RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780424|ref|YP_003064837.1| transcriptional regulator
protein [Candidatus Liberibacter asiaticus str. psy62]
(144 letters)
>gnl|CDD|28977 cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins.
Prokaryotic DNA binding proteins belonging to the
xenobiotic response element family of transcriptional
regulators..
Length = 58
Score = 52.1 bits (125), Expect = 5e-08
Identities = 14/58 (24%), Positives = 29/58 (50%)
Query: 16 GKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFF 73
G+R++ R G++QE+L E LG++ + + E G L+ +++ L +
Sbjct: 1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
>gnl|CDD|144828 pfam01381, HTH_3, Helix-turn-helix. This large family of DNA
binding helix-turn helix proteins includes Cro and CI.
Length = 55
Score = 45.2 bits (108), Expect = 6e-06
Identities = 16/55 (29%), Positives = 27/55 (49%)
Query: 19 IRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFF 73
++ R LG+SQE+L E LG++ + K E G L+ ++E L +
Sbjct: 1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
>gnl|CDD|31586 COG1396, HipB, Predicted transcriptional regulators
[Transcription].
Length = 120
Score = 44.6 bits (103), Expect = 9e-06
Identities = 17/94 (18%), Positives = 37/94 (39%), Gaps = 1/94 (1%)
Query: 15 VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKG-VNRVGASRLQHISEVLESPISFF 73
+G+R++ R G+SQE+L E LG++ + + E+G L ++ L +
Sbjct: 2 IGERLKELRKKKGLSQEELAERLGVSRSTISRIERGRSESPSLELLARLAAALGVSLDEL 61
Query: 74 FDVSPTVCSDISSEENNVMDFISTPDGLQLNRYF 107
+ + + +E ++ L
Sbjct: 62 LEEEEELEIEELNELAKLLLLEEEELLAILEELI 95
>gnl|CDD|31585 COG1395, COG1395, Predicted transcriptional regulator
[Transcription].
Length = 313
Score = 32.9 bits (75), Expect = 0.032
Identities = 21/73 (28%), Positives = 35/73 (47%)
Query: 16 GKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFD 75
G+++R +R +G+S L LG++ + V KYEKG++ + E+ I D
Sbjct: 127 GEKLREKREEMGLSLGDLATMLGVSRKTVYKYEKGLSDASLEVALKLEEIFGEDIVKPID 186
Query: 76 VSPTVCSDISSEE 88
+ DI EE
Sbjct: 187 ILKIPEDDIKLEE 199
>gnl|CDD|32182 COG1999, COG1999, Uncharacterized protein SCO1/SenC/PrrC, involved
in biogenesis of respiratory and photosynthetic systems
[General function prediction only].
Length = 207
Score = 31.9 bits (72), Expect = 0.059
Identities = 9/42 (21%), Positives = 18/42 (42%)
Query: 70 ISFFFDVSPTVCSDISSEENNVMDFISTPDGLQLNRYFIQID 111
+ F + P VC +E ++ + +G + FI +D
Sbjct: 72 VFFGYTHCPDVCPTTLAELKALLKKLGEGEGDDVQVVFITVD 113
>gnl|CDD|31665 COG1476, COG1476, Predicted transcriptional regulators
[Transcription].
Length = 68
Score = 30.6 bits (69), Expect = 0.17
Identities = 11/33 (33%), Positives = 22/33 (66%)
Query: 18 RIRLRRMILGMSQEKLGECLGITFQQVQKYEKG 50
+++ R LG++QE+L + +G++ Q + EKG
Sbjct: 5 KLKELRAELGLTQEELAKLVGVSRQTIIAIEKG 37
>gnl|CDD|31998 COG1813, COG1813, Predicted transcription factor, homolog of
eukaryotic MBF1 [Transcription].
Length = 165
Score = 30.3 bits (68), Expect = 0.21
Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 3/56 (5%)
Query: 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKG---VNRVGASRLQHISEVL 66
+ G+RIR R G+SQE L L +++ E+G N A +L+ + +
Sbjct: 79 DYGERIREAREKRGLSQEDLAAKLKEKVSVIRRIERGEATPNIKVAKKLEKLLGIK 134
>gnl|CDD|32767 COG2944, COG2944, Predicted transcriptional regulator
[Transcription].
