RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780376|ref|YP_003064789.1| flagellar basal body P-ring protein [Candidatus Liberibacter asiaticus str. psy62] (369 letters) >gnl|CDD|180004 PRK05303, flgI, flagellar basal body P-ring protein; Provisional. Length = 367 Score = 476 bits (1229), Expect = e-135 Identities = 187/372 (50%), Positives = 237/372 (63%), Gaps = 8/372 (2%) Query: 1 MIFRIAFLIFSLIGLHEISAQVVSRIKDVVSLQSGRDNQLIGYGLVVGLQGTGDSLRSSP 60 M L L+ L ++ RIKD+ S+Q RDNQLIGYGLVVGL GTGD +P Sbjct: 1 MKMLKLLLALLLLLLLLLAPAAAERIKDLASVQGVRDNQLIGYGLVVGLDGTGDQTTQTP 60 Query: 61 FTEQSMRSLLQNLGISTPGG-RLGSKNVAAVMVTANLPPFASPGSRIDVSINSLGDASSL 119 FT QS+ ++L+ LG++ P G KNVAAVMVTA LPPFA PG RIDV+++S+GDA SL Sbjct: 61 FTTQSLANMLEQLGVNVPPGTNPKLKNVAAVMVTATLPPFARPGQRIDVTVSSIGDAKSL 120 Query: 120 RGGILVMTSLLGADGNIYAVAQGSVVVSGLFVKGQSSSFMEGISTGGKIVNGAIVERELP 179 RGG L+MT L GADG +YAVAQG++VV G G SS + T G+I NGAIVERE+P Sbjct: 121 RGGTLLMTPLKGADGQVYAVAQGNLVVGGFGASGDGSSVTVNVPTVGRIPNGAIVEREVP 180 Query: 180 KKFKDSADLILQLRNPDFSTAIRIADQINSYSLNRFSRPIAEAYDSRTVKVSKPT-NIDL 238 F L L LRNPDF+TA RIAD IN F +A A D+RTV+V P Sbjct: 181 SDFGQGNSLTLNLRNPDFTTAQRIADAIN----RLFGPGVATALDARTVQVRAPADPSQR 236 Query: 239 TRLMSEVEMLTVETDTPARVIINERTGTIVIGDNVRISKVVVSYGNLTVQITENEQVVQP 298 R ++ +E L VE D PA+V+INERTGTIV+G +VR+S V VS+GNLTV ITE QV QP Sbjct: 237 VRFLARIENLEVEPDAPAKVVINERTGTIVMGQDVRVSPVAVSHGNLTVTITEQPQVSQP 296 Query: 299 NAFSSNGSTVTQNNTDLKVSDNKGSFSLIDA-PDLNSLISGMNSIGLKTDGIISILQGIK 357 N F S G TV T + V + G ++ L L+ +N++G +I+ILQ +K Sbjct: 297 NPF-SGGQTVVTPQTQIDVEEEGGRLFVVPEGATLADLVRALNALGATPRDLIAILQALK 355 Query: 358 AAGALQSEIIIQ 369 AAGAL +E+ + Sbjct: 356 AAGALHAELEVI 367 >gnl|CDD|183746 PRK12789, flgI, flagellar basal body P-ring protein; Reviewed. Length = 367 Score = 435 bits (1121), Expect = e-123 Identities = 196/370 (52%), Positives = 272/370 (73%), Gaps = 4/370 (1%) Query: 1 MIFRIAF-LIFSLIGLHEISAQVVSRIKDVVSLQSGRDNQLIGYGLVVGLQGTGDSLRSS 59 MI R+ ++ L L A +RIKD+ +L+ RDNQL+GYGLV GLQGTGD+LR++ Sbjct: 1 MIRRLLLAVLLGL--LAGPVAAAGTRIKDIATLKGVRDNQLVGYGLVTGLQGTGDTLRNA 58 Query: 60 PFTEQSMRSLLQNLGISTPGGRLGSKNVAAVMVTANLPPFASPGSRIDVSINSLGDASSL 119 FTEQS++S+L +GI+ RL ++NVAAVMVTA+LPPF PGSRIDV+++SLGDA+SL Sbjct: 59 QFTEQSLQSMLDRMGINVRDARLRTRNVAAVMVTADLPPFTGPGSRIDVTVSSLGDATSL 118 Query: 120 RGGILVMTSLLGADGNIYAVAQGSVVVSGLFVKGQSSSFMEGISTGGKIVNGAIVERELP 179 RGG L+MTSL G DG +YAVAQG + VSG V+GQ+ S +G+ T G+I NGA++ERE+P Sbjct: 119 RGGTLLMTSLTGGDGLVYAVAQGPLAVSGFSVQGQAESLTQGVPTAGRIPNGALIEREVP 178 Query: 180 KKFKDSADLILQLRNPDFSTAIRIADQINSYSLNRFSRPIAEAYDSRTVKVSKPTNIDLT 239 F+D +L+L+L+NPDF TA +I+D IN+YSL R+ R IA D RTV + +P + T Sbjct: 179 GTFRDLPELVLELKNPDFKTATQISDAINAYSLGRYGRRIASERDQRTVVLMRPRQMAQT 238 Query: 240 RLMSEVEMLTVETDTPARVIINERTGTIVIGDNVRISKVVVSYGNLTVQITENEQVVQPN 299 R ++E+ LT+E DTPARV++++RTGT+VIG NV+IS V V++GNLTV++TE +V QP Sbjct: 239 RFIAEIGDLTIEPDTPARVVVDQRTGTVVIGRNVQISTVAVTHGNLTVRVTEAPEVSQPA 298 Query: 300 AFSSNGSTVTQNNTDLKVSDNKGSFSLIDAPDLNSLISGMNSIGLKTDGIISILQGIKAA 