RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254781031|ref|YP_003065444.1| exsB protein [Candidatus Liberibacter asiaticus str. psy62] (240 letters) >gnl|CDD|129461 TIGR00364, TIGR00364, exsB protein. This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome. In Rhizobium meliloti, a species in which the exo genes make succinoglycan, a symbiotically important exopolysaccharide, exsB is located nearby and affects succinoglycan levels, probably through polar effects on exsA expression or the same polycistronic mRNA. In Arthrobacter viscosus, the homologous gene is designated ALU1 and is associated with an aluminum tolerance phenotype. The function is unknown. Length = 201 Score = 236 bits (603), Expect = 5e-63 Identities = 96/222 (43%), Positives = 133/222 (59%), Gaps = 26/222 (11%) Query: 11 ALLLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVELECRLCVRKKIVELMPKWKDS 70 A+++ SGGQDS+TCL+ A D V ++FDYGQR+ ELE +KI E Sbjct: 1 AVVVLSGGQDSTTCLAIAKDEGYEVHAITFDYGQRHSRELESA----RKIAEA------- 49 Query: 71 LG-EDHILPLAILGDISHSSLTKNVAMKIQ----DNNLPNTFVPGRNIIFLVFAATLAYR 125 LG E H++ L++L + S+LT + Q ++ LPNTFVPGRN IFL AA+ A Sbjct: 50 LGIEHHVIDLSLLKQLGGSALTDESEIPPQKSNEEDTLPNTFVPGRNAIFLSIAASYAEA 109 Query: 126 LGITNIVIGVCETDYSGYPDCRHDTIRAIETAINLGMESHVTVHTPLMWLKKYETWKLAQ 185 LG ++ GVCETD+SGYPDCR + ++A A+NLGM + V + PLM L K E +LA Sbjct: 110 LGAEAVITGVCETDFSGYPDCRDEFVKAFNHALNLGMLTPVKIRAPLMDLTKAEIVQLAD 169 Query: 186 DIGGQDLVNLILEESHTCYLGKRDKRYEWGYGCNSCPACYLR 227 ++G DLV ++ +++CY G G GC CP+C LR Sbjct: 170 ELGVLDLV---IKLTYSCYAGG-------GEGCGKCPSCMLR 201 >gnl|CDD|182967 PRK11106, PRK11106, queuosine biosynthesis protein QueC; Provisional. Length = 231 Score = 217 bits (555), Expect = 2e-57 Identities = 97/226 (42%), Positives = 139/226 (61%), Gaps = 26/226 (11%) Query: 11 ALLLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVELECRLCVRKKIVELMPKWKDS 70 A+++FSGGQDS+TCL AL ++D V ++FDYGQR++ E++ V +++ Sbjct: 4 AVVVFSGGQDSTTCLIQALQQYDEVHCVTFDYGQRHRAEID----VARELAL-------K 52 Query: 71 LG-EDH-ILPLAILGDISHSSLTKN----VAMKIQDNNLPNTFVPGRNIIFLVFAATLAY 124 LG H +L + +L +++ SSLT++ + + + LPNTFVPGRNI+FL AA AY Sbjct: 53 LGARAHKVLDVTLLNELAVSSLTRDSIPVPDYEPEADGLPNTFVPGRNILFLTLAAIYAY 112 Query: 125 RLGITNIVIGVCETDYSGYPDCRHDTIRAIETAINLGMESHVTVHTPLMWLKKYETWKLA 184 ++ ++ GVCETD+SGYPDCR + ++A+ A++LGM + TPLMWL K ETW LA Sbjct: 113 QVKAEAVITGVCETDFSGYPDCRDEFVKALNHAVSLGMAKDIRFETPLMWLNKAETWALA 172 Query: 185 QDIGGQDLVNLILEESHTCYLGKRDKRYEWGYGCNSCPACYLRQKG 230 G DLV E+ TCY G + G GC C AC+LR G Sbjct: 173 DYYGQLDLVR---HETLTCYNGIK------GDGCGHCAACHLRANG 209 >gnl|CDD|148238 pfam06508, ExsB, ExsB. This family includes putative transcriptional regulators from Bacteria and Archaea. Length = 137 Score = 184 bits (470), Expect = 1e-47 Identities = 67/148 (45%), Positives = 92/148 (62%), Gaps = 18/148 (12%) Query: 11 ALLLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVELECRLCVRKKIVELMPKWKDS 70 A++L SGG DS+TCL+WA V L+FDYGQR+ ELEC KKI + Sbjct: 2 