RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780694|ref|YP_003065107.1| probable transcriptional regulator protein, LuxR family [Candidatus Liberibacter asiaticus str. psy62] (246 letters) >gnl|CDD|128698 smart00421, HTH_LUXR, helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon. Length = 58 Score = 77.2 bits (191), Expect = 3e-15 Identities = 25/55 (45%), Positives = 36/55 (65%) Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYA 240 LT RE E L ++EG T+ EIA LGIS TV ++++IMRK ++R+ A+ A Sbjct: 4 LTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 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 = 63.3 bits (154), Expect = 6e-11 Identities = 26/57 (45%), Positives = 38/57 (66%) Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVR 242 +T RE E L W+ +GKT++EIA ILGIS TV N++ I +K + R+ A+A A+ Sbjct: 191 ITAREAEILAWVRDGKTNEEIAAILGISSLTVKNHLQHIFKKLDVRNRAQAVAKAIA 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 = 53.2 bits (128), Expect = 5e-08 Identities = 26/57 (45%), Positives = 34/57 (59%) Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVR 242 L+ RE E L W + G+ +IA ILGIS TV N++ S RK T + AIA A+R Sbjct: 172 LSEREREVLAWTALGRRQADIAAILGISERTVENHLRSARRKLGVATTAQAIAIALR 228 >gnl|CDD|182292 PRK10188, PRK10188, DNA-binding transcriptional activator SdiA; Provisional. Length = 240 Score = 52.1 bits (125), Expect = 1e-07 Identities = 24/53 (45%), Positives = 32/53 (60%) Query: 189 REVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAV 241 RE E L W +EGKTS EIA+IL IS NTVN + ++ +K ++ YA Sbjct: 183 REKEILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQIACYAA 235 >gnl|CDD|182241 PRK10100, PRK10100, DNA-binding transcriptional regulator CsgD; Provisional. Length = 216 Score = 43.3 bits (102), Expect = 6e-05 Identities = 23/58 (39%), Positives = 36/58 (62%) Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRN 243 LT RE E L + G +++EIA L IS NTV ++ ++ +K A K R+ A+++A N Sbjct: 156 LTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAVSWANDN 213 >gnl|CDD|182431 PRK10403, PRK10403, transcriptional regulator NarP; Provisional. Length = 215 Score = 39.5 bits (92), Expect = 0.001 Identities = 18/51 (35%), Positives = 33/51 (64%) Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGA 236 LT RE++ L +++G ++ +IA +L IS TV +I +++RK ++R A Sbjct: 154 LTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAA 204 >gnl|CDD|182619 PRK10651, PRK10651, transcriptional regulator NarL; Provisional. Length = 216 Score = 39.2 bits (92), Expect = 0.001 Identities = 26/96 (27%), Positives = 48/96 (50%), Gaps = 7/96 (7%) Query: 151 GRIILRDRLWEIGLLAAYQANMFKSYDVHWGKDFE-LTGREVECLTWISEGKTSDEIAVI 209 G ++L + L + L A+ +AN + +D LT RE + L I++G + IA Sbjct: 126 GEMVLSEALTPV-LAASLRANRATT-----ERDVNQLTPRERDILKLIAQGLPNKMIARR 179 Query: 210 LGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNI 245 L I+ +TV ++ +++K K+R A + + I Sbjct: 180 LDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQERI 215 >gnl|CDD|172390 PRK13870, PRK13870, transcriptional regulator TraR; Provisional. Length = 234 Score = 36.5 bits (84), Expect = 0.006 Identities = 18/61 (29%), Positives = 34/61 (55%) Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNI 245 L +E L WI+ GKT +EIA + G+ N+V + M++ ++++ A A+R + Sbjct: 174 LDPKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTALAIRRKL 233 Query: 246 V 246 + Sbjct: 234 I 234 >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 = 35.1 bits (82), Expect = 0.015 Identities = 12/29 (41%), Positives = 18/29 (62%) Query: 199 EGKTSDEIAVILGISRNTVNNYIASIMRK 227 EG + EIA +LGIS TV + ++ +K Sbjct: 25 EGLSYAEIAELLGISEGTVKSRLSRARKK 53 >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 = 35.4 bits (82), Expect = 0.015 Identities = 17/39 (43%), Positives = 22/39 (56%), Gaps = 1/39 (2%) Query: 189 REVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRK 227 REV L ++ EG + EIA ILGIS TV + +K Sbjct: 116 REVLVLRYL-EGLSYKEIAEILGISVGTVKRRLKRARKK 153 >gnl|CDD|185267 PRK15369, PRK15369, two component system sensor kinase SsrB; Provisional. Length = 211 Score = 34.7 bits (80), Expect = 0.021 Identities = 19/42 (45%), Positives = 26/42 (61%) Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRK 227 LT RE + L I+EG T+ +IA L IS TV + ++MRK Sbjct: 150 LTPRERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRK 191 >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 = 34.5 bits (80), Expect = 0.029 Identities = 15/32 (46%), Positives = 19/32 (59%), Gaps = 3/32 (9%) Query: 199 EGKTSDEIAVILGISRNTVNNYIA---SIMRK 227 EGK+ EIA LGIS TV +I+ +RK Sbjct: 128 EGKSYKEIAEELGISVKTVEYHISKALKELRK 159 >gnl|CDD|184041 PRK13413, mpi, multiple promoter invertase; Provisional. Length = 200 Score = 33.9 bits (78), Expect = 0.044 Identities = 14/40 (35%), Positives = 25/40 (62%) Query: 182 KDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYI 221 K ++LTG+E + + +G + EIA LG+SR T+ ++ Sbjct: 154 KKYKLTGKEEKIKKLLDKGTSKSEIARKLGVSRTTLARFL 193 >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 = 33.6 bits (77), Expect = 0.051 Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 20/61 (32%) Query: 191 VECLTWIS-------------EGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAI 237 E LTW+ GKT+ EIA LG + TV N++ +T++G + Sbjct: 10 AERLTWVDSLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG-------ETKAGGL 62 Query: 238 A 238 Sbjct: 63 V 63 >gnl|CDD|182168 PRK09958, PRK09958, DNA-binding transcriptional activator EvgA; Provisional. Length = 204 Score = 32.9 bits (75), Expect = 0.069 Identities = 19/60 (31%), Positives = 34/60 (56%) Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNI 245 L+ +E+ + +I +GK +++IA + IS TV+ Y + +M K K+ +A RN I Sbjct: 144 LSKQEISVMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKLECKSLMDLYTFAQRNKI 203 >gnl|CDD|116512 pfam07900, DUF1670, Protein of unknown function (DUF1670). The hypothetical eukaryotic proteins found in this family are of unknown function. Length = 220 Score = 31.3 bits (71), Expect = 0.25 Identities = 16/40 (40%), Positives = 20/40 (50%), Gaps = 6/40 (15%) Query: 182 KDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYI 221 KDF VE LT +G + +EI I GIS V Y+ Sbjct: 185 KDFT----RVEKLT--EKGMSEEEIRYITGISERLVEEYV 218 >gnl|CDD|182154 PRK09935, PRK09935, transcriptional regulator FimZ; Provisional. Length = 210 Score = 31.0 bits (70), Expect = 0.30 Identities = 19/58 (32%), Positives = 30/58 (51%) Query: 183 DFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYA 240 D L+ REV L ++ G ++ EIA L +S TV+ + ++I K + I YA