Length = 104
Score = 29.5 bits (66), Expect = 0.34
Identities = 14/49 (28%), Positives = 22/49 (44%)
Query: 5 KKIPNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNR 53
K V I+ R LG+SQ LG++ V+K+E+G +
Sbjct: 35 KACLLKVKTLSPTEIKAIREKLGLSQPVFARYLGVSVSTVRKWEQGRKK 83
>gnl|CDD|33419 COG3620, COG3620, Predicted transcriptional regulator with
C-terminal CBS domains [Transcription].
Length = 187
Score = 28.7 bits (64), Expect = 0.52
Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 6/61 (9%)
Query: 7 IPNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVL 66
+P P D+ R RR LG++Q+ L G++ + + E G S ++ I E L
Sbjct: 4 LPTPEDL------RKRRKELGITQKDLARRAGVSQPYIARLEAGKVDPRLSTVKRILEAL 57
Query: 67 E 67
E
Sbjct: 58 E 58
>gnl|CDD|35671 KOG0450, KOG0450, KOG0450, 2-oxoglutarate dehydrogenase, E1 subunit
[Carbohydrate transport and metabolism].
Length = 1017
Score = 27.2 bits (60), Expect = 1.7
Identities = 28/121 (23%), Positives = 51/121 (42%), Gaps = 18/121 (14%)
Query: 17 KRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRV-----GASR---LQHISEVLES 68
K+IR + +L EKL ++ Q+V + K + + S+ HI + L+S
Sbjct: 527 KQIRKHKPVLQKYAEKLLSEGTVSQQEVDEEIKKYDNILEEAFERSKDYKPLHIRDWLDS 586
Query: 69 PISFFFDVS----PTVCSDISSEENNVMD----FISTPDGLQLNRYFIQIDDVKVRQKII 120
P FF C +E + S P+G +++R +I +K R ++I
Sbjct: 587 PWPGFFSPDGQPKILPCPSTGVKEEILKHIGKVASSVPEGFKIHRGLKRI--LKNRAQMI 644
Query: 121 E 121
+
Sbjct: 645 K 645
>gnl|CDD|48517 cd02968, SCO, SCO (an acronym for Synthesis of Cytochrome c
Oxidase) family; composed of proteins similar to Sco1, a
membrane-anchored protein possessing a soluble domain
with a TRX fold. Members of this family are required for
the proper assembly of cytochrome c oxidase (COX). They
contain a metal binding motif, typically CXXXC, which is
located in a flexible loop. COX, the terminal enzyme in
the respiratory chain, is imbedded in the inner
mitochondrial membrane of all eukaryotes and in the
plasma membrane of some prokaryotes. It is composed of
two subunits, COX I and COX II. It has been proposed
that Sco1 specifically delivers copper to the CuA site,
a dinuclear copper center, of the COX II subunit.
Mutations in human Sco1 and Sco2 cause fatal infantile
hepatoencephalomyopathy and cardioencephalomyopathy,
respectively. Both disorders are associated with severe
COX deficiency in affected tissues. More recently, it
has been argued that the redox sensitivity of the copper
binding properties of Sco1 implies that it participates
in signaling events rather than functioning as a
chaperone that transfers copper to COX II..
Length = 142
Score = 27.1 bits (60), Expect = 2.0
Identities = 8/42 (19%), Positives = 15/42 (35%)
Query: 70 ISFFFDVSPTVCSDISSEENNVMDFISTPDGLQLNRYFIQID 111
+ F + P VC + + + G + FI +D
Sbjct: 27 VYFGYTHCPDVCPTTLANLAQALKQLGADGGDDVQVVFISVD 68
>gnl|CDD|143925 pfam00157, Pou, Pou domain - N-terminal to homeobox domain.
Length = 75
Score = 26.9 bits (60), Expect = 2.3
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 17 KRIRLRRMILGMSQEKLGECLGITF 41
K + RR+ LG +Q +G LG +
Sbjct: 14 KEFKQRRIKLGYTQADVGLALGALY 38
>gnl|CDD|34535 COG4926, PblB, Phage-related protein [Function unknown].
