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= 0020.0122.p (350 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... 709 0.0 gi|300310145|ref|YP_003774237.1| general secretion pathway prote... 136 3e-33 gi|300310151|ref|YP_003774243.1| twitching mobility PilT protein... 103 2e-23 gi|300313098|ref|YP_003777190.1| Tfp pilus assembly protein, pil... 94 1e-20 >gi|300309699|ref|YP_003773791.1| ATPase PilB [Herbaspirillum seropedicae SmR1] Length = 377 Score = 709 bits (1829), Expect = 0.0, Method: Compositional matrix adjust. Identities = 350/350 (100%), Positives = 350/350 (100%) Query: 1 MGASDLHFEPFEHYCRVRLRIDGILHELAQPPLSLKDKLATRLKILARLDIAEKRLPQDG 60 MGASDLHFEPFEHYCRVRLRIDGILHELAQPPLSLKDKLATRLKILARLDIAEKRLPQDG Sbjct: 28 MGASDLHFEPFEHYCRVRLRIDGILHELAQPPLSLKDKLATRLKILARLDIAEKRLPQDG 87 Query: 61 KMRLALETRTVDFRVSTLPTQFGEKIVLRILDTEQATLALEQLGYEPAQLQALQQAIARP 120 KMRLALETRTVDFRVSTLPTQFGEKIVLRILDTEQATLALEQLGYEPAQLQALQQAIARP Sbjct: 88 KMRLALETRTVDFRVSTLPTQFGEKIVLRILDTEQATLALEQLGYEPAQLQALQQAIARP 147 Query: 121 HGMVLMTGPTGSGKTVSLYACLQRLNRPGINIATAEDPVEINLPGINQVSINERAGLNFA 180 HGMVLMTGPTGSGKTVSLYACLQRLNRPGINIATAEDPVEINLPGINQVSINERAGLNFA Sbjct: 148 HGMVLMTGPTGSGKTVSLYACLQRLNRPGINIATAEDPVEINLPGINQVSINERAGLNFA 207 Query: 181 VALRAFLRQDPDVLMVGEIRDLDTADIAIKAAQTGHLVLSTLHTNDAPATLTRLLNMGVP 240 VALRAFLRQDPDVLMVGEIRDLDTADIAIKAAQTGHLVLSTLHTNDAPATLTRLLNMGVP Sbjct: 208 VALRAFLRQDPDVLMVGEIRDLDTADIAIKAAQTGHLVLSTLHTNDAPATLTRLLNMGVP 267 Query: 241 AYNIAASVSLIVAQRLVRRLCSCRRPARDASGSFVPHGCPACSHTGYRGRTGIYQVMPVS 300 AYNIAASVSLIVAQRLVRRLCSCRRPARDASGSFVPHGCPACSHTGYRGRTGIYQVMPVS Sbjct: 268 AYNIAASVSLIVAQRLVRRLCSCRRPARDASGSFVPHGCPACSHTGYRGRTGIYQVMPVS 327 Query: 301 ATMQSLIQAQAGTQDIARQARAEGVIDLRRAGLLKALRGDTSLGEVLAST 350 ATMQSLIQAQAGTQDIARQARAEGVIDLRRAGLLKALRGDTSLGEVLAST Sbjct: 328 ATMQSLIQAQAGTQDIARQARAEGVIDLRRAGLLKALRGDTSLGEVLAST 377 >gi|300310145|ref|YP_003774237.1| general secretion pathway protein E [Herbaspirillum seropedicae SmR1] Length = 541 Score = 136 bits (342), Expect = 3e-33, Method: Compositional matrix adjust. Identities = 89/257 (34%), Positives = 139/257 (54%), Gaps = 33/257 (12%) Query: 74 RVSTLPTQFGEKIVLRILDTEQA-TLALEQLGYEPAQLQALQQAIARPHGMVLMTGPTGS 132 R++T+PT G +VLR+L + + L LG+ A ALQ+ +P GM +++GPTGS Sbjct: 209 RIATVPTSEGSVMVLRLLYNDAGDNIDLRPLGFSEAHASALQKLKEQPVGMNIISGPTGS 268 Query: 133 GKTVSLYACL--QRLNRPG-INIATAEDPVEINLPGINQVSI-----NERAGLNFAVALR 184 GK+ +L L + + G +++ T EDPVE + G Q ++ E FA A+ Sbjct: 269 GKSTTLQRVLTGEIIEAEGKLHVLTIEDPVEYPIDGAVQTAVTNAGSEEERSRAFAAAIS 328 Query: 185 AFLRQDPDVLMVGEIRDLDTADIAIKAAQTGHLVLSTLHTNDAPATLTRLLNMGVPAYNI 244 +R DPD +M+GE+RD TA A++A+ TGH V +T+H N A A + RLL++G+PA + Sbjct: 329 NAMRLDPDTIMIGEVRDRATAQNALRASMTGHQVWTTVHANSALAIIDRLLDLGLPASLV 388 Query: 245 