Sbjct: 147 DTVLSNREVTILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHSIVELIDYA 204 >gnl|CDD|116863 pfam08279, HTH_11, HTH domain. This family includes helix-turn-helix domains in a wide variety of proteins. Length = 55 Score = 30.5 bits (70), Expect = 0.45 Identities = 8/23 (34%), Positives = 14/23 (60%) Query: 202 TSDEIAVILGISRNTVNNYIASI 224 + E+A LG+SR T+ I ++ Sbjct: 17 SGQELAEKLGVSRRTIRRDIKAL 39 >gnl|CDD|182408 PRK10360, PRK10360, DNA-binding transcriptional activator UhpA; Provisional. Length = 196 Score = 30.3 bits (68), Expect = 0.48 Identities = 17/47 (36%), Positives = 27/47 (57%) Query: 181 GKDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRK 227 G+ LT RE + +++G EIA LG+S TV+ + A++M K Sbjct: 133 GRQDPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEK 179 >gnl|CDD|162580 TIGR01884, cas_HTH, CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity. Length = 203 Score = 29.6 bits (67), Expect = 0.70 Identities = 12/43 (27%), Positives = 22/43 (51%), Gaps = 2/43 (4%) Query: 182 KDFELTGREVECL-TWISEGKTS-DEIAVILGISRNTVNNYIA 222 L+ E++ L +EG+ S IA LG S +T++ ++ Sbjct: 137 LLAGLSREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLR 179 >gnl|CDD|182165 PRK09954, PRK09954, putative kinase; Provisional. Length = 362 Score = 29.9 bits (67), Expect = 0.71 Identities = 14/28 (50%), Positives = 18/28 (64%) Query: 204 DEIAVILGISRNTVNNYIASIMRKTATK 231 +EIA IL ISR+ V +I +MRK K Sbjct: 21 NEIADILQISRSRVAAHIMDLMRKGRIK 48 >gnl|CDD|180757 PRK06930, PRK06930, positive control sigma-like factor; Validated. Length = 170 Score = 29.7 bits (67), Expect = 0.80 Identities = 17/48 (35%), Positives = 23/48 (47%), Gaps = 1/48 (2%) Query: 186 LTGREVEC-LTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKT 232 LT RE E L G + EIA L I ++TV + I +K A + Sbjct: 115 LTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQI 162 >gnl|CDD|179885 PRK04841, PRK04841, transcriptional regulator MalT; Provisional. Length = 903 Score = 29.1 bits (66), Expect = 1.0 Identities = 16/55 (29%), Positives = 30/55 (54%) Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYA 240 LT RE + L I G ++++IA L ++ T+ +I ++ +K R A+ +A Sbjct: 839 LTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEAVQHA 893 >gnl|CDD|171560 PRK12527, PRK12527, RNA polymerase sigma factor; Reviewed. Length = 159 Score = 29.4 bits (66), Expect = 1.0 Identities = 13/35 (37%), Positives = 20/35 (57%) Query: 199 EGKTSDEIAVILGISRNTVNNYIASIMRKTATKTR 233 EG + +IA LGISR+ V +I + M+ + R Sbjct: 120 EGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMR 154 >gnl|CDD|180266 PRK05803, PRK05803, sporulation sigma factor SigK; Reviewed. Length = 233 Score = 29.1 bits (66), Expect = 1.2 Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 9/51 (17%) Query: 186 LTGREVECLT-----WISEGKTSDEIAVILGISRNTVNNYIASIMRKTATK 231 L RE E + + KT EIA LGISR +Y++ I ++ K Sbjct: 176 LDEREKEVIEMRYGLGNGKEKTQREIAKALGISR----SYVSRIEKRALKK 222 >gnl|CDD|185123 PRK15201, PRK15201, fimbriae regulatory protein FimW; Provisional. Length = 198 Score = 28.5 bits (63), Expect = 1.7 Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 3/64 (4%) Query: 182 KDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAV 241 + F +T R + L I+ G E A +L +S + SIMRK KT + Y + Sbjct: 