AVVLLSGGLDSTTCLAWAKKEGYEVYALTFDYGQRHSKELECA----KKIAKA------- 50 Query: 71 LGEDH-ILPLAILGDISHSSLTKNVAMKIQDNNL-----PNTFVPGRNIIFLVFAATLAY 124 LG +H I+ L L I S+LT + ++++ D+ L PNT+VPGRN+IFL AA+ A Sbjct: 51 LGVEHKIVDLDFLKQIGGSALTDD-SIEVPDSELESEEIPNTYVPGRNLIFLSIAASYAE 109 Query: 125 RLGITNIVIGVCETDYSGYPDCRHDTIR 152 +G +I IGV E D+SGYPDCR + ++ Sbjct: 110 AIGANDIFIGVNEEDFSGYPDCRPEFVK 137 >gnl|CDD|184745 PRK14561, PRK14561, hypothetical protein; Provisional. Length = 194 Score = 35.2 bits (82), Expect = 0.014 Identities = 15/39 (38%), Positives = 25/39 (64%), Gaps = 3/39 (7%) Query: 13 LLFSGGQDSSTCLS-WALDRFDRVETLSFDYGQRNKVEL 50 +LFSGG+DSS L+ L+RF VE ++ ++G + + Sbjct: 5 VLFSGGKDSS--LAAILLERFYDVELVTVNFGVLDSWKH 41 >gnl|CDD|173244 PRK14783, PRK14783, lipoprotein signal peptidase; Provisional. Length = 182 Score = 32.1 bits (73), Expect = 0.12 Identities = 14/43 (32%), Positives = 20/43 (46%), Gaps = 3/43 (6%) Query: 79 LAILGDISHSSLTKNVAM---KIQDNNLPNTFVPGRNIIFLVF 118 L +LG +LT N QDN +P+ G I+FL+ Sbjct: 44 LEVLGSFFRMTLTFNTGFVFGAFQDNAIPSLIATGFAIVFLIG 86 >gnl|CDD|129143 TIGR00032, argG, argininosuccinate synthase. argG in bacteria, ARG1 in Saccharomyces cerevisiae. There is a very unusual clustering in the alignment, with a deep split between one cohort of E. coli, H. influenzae, and Streptomyces, and the other cohort of eukaryotes, archaea, and the rest of the eubacteria. Length = 394 Score = 31.2 bits (71), Expect = 0.24 Identities = 13/32 (40%), Positives = 18/32 (56%) Query: 13 LLFSGGQDSSTCLSWALDRFDRVETLSFDYGQ 44 L +SGG D+S CL W ++ V + D GQ Sbjct: 4 LAYSGGLDTSVCLKWLREKGYEVIAYTADVGQ 35 >gnl|CDD|183452 PRK12337, PRK12337, 2-phosphoglycerate kinase; Provisional. Length = 475 Score = 30.9 bits (70), Expect = 0.27 Identities = 12/16 (75%), Positives = 13/16 (81%) Query: 117 VFAATLAYRLGITNIV 132 V A+ LAYRLGIT IV Sbjct: 270 VLASALAYRLGITRIV 285 >gnl|CDD|184346 PRK13820, PRK13820, argininosuccinate synthase; Provisional. Length = 394 Score = 30.3 bits (69), Expect = 0.48 Identities = 13/36 (36%), Positives = 22/36 (61%), Gaps = 2/36 (5%) Query: 11 ALLLFSGGQDSSTCLSWALDR--FDRVETLSFDYGQ 44 +L +SGG D+S C+ ++ +D V T++ D GQ Sbjct: 5 VVLAYSGGLDTSVCVPLLKEKYGYDEVITVTVDVGQ 40 >gnl|CDD|178475 PLN02887, PLN02887, hydrolase family protein. Length = 580 Score = 29.8 bits (67), Expect = 0.56 Identities = 27/92 (29%), Positives = 37/92 (40%), Gaps = 27/92 (29%) Query: 9 PSAL-LLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVELECRLCVRKKIVELMPKW 67 P A+ L F G +DS + +T D G + VEL LC I +L +W Sbjct: 129 PMAMKLAFDGLKDSK---------YKTRDTDISDVGGYDSVELSVMLCNDDFIRKLNKEW 179 Query: 68 KDSLGEDHI--------------LPLAILGDI 85 + EDH LP+ +LGDI Sbjct: 180 RG---EDHATDVLSMSQHVPGLKLPVLMLGDI 208 >gnl|CDD|179917 PRK05031, PRK05031, tRNA (uracil-5-)-methyltransferase; Validated. Length = 362 Score = 29.0 bits (66), Expect = 1.1 Identities = 8/38 (21%), Positives = 17/38 (44%) Query: 40 FDYGQRNKVELECRLCVRKKIVELMPKWKDSLGEDHIL 77 FD + ++ ++ + I LMP +L + +L Sbjct: 64 FDQQTKQRIRIDQFPIASELINALMPALLAALRANPVL 