RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780693|ref|YP_003065106.1| transcriptional regulator protein [Candidatus Liberibacter asiaticus str. psy62] (235 letters) >gnl|CDD|128698 smart00421, HTH_LUXR, helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon. Length = 58 Score = 73.3 bits (181), Expect = 4e-14 Identities = 24/58 (41%), Positives = 35/58 (60%) Query: 171 ARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKA 228 +LT RE L+L +G T++EIAE+LG+S TV +L + KL +R QA+ A Sbjct: 1 LASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58 >gnl|CDD|163106 TIGR03020, EpsA, transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes. Length = 247 Score = 53.6 bits (129), Expect = 4e-08 Identities = 29/61 (47%), Positives = 35/61 (57%) Query: 170 AARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAI 229 +A +T RE L DG T+EEIA LG+S TV +L KLD NR QA+AKAI Sbjct: 187 SAGLITAREAEILAWVRDGKTNEEIAAILGISSLTVKNHLQHIFKKLDVRNRAQAVAKAI 246 Query: 230 R 230 Sbjct: 247 A 247 >gnl|CDD|132580 TIGR03541, reg_near_HchA, LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene. Length = 232 Score = 49.4 bits (118), Expect = 8e-07 Identities = 27/79 (34%), Positives = 34/79 (43%), Gaps = 4/79 (5%) Query: 160 FLELFKKRSSAARN----LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVK 215 F + + L+ERE L G +IA LG+S TV +L SA K Sbjct: 154 FFAARRLLEAPLLREAGVLSEREREVLAWTALGRRQADIAAILGISERTVENHLRSARRK 213 Query: 216 LDAVNRIQAIAKAIRFGYI 234 L QAIA A+R G I Sbjct: 214 LGVATTAQAIAIALRKGDI 232 >gnl|CDD|185267 PRK15369, PRK15369, two component system sensor kinase SsrB; Provisional. Length = 211 Score = 40.1 bits (94), Expect = 6e-04 Identities = 23/61 (37%), Positives = 34/61 (55%) Query: 174 LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGY 233 LT RE L+L +GYT+ +IAE+L +S+ TV + + KLD + + A R G Sbjct: 150 LTPRERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELLNWARRLGL 209 Query: 234 I 234 I Sbjct: 210 I 210 >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 = 38.1 bits (89), Expect = 0.002 Identities = 22/48 (45%), Positives = 26/48 (54%), Gaps = 1/48 (2%) Query: 170 AARNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 A L ERE L L +G + +EIAE LG+SV TV L A KL Sbjct: 107 ALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154 >gnl|CDD|182408 PRK10360, PRK10360, DNA-binding transcriptional activator UhpA; Provisional. Length = 196 Score = 38.0 bits (88), Expect = 0.002 Identities = 23/75 (30%), Positives = 34/75 (45%), Gaps = 3/75 (4%) Query: 149 AHGACYQVITDFLELFKKRSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAY 208 A G CY ++L R LT+RE + G +EIA +LGLS TV+ + Sbjct: 116 ATGGCYLTPDIAIKLASGRQDP---LTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVH 172 Query: 209 LGSATVKLDAVNRIQ 223 + KL N ++ Sbjct: 173 RANLMEKLGVSNDVE 187 >gnl|CDD|182292 PRK10188, PRK10188, DNA-binding transcriptional activator SdiA; Provisional. Length = 240 Score = 35.9 bits (83), Expect = 0.009 Identities = 22/62 (35%), Positives = 32/62 (51%) Query: 173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFG 232 N ++RE L+ +G TS EIA L +S +TVN + + K +A N+ Q A G Sbjct: 179 NFSKREKEILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQIACYAAATG 238 Query: 233 YI 234 I Sbjct: 239 LI 240 >gnl|CDD|182771 PRK10840, PRK10840, transcriptional regulator RcsB; Provisional. Length = 216 Score = 36.0 bits (83), Expect = 0.009 Identities = 21/67 (31%), Positives = 