BLASTP 2.2.18 [Mar-02-2008] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= 0001.0330.p (378 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309699|ref|YP_003773791.1| ATPase PilB [Herbaspirillum ser... 640 0.0 gi|300310145|ref|YP_003774237.1| general secretion pathway prote... 140 1e-34 gi|300310151|ref|YP_003774243.1| twitching mobility PilT protein... 97 3e-21 gi|300313098|ref|YP_003777190.1| Tfp pilus assembly protein, pil... 86 3e-18 >gi|300309699|ref|YP_003773791.1| ATPase PilB [Herbaspirillum seropedicae SmR1] Length = 377 Score = 640 bits (1651), Expect = 0.0, Method: Compositional matrix adjust. Identities = 315/378 (83%), Positives = 347/378 (91%), Gaps = 1/378 (0%) Query: 1 MQAPDTAVADDDVPVVRLLHKLLADAVGRGASDLHFEPFESVFRVRLRVDGVLHELAQPP 60 MQA +T +ADD VPVVRLL+KLLADAV GASDLHFEPFE RVRLR+DG+LHELAQPP Sbjct: 1 MQASETPLADD-VPVVRLLYKLLADAVSMGASDLHFEPFEHYCRVRLRIDGILHELAQPP 59 Query: 61 LSLREKLATRLKILARLDIAEKRLPQDGKMRLALAERSVDFRVSTLPTQFGEKIVLRILD 120 LSL++KLATRLKILARLDIAEKRLPQDGKMRLAL R+VDFRVSTLPTQFGEKIVLRILD Sbjct: 60 LSLKDKLATRLKILARLDIAEKRLPQDGKMRLALETRTVDFRVSTLPTQFGEKIVLRILD 119 Query: 121 TAQATLSIAELGYEPAQQQALLHAITKPHGLVLMTGPTGSGKTVSLYACLQRLNQPGVNI 180 T QATL++ +LGYEPAQ QAL AI +PHG+VLMTGPTGSGKTVSLYACLQRLN+PG+NI Sbjct: 120 TEQATLALEQLGYEPAQLQALQQAIARPHGMVLMTGPTGSGKTVSLYACLQRLNRPGINI 179 Query: 181 ATAEDPVEINLPGVNQVSINERTGLDFALALRAFLRQDPDVLMVGEIRDLETADIAVKAS 240 ATAEDPVEINLPG+NQVSINER GL+FA+ALRAFLRQDPDVLMVGEIRDL+TADIA+KA+ Sbjct: 180 ATAEDPVEINLPGINQVSINERAGLNFAVALRAFLRQDPDVLMVGEIRDLDTADIAIKAA 239 Query: 241 QTGHLVLSTLHTNDAPATLTRLLNMGVPAYNIAASVSLIVAQRLVRKLCHCRRPAGGRPA 300 QTGHLVLSTLHTNDAPATLTRLLNMGVPAYNIAASVSLIVAQRLVR+LC CRRPA Sbjct: 240 QTGHLVLSTLHTNDAPATLTRLLNMGVPAYNIAASVSLIVAQRLVRRLCSCRRPARDASG 299 Query: 301 TFVAQGCPACNHTGFRGRTGIYQVMPVSPAMQSLILAQAGTLELARQAQAEGIIDLRRAG 360 +FV GCPAC+HTG+RGRTGIYQVMPVS MQSLI AQAGT ++ARQA+AEG+IDLRRAG Sbjct: 300 SFVPHGCPACSHTGYRGRTGIYQVMPVSATMQSLIQAQAGTQDIARQARAEGVIDLRRAG 359 Query: 361 LLKVLRGETSVGEILACT 378 LLK LRG+TS+GE+LA T Sbjct: 360 LLKALRGDTSLGEVLAST 377 >gi|300310145|ref|YP_003774237.1| general secretion pathway protein E [Herbaspirillum seropedicae SmR1] Length = 541 Score = 140 bits (354), Expect = 1e-34, Method: Compositional matrix adjust. Identities = 107/343 (31%), Positives = 169/343 (49%), Gaps = 40/343 (11%) Query: 22 LLADAVGRGASDLHFEPFESVFRVRLRVDGVLHELAQPPLSLREKLATRLKILARLDIAE 81 LL A ASD+H ++ + R+ L ++ E+L L A +++ Sbjct: 124 LLNKACRSRASDIHLRVRKNCTEIYFRIHNDLVQVGGQTREYGERLLATL-YGAMTSVSD 182 Query: 82 KRLPQDGKMRLALAERS------VDFRVSTLPTQFGEKIVLRIL-DTAQATLSIAELGYE 134 + A+A+R R++T+PT G +VLR+L + A + + LG+ Sbjct: 183 SSYKPTERQDAAIADRDKLPPALYGVRIATVPTSEGSVMVLRLLYNDAGDNIDLRPLGFS 242 Query: 135 PAQQQALLHAITKPHGLVLMTGPTGSGKTVSLYACL--QRLNQPG-VNIATAEDPVEINL 191 A AL +P G+ +++GPTGSGK+ +L L + + G +++ T EDPVE + Sbjct: 243 EAHASALQKLKEQPVGMNIISGPTGSGKSTTLQRVLTGEIIEAEGKLHVLTIEDPVEYPI 