101 >gnl|CDD|162012 TIGR00728, OPT_sfam, oligopeptide transporters, OPT superfamily. Homology between the two branches of the superfamily is seen most easily at the ends of the protein. The central regions are poorly conserved within each branch and may not be homologous between branches. Length = 654 Score = 28.6 bits (64), Expect = 1.6 Identities = 10/23 (43%), Positives = 12/23 (52%) Query: 113 IIFLVFAATLAYRLGITNIVIGV 135 II V A + GITN V G+ Sbjct: 415 IIAFVLAIPIGILAGITNPVSGL 437 >gnl|CDD|163392 TIGR03679, arCOG00187, arCOG00187 universal archaeal metal-binding-domain/4Fe-4S-binding-domain containing ABC transporter, ATP-binding protein. This model has the same scope as an archaeal COG (arCOG00187) and is found in all completely sequenced archaea and does not recognize any known non-archaeal genes. Length = 218 Score = 28.4 bits (64), Expect = 1.9 Identities = 11/25 (44%), Positives = 15/25 (60%) Query: 14 LFSGGQDSSTCLSWALDRFDRVETL 38 L+SGG+DS+ L AL+ V L Sbjct: 3 LYSGGKDSNYALYKALEEGHEVRCL 27 >gnl|CDD|129390 TIGR00289, TIGR00289, conserved hypothetical protein TIGR00289. Homologous proteins related to MJ0570 of Methanococcus jannaschii include both the apparent orthologs found by this model above the trusted cutoff, the much longer protein YLR143W from Saccharomyces cerevisiae, and second homologous proteins from Archaeoglobus fulgidus and Pyrococcus horikoshii that appear to represent a second orthologous group. Length = 222 Score = 28.3 bits (63), Expect = 2.0 Identities = 11/25 (44%), Positives = 16/25 (64%), Gaps = 1/25 (4%) Query: 14 LFSGGQDSSTCLSWALDRFDRVETL 38 L+SGG+DS L AL+ + V +L Sbjct: 6 LYSGGKDSILALYKALEEHE-VISL 29 >gnl|CDD|181483 PRK08576, PRK08576, hypothetical protein; Provisional. Length = 438 Score = 27.7 bits (62), Expect = 2.5 Identities = 11/29 (37%), Positives = 15/29 (51%) Query: 15 FSGGQDSSTCLSWALDRFDRVETLSFDYG 43 +SGG+DS+ L A F V + D G Sbjct: 241 WSGGKDSTAALLLAKKAFGDVTAVYVDTG 269 >gnl|CDD|178336 PLN02735, PLN02735, carbamoyl-phosphate synthase. Length = 1102 Score = 27.8 bits (62), Expect = 2.7 Identities = 13/23 (56%), Positives = 14/23 (60%), Gaps = 1/23 (4%) Query: 126 LGITNIVIG-VCETDYSGYPDCR 147 LG IVIG CE DYSG C+ Sbjct: 29 LGAGPIVIGQACEFDYSGTQACK 51 >gnl|CDD|172452 PRK13943, PRK13943, protein-L-isoaspartate O-methyltransferase; Provisional. Length = 322 Score = 27.1 bits (60), Expect = 3.6 Identities = 11/31 (35%), Positives = 14/31 (45%), Gaps = 1/31 (3%) Query: 115 FLVFAATLAYRLGITNIVIGVCETDYSGYPD 145 A RLGI N++ VC Y G P+ Sbjct: 117 ICEIAKRNVRRLGIENVIF-VCGDGYYGVPE 146 >gnl|CDD|177791 PLN00200, PLN00200, argininosuccinate synthase; Provisional. Length = 404 Score = 27.0 bits (60), Expect = 3.9 Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 2/46 (4%) Query: 7 KAPSALLLFSGGQDSSTCLSWALDRFD-RVETLSFDYGQRNKVELE 51 K +L +SGG D+S L W + + V + D GQ + ELE Sbjct: 4 KLNKVVLAYSGGLDTSVILKWLRENYGCEVVCFTADVGQGIE-ELE 48 >gnl|CDD|185096 PRK15174, PRK15174, Vi polysaccharide export