRRHQEEEERLEEEWRKHKAARERQRRI 69
KL+ E +L +Q + + + E E L EE + + AR+ +RR+
Sbjct: 18 KLESIAEALPELLEQAADCKEWGYAEFLEYLLEEEKLAREARKIERRL 65
>gnl|CDD|241528 cd13377, PH_SynGAP_2, Synaptic Ras-GTPase activating protein
Pleckstrin homology (PH) domain. SynGAP is a member of
the RasSynGAP family along with DOC-2/DAB2-interacting
protein (DAB2IP) and neuronal growth-associated protein
(nGAP/RASAL2). SynGAP, a neuronal Ras-GAP, has been
shown display both Ras-GAP activity and Ras-related
protein (Rap)-GAP activity. Saccharomyces cerevisiae
Bud2 and GAP1 members CAPRI (Ca2+-promoted Ras
inactivator) and RASAL (Ras-GTPase-activating-like
protein) also possess this dual activity. Human
DOC-2/DAB2-interacting protein (DAB2IP) is encoded by a
tumor suppressor gene and a newly recognized member of
the Ras-GTPase-activating family. Members here include
nematodes, insects, arthropods, and cnidarians. PH
domains are only found in eukaryotes. They share little
sequence conservation, but all have a common fold, which
is electrostatically polarized. PH domains have diverse
functions, but in general are involved in targeting
proteins to the appropriate cellular location or in the
interaction with a binding partner. They share little
sequence conservation, but all have a common fold, which
is electrostatically polarized. Less than 10% of PH
domains bind phosphoinositide phosphates (PIPs) with
high affinity and specificity. PH domains are
distinguished from other PIP-binding domains by their
specific high-affinity binding to PIPs with two vicinal
phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or
PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 129
Score = 26.7 bits (59), Expect = 8.0
Identities = 22/89 (24%), Positives = 31/89 (34%), Gaps = 21/89 (23%)
Query: 57 RKHKAARER-QRRIENRERGSRSNSEDRWTTEDTSSLCSYQTSTGGYRSTEEDLRIG-MH 114
RK R + + R R SRS+ SL S Q+S +R+ +H
Sbjct: 30 RKSATKLARSKVQATGRLRSSRSH----------ESLLSSQSSAHMILEGPAGVRLHPLH 79
Query: 115 -KVMNRLKSHEDAWPFCDPVDEATAPNYY 142
V+ R P C V T Y+
Sbjct: 80 PSVLGR--------PHCFQVSTPTDTTYF 100
>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family. This model
represents a subfamily of RNA splicing factors
including the Pad-1 protein (N. crassa), CAPER (M.
musculus) and CC1.3 (H.sapiens). These proteins are
characterized by an N-terminal arginine-rich, low
complexity domain followed by three (or in the case of
4 H. sapiens paralogs, two) RNA recognition domains
(rrm: pfam00706). These splicing factors are closely
related to the U2AF splicing factor family (TIGR01642).
A homologous gene from Plasmodium falciparum was
identified in the course of the analysis of that genome
at TIGR and was included in the seed.
Length = 457
Score = 27.6 bits (61), Expect = 8.3
Identities = 14/43 (32%), Positives = 19/43 (44%), Gaps = 1/43 (2%)
Query: 43 RRHQEEEERLEEEWRKHKAARERQRRIE-NRERGSRSNSEDRW 84
R E RL + R+ RER RR +R+R R D +
Sbjct: 1 RYRDRERGRLRNDTRRSDKGRERSRRRSRSRDRSRRRRDRDYY 43
>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC;
Provisional.
Length = 695
Score = 27.6 bits (62), Expect = 8.4
Identities = 17/54 (31%), Positives = 23/54 (42%), Gaps = 11/54 (20%)
Query: 20 RIEKLKHSKEI-ERKLQKQKEEETR-RHQE-----EEERLEEEWRKHKAARERQ 66
R K EI + +K+K EE + R + E E+ E R KAA R
Sbjct: 432 RQAK----AEIRAIEQEKKKAEEAKARFEARQARLEREKAAREARHKKAAEARA 481
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 27.7 bits (62), Expect = 8.5
Identities = 19/42 (45%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 219 DEEEMAVEFQEELPPKPK-GKRGRKKKIVLSPRSLTPTDEEE 259
DEE M+V +E +PP K GK G K + LS + LT + EE
Sbjct: 147 DEETMSVHLKEGVPPMAKKGKPGEWKLVRLSDKPLTREELEE 188
>gnl|CDD|220369 pfam09731, Mitofilin, Mitochondrial inner membrane protein.
Mitofilin controls mitochondrial cristae morphology.
Mitofilin is enriched in the narrow space between the
inner boundary and the outer membranes, where it forms a
homotypic interaction and assembles into a large
multimeric protein complex. The first 78 amino acids
contain a typical amino-terminal-cleavable mitochondrial
presequence rich in positive-charged and hydroxylated
residues and a membrane anchor domain. In addition, it
has three centrally located coiled coil domains.