36/67 (53%), Gaps = 3/67 (4%) Query: 159 DFLELFKKRSSAA---RNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVK 215 L +K S+ + L+ +E+ L+L +G+ EIA+KL S+ T+++ SA +K Sbjct: 133 SVSRLLEKISAGGYGDKRLSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMK 192 Query: 216 LDAVNRI 222 L N I Sbjct: 193 LGVENDI 199 >gnl|CDD|182431 PRK10403, PRK10403, transcriptional regulator NarP; Provisional. Length = 215 Score = 35.2 bits (81), Expect = 0.014 Identities = 19/63 (30%), Positives = 31/63 (49%) Query: 162 ELFKKRSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNR 221 E+F LTERE L G ++++IA L +S TV ++ + KL+ +R Sbjct: 142 EMFGAEEDPFSVLTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSR 201 Query: 222 IQA 224 + A Sbjct: 202 VAA 204 >gnl|CDD|181897 PRK09483, PRK09483, response regulator; Provisional. Length = 217 Score = 34.7 bits (80), Expect = 0.019 Identities = 21/59 (35%), Positives = 30/59 (50%) Query: 174 LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFG 232 L+ERE + + G EI+E+L LS TVN+Y KL+ ++ AIR G Sbjct: 149 LSERELQIMLMITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVELTHLAIRHG 207 >gnl|CDD|116865 pfam08281, Sigma70_r4_2, Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Length = 54 Score = 34.4 bits (80), Expect = 0.030 Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 1/37 (2%) Query: 174 LTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYL 209 L R+ L +G + EIAE LG+S TV + L Sbjct: 11 LPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRL 47 >gnl|CDD|132030 TIGR02985, Sig70_bacteroi1, RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium. Length = 161 Score = 33.3 bits (77), Expect = 0.048 Identities = 13/29 (44%), Positives = 20/29 (68%) Query: 188 GYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 G + +EIAE+LG+SV TV ++ A +L Sbjct: 129 GKSYKEIAEELGISVKTVEYHISKALKEL 157 >gnl|CDD|184142 PRK13558, PRK13558, bacterio-opsin activator; Provisional. Length = 665 Score = 33.3 bits (76), Expect = 0.053 Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 8/58 (13%) Query: 167 RSSAARNLTERETSCLQLAG-DGY-------TSEEIAEKLGLSVHTVNAYLGSATVKL 216 R+S +LT+R+ + LQ A GY EE+AE +G+S T + +L +A KL Sbjct: 601 RASLENDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQHLRAAERKL 658 >gnl|CDD|182154 PRK09935, PRK09935, transcriptional regulator FimZ; Provisional. Length = 210 Score = 32.9 bits (75), Expect = 0.066 Identities = 20/63 (31%), Positives = 34/63 (53%) Query: 166 KRSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAI 225 SS L+ RE + L+ G +++EIA++L LS TV+A+ + KL + ++ I Sbjct: 142 TNSSTDTVLSNREVTILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHSIVELI 201 Query: 226 AKA 228 A Sbjct: 202 DYA 204 >gnl|CDD|182619 PRK10651, PRK10651, transcriptional regulator NarL; Provisional. Length = 216 Score = 33.1 bits (76), Expect = 0.073 Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 3/65 (4%) Query: 163 LFKKRSSAAR---NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAV 219 L R++ R LT RE L+L G ++ IA +L ++ TV ++ K+ Sbjct: 142 LRANRATTERDVNQLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLK 201 Query: 220 NRIQA 224 +R++A Sbjct: 202 SRVEA 206 >gnl|CDD|179885 PRK04841, PRK04841, transcriptional regulator MalT; Provisional. Length = 903 Score = 33.0 bits (76), Expect = 0.076 Identities = 18/55 (32%), Positives = 32/55 (58%) Query: 174 LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKA 228 LT+RE L L GY++E+IA +L ++ T+ ++ + KL +R +A+ A Sbjct: 839 LTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEAVQHA 893 >gnl|CDD|182241 PRK10100, PRK10100, DNA-binding transcriptional regulator CsgD; Provisional. Length = 216 Score = 32.5 bits (74), Expect = 0.094 Identities = 20/55 (36%), Positives = 29/55 (52%) Query: 174 LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKA 228 LT RE L G ++ EIA L +S +TV +L + K+ NR QA++ A Sbjct: 156 LTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAVSWA 210 >gnl|CDD|182015 PRK09646, PRK09646, RNA polymerase sigma factor SigK; Reviewed. Length = 194 Score = 32.3 bits (74), Expect = 0.11 Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 1/35 (2%) Query: 172 RNLTERETSCLQLAG-DGYTSEEIAEKLGLSVHTV 205 LT+ + + LA G T E+AE+L + + TV Sbjct: 141 DALTDTQRESVTLAYYGGLTYREVAERLAVPLGTV 175 >gnl|CDD|132028 TIGR02983, SigE-fam_strep, RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives. Length = 162 Score = 31.6 bits (72), Expect = 0.18 Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 1/48 (2%) Query: 170 AARNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 A R L R+ + + L + + ++AE LG+SV TV + L A +L Sbjct: 107 ALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARL 154 >gnl|CDD|179690 PRK03975, tfx, putative transcriptional regulator; Provisional. Length = 141 Score = 31.0 bits (71), Expect = 0.24 Identities = 14/29 (48%), Positives = 18/29 (62%) Query: 173 NLTERETSCLQLAGDGYTSEEIAEKLGLS 201 LTER+ L+L G T +EIA+ LG S Sbjct: 6 FLTERQIEVLRLRERGLTQQEIADILGTS 34 >gnl|CDD|182011 PRK09639, PRK09639, RNA polymerase sigma factor SigX; Provisional. Length = 166 Score = 30.7 bits (70), Expect = 0.32 Identities = 14/33 (42%), Positives = 21/33 (63%) Query: 173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTV 205 +TER+ + L L GY+ +EIAE LG+ +V Sbjct: 112 KMTERDRTVLLLRFSGYSYKEIAEALGIKESSV 144 >gnl|CDD|163591 TIGR03879, near_KaiC_dom, probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation. Length = 73 Score = 30.1 bits (68), Expect = 0.46 Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 9/51 (17%) Query: 172 RNLTERET-------SCLQLAGD--GYTSEEIAEKLGLSVHTVNAYLGSAT 213 + L ER T + LA + G T+ EIAE+LG + TV +L T Sbjct: 7 KKLAERLTWVDSLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKGET 57 >gnl|CDD|183569 PRK12517, PRK12517, RNA polymerase sigma factor; Provisional. Length = 188 Score = 30.0 bits (68), Expect = 0.50 Identities = 16/33 (48%), Positives = 21/33 (63%), Gaps = 1/33 (3%) Query: 177 RETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYL 209 RE LQ+ G G++ EEIAE L L+ +TV L Sbjct: 134 REPLLLQVIG-GFSGEEIAEILDLNKNTVMTRL 165 >gnl|CDD|183572 PRK12523, PRK12523, RNA polymerase sigma factor; Reviewed. Length = 172 Score = 30.2 bits (68), Expect = 0.50 Identities = 13/26 (50%), Positives = 15/26 (57%) Query: 187 DGYTSEEIAEKLGLSVHTVNAYLGSA 212 DG EIAE+LG+SV V YL Sbjct: 134 DGMGHAEIAERLGVSVSRVRQYLAQG 159 >gnl|CDD|182018 PRK09651, PRK09651, RNA polymerase sigma factor FecI; Provisional. Length = 172 Score = 30.2 bits (68), Expect = 0.53 Identities = 15/27 (55%), Positives = 18/27 (66%) Query: 187 DGYTSEEIAEKLGLSVHTVNAYLGSAT 213 DG T EIA KLG+SV +V Y+ AT Sbjct: 134 DGLTYSEIAHKLGVSVSSVKKYVAKAT 160 >gnl|CDD|116253 pfam07638, Sigma70_ECF, ECF sigma factor. These proteins are probably RNA polymerase sigma factors belonging to the extra-cytoplasmic function (ECF) subfamily and show sequence similarity to pfam04542 