132 RHFSVTERHL--LKLIASGYHLSETAALLSLSEEQTKSLRRSIMRKLHVKTEQQFLKY-I 188 Query: 242 RNNI 245 R N+ Sbjct: 189 RVNL 192 >gnl|CDD|131893 TIGR02846, spore_sigmaK, RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K. Length = 227 Score = 28.5 bits (64), Expect = 1.7 Identities = 20/51 (39%), Positives = 28/51 (54%), Gaps = 9/51 (17%) Query: 186 LTGREVECLTW---ISEG--KTSDEIAVILGISRNTVNNYIASIMRKTATK 231 L GRE E + + +G KT EIA ILGISR +Y++ I ++ K Sbjct: 175 LDGREREVIEMRYGLGDGRRKTQREIAKILGISR----SYVSRIEKRALMK 221 >gnl|CDD|182069 PRK09775, PRK09775, putative DNA-binding transcriptional regulator; Provisional. Length = 442 Score = 28.0 bits (63), Expect = 2.2 Identities = 12/52 (23%), Positives = 29/52 (55%), Gaps = 1/52 (1%) Query: 195 TWISEGK-TSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNI 245 T + +G ++ E+A LG+S+ T++ +A++ + ++ A YA+ + Sbjct: 7 TLLLQGPLSAAELAARLGVSQATLSRLLAALGDQVVRFGKARATRYALLRPL 58 >gnl|CDD|181815 PRK09390, fixJ, response regulator FixJ; Provisional. Length = 202 Score = 27.7 bits (62), Expect = 2.8 Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 4/58 (6%) Query: 185 ELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVR 242 L+ RE + + + G ++ IA L IS TV Y A++M TK ++G+++ VR Sbjct: 141 SLSERERQVMDGLVAGLSNKVIARDLDISPRTVEVYRANVM----TKMQAGSLSELVR 194 >gnl|CDD|181897 PRK09483, PRK09483, response regulator; Provisional. Length = 217 Score = 27.8 bits (62), Expect = 2.9 Identities = 13/35 (37%), Positives = 24/35 (68%) Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNY 220 L+ RE++ + I++G+ +EI+ L +S TVN+Y Sbjct: 149 LSERELQIMLMITKGQKVNEISEQLNLSPKTVNSY 183 >gnl|CDD|183384 PRK11924, PRK11924, RNA polymerase sigma factor; Provisional. Length = 179 Score = 27.6 bits (62), Expect = 3.4 Identities = 10/24 (41%), Positives = 14/24 (58%) Query: 199 EGKTSDEIAVILGISRNTVNNYIA 222 EG + EIA ILG+ TV + + Sbjct: 140 EGLSYREIAEILGVPVGTVKSRLR 163 >gnl|CDD|152436 pfam12001, DUF3496, Domain of unknown function (DUF3496). This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is about 110 amino acids in length. Length = 111 Score = 27.5 bits (61), Expect = 3.5 Identities = 14/31 (45%), Positives = 18/31 (58%) Query: 2 NFEIQQVNIVLNREDEQRTSFVSHLPTRSDL 32 N + +V+ L E EQ S +S LPTR DL Sbjct: 56 NERLAEVSTKLLMEKEQSRSLLSTLPTRPDL 86 >gnl|CDD|147812 pfam05858, BIV_Env, Bovine immunodeficiency virus surface protein (SU). The bovine lentivirus also known as the bovine immunodeficiency-like virus (BIV) has conserved and hypervariable regions in the surface envelope gene. This family corresponds to the SU surface protein. Length = 548 Score = 27.3 bits (60), Expect = 3.6 Identities = 18/56 (32%), Positives = 24/56 (42%), Gaps = 5/56 (8%) Query: 115 TLPENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILRDRLWEIGLLAAYQA 170 ++PENIT D +L +GL+ G II R G+LAA A Sbjct: 130 SVPENITKIPIKDTDPWTLILLGLVCILGLL-----GVIIAMRRSNPEGILAARDA 180 >gnl|CDD|179690 PRK03975, tfx, putative transcriptional regulator; Provisional. Length = 141 Score = 26.8 bits (60), Expect = 4.9 Identities = 19/44 (43%), Positives = 22/44 (50%), Gaps = 5/44 (11%) Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 LT R++E L G T EIA ILG SR V S + K A Sbjct: 7 LTERQIEVLRLRERGLTQQEIADILGTSRANV-----SSIEKRA 45 >gnl|CDD|183569 