Length = 493
Score = 27.7 bits (62), Expect = 8.5
Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 5/58 (8%)
Query: 18 STRIEKLKHS--KEIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQRRIENRE 73
S ++ +LK +E+ER L++++EE + EE L +AA E+Q R+E
Sbjct: 176 SKKLAELKAEEEEELERALKEKREELLS---KLEEELLARLESKEAALEKQLRLEFER 230
>gnl|CDD|233973 TIGR02680, TIGR02680, TIGR02680 family protein. Members of this
protein family belong to a conserved gene four-gene
neighborhood found sporadically in a phylogenetically
broad range of bacteria: Nocardia farcinica,
Symbiobacterium thermophilum, and Streptomyces
avermitilis (Actinobacteria), Geobacillus kaustophilus
(Firmicutes), Azoarcus sp. EbN1 and Ralstonia
solanacearum (Betaproteobacteria). Proteins in this
family average over 1400 amino acids in length
[Hypothetical proteins, Conserved].
Length = 1353
Score = 27.9 bits (62), Expect = 9.0
Identities = 12/57 (21%), Positives = 17/57 (29%), Gaps = 2/57 (3%)
Query: 32 RKLQKQKEEETRRHQEEEERLEE--EWRKHKAARERQRRIENRERGSRSNSEDRWTT 86
R+ + H R +E E + AAR G+R D W
Sbjct: 445 RRRDDVADRAEATHAAARARRDELDEEAEQAAARAELADEAVHREGARLAWVDAWQA 501
>gnl|CDD|237722 PRK14476, PRK14476, nitrogenase molybdenum-cofactor biosynthesis
protein NifN; Provisional.
Length = 455
Score = 27.5 bits (62), Expect = 9.2
Identities = 16/41 (39%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 224 AVE-FQEELPPKPKGKRGRKKKIVLSPRS-LTPTDEEEDKE 262
AVE E L P R +++ + P S LTP D EE +E
Sbjct: 149 AVEAIVEALVPPASSTGRRPRQVNVLPGSHLTPGDIEELRE 189
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family. Emg1 and Nop14 are novel
proteins whose interaction is required for the
maturation of the 18S rRNA and for 40S ribosome
production.
Length = 809
Score = 27.7 bits (62), Expect = 9.2
Identities = 13/42 (30%), Positives = 18/42 (42%)
Query: 47 EEEERLEEEWRKHKAARERQRRIENRERGSRSNSEDRWTTED 88
EEE EE R K ER RR+ E + + + +D
Sbjct: 260 EEELAKEEAERLKKLEAERLRRMRGEEEDDEEEEDSKESADD 301
>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function
unknown].
Length = 652
Score = 27.4 bits (61), Expect = 9.3
Identities = 15/59 (25%), Positives = 32/59 (54%), Gaps = 4/59 (6%)
Query: 20 RIEKLK-HSKEIERK---LQKQKEEETRRHQEEEERLEEEWRKHKAARERQRRIENRER 74
+E+L+ + E++R+ L+++ E+ + + ++ RK + R R RRIE E+
Sbjct: 430 TVERLEEENSELKRELEELKREIEKLESELERFRREVRDKVRKDREIRARDRRIERLEK 488
>gnl|CDD|163696 cd08065, MPN_eIF3h, Mpr1p, Pad1p N-terminal (MPN) domains without
catalytic isopeptidase activity, found in eIF2h.
Eukaryotic translation initiation factor 3 (eIF3)
subunit h (eIF3h; eIF3 subunit 3; eIF3S3; eIF3-gamma;
eIF3-p40) is an evolutionarily non-conserved subunit of
the functional core that comprises eIF3a, eIF3b, eIF3c,
eIF3e, eIF3f, and eIF3h, and contains the MPN domain.
However, it lacks the canonical JAMM motif, and
therefore does not show catalytic isopeptidase
activity.Together with eIF3e and eIF3f, eIF3h stabilizes
the eIF3 complex. Results suggest that eIF3h regulates
cell growth and viability, and that over-expression of
the gene may provide growth advantage to prostate,
breast, and liver cancer cells. For example, EIF3h gene
amplification is common in late-stage prostate cancer
suggesting that it may be functionally involved in the
progression of the disease. It has been shown that
coamplification of MYC, a well characterized oncogene
involved in cell growth, differentiation, and apoptosis,
and EIF3h in patients with non-small cell lung cancer
(NSCLC) improves survival if treated with the Epidermal
Growth Factor Receptor Tyrosine Kinase Inhibitor
(EGFR-TKI), Gefitinib. Plant eIF3h is implicated in
translation of specific mRNAs.
Length = 266
Score = 27.2 bits (61), Expect = 9.3
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 25 KHSKEIERKLQKQKEEETRRHQEEEERLEEE 55
+ +I++ LQK+K E +R EE L EE
Sbjct: 235 RQQAQIQQWLQKRKAENAQREARGEEPLPEE 265
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
0.311 0.129 0.369
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,544,867
Number of extensions: 1422131
Number of successful extensions: 4418
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3648
Number of HSP's successfully gapped: 695
Length of query: 277
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 181
Effective length of database: 6,679,618
Effective search space: 1209010858
Effective search space used: 1209010858
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 58 (26.2 bits)