Length = 698
Score = 25.8 bits (56), Expect = 4.3
Identities = 18/53 (33%), Positives = 23/53 (43%), Gaps = 2/53 (3%)
Query: 54 VGASRLQHISEVLESPISFFFDVSPTVCSDISSEENNVMDFISTPDGLQLNRY 106
A L S V E P FF D+S + E NV++ I DG L+ Y
Sbjct: 113 ATAMELLKDSLVGEHPFEFFSDISTL--GSFNWEIKNVLEAIGGLDGSILDVY 163
>gnl|CDD|37039 KOG1828, KOG1828, KOG1828, IRF-2-binding protein CELTIX-1, contains
BROMO domain [Transcription].
Length = 418
Score = 25.8 bits (56), Expect = 4.8
Identities = 11/54 (20%), Positives = 20/54 (37%), Gaps = 3/54 (5%)
Query: 56 ASRLQHISEVLES--PISFF-FDVSPTVCSDISSEENNVMDFISTPDGLQLNRY 106
+ +H L S P F F ++ + + + MD I+ + RY
Sbjct: 21 SGDAEHHLRKLPSKDPKQKFAFPLTDKMAPNYLEIISEPMDRITKRSKIDDTRY 74
>gnl|CDD|147776 pfam05804, KAP, Kinesin-associated protein (KAP). This family
consists of several eukaryotic kinesin-associated (KAP)
proteins. Kinesins are intracellular multimeric
transport motor proteins that move cellular cargo on
microtubule tracks. It has been shown that the sea
urchin KRP85/95 holoenzyme associates with a KAP115
non-motor protein, forming a heterotrimeric complex in
vitro, called the Kinesin-II.
Length = 708
Score = 25.6 bits (56), Expect = 5.1
Identities = 16/84 (19%), Positives = 36/84 (42%), Gaps = 5/84 (5%)
Query: 17 KRIRLRRM-----ILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPIS 71
K IRL+ + I +++E + +C I ++ + E+ + + + S S +
Sbjct: 42 KIIRLKSLNADTDIAALAREVVEKCKLIHPSKLNEVEQLLFYLQNRKDSRSSARSRSSSA 101
Query: 72 FFFDVSPTVCSDISSEENNVMDFI 95
D P I + N++ ++I
Sbjct: 102 KSKDPPPIEGPTIDANINDIDEYI 125
>gnl|CDD|147229 pfam04952, AstE_AspA, Succinylglutamate desuccinylase /
Aspartoacylase family. This family includes
Succinylglutamate desuccinylase EC:3.1.-.- that
catalyses the fifth and last step in arginine catabolism
by the arginine succinyltransferase pathway. The family
also include aspartoacylase EC:3.5.1.15 which cleaves
acylaspartate into a fatty acid and aspartate. Mutations
in human aspartoacylase (ACY-2) lead to Canavan disease.
This family is probably structurally related to
pfam00246 (Bateman A pers. obs.).
Length = 289
Score = 25.4 bits (56), Expect = 5.5
Identities = 10/40 (25%), Positives = 17/40 (42%), Gaps = 5/40 (12%)
Query: 33 LGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISF 72
LG + + + GV V L+HI V+ ++F
Sbjct: 168 LGGAGVLGADLISRTAAGVLNV----LRHI-GVVAGGLTF 202
>gnl|CDD|34678 COG5074, COG5074, t-SNARE complex subunit, syntaxin [Intracellular
trafficking and secretion].