protein VexE; Provisional. Length = 656 Score = 27.0 bits (59), Expect = 4.0 Identities = 12/62 (19%), Positives = 25/62 (40%), Gaps = 14/62 (22%) Query: 70 SLGEDHILPLAILGDISHSSLTKNVAMKIQDNNLPNTFVPGRNIIFLVFAATLAYRLGIT 129 +L L +AI G ++ S+ P G+ I + F + LA+++ + Sbjct: 541 TLHSGQSLVVAIDGALNLSA--------------PTIDFFGQQITYSTFCSRLAWKMHLP 586 Query: 130 NI 131 + Sbjct: 587 TV 588 >gnl|CDD|182369 PRK10307, PRK10307, putative glycosyl transferase; Provisional. Length = 412 Score = 26.9 bits (60), Expect = 4.7 Identities = 11/47 (23%), Positives = 18/47 (38%), Gaps = 11/47 (23%) Query: 26 SWALDRFDRVETLS---FDYGQRNKVELECRLCVRKKIVELMPKWKD 69 L RFD V T+S + + V +K++ P W + Sbjct: 166 RSLLRRFDNVSTISRSMMNKAREKGV-------AAEKVIFF-PNWSE 204 >gnl|CDD|161976 TIGR00644, recJ, single-stranded-DNA-specific exonuclease RecJ. All proteins in this family are 5'-3' single-strand DNA exonucleases. These proteins are used in some aspects of mismatch repair, recombination, and recombinational repair. Length = 539 Score = 26.9 bits (60), Expect = 5.5 Identities = 18/99 (18%), Positives = 38/99 (38%), Gaps = 23/99 (23%) Query: 1 MNDIIKKAPSALLLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVELECRLCVRKKI 60 + D++ + AL L GG + L+ +R +E R+K+ Sbjct: 377 LYDLLSELREALFLKFGGHAMAAGLTL----------------KRENLEE-----FREKL 415 Query: 61 VELMPKWKDSLGEDHILPLAILGDISHSSLTKNVAMKIQ 99 E K + + ILP + ++ +T+ + +I+ Sbjct: 416 EEKFKKILFADESEEILP--VDAELKAEEITRELIEQIE 452 >gnl|CDD|119242 pfam10722, YbjN, Putative bacterial sensory transduction regulator. YbjN is a putative sensory transduction regulator protein found in Proteobacteria. As it is a multi-copy suppressor of the coenzyme A-associated temperature sensitivity in temperature-sensitive mutant strains of Escherichia coli the suggestion is that it both helps CoA-A1 and possibly works as a general stabilizer for some other unstable proteins. Length = 157 Score = 26.5 bits (59), Expect = 5.7 Identities = 15/30 (50%), Positives = 19/30 (63%), Gaps = 1/30 (3%) Query: 76 ILPL-AILGDISHSSLTKNVAMKIQDNNLP 104 +LPL A L I+ S LT + IQD+NLP Sbjct: 68 LLPLVADLSRINASYLTVKAFLDIQDDNLP 97 >gnl|CDD|178474 PLN02886, PLN02886, aminoacyl-tRNA ligase. Length = 389 Score = 26.7 bits (59), Expect = 5.9 Identities = 8/13 (61%), Positives = 9/13 (69%) Query: 163 ESHVTVHTPLMWL 175 +SHV H LMWL Sbjct: 125 QSHVPAHAELMWL 137 >gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional. Length = 632 Score = 26.4 bits (59), Expect = 6.8 Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 2/49 (4%) Query: 122 LAYRLGITNIVIGVCETDYSGYPDCRHDTIRA--IETAINLGMESHVTV 168 +A LGI ++V+ V + D Y D I A A LG+ + Sbjct: 151 IASLLGIRHVVLAVNKMDLVDYDQEVFDEIVADYRAFAAKLGLHDVTFI 199 >gnl|CDD|184427 PRK13969, PRK13969, proline racemase; Provisional. Length = 334 Score = 26.4 bits (58), Expect = 7.1 Identities = 12/45 (26%), Positives = 20/45 (44%), Gaps = 7/45 (15%) Query: 134 GVCETDYSGYPD-CRHDTIRAIETAINLGME------SHVTVHTP 171 G+ D GY + C H +I A A+ G+ +H+ + P Sbjct: 78 