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)