RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780424|ref|YP_003064837.1| transcriptional regulator
protein [Candidatus Liberibacter asiaticus str. psy62]
(144 letters)
>gnl|CDD|128803 smart00530, HTH_XRE, Helix-turn-helix XRE-family like proteins.
Length = 56
Score = 50.6 bits (122), Expect = 1e-07
Identities = 13/56 (23%), Positives = 28/56 (50%)
Query: 18 RIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFF 73
R++ R G++QE+L E LG++ + + E G + L+ +++ L +
Sbjct: 1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
>gnl|CDD|182039 PRK09706, PRK09706, transcriptional repressor DicA; Reviewed.
Length = 135
Score = 39.1 bits (91), Expect = 4e-04
Identities = 30/134 (22%), Positives = 55/134 (41%), Gaps = 28/134 (20%)
Query: 15 VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLE-SPISFF 73
+G+RIR RR L +SQ L + + ++ + ++E+ L +++ L+ SP
Sbjct: 6 LGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSPTWLL 65
Query: 74 F---DVSPTVCSDISSEENNVMDFISTPDGLQLNRYFIQIDDVKVRQK-IIELVRSIVSS 129
F D PT P L +++ + QK ++EL ++ S
Sbjct: 66 FGDEDKQPT-----------------PPVPLNQP---VELSE---DQKELLELFDALPES 102
Query: 130 EKKYRTIEEECMVE 143
E+ + E VE
Sbjct: 103 EQDAQLSEMRARVE 116
>gnl|CDD|182158 PRK09943, PRK09943, DNA-binding transcriptional repressor PuuR;
Provisional.
Length = 185
Score = 35.9 bits (83), Expect = 0.004
Identities = 18/66 (27%), Positives = 29/66 (43%)
Query: 9 NPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLES 68
+ + GKR+ R G+SQ + E G+T + E+ S LQ + +V
Sbjct: 2 SDEGLAPGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGL 61
Query: 69 PISFFF 74
+S FF
Sbjct: 62 SLSEFF 67
>gnl|CDD|179747 PRK04140, PRK04140, hypothetical protein; Provisional.
Length = 317
Score = 33.3 bits (77), Expect = 0.022
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 11 VDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPI 70
V I+ G +R R LG+S +L LG++ + + KYE G + E+L+ P+
Sbjct: 124 VKID-GDVLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDVPL 182
>gnl|CDD|181256 PRK08154, PRK08154, anaerobic benzoate catabolism transcriptional
regulator; Reviewed.
Length = 309
Score = 33.0 bits (76), Expect = 0.028
Identities = 14/56 (25%), Positives = 29/56 (51%)
Query: 15 VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPI 70
+G+R+R R GMS++ L + G++ + + + E G V L+ ++ L +
Sbjct: 29 LGERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSL 84
>gnl|CDD|163542 TIGR03830, CxxCG_CxxCG_HTH, putative zinc finger/helix-turn-helix
protein, YgiT family. This model describes a family of
predicted regulatory proteins with a conserved zinc
finger/HTH architecture. The amino-terminal region
contains a novel domain, featuring two CXXC motifs and
occuring in a number of small bacterial proteins as well
as in the present family. The carboxyl-terminal region
consists of a helix-turn-helix domain, modeled by
pfam01381. The predicted function is DNA binding and
transcriptional regulation.
Length = 127
Score = 29.1 bits (66), Expect = 0.43
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 17 KRIRLRRMILGMSQEKLGECLGITFQQVQKYEKG 50
+RIR + LG+SQ + E LG +YE+G
Sbjct: 71 RRIRKK---LGLSQREAAELLGGGVNAFSRYERG 101
>gnl|CDD|163124 TIGR03070, couple_hipB, transcriptional regulator, y4mF family.
Members of this family belong to a clade of
helix-turn-helix DNA-binding proteins, among the larger
family pfam01381 (HTH_3; Helix-turn-helix). Members are
similar in sequence to the HipB protein of E. coli.
Genes for members of the seed alignment for this
protein family were found to be closely linked to genes
encoding proteins related to HipA. The HibBA operon
appears to have some features in common with
toxin-antitoxin post-segregational killing systems.
