RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780551|ref|YP_003064964.1| tolQ protein [Candidatus Liberibacter asiaticus str. psy62] (230 letters) >gnl|CDD|131843 TIGR02796, tolQ, TolQ protein. TolQ is one of the essential components of the Tol-Pal system. Together with TolR, it harnesses protonmotive force to energize TolA, which spans the periplasm to reach the complex of TolB and Pal at the outer member. The tol-pal system proves to be important for maintaining outer membrane integrity. Gene pairs similar to the TolQ and TolR gene pair often number several per genome, but this model describes specificially TolQ per se, as found in tol-pal operons. A close homolog, excluded from this model, is ExbB of the ExbB/ExbD/TonB protein complex, which powers transport of siderophores and vitamin B12 across the bacterial outer membrane. The Tol-Pal system is exploited by colicin and filamentous phage DNA to enter the cell. It is also implicated in pathogenesis in several bacterial species. Length = 215 Score = 200 bits (510), Expect = 3e-52 Identities = 86/215 (40%), Positives = 123/215 (57%), Gaps = 3/215 (1%) Query: 12 SIFALFMQMGLAVKCIITLLFIFSILSWSVIIQKSVNFITLRRQFREFEQLFWSGQSLET 71 SI LF+Q VK ++ +L + SI+SW++I QK F RR+ EFE FWSG LE Sbjct: 1 SILDLFLQASFVVKLVMLILLLASIISWAIIFQKFFIFRRARREAEEFEDRFWSGGDLEK 60 Query: 72 VCKSLKNHHNI-GLAAIFMSAMSEWKKSCDKGARSPIGIQDRIDRMMDVAIARELEEITE 130 + SL N+ GL +IF + E+ + KG P + +RIDR M VA+ RE E++ Sbjct: 61 LYNSLSNNKPTSGLESIFCAGFKEFSRLKSKGELDPGVVIERIDRAMRVALNRESEKLES 120 Query: 131 KLSFLGSMSSAGLLVGILGAVLGMMGFFQSIAGYYSNNVVSI--PGIIESLISILLGLCV 188 L FL ++ S +G+ G V G+M FQ+I G + +++ PGI E+LI+ +GL Sbjct: 121 GLPFLATIGSTSPFIGLFGTVWGIMHSFQAIGGSKNQATLAVVAPGIAEALIATAIGLFA 180 Query: 189 SIPSSIAYNKFIEDSKKFAMQMEGFANEFSAILSR 223 +IP+ IAYNK K + E FA+EFS IL R Sbjct: 181 AIPAVIAYNKLSTQVNKIEQRYENFADEFSTILQR 215 >gnl|CDD|182743 PRK10801, PRK10801, colicin uptake protein TolQ; Provisional. Length = 227 Score = 112 bits (282), Expect = 6e-26 Identities = 68/217 (31%), Positives = 114/217 (52%), Gaps = 3/217 (1%) Query: 11 ISIFALFMQMGLAVKCIITLLFIFSILSWSVIIQKSVNFITLRRQFREFEQLFWSGQSLE 70 ++I LF++ L VK I+ +L FSI SW++IIQ++ R+ FE FWSG L Sbjct: 1 MNILDLFLKASLLVKLIMLILIGFSIASWAIIIQRTRILNAAAREAEAFEDKFWSGIELS 60 Query: 71 TVCKSLKNHHNI--GLAAIFMSAMSEWKKSCDKGARSPIGIQDRIDRMMDVAIARELEEI 128 + + + + G IF S E+ + + +P + + R M +++ RELE + Sbjct: 61 RLYQESQGRRDNLSGSEQIFYSGFKEFVRLHRANSHAPEAVVEGASRAMRISMNRELETL 120 Query: 129 TEKLSFLGSMSSAGLLVGILGAVLGMMGFFQSIAGYYSNNVVSI-PGIIESLISILLGLC 187 + FLG++ S +G+ G V G+M F ++ + + PGI E+LI+ +GL Sbjct: 121 ETHIPFLGTVGSISPYIGLFGTVWGIMHAFIALGAVKQATLQMVAPGIAEALIATAIGLF 180 Query: 188 VSIPSSIAYNKFIEDSKKFAMQMEGFANEFSAILSRQ 224 +IP+ +AYN+ + K + + F EF+AIL RQ Sbjct: 181 AAIPAVMAYNRLNQRVNKLELNYDNFMEEFTAILHRQ 