302 Query: 192 PGVNQVSI-----NERTGLDFALALRAFLRQDPDVLMVGEIRDLETADIAVKASQTGHLV 246 G Q ++ E FA A+ +R DPD +M+GE+RD TA A++AS TGH V Sbjct: 303 DGAVQTAVTNAGSEEERSRAFAAAISNAMRLDPDTIMIGEVRDRATAQNALRASMTGHQV 362 Query: 247 LSTLHTNDAPATLTRLLNMGVPAYNIA--ASVSLIVAQRLVRKLCH-CRRPAGGRPATFV 303 +T+H N A A + RLL++G+PA +A A V+ +++QRLV+KLC CR+P RP Sbjct: 363 WTTVHANSALAIIDRLLDLGLPASLVADHAVVTGLISQRLVKKLCPCCRQPLAARPEVLP 422 Query: 304 AQ---------------------GCPACNHTGFRGRTGIYQVM 325 A GC C G GRT + +++ Sbjct: 423 AAVLARVRQAVSPSLDGVCVTGPGCEHCAGQGTVGRTVVAEII 465 >gi|300310151|ref|YP_003774243.1| twitching mobility PilT protein [Herbaspirillum seropedicae SmR1] Length = 365 Score = 96.7 bits (239), Expect = 3e-21, Method: Compositional matrix adjust. Identities = 53/118 (44%), Positives = 75/118 (63%), Gaps = 4/118 (3%) Query: 150 GLVLMTGPTGSGKTVSLYACLQRLNQPGV-NIATAEDPVEINLPGVNQVSINERTGLD-- 206 G++L+TGPTG+GKT ++ + L +N +I T E+P+E L + + D Sbjct: 133 GIILVTGPTGAGKTTTIASMLDYINASRRGHIITIEEPIEYELQRKQSMISQKEVPTDTE 192 Query: 207 -FALALRAFLRQDPDVLMVGEIRDLETADIAVKASQTGHLVLSTLHTNDAPATLTRLL 263 F+ LR LRQ PDVLMVGEIRD +TAD + A ++GHLVL+TLHT+ A +T+LL Sbjct: 193 SFSSGLREALRQKPDVLMVGEIRDFDTADTVLHAGESGHLVLATLHTSSAVRAITKLL 250 >gi|300313098|ref|YP_003777190.1| Tfp pilus assembly protein, pilus retraction ATPase PilT protein [Herbaspirillum seropedicae SmR1] Length = 351 Score = 86.3 bits (212), Expect = 3e-18, Method: Compositional matrix adjust. Identities = 78/197 (39%), Positives = 113/197 (57%), Gaps = 20/197 (10%) Query: 101 FRVSTLPTQFGEKIVLRILDTAQATLSIAELGYEPAQQQALLHAITKPHGLVLMTGPTGS 160 FRV Q G + +R L TL A+LG P + + GLVL+TGPTG+ Sbjct: 81 FRVHAFLRQGGPAVAIRHLGREPPTL--AQLGAPPLCAEL----AERAGGLVLVTGPTGA 134 Query: 161 GKTVSLYACLQRLNQP-GVNIATAEDPVE-INLPG---VNQVSINERTGLDFALALRAFL 215 GK+ +L A ++ LN+ ++I T EDP+E I+ P ++Q + T D ALRA L Sbjct: 135 GKSSTLAAMIRHLNETRALHILTIEDPIEFIHTPQRALISQRELGTHT-ADLPAALRAAL 193 Query: 216 RQDPDVLMVGEIRDLETADIAVKASQTGHLVLSTLHTNDAPATLTRLLNMGVPAYN---- 271 R DPDVL+VGE+RD +T +A+ A++TGHLVL TLH A T+ R+L++ PA Sbjct: 194 RADPDVLLVGELRDADTIRLALTAAETGHLVLGTLHAASAARTVERMLDV-FPAGEKEPA 252 Query: 272 ---IAASVSLIVAQRLV 285 +A S+ ++AQ L+ Sbjct: 253 RAMLAESLQGVIAQTLL 269 Database: BlastDatabases/689/689 Posted date: Apr 10, 2011 12:15 AM Number of letters in database: 1,619,870 Number of sequences in database: 4735 Lambda K H 0.321 0.136 0.388 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 4735 Number of Hits to DB: 1,084,320 Number of extensions: 43961 Number of successful extensions: 208 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 203 Number of HSP's successfully gapped: 4 Length of query: 378 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 291 Effective length of database: 1,207,925 Effective search space: 351506175 Effective search space used: 351506175 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: 131 (55.1 bits)