359 F SNG TV T++ ++ G +++ DL +L+ G+N IGLK II+ILQ IK A Sbjct: 299 PF-SNGQTVVVPRTEIDANEEGGKLAILRGSDLQTLVRGLNQIGLKPSDIIAILQAIKTA 357 Query: 360 GALQSEIIIQ 369 GALQ+E+++Q Sbjct: 358 GALQAELVVQ 367 >gnl|CDD|183694 PRK12706, flgI, flagellar basal body P-ring protein; Provisional. Length = 328 Score = 73.3 bits (180), Expect = 8e-14 Identities = 94/354 (26%), Positives = 151/354 (42%), Gaps = 62/354 (17%) Query: 17 EISAQVVSRIKDVVSLQSGRDNQLIGYGLVVGLQGTGDSLRSSPFTEQSMRSLLQNLGIS 76 +IS V ++K++ + N L G G+V GL GDSL+ + +L +GI+ Sbjct: 35 QISESV--KLKNIAEICPTNSNFLTGIGIVAGLADKGDSLKQKDILNK----ILNEIGIN 88 Query: 77 TPG-GRLGSKNVAAVMVTANLPPFASPGSRIDVSINSLGDASSLRGGILVMTSLLGADGN 135 +GSKN+A V V+ + GS+ +V I S+ D+ L GIL+ T L +G Sbjct: 89 EIDLTNIGSKNIALVNVSLQINGNMIKGSKHNVYIASMLDSKDLTNGILLKTELKDKEGK 148 Query: 136 IYAVAQGSVVVSGLFVKGQSSSFMEGISTGGKIVNGAIVERELPKKFKDSADLILQLRNP 195 I A A G ++ + KG G I+NGA + ++ + L+ Sbjct: 149 ILATASGPIITNNK-SKGT-----------GYILNGATIHEN-----QNYTHYNIILKKG 191 Query: 196 DFSTAIRIADQINSYSLNRFSRPIAEAYDSRTVKVSKPTNIDLTRLMSEVEMLTVETDTP 255 D++ IN S S+ I S + + NI L+ E+E + +ET Sbjct: 192 DYTL-------INRISKILTSKNIKNNIKSGNIIEIEVKNI---GLLEEIENIEIETM-- 239 Query: 256 ARVIINERTGTIVIGDNVRISKVVVSYGNLTVQITENEQVVQPNAFSSNGSTVTQNNTDL 315 +V+I+E+ I+ N I G LT I ++Q N F++ NN + Sbjct: 240 PKVLIDEQNKIILASTNAEI-------GPLTFSIERDDQ----NLFNNK------NNKTI 282 Query: 316 KVSDNKGSFSLIDAPDLNSLISGMNSIGLKTDGIISILQGIKAAGALQSEIIIQ 369 K+ K LN IS NS L +I I++ K L E+I++ Sbjct: 283 KIQIQKMK--------LNEFISK-NSNNLSNKELIQIIKAAKKINKLNGELILE 327 >gnl|CDD|129562 TIGR00470, sepS, O-phosphoseryl-tRNA(Cys) synthetase. This family of archaeal proteins resembles known phenylalanyl-tRNA synthetase alpha chains. Recently, it was shown to act in a proposed pathway of tRNA(Cys) indirect aminoacylation, resulting in Cys biosynthesis from O-phosphoserine, in certain archaea. It charges tRNA(Cys) with O-phosphoserine. The pscS gene product converts the phosphoserine to Cys. Length = 533 Score = 29.8 bits (67), Expect = 1.2 Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 5/73 (6%) Query: 103 GSRIDVSINSLGDASSLRGGILVMTSLLGADGNIYAVAQGSVVVSGLFVKGQSSSFMEGI 162 G RI V I + + L G V+ + DGNIY + V ++K + EG+ Sbjct: 403 GRRIKVEIFENEENTKLLGPA-VLNEVYVYDGNIYGIPPTFEGVKEQYIK----AKEEGV 457 Query: 163 STGGKIVNGAIVE 175 STG + ++G + Sbjct: 458 STGIRYIDGIAYK 470 >gnl|CDD|163210 TIGR03303, OM_YaeT, outer membrane protein assembly complex, YaeT protein. Members of this protein family are the YaeT protein of the YaeT/YfiO complex for assembling proteins into the outer membrane of Gram-negative bacteria. This protein is similar in sequence and function to a non-essential paralog, YtfM, that is also in the Omp85 family. Members of this family typically have five tandem copies of the surface antigen variable number repeat (pfam07244), followed by an outer membrane beta-barrel domain (pfam01103), while the YtfM family typically has a single pfam07244 repeat. Length = 741 Score = 28.7 bits (65), Expect = 2.2 Identities = 15/55 (27%), Positives = 25/55 (45%), Gaps = 6/55 (10%) Query: 221 EAYDSRTVKVSKPTNIDLTRLMSEVEMLTVETDTPARVIIN----ER-TGTIVIG 270 + Y +K SK ++ V + TV +P +V +N E+ TG+I G Sbjct: 350 DWYSLSKIKRSK-RRLERLGYFETVNIETVPVGSPDQVDLNVKVKEQPTGSISFG 403 >gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional. Length = 2836 Score = 27.7 bits (61), Expect = 5.0 Identities = 15/49 (30%), Positives = 26/49 (53%) Query: 79 GGRLGSKNVAAVMVTANLPPFASPGSRIDVSINSLGDASSLRGGILVMT 127 GR G+K V + +V P+ G+ +D+ +N LG S + G ++ T Sbjct: 1088 AGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILET 1136 >gnl|CDD|161995 TIGR00682, lpxK, tetraacyldisaccharide 4'-kinase. Also called lipid-A 4'-kinase. This essential gene encodes an enzyme in the pathway of lipid A biosynthesis in Gram-negative organisms. A single copy of this protein is found in Gram-negative bacteria. PSI-BLAST converges on this set of apparent orthologs without identifying any other homologs. Length = 311 Score = 27.4 bits (61), Expect = 6.2 Identities = 8/40 (20%), Positives = 15/40 (37%), Gaps = 1/40 (2%) Query: 176 RELPKKFKDSADLILQLR-NPDFSTAIRIADQINSYSLNR 214 RE PK+ K + +I+ N + + +I Sbjct: 163 REFPKRLKSADAVIVNGGENQSGFIPMFLMPRIACCVNLS 202 >gnl|CDD|180856 PRK07133, PRK07133, DNA polymerase III subunits gamma and tau; Validated. Length = 725 Score = 26.7 bits (59), Expect = 8.7 Identities = 12/41 (29%), Positives = 23/41 (56%) Query: 173 IVERELPKKFKDSADLILQLRNPDFSTAIRIADQINSYSLN 213 I+E+E K++ LI +L + A+ IA+Q++ + N Sbjct: 189 ILEKENISYEKNALKLIAKLSSGSLRDALSIAEQVSIFGNN 229 >gnl|CDD|131892 TIGR02845, spore_V_AD, stage V sporulation protein AD. Bacillus and Clostridium species contain about 10 % dipicolinic acid (pyridine-2,6-dicarboxylic acid) by weight. This protein family, SpoVAD, belongs to the spoVA operon that is suggested to act in the transport of dipicolinic acid (DPA) from the mother cell, where DPA is synthesized, to the forespore, a process essential to sporulation. Members of this protein family are found, so far, in exactly those species believed capable of endospore formation. Length = 327 Score = 27.0 bits (60), Expect = 9.0 Identities = 11/31 (35%), Positives = 18/31 (58%), Gaps = 2/31 (6%) Query: 148 GLFVKGQSSSFMEGISTGGKIVNGAIVEREL 178 GL+ G S+ ME ++ G +V+G +R L Sbjct: 100 GLY--GACSTSMETLALGAMLVDGGFADRVL 128 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 0.315 0.133 0.355 Gapped Lambda K H 0.267 0.0789 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 5,693,696 Number of extensions: 365566 Number of successful extensions: 829 Number of sequences better than 10.0: 1 Number of HSP's gapped: 823 Number of HSP's successfully gapped: 26 Length of query: 369 Length of database: 5,994,473 Length adjustment: 95 Effective length of query: 274 Effective length of database: 3,941,713 Effective search space: 1080029362 Effective search space used: 1080029362 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 58 (26.0 bits)