GIIFMDGGGYLNMCGHGSIGAATCAVETGIVKVEEPYTHIKLEAP 122 >gnl|CDD|179998 PRK05294, carB, carbamoyl phosphate synthase large subunit; Reviewed. Length = 1066 Score = 26.2 bits (59), Expect = 7.2 Identities = 10/13 (76%), Positives = 10/13 (76%), Gaps = 1/13 (7%) Query: 131 IVIG-VCETDYSG 142 IVIG CE DYSG Sbjct: 18 IVIGQACEFDYSG 30 >gnl|CDD|161881 TIGR00442, hisS, histidyl-tRNA synthetase. This model finds a histidyl-tRNA synthetase in every completed genome. Apparent second copies from Bacillus subtilis, Synechocystis sp., and Aquifex aeolicus are slightly shorter, more closely related to each other than to other hisS proteins, and actually serve as regulatory subunits for an enzyme of histidine biosynthesis. They were excluded from the seed alignment and score much lower than do single copy histidyl-tRNA synthetases of other genomes not included in the seed alignment. These putative second copies of HisS score below the trusted cutoff. The regulatory protein kinase GCN2 of Saccharomyces cerevisiae (YDR283c), and related proteins from other species designated eIF-2 alpha kinase, have a domain closely related to histidyl-tRNA synthetase that may serve to detect and respond to uncharged tRNA(his), an indicator of amino acid starvation; these regulatory proteins are not orthologous and so score below the noise cutoff. Length = 397 Score = 25.9 bits (58), Expect = 8.6 Identities = 15/40 (37%), Positives = 19/40 (47%), Gaps = 5/40 (12%) Query: 50 LECRLCVRKKIVELMPKWKDSLGED-----HILPLAILGD 84 LE RL R+ ++ + K D LGED PL IL Sbjct: 165 LEGRLEYREALLRYLDKHLDKLGEDSVRRLEKNPLRILDS 204 >gnl|CDD|150923 pfam10327, 7TM_GPCR_Sri, Serpentine type 7TM GPCR chemoreceptor Sri. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Sri is part of the Str superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. Length = 303 Score = 26.0 bits (58), Expect = 9.3 Identities = 7/31 (22%), Positives = 11/31 (35%) Query: 75 HILPLAILGDISHSSLTKNVAMKIQDNNLPN 105 HI P S L++ ++ N P Sbjct: 141 HIFPFLTAFLFYQSGLSREEQLEYVKENYPE 171 >gnl|CDD|179051 PRK00509, PRK00509, argininosuccinate synthase; Provisional. Length = 399 Score = 25.8 bits (58), Expect = 9.4 Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 3/40 (7%) Query: 13 LLFSGGQDSSTCLSWALDRFDR-VETLSFDYGQRNKVELE 51 L +SGG D+S + W + + V + D GQ ELE Sbjct: 7 LAYSGGLDTSVIIKWLKETYGCEVIAFTADVGQGE--ELE 44 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 0.322 0.138 0.438 Gapped Lambda K H 0.267 0.0755 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 3,925,980 Number of extensions: 236463 Number of successful extensions: 506 Number of sequences better than 10.0: 1 Number of HSP's gapped: 498 Number of HSP's successfully gapped: 32 Length of query: 240 Length of database: 5,994,473 Length adjustment: 91 Effective length of query: 149 Effective length of database: 4,028,145 Effective search space: 600193605 Effective search space used: 600193605 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 (25.3 bits)