and pfam04545. Length = 185 Score = 30.1 bits (68), Expect = 0.58 Identities = 10/19 (52%), Positives = 15/19 (78%) Query: 187 DGYTSEEIAEKLGLSVHTV 205 G +++EIAE+LG+S TV Sbjct: 150 AGLSNDEIAERLGVSERTV 168 >gnl|CDD|171561 PRK12528, PRK12528, RNA polymerase sigma factor; Provisional. Length = 161 Score = 29.4 bits (66), Expect = 0.81 Identities = 13/29 (44%), Positives = 18/29 (62%) Query: 187 DGYTSEEIAEKLGLSVHTVNAYLGSATVK 215 DG EIA +LG+S+ TV YL A ++ Sbjct: 128 DGLGYGEIATELGISLATVKRYLNKAAMR 156 >gnl|CDD|164986 PHA02591, PHA02591, hypothetical protein; Provisional. Length = 83 Score = 29.3 bits (65), Expect = 0.88 Identities = 15/29 (51%), Positives = 19/29 (65%) Query: 183 QLAGDGYTSEEIAEKLGLSVHTVNAYLGS 211 +LA G+T E+IA LG+SV V YL S Sbjct: 54 ELARKGFTVEKIASLLGVSVRKVRRYLES 82 >gnl|CDD|165035 PHA02656, PHA02656, viral TNFR II-like protein; Provisional. Length = 199 Score = 29.2 bits (65), Expect = 0.89 Identities = 14/54 (25%), Positives = 28/54 (51%) Query: 149 AHGACYQVITDFLELFKKRSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSV 202 + G+ Y+ I + +F + +NL R+ SC++ D + S I +K +S+ Sbjct: 20 SKGSNYEEIQNKFTMFVDLTVYDKNLINRDVSCIRYDHDDFYSMYIIDKFNVSI 73 >gnl|CDD|179909 PRK04984, PRK04984, fatty acid metabolism regulator; Provisional. Length = 239 Score = 28.7 bits (65), Expect = 1.3 Identities = 15/55 (27%), Positives = 22/55 (40%), Gaps = 14/55 (25%) Query: 41 ALDFPRRQQLICELHNYDLDSGDIPNILIETYGDDFLFHFNSGLLPIIWQSIQEE 95 AL F + +CE N+D +P + YG SG IW +Q+ Sbjct: 189 ALGFYHKLSALCEEGNHD----QVPE-CVRQYG------IESGE---IWHRMQKN 229 >gnl|CDD|132044 TIGR02999, Sig-70_X6, RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five. Length = 183 Score = 28.8 bits (65), Expect = 1.4 Identities = 13/18 (72%), Positives = 14/18 (77%) Query: 188 GYTSEEIAEKLGLSVHTV 205 G T EEIAE LG+SV TV Sbjct: 150 GLTVEEIAELLGVSVRTV 167 >gnl|CDD|171568 PRK12537, PRK12537, RNA polymerase sigma factor; Provisional. Length = 182 Score = 28.6 bits (64), Expect = 1.7 Identities = 12/33 (36%), Positives = 18/33 (54%) Query: 177 RETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYL 209 R L DG + EIA++LG + TV A++ Sbjct: 138 RRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWI 170 >gnl|CDD|128803 smart00530, HTH_XRE, Helix-turn-helix XRE-family like proteins. Length = 56 Score = 28.3 bits (64), Expect = 2.0 Identities = 16/44 (36%), Positives = 25/44 (56%), Gaps = 4/44 (9%) Query: 188 GYTSEEIAEKLGLSVHTVNAYL-GSATVKLDAVNRIQAIAKAIR 230 G T EE+AEKLG+S T++ G L+ ++ +AKA+ Sbjct: 10 GLTQEELAEKLGVSRSTLSRIENGKRKPSLE---TLKKLAKALG 50 >gnl|CDD|132005 TIGR02960, SigX5, RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. Length = 324 Score = 27.9 bits (62), Expect = 2.6 Identities = 14/32 (43%), Positives = 18/32 (56%) Query: 188 GYTSEEIAEKLGLSVHTVNAYLGSATVKLDAV 219 G+ + E AE LG S +VN+ L A LD V Sbjct: 158 GWRAAETAELLGTSTASVNSALQRARATLDEV 189 >gnl|CDD|181072 PRK07661, PRK07661, acetyl-CoA acetyltransferase; Provisional. Length = 391 Score = 27.8 bits (62), Expect = 2.8 Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 9/47 (19%) Query: 186 GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFG 232 G G+T+E++A K G+S +A+ AV Q AKA+ G Sbjct: 146 GMGHTAEQVAVKYGISREDQDAF---------AVRSHQRAAKALAEG 183 >gnl|CDD|132034 TIGR02989, Sig-70_gvs1, RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2). Length = 159 Score = 27.2 bits (61), Expect = 3.4 Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 