PRK12517, PRK12517, RNA polymerase sigma factor; Provisional. Length = 188 Score = 26.6 bits (59), Expect = 6.4 Identities = 9/19 (47%), Positives = 14/19 (73%) Query: 200 GKTSDEIAVILGISRNTVN 218 G + +EIA IL +++NTV Sbjct: 144 GFSGEEIAEILDLNKNTVM 162 >gnl|CDD|181871 PRK09455, rseB, anti-sigma E factor; Provisional. Length = 319 Score = 26.0 bits (58), Expect = 8.7 Identities = 11/26 (42%), Positives = 13/26 (50%), Gaps = 6/26 (23%) Query: 16 DEQRTSFV------SHLPTRSDLLAR 35 D R S++ S LP R DLL R Sbjct: 151 DGTRYSYIVWIDEESKLPLRVDLLDR 176 >gnl|CDD|163020 TIGR02786, addB_alphas, double-strand break repair protein AddB, alphaproteobacterial type. AddAB is a system well described in the Firmicutes as a replacement for RecBCD in many prokaryotes for the repair of double stranded break DNA damage. More recently, a distantly related gene pair conserved in many alphaproteobacteria was shown also to function in double-stranded break repair in Rhizobium etli. This family consists of AddB proteins of the alphaproteobacteial type. Length = 1021 Score = 26.2 bits (58), Expect = 8.7 Identities = 10/21 (47%), Positives = 13/21 (61%) Query: 19 RTSFVSHLPTRSDLLARMIPL 39 R +FV L R+ LL R+ PL Sbjct: 55 REAFVDVLDGRAALLPRIRPL 75 >gnl|CDD|163347 TIGR03599, YloV, DAK2 domain fusion protein YloV. This model describes a protein family that contains an N-terminal DAK2 domain (pfam02734), so named because of similarity to the dihydroxyacetone kinase family family. The GTP-binding protein CgtA (a member of the obg family) is a bacterial GTPase associated with ribosome biogenesis, and it has a characteristic extension (TIGR03595) in certain lineages. This protein family described here was found, by the method of partial phylognetic profiling, to have a phylogenetic distribution strongly correlated to that of TIGR03595. This correlation implies some form of functional coupling. Length = 530 Score = 26.0 bits (58), Expect = 8.9 Identities = 8/22 (36%), Positives = 11/22 (50%) Query: 222 ASIMRKTATKTRSGAIAYAVRN 243 M + RSG + YAVR+ Sbjct: 416 KEAMEEAIKAVRSGEVTYAVRD 437 >gnl|CDD|180310 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional. Length = 509 Score = 26.1 bits (58), Expect = 9.6 Identities = 9/27 (33%), Positives = 15/27 (55%) Query: 201 KTSDEIAVILGISRNTVNNYIASIMRK 227 KT DEI + G++R + + +RK Sbjct: 468 KTLDEIGQVYGVTRERIRQIESKTLRK 494 >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 = 25.9 bits (57), Expect = 10.0 Identities = 12/31 (38%), Positives = 18/31 (58%), Gaps = 4/31 (12%) Query: 202 TSDEIAVILGISRNTVNNYIASIMRKTATKT 232 T +E+A + G SR T+N ++ RK KT Sbjct: 2 TPEELAELTGYSRQTINRWV----RKEGWKT 28 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 0.324 0.137 0.423 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: 4,061,959 Number of extensions: 255195 Number of successful extensions: 618 Number of sequences better than 10.0: 1 Number of HSP's gapped: 618 Number of HSP's successfully gapped: 43 Length of query: 246 Length of database: 5,994,473 Length adjustment: 91 Effective length of query: 155 Effective length of database: 4,028,145 Effective search space: 624362475 Effective search space used: 624362475 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 56 (25.5 bits)