217 >gnl|CDD|131844 TIGR02797, exbB, tonB-system energizer ExbB. This model describes ExbB proteins, part of the MotA/TolQ/ExbB protein family. The paired proteins MotA and MotB, TolQ and TolR, and ExbB and ExbD harness the proton-motive force to drive the flagellar motor, energize the Tol-Pal system, or energize TonB, respectively. Tol-Pal and TonB are both active at the outer membrane. Genomes may have many different TonB-dependent receptors, of which many of those characterized are involved in siderophore transport across the outer membrane. Length = 211 Score = 77.1 bits (190), Expect = 4e-15 Identities = 48/189 (25%), Positives = 93/189 (49%), Gaps = 3/189 (1%) Query: 12 SIFALFMQMGLAVKCIITLLFIFSILSWSVIIQKSVNFITLRRQFREFEQLFWSGQSLET 71 S + +F+ + VK ++ L + S+++W++ I KSV RR+ + + ++L Sbjct: 1 SPWGMFLAADIVVKAVMIGLALASVVTWTIWIAKSVELAGARRRLKRALKALGEARTLAE 60 Query: 72 VCKSLKNHHNIGLAAIFMSAMSEWKKSCDKGARSPIGIQDRIDRMMDVAIARELEEITEK 131 ++L + AA+ +A E + S G GI++R+ ++ A ++ Sbjct: 61 AQEALGDRGGPA-AALVRAAEEEMELS-AAGLSDGEGIKERVASRLERIEAAAGRRMSRG 118 Query: 132 LSFLGSMSSAGLLVGILGAVLGMMGFFQSIAGYYSNNV-VSIPGIIESLISILLGLCVSI 190 L ++ + VG+ G V G+M F I+ + N+ V PGI E+L++ +GL +I Sbjct: 119 TGVLATIGATAPFVGLFGTVWGIMNSFIGISKSQTTNLAVVAPGIAEALLATAIGLVAAI 178 Query: 191 PSSIAYNKF 199 P+ + YN F Sbjct: 179 PAVVIYNVF 187 >gnl|CDD|182439 PRK10414, PRK10414, biopolymer transport protein ExbB; Provisional. Length = 244 Score = 74.5 bits (183), Expect = 2e-14 Identities = 50/193 (25%), Positives = 101/193 (52%), Gaps = 4/193 (2%) Query: 9 MDISIFALFMQMGLAVKCIITLLFIFSILSWSVIIQKSVNFITLRRQFREFEQLFWSGQS 68 D+S++ ++ + VKC++ L + S+++W++ KSV F +R+ + +QL +S Sbjct: 8 TDLSVWGMYQHADIVVKCVMIGLILASVVTWAIFFSKSVEFFNQKRRLKREQQLLAEARS 67 Query: 69 LETVCKSLKNHHNIGLAAIFMS-AMSEWKKSCDKGARSPIGIQDRIDRMMDVAIARELEE 127 L+ + + L+ ++ A +E + S +G+ GI++R ++ +A + Sbjct: 68 LDQANDIAADFGSKSLSLHLLNEAQNELELS--EGSDDNEGIKERTSFRLERRVAAVGRQ 125 Query: 128 ITEKLSFLGSMSSAGLLVGILGAVLGMMGFFQSIAGYYSNNV-VSIPGIIESLISILLGL 186 + +L ++ + VG+ G V G+M F IA + N+ V PGI E+L++ +GL Sbjct: 126 MGRGNGYLATIGAISPFVGLFGTVWGIMNSFIGIAQTQTTNLAVVAPGIAEALLATAIGL 185 Query: 187 CVSIPSSIAYNKF 199 +IP+ + YN F Sbjct: 186 VAAIPAVVIYNVF 198 >gnl|CDD|131852 TIGR02805, exbB2, tonB-system energizer ExbB, group 2. Members of this protein family appear to be the ExbB protein of an ExbBD proton-transporting membrane complex that, by means of TonB, energizes transport by TonB-dependent receptors. Note that this family represents one of at least two distinct groups TolQ homologs designated ExbB - see also TIGR02797. Each group associates with a distinct group of ExbD proteins, and a single species may have two ExbB/ExbD/TonB systems. Length = 138 Score = 35.5 bits (82), Expect = 0.011 Identities = 22/73 (30%), Positives = 40/73 (54%), Gaps = 3/73 (4%) Query: 127 EITEKLSFLGSMSSAGLLVGILGAVLGMMGFFQSI--AGYYSNNVVSIPGIIESLISILL 184 ++ L+ + + S +G+LG V+G+M F + G +V+ + G+ +L + L Sbjct: 50 DLNRNLTVISIIGSNAPYIGLLGTVIGIMVTFYQMGHGGGIDPSVIML-GLSLALKATAL 108 Query: 185 GLCVSIPSSIAYN 197 GL V+IPS + YN Sbjct: 109 GLLVAIPSLVFYN 121 >gnl|CDD|172363 PRK13836, PRK13836, conjugal transfer protein TrbF; Provisional. Length = 220 Score = 29.8 bits (67), Expect = 0.61 Identities = 17/52 (32%), Positives = 27/52 (51%), Gaps = 2/52 (3%) Query: 126 EEITEKLSFLGSMSSAGLLVGILGAVLGMMGFFQSIAGYYSNNVVSIPGIIE 177 +E E+ ++A +VGILG + ++GF A Y S V +P I+E Sbjct: 16 QEWNERYGSYVKAAAAWRIVGILGLTMAVIGF--GYALYQSTQVKLVPYIVE 65 >gnl|CDD|179889 PRK04885, ppnK, inorganic polyphosphate/ATP-NAD kinase; Provisional. Length = 265 Score = 29.4 bits (67), Expect = 0.71 Identities = 11/15 (73%), Positives = 12/15 (80%), Gaps = 1/15 (6%) Query: 185 GLCVSIPS-SIAYNK 198 GLCVS P+ S AYNK Sbjct: 150 GLCVSTPTGSTAYNK 164 >gnl|CDD|115462 pfam06805, Lambda_tail_I, Bacteriophage lambda tail assembly protein I. This family consists of several Bacteriophage lambda tail assembly protein I and related phage and bacterial sequences. Members of this family are typically around 200 residues in length. The function of this family is unknown. Length = 194 Score = 28.2 bits (63), Expect = 1.9 Identities = 21/83 (25%), Positives = 35/83 (42%), Gaps = 3/83 (3%) Query: 103 ARSPIGIQDRIDRMMDVAIARELEEITEKLSFLGSMSSAGLLVGILGAVLGMMGFFQSIA 162 A I + + R+ + + I ++ GS GL ILGAVL + GFF + A Sbjct: 53 AGKNISVDELTARLHEPLPGGAVIRIVPVVA--GS-KKGGLFQTILGAVLIVAGFFTAGA 109 Query: 163 GYYSNNVVSIPGIIESLISILLG 185 + + + S++LG Sbjct: 110 SAGAGAAGAGAFLFSLGASMVLG 132 >gnl|CDD|181950 PRK09556, uhpT, sugar phosphate antiporter; Reviewed. Length = 467 Score = 27.7 bits (62), Expect = 2.4 Identities = 11/35 (31%), Positives = 21/35 (60%) Query: 137 SMSSAGLLVGILGAVLGMMGFFQSIAGYYSNNVVS 171 S+ S + +G++ A+ + GFFQS G S + ++ Sbjct: 114 SLGSGSVSLGLMIALWALSGFFQSTGGPCSYSTIT 148 >gnl|CDD|179210 PRK01030, PRK01030, tetrahydromethanopterin S-methyltransferase subunit C; Provisional. Length = 264 Score = 27.6 bits (62), Expect = 3.0 Identities = 17/77 (22%), Positives = 31/77 (40%), Gaps = 13/77 (16%) Query: 135 LGSMSSAGLLVGILGAVLGMM-GFFQSIAGYYSNNVVS--IPGIIESLISI-------LL 184 +G L I+ ++ + G + G +NNVV IP + S+ + +L Sbjct: 86 IGDALGIVLAGPIVALIIAAIIGA---VVGKLANNVVGMKIPIMERSMTELSGAGALAIL 142 Query: 185 GLCVSIPSSIAYNKFIE 201 G +I S ++ I Sbjct: 143 GFSTAIAGSFDFDAIIT 159 >gnl|CDD|162643 TIGR01989, COQ6, Ubiquinone biosynthesis mono0xygenase COQ6. This model represents the monooxygenase responsible for the 4-hydroxylateion of the phenol ring in the aerobic biosynthesis of ubiquinone. Length = 437 Score = 27.0 bits (60), Expect = 4.0 Identities = 17/53 (32%), Positives = 21/53 (39%), Gaps = 5/53 (9%) Query: 135 LGSMSS-AGLLVGILGAVLGM---MGFFQSIAGYYSNNVVSI-PGIIESLISI 182 LG+ L V +L AV ++ G YSN V SI P I I Sbjct: 19 LGNNPLTKDLKVLLLDAVDNPKLKSRNYEKPDGPYSNRVSSITPASISFFKKI 71 >gnl|CDD|183338 PRK11855, PRK11855, dihydrolipoamide acetyltransferase; Reviewed. Length = 547 Score = 26.7 bits (60), Expect = 4.6 Identities = 20/71 (28%), Positives = 30/71 (42%), Gaps = 25/71 (35%) Query: 68 SLETVCKSL--KNHHNIGLAAIFMSAMSEWKKSCDKGARSPIG-----IQDRIDRMMDVA 120 SL+ L K + NIG A D +P G I+D +D+ + Sbjct: 397 SLDEDGDELTYKKYFNIGFAV-------------D----TPNGLVVPVIKD-VDKKSLLE 438 Query: 121 IARELEEITEK 131 IARE+ E+ +K Sbjct: 439 IAREIAELAKK 449 >gnl|CDD|129816 TIGR00733, TIGR00733, putative oligopeptide transporter, OPT family. This protein represents a small family of integral membrane proteins from Gram-negative bacteria, a Gram-positive bacteria, and an archaeal species. Members of this family contain 15 to 18 GES predicted transmembrane regions, and this family has extensive homology to a family of yeast tetrapeptide transporters, including isp4 (Schizosaccharomyces pombe) and Opt1 (Candida albicans). EspB, an apparent equivalog from Myxococcus xanthus, shares an operon with a two component system regulatory protein, and is required for the normal timing of sporulation after the aggregation of cells. This is consistent with a role in transporting oligopeptides as signals across the membrane. Length = 591 Score = 26.4 bits (58), Expect = 7.0 Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 1/41 (2%) Query: 106 PIGIQDRIDRMMDVAIARELEEITEKLSFLGSMSSAGLLVG 146 PI + + R++ +E E T+K G + +AGL+VG Sbjct: 539 PILLGAFLARILVSRGRKEGESFTDKKRL-GVLGAAGLIVG 578 >gnl|CDD|131878 TIGR02831, spo_II_M, stage II sporulation protein M. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This predicted integral membrane protein is designated stage II sporulation protein M. Length = 200 Score = 26.1 bits (58), Expect = 8.6 Identities = 14/35 (40%), Positives = 18/35 (51%) Query: 142 GLLVGILGAVLGMMGFFQSIAGYYSNNVVSIPGII 176 G VG L LGM G + G N++ IPGI+ Sbjct: 105 GFTVGFLVNQLGMKGVLLAFLGVLPQNLIIIPGIL 139 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 0.325 0.138 0.394 Gapped Lambda K H 0.267 0.0808 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 3,694,624 Number of extensions: 236207 Number of successful extensions: 937 Number of sequences better than 10.0: 1 Number of HSP's gapped: 925 Number of HSP's successfully gapped: 49 Length of query: 230 Length of database: 5,994,473 Length adjustment: 90 Effective length of query: 140 Effective length of database: 4,049,753 Effective search space: 566965420 Effective search space used: 566965420 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: 55 (24.8 bits)