Length = 280
Score = 25.4 bits (55), Expect = 5.6
Identities = 23/103 (22%), Positives = 42/103 (40%), Gaps = 4/103 (3%)
Query: 44 VQKYEKGVNRVGASRLQHISEVLESPISFFFDVSPTVCSDISSEENNVMD--FISTPDGL 101
+ YEK +N++ ++EV E S + + N+ + DG+
Sbjct: 34 LSVYEKEINQIDNLHKDLLTEVFEEQSRKLRRSLDNFSSQTTDLQRNLKKDIKSAERDGI 93
Query: 102 QLNRYFIQIDDVKVRQKIIELVRSIVSSEKKYRTIEEECMVEQ 144
L Q ++V RQK ++L++ + YR E+E Q
Sbjct: 94 HLANKQAQAENV--RQKFLKLIQDYRIIDSNYREEEKEQARRQ 134
>gnl|CDD|153288 cd07604, BAR_ASAPs, The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP
with SH3 domain, ANK repeat and PH domain containing
proteins. BAR domains are dimerization, lipid binding
and curvature sensing modules found in many different
proteins with diverse functions. This subfamily is
composed of ASAPs (ArfGAP with SH3 domain, ANK repeat
and PH domain containing proteins), which are Arf GTPase
activating proteins (GAPs) with similarity to ACAPs
(ArfGAP with Coiled-coil, ANK repeat and PH domain
containing proteins) in that they contain an N-terminal
BAR domain, followed by a Pleckstrin homology (PH)
domain, an Arf GAP domain, and ankyrin (ANK) repeats.
However, ASAPs contain an additional C-terminal SH3
domain. ASAPs function in regulating cell growth,
migration, and invasion. Vertebrates contain at least
three members, ASAP1, ASAP2, and ASAP3. ASAP1 and ASAP2
shows GTPase activating protein (GAP) activity towards
Arf1 and Arf5. They do not show GAP activity towards
Arf6, but is able to mediate Arf6 signaling by binding
stably to GTP-Arf6. ASAP3 is an Arf6-specific GAP. BAR
domains form dimers that bind to membranes, induce
membrane bending and curvature, and may also be involved
in protein-protein interactions. The BAR domain of ASAP1
mediates membrane bending, is essential for function,
and autoinhibits GAP activity by interacting with the PH
and/or Arf GAP domains.
Length = 215
Score = 25.1 bits (55), Expect = 7.0
Identities = 7/27 (25%), Positives = 20/27 (74%), Gaps = 1/27 (3%)
Query: 101 LQLNRYFIQIDDVKVRQKIIELVRSIV 127
LQ+ Y I+++++K ++ ++L++ +V
Sbjct: 163 LQMCEYLIKVNEIKTKKG-VDLLQHLV 188
>gnl|CDD|32592 COG2522, COG2522, Predicted transcriptional regulator [General
function prediction only].
Length = 119
Score = 24.9 bits (54), Expect = 8.0
Identities = 15/41 (36%), Positives = 25/41 (60%), Gaps = 2/41 (4%)
Query: 27 GMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLE 67
G+SQ ++ + LG+T V +Y G + G++RL+ I E E
Sbjct: 22 GLSQYRIAKLLGLTQAAVSQYLSG--KRGSARLEDIGETDE 60
>gnl|CDD|31895 COG1709, COG1709, Predicted transcriptional regulator
[Transcription].
Length = 241
Score = 24.8 bits (54), Expect = 8.6
Identities = 12/37 (32%), Positives = 20/37 (54%)
Query: 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKG 50
+ G+ +R R I +SQ +L LG++ + YE G
Sbjct: 27 DPGETLRKWREIFNVSQTELARELGVSPSVISDYESG 63
>gnl|CDD|31615 COG1426, COG1426, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 284
Score = 24.7 bits (53), Expect = 9.7
Identities = 10/38 (26%), Positives = 18/38 (47%)
Query: 13 INVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKG 50
+G+R+R R G+S E + I ++ E+G
Sbjct: 2 KTLGERLRQAREEKGLSLEDVAARTKIRKSYLRALEEG 39
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.319 0.137 0.378
Gapped
Lambda K H
0.267 0.0615 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,706,370
Number of extensions: 82174
Number of successful extensions: 223
Number of sequences better than 10.0: 1
Number of HSP's gapped: 223
Number of HSP's successfully gapped: 31
Length of query: 144
Length of database: 6,263,737
Length adjustment: 85
Effective length of query: 59
Effective length of database: 4,426,972
Effective search space: 261191348
Effective search space used: 261191348
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: 52 (24.1 bits)