1/44 (2%) Query: 174 LTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 L ER+ LQL G + +AE+LG +V+ V L V+L Sbjct: 112 LPERQRELLQLRYQRGVSLTALAEQLGRTVNAVYKALSRLRVRL 155 >gnl|CDD|116452 pfam07840, FadR_C, FadR C-terminal domain. This family contains sequences that are similar to the fatty acid metabolism regulator protein (FadR). This functions as a dimer, with each monomer being composed of an N-terminal DNA-binding domain and a regulatory C-terminal domain. A linker comprising two short alpha helices joins the two domains. In the C-terminal domain, an antiparallel array of six alpha helices forms a barrel-like structure, while a seventh alpha helix forms a 'lid' at the end closest to the N-terminal domain. This structure was found to be similar to that of the C-terminal domain of the Tet repressor. Long-chain acyl-CoA thioesters interact directly and reversibly with the C-terminal domain, and this interaction affects the structure and therefore the DNA binding properties of the N-terminal domain. Length = 164 Score = 27.2 bits (61), Expect = 3.5 Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 14/55 (25%) Query: 41 ALDFPRRQQLICELHNYDLDSGDIPNILIETYGDDFLFHFNSGLLPIIWQSIQEE 95 AL F R +CE NYD +P++ + YG SG IWQS+++E Sbjct: 118 ALKFYRDLLELCEEGNYD----KVPDV-VRQYG------IESGK---IWQSMRDE 158 >gnl|CDD|129804 TIGR00721, tfx, DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter. Length = 137 Score = 27.1 bits (60), Expect = 3.7 Identities = 13/34 (38%), Positives = 21/34 (61%) Query: 174 LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNA 207 LTER+ L+L G + +EIA++L + V+A Sbjct: 7 LTERQIKVLELREKGLSQKEIAKELKTTRANVSA 40 >gnl|CDD|181003 PRK07500, rpoH2, RNA polymerase factor sigma-32; Reviewed. Length = 289 Score = 27.3 bits (61), Expect = 3.7 Identities = 14/36 (38%), Positives = 20/36 (55%), Gaps = 3/36 (8%) Query: 169 SAARNLTERETSCL---QLAGDGYTSEEIAEKLGLS 201 A + L ERE + +L DG T E + E+LG+S Sbjct: 223 QALQTLNERELRIIRERRLREDGATLEALGEELGIS 258 >gnl|CDD|128648 smart00354, HTH_LACI, helix_turn _helix lactose operon repressor. Length = 70 Score = 27.2 bits (61), Expect = 3.8 Identities = 13/46 (28%), Positives = 23/46 (50%), Gaps = 3/46 (6%) Query: 190 TSEEIAEKLGLSVHTVNAYL-GSATVKLDAVNRIQAIAKAIRFGYI 234 T +++A G+S TV+ L G+ V + ++ A + GYI Sbjct: 2 TIKDVARLAGVSKATVSRVLNGNGRVSEETREKVLAAME--ELGYI 45 >gnl|CDD|172390 PRK13870, PRK13870, transcriptional regulator TraR; Provisional. Length = 234 Score = 27.3 bits (60), Expect = 3.9 Identities = 18/57 (31%), Positives = 28/57 (49%) Query: 174 LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIR 230 L +E + L+ G T EEIA+ G+ ++V L A + D ++ A AIR Sbjct: 174 LDPKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTALAIR 230 >gnl|CDD|128696 smart00419, HTH_CRP, helix_turn_helix, cAMP Regulatory protein. Length = 48 Score = 27.0 bits (61), Expect = 4.2 Identities = 10/17 (58%), Positives = 13/17 (76%) Query: 190 TSEEIAEKLGLSVHTVN 206 T +EIAE LGL+ TV+ Sbjct: 10 TRQEIAELLGLTRETVS 26 >gnl|CDD|182019 PRK09652, PRK09652, RNA polymerase sigma factor RpoE; Provisional. Length = 182 Score = 27.1 bits (61), Expect = 4.5 Identities = 9/19 (47%), Positives = 13/19 (68%) Query: 187 DGYTSEEIAEKLGLSVHTV 205 +G + EEIAE +G + TV Sbjct: 143 EGLSYEEIAEIMGCPIGTV 161 >gnl|CDD|181314 PRK08241, PRK08241, RNA polymerase factor sigma-70; Validated. Length = 339 Score = 26.8 bits (60), Expect = 4.8 Identities = 13/37 (35%), Positives = 18/37 (48%) Query: 188 GYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQA 224 G+++ E+AE L SV VN+ L A L A Sbjct: 169 GWSAAEVAELLDTSVAAVNSALQRARATLAERGPSAA 205 >gnl|CDD|179404 PRK02277, PRK02277, orotate phosphoribosyltransferase-like protein; Provisional. Length = 200 Score = 26.8 bits (60), Expect = 5.2 Identities = 8/24 (33%), Positives = 14/24 (58%) Query: 182 LQLAGDGYTSEEIAEKLGLSVHTV 205 +L G ++ EIA++L +S T Sbjct: 12 AELKNKGLSTGEIADELNVSRETA 35 >gnl|CDD|148279 pfam06577, DUF1134, Protein of unknown function (DUF1134). This family consists of several hypothetical bacterial proteins of unknown function. Length = 161 Score = 26.4 bits (59), Expect = 5.9 Identities = 7/20 (35%), Positives = 11/20 (55%) Query: 71 TYGDDFLFHFNSGLLPIIWQ 90 YG+ L+ N+G + WQ Sbjct: 56 RYGEGTLYTKNAGEHKVYWQ 75 >gnl|CDD|181361 PRK08295, PRK08295, RNA polymerase factor sigma-70; Validated. Length = 208 Score = 26.4 bits (59), Expect = 6.5 Identities = 15/36 (41%), Positives = 22/36 (61%), Gaps = 1/36 (2%) Query: 173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTV-NA 207 L+E E L+L DG + +EIAE+L V ++ NA Sbjct: 155 LLSELEKEVLELYLDGKSYQEIAEELNRHVKSIDNA 190 >gnl|CDD|132004 TIGR02959, SigZ, RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded). Length = 170 Score = 26.6 bits (59), Expect = 6.7 Identities = 12/30 (40%), Positives = 18/30 (60%) Query: 187 DGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 +G + +EIAEKLGLS+ + + KL Sbjct: 115 EGLSQQEIAEKLGLSLSGAKSRVQRGRKKL 144 >gnl|CDD|183384 PRK11924, PRK11924, RNA polymerase sigma factor; Provisional. Length = 179 Score = 26.5 bits (59), Expect = 6.8 Identities = 13/30 (43%), Positives = 17/30 (56%) Query: 187 DGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 +G + EIAE LG+ V TV + L A L Sbjct: 140 EGLSYREIAEILGVPVGTVKSRLRRARQLL 169 >gnl|CDD|114760 pfam06056, Terminase_5, Putative ATPase subunit of terminase (gpP-like). This family of proteins are annotated as ATPase subunits of phage terminase after. Terminases are viral proteins that are involved in packaging viral DNA into the capsid. Length = 58 Score = 26.1 bits (58), Expect = 7.2 Identities = 10/21 (47%), Positives = 14/21 (66%) Query: 188 GYTSEEIAEKLGLSVHTVNAY 208 GY EIA++LGL TV ++ Sbjct: 13 GYRPAEIAQELGLKARTVYSW 33 >gnl|CDD|185431 PTZ00077, PTZ00077, asparagine synthetase-like protein; Provisional. Length = 586 Score = 26.2 bits (58), Expect = 7.6 Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 8/36 (22%) Query: 121 PVRLGFHKNGYVIFTSEFLMLANEVIIEAHGACYQV 156 P+ +G+ K+G + F+SE L H C +V Sbjct: 152 PLYIGYAKDGSIWFSSELKAL--------HDQCVEV 179 >gnl|CDD|179124 PRK00783, PRK00783, DNA-directed RNA polymerase subunit D; Provisional. Length = 263 Score = 26.0 bits (58), Expect = 7.8 Identities = 14/61 (22%), Positives = 24/61 (39%), Gaps = 7/61 (11%) Query: 50 LICELHNYDLDSGDIPNILIETYGDDFLFHFNS-GLLPIIWQSIQEETVIESSGQLSVRL 108 L C L + I + + F+F S G LP+ EE ++E+ L + Sbjct: 199 LNCSLCKLCERACPGKAIRVSDDENKFIFTVESDGSLPV------EEILLEALKILKRKA 252 Query: 109 E 109 + Sbjct: 253 D 253 >gnl|CDD|183153 PRK11475, PRK11475, DNA-binding transcriptional activator BglJ; Provisional. Length = 207 Score = 26.2 bits (58), Expect = 7.9 Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 2/42 (4%) Query: 175 TERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 TERE L+ GY+ +IAE+L ++ T+ A+ + KL Sbjct: 138 TEREI--LRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKL 177 >gnl|CDD|180498 PRK06266, PRK06266, transcription initiation factor E subunit alpha; Validated. Length = 178 Score = 26.1 bits (58), Expect = 8.4 Identities = 9/16 (56%), Positives = 13/16 (81%) Query: 190 TSEEIAEKLGLSVHTV 205 T EEIAE+ G+ ++TV Sbjct: 38 TDEEIAEQTGIKLNTV 53 >gnl|CDD|184041 PRK13413, mpi, multiple promoter invertase; Provisional. Length = 200 Score = 26.2 bits (58), Expect = 8.5 Identities = 15/45 (33%), Positives = 22/45 (48%) Query: 165 KKRSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYL 209 K + LT +E +L G + EIA KLG+S T+ +L Sbjct: 149 KGSTPKKYKLTGKEEKIKKLLDKGTSKSEIARKLGVSRTTLARFL 193 >gnl|CDD|184503 PRK14096, pgi, glucose-6-phosphate isomerase; Provisional. Length = 528 Score = 26.0 bits (58), Expect = 8.5 Identities = 12/35 (34%), Positives = 19/35 (54%) Query: 165 KKRSSAARNLTERETSCLQLAGDGYTSEEIAEKLG 199 KK ++A +L ++ L+ G + EEIA LG Sbjct: 455 KKAAAAILDLQKKVEELLKEDGGELSIEEIAAALG 489 >gnl|CDD|163028 TIGR02812, fadR_gamma, fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function. Length = 235 Score = 25.8 bits (57), Expect = 8.9 Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 14/55 (25%) Query: 41 ALDFPRRQQLICELHNYDLDSGDIPNILIETYGDDFLFHFNSGLLPIIWQSIQEE 95 AL F + Q +C+ N+D ++P+ I YG SG IW +Q+E Sbjct: 188 ALQFYKELQALCKAGNHD----EVPD-CIRQYG------IESGE---IWHQMQDE 228 >gnl|CDD|182010 PRK09638, PRK09638, RNA polymerase sigma factor SigY; Reviewed. Length = 176 Score = 25.8 bits (57), Expect = 9.1 Identities = 10/18 (55%), Positives = 12/18 (66%) Query: 188 GYTSEEIAEKLGLSVHTV 205 GYT EEIA+ L + TV Sbjct: 142 GYTYEEIAKMLNIPEGTV 159 >gnl|CDD|137446 PRK09637, PRK09637, RNA polymerase sigma factor SigZ; Provisional. Length = 181 Score = 26.1 bits (58), Expect = 9.3 Identities = 10/19 (52%), Positives = 14/19 (73%) Query: 187 DGYTSEEIAEKLGLSVHTV 205 +G + +EIAEKLGLS+ Sbjct: 121 EGLSQKEIAEKLGLSLSGA 139 >gnl|CDD|179487 PRK02866, PRK02866, cyanate hydratase; Validated. Length = 147 Score = 25.9 bits (58), Expect = 9.3 Identities = 13/27 (48%), Positives = 15/27 (55%), Gaps = 1/27 (3%) Query: 188 GYTSEEIAEKLGLS-VHTVNAYLGSAT 213 G T +IAE +GLS V A LG T Sbjct: 18 GLTWADIAEAIGLSEVWVTAALLGQMT 44 >gnl|CDD|139037 PRK12525, PRK12525, RNA polymerase sigma factor; Provisional. Length = 168 Score = 26.1 bits (57), Expect = 9.4 Identities = 10/26 (38%), Positives = 17/26 (65%) Query: 187 DGYTSEEIAEKLGLSVHTVNAYLGSA 212 +G T EI E+LG+S+ ++ Y+ A Sbjct: 133 EGLTYVEIGERLGVSLSRIHQYMVEA 158 >gnl|CDD|128638 smart00344, HTH_ASNC, helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli. Length = 108 Score = 25.9 bits (58), Expect = 9.5 Identities = 11/23 (47%), Positives = 14/23 (60%), Gaps = 1/23 (4%) Query: 184 LAGDGYTS-EEIAEKLGLSVHTV 205 L D S E+A+K+GLS TV Sbjct: 12 LQKDARISLAELAKKVGLSPSTV 34 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 0.321 0.138 0.395 Gapped Lambda K H 0.267 0.0675 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 3,756,961 Number of extensions: 237941 Number of successful extensions: 682 Number of sequences better than 10.0: 1 Number of HSP's gapped: 682 Number of HSP's successfully gapped: 77 Length of query: 235 Length of database: 5,994,473 Length adjustment: 90 Effective length of query: 145 Effective length of database: 4,049,753 Effective search space: 587214185 Effective search space used: 587214185 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 (21.9 bits) S2: 56 (25.5 bits)