Length = 58
Score = 28.8 bits (65), Expect = 0.51
Identities = 16/54 (29%), Positives = 28/54 (51%), Gaps = 3/54 (5%)
Query: 15 VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLES 68
+G +R RR LG++Q L + G+ + ++ E G V RL + VL++
Sbjct: 3 IGMLVRARRKALGLTQADLADLAGVGLRFIRDVENGKPTV---RLDKVLRVLDA 53
>gnl|CDD|131661 TIGR02612, mob_myst_A, mobile mystery protein A. Members of this
protein family are found in mobization-related contexts
more often than not, including within a
CRISPR-associated gene region in Geobacter
sulfurreducens PCA, and on plasmids in Agrobacterium
tumefaciens and Coxiella burnetii, always together with
mobile mystery protein B, a member of the Fic protein
family (pfam02661). This protein is encoded by the
upstream member of the gene pair and belongs to a
family of helix-turn-helix DNA binding proteins
(pfam01381).
Length = 150
Score = 27.9 bits (62), Expect = 1.1
Identities = 14/31 (45%), Positives = 19/31 (61%)
Query: 19 IRLRRMILGMSQEKLGECLGITFQQVQKYEK 49
+R R LGMS +L LG+T Q+V+ EK
Sbjct: 30 VRAIRKALGMSGAQLAGRLGVTPQRVEALEK 60
>gnl|CDD|148573 pfam07037, DUF1323, Putative transcription regulator (DUF1323).
This family consists of several hypothetical
Enterobacterial proteins of around 120 residues in
length. This family appears to have an HTH domain and
is therefore likely to act as a transcriptional
regulator.
Length = 122
Score = 27.4 bits (61), Expect = 1.5
Identities = 13/46 (28%), Positives = 22/46 (47%), Gaps = 9/46 (19%)
Query: 28 MSQEKLGECLGITFQQVQKY--EKGVNRV-------GASRLQHISE 64
M+ E+L E G + Q + ++ ++G G +RL HI E
Sbjct: 1 MTPEELAELTGYSRQTINRWVRKEGWKTSPKPGVKGGKARLIHIDE 46
>gnl|CDD|183883 PRK13188, PRK13188, bifunctional UDP-3-O-[3-hydroxymyristoyl]
N-acetylglucosamine
deacetylase/(3R)-hydroxymyristoyl-[acyl-carrier-protein]
dehydratase; Reviewed.
Length = 464
Score = 26.0 bits (58), Expect = 3.6
Identities = 9/15 (60%), Positives = 13/15 (86%)
Query: 106 YFIQIDDVKVRQKII 120
YF++ID VK RQK++
Sbjct: 403 YFMKIDKVKFRQKVV 417
>gnl|CDD|163078 TIGR02937, sigma70-ECF, RNA polymerase sigma factor, sigma-70
family. Several PFAM models hit segments of these
sequences including Sigma-70 region 2 (pfam04542) and
Sigma-70, region 4 (pfam04545), but not always above
their respective trusted cutoffs.
Length = 158
Score = 26.2 bits (58), Expect = 3.8
Identities = 9/33 (27%), Positives = 20/33 (60%)
Query: 17 KRIRLRRMILGMSQEKLGECLGITFQQVQKYEK 49
+ + + R + G+S +++ E LGI+ V++ K
Sbjct: 116 REVLVLRYLEGLSYKEIAEILGISVGTVKRRLK 148
>gnl|CDD|163142 TIGR03117, cas_csf4, CRISPR-associated DEAD/DEAH-box helicase Csf4.
Members of this family show up near CRISPR repeats in
Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp.
EbN1, and Rhodoferax ferrireducens DSM 15236. In the
latter two species, the CRISPR/cas locus is found on a
plasmid. This family is one of several characteristic of
a type of CRISPR-associated (cas) gene cluster we
designate Aferr after A. ferrooxidans, where it is both
chromosomal and the only type of cas gene cluster found.
The gene is designated csf4 (CRISPR/cas Subtype as in A.
ferrooxidans protein 1), as it lies farthest (fourth
closest) from the repeats in the A. ferrooxidans genome.