A--ASVSLIVAQRLVRRLCSCRRPARDASGSFVPH----------------------GCP 280 A A V+ +++QRLV++LC C R A +P GC Sbjct: 389 ADHAVVTGLISQRLVKKLCPCCRQPLAARPEVLPAAVLARVRQAVSPSLDGVCVTGPGCE 448 Query: 281 ACSHTGYRGRTGIYQVM 297 C+ G GRT + +++ Sbjct: 449 HCAGQGTVGRTVVAEII 465 >gi|300310151|ref|YP_003774243.1| twitching mobility PilT protein [Herbaspirillum seropedicae SmR1] Length = 365 Score = 103 bits (258), Expect = 2e-23, Method: Compositional matrix adjust. Identities = 67/159 (42%), Positives = 98/159 (61%), Gaps = 12/159 (7%) Query: 83 GEKIVLRILDTEQATLALEQLGYEPAQLQALQQAIARPHGMVLMTGPTGSGKTVSLYACL 142 G K+ + I LALE+ G P+ ++ + +A G++L+TGPTG+GKT ++ + L Sbjct: 98 GSKVAVSIRRFPLEPLALERTGL-PSYVKTVLEATK---GIILVTGPTGAGKTTTIASML 153 Query: 143 QRLN--RPGINIATAEDPVEINLPGINQVSINERA----GLNFAVALRAFLRQDPDVLMV 196 +N R G +I T E+P+E L Q I+++ +F+ LR LRQ PDVLMV Sbjct: 154 DYINASRRG-HIITIEEPIEYELQR-KQSMISQKEVPTDTESFSSGLREALRQKPDVLMV 211 Query: 197 GEIRDLDTADIAIKAAQTGHLVLSTLHTNDAPATLTRLL 235 GEIRD DTAD + A ++GHLVL+TLHT+ A +T+LL Sbjct: 212 GEIRDFDTADTVLHAGESGHLVLATLHTSSAVRAITKLL 250 >gi|300313098|ref|YP_003777190.1| Tfp pilus assembly protein, pilus retraction ATPase PilT protein [Herbaspirillum seropedicae SmR1] Length = 351 Score = 94.4 bits (233), Expect = 1e-20, Method: Compositional matrix adjust. Identities = 93/264 (35%), Positives = 133/264 (50%), Gaps = 30/264 (11%) Query: 73 FRVSTLPTQFGEKIVLRILDTEQATLALEQLGYEPAQLQALQQAIARPHGMVLMTGPTGS 132 FRV Q G + +R L E TLA QLG P + ++A G+VL+TGPTG+ Sbjct: 81 FRVHAFLRQGGPAVAIRHLGREPPTLA--QLGAPPLCAELAERA----GGLVLVTGPTGA 134 Query: 133 GKTVSLYACLQRLNRP-GINIATAEDPVE-INLPGINQVSINERAG--LNFAVALRAFLR 188 GK+ +L A ++ LN ++I T EDP+E I+ P +S E + ALRA LR Sbjct: 135 GKSSTLAAMIRHLNETRALHILTIEDPIEFIHTPQRALISQRELGTHTADLPAALRAALR 194 Query: 189 QDPDVLMVGEIRDLDTADIAIKAAQTGHLVLSTLHTNDAPATLTRLLNMGVPAYN----- 243 DPDVL+VGE+RD DT +A+ AA+TGHLVL TLH A T+ R+L++ PA Sbjct: 195 ADPDVLLVGELRDADTIRLALTAAETGHLVLGTLHAASAARTVERMLDV-FPAGEKEPAR 253 Query: 244 --IAASVSLIVAQRLVRRLCSCRRPARDASGSFVPH----GCPACSHTGYRGRTGIYQVM 297 +A S+ ++AQ L+ P D H PA + GR+ + Sbjct: 254 AMLAESLQGVIAQTLL--------PTADGRARVAAHELLVATPAVRNLIREGRSAQLLSL 305 Query: 298 PVSATMQSLIQAQAGTQDIARQAR 321 + Q + +A Q + +Q R Sbjct: 306 MQAGAAQGMQTLEAALQRLHQQGR 329 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 0.322 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: 972,339 Number of extensions: 37381 Number of successful extensions: 207 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 201 Number of HSP's successfully gapped: 4 Length of query: 350 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 264 Effective length of database: 1,212,660 Effective search space: 320142240 Effective search space used: 320142240 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)