Length = 636
Score = 25.7 bits (56), Expect = 4.2
Identities = 19/103 (18%), Positives = 36/103 (34%), Gaps = 8/103 (7%)
Query: 19 IRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDVSP 78
+ LRR+ L + + G GI V + R+ A + + L D
Sbjct: 230 LSLRRLHLYVEKRHTGAGKGIVSAAVAAVSHCIQRLRALDVFGDGQTLC------LDAGN 283
Query: 79 TVCSDISSEENNVMDFISTPDGLQLNRY-FIQIDDVKVRQKII 120
+ ++ + +D S N+ + DVK + + I
Sbjct: 284 KELETLFADLDAALDACSVGRNRDENKKALSVVKDVK-KARFI 325
>gnl|CDD|183574 PRK12529, PRK12529, RNA polymerase sigma factor; Provisional.
Length = 178
Score = 25.7 bits (56), Expect = 4.9
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 5/35 (14%)
Query: 18 RIRLRRMIL-----GMSQEKLGECLGITFQQVQKY 47
R R+++ L GM Q+ + + L I V+KY
Sbjct: 129 RPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKY 163
>gnl|CDD|185111 PRK15189, PRK15189, fimbrial protein BcfD; Provisional.
Length = 335
Score = 25.5 bits (55), Expect = 5.7
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 78 PTVCSDISSEENNVMDFISTPD 99
P CS + S+ N M I+TPD
Sbjct: 237 PVKCSGLDSQVNLTMRLIATPD 258
>gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation
factor; Provisional.
Length = 614
Score = 25.0 bits (55), Expect = 6.9
Identities = 11/20 (55%), Positives = 11/20 (55%)
Query: 18 RIRLRRMILGMSQEKLGECL 37
R RLRRM L M E L L
Sbjct: 442 RERLRRMALPMEDEALVLLL 461
>gnl|CDD|180858 PRK07139, PRK07139, amidase; Provisional.
Length = 439
Score = 25.0 bits (55), Expect = 7.2
Identities = 19/85 (22%), Positives = 32/85 (37%), Gaps = 23/85 (27%)
Query: 22 RRMILGM------SQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFD 75
+R+ILG +QEK F + +K V RV + + +
Sbjct: 316 KRLILGSYFLEEENQEKY-------FLKAKK----VRRVIK---NYYESIHNKFDIVIYP 361
Query: 76 VSPTVCSDI---SSEENNVMDFIST 97
+ DI ++ +N MD+I T
Sbjct: 362 AYADIAPDIDENENKSDNYMDYILT 386
>gnl|CDD|185607 PTZ00422, PTZ00422, glideosome-associated protein 50; Provisional.
Length = 394
Score = 24.8 bits (54), Expect = 7.8
Identities = 13/68 (19%), Positives = 25/68 (36%)
Query: 55 GASRLQHISEVLESPISFFFDVSPTVCSDISSEENNVMDFISTPDGLQLNRYFIQIDDVK 114
G+ ++++ S F+ C + E V F+S G L + + K
Sbjct: 274 GSGGNSGRKSIMKNSKSLFYSEDIGFCIHELNAEGMVTKFVSGNTGEVLYTHKQPLKKRK 333
Query: 115 VRQKIIEL 122
+R + L
Sbjct: 334 LRFQGNAL 341
>gnl|CDD|180894 PRK07226, PRK07226, fructose-bisphosphate aldolase; Provisional.
Length = 267
Score = 24.8 bits (55), Expect = 9.7
Identities = 8/12 (66%), Positives = 10/12 (83%)
Query: 14 NVGKRIRLRRMI 25
N+GKRIRL R+
Sbjct: 3 NIGKRIRLERIF 14
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.319 0.137 0.378
Gapped
Lambda K H
0.267 0.0763 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,331,868
Number of extensions: 136488
Number of successful extensions: 288
Number of sequences better than 10.0: 1
Number of HSP's gapped: 287
Number of HSP's successfully gapped: 31
Length of query: 144
Length of database: 5,994,473
Length adjustment: 84
Effective length of query: 60
Effective length of database: 4,179,401
Effective search space: 250764060
Effective search space used: 250764060
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 (23.7 bits)