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= 0027.0008.p (485 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310145|ref|YP_003774237.1| general secretion pathway prote... 732 0.0 gi|300309699|ref|YP_003773791.1| ATPase PilB [Herbaspirillum ser... 130 3e-31 gi|300310151|ref|YP_003774243.1| twitching mobility PilT protein... 83 5e-17 gi|300313098|ref|YP_003777190.1| Tfp pilus assembly protein, pil... 69 9e-13 >gi|300310145|ref|YP_003774237.1| general secretion pathway protein E [Herbaspirillum seropedicae SmR1] Length = 541 Score = 732 bits (1889), Expect = 0.0, Method: Compositional matrix adjust. Identities = 362/473 (76%), Positives = 403/473 (85%), Gaps = 5/473 (1%) Query: 1 MKLRIARHNEQTQQHTYNMSFADINDVSSADILSNTGAFEASEEERKLLCLLADGRLLVV 60 MKLR+ R EQ + + + A ILS++G EA +EERKLLCLLADGRLLVV Sbjct: 1 MKLRLPRRREQAFS-SAGGAIEIVPGFDGAQILSHSGMLEAGQEERKLLCLLADGRLLVV 59 Query: 61 AGQNLNPHVMSYQGRLERMGRKHHVVFTSVEVISRINQNSNS----SVADRHQEHSMMQV 116 AGQ LNPHV SY GRLER+G+ + +V + VI R+N+ S +RHQEH+MMQV Sbjct: 60 AGQELNPHVQSYIGRLERLGQPYQLVPGDIAVIYRMNRISTRIGGPQPEERHQEHTMMQV 119 Query: 117 TAKDLLTKAWRARASDVHIRVRKNCTEIYFRIHNDLVPVGGQTREYGERLLATMYGAMTS 176 TAKDLL KA R+RASD+H+RVRKNCTEIYFRIHNDLV VGGQTREYGERLLAT+YGAMTS Sbjct: 120 TAKDLLNKACRSRASDIHLRVRKNCTEIYFRIHNDLVQVGGQTREYGERLLATLYGAMTS 179 Query: 177 VSDSSYKPTERQDASIADRDKLPPGLYGVRIATVPTNEGSVMVLRLLYNDAGENTDLRPL 236 VSDSSYKPTERQDA+IADRDKLPP LYGVRIATVPT+EGSVMVLRLLYNDAG+N DLRPL Sbjct: 180 VSDSSYKPTERQDAAIADRDKLPPALYGVRIATVPTSEGSVMVLRLLYNDAGDNIDLRPL 239 Query: 237 GFSDAHAAALQHLKEQPVGINIISGPTGSGKSTTLQRILTGEIIEAGGKMHVLTIEDPVE 296 GFS+AHA+ALQ LKEQPVG+NIISGPTGSGKSTTLQR+LTGEIIEA GK+HVLTIEDPVE Sbjct: 240 GFSEAHASALQKLKEQPVGMNIISGPTGSGKSTTLQRVLTGEIIEAEGKLHVLTIEDPVE 299 Query: 297 YPIEGAVQTAVTNAGTEEERSRLFAAAISNAMRLDPDTIMIGEVRDKASAQNALRASMTG 356 YPI+GAVQTAVTNAG+EEERSR FAAAISNAMRLDPDTIMIGEVRD+A+AQNALRASMTG Sbjct: 300 YPIDGAVQTAVTNAGSEEERSRAFAAAISNAMRLDPDTIMIGEVRDRATAQNALRASMTG 359 Query: 357 HQVWTTVHANSALAIMDRLTDLGLPPNLTADYTVVTGLISQRLVKTLCQDCRLPLATHQD 416 HQVWTTVHANSALAI+DRL DLGLP +L AD+ VVTGLISQRLVK LC CR PLA + Sbjct: 360 HQVWTTVHANSALAIIDRLLDLGLPASLVADHAVVTGLISQRLVKKLCPCCRQPLAARPE 419 Query: 417 QLPPAVLARVKQAVSPALEGVCILGPGCPTCGHHGTIGRTVVAEIIIPDDEFF 469 LP AVLARV+QAVSP+L+GVC+ GPGC C GT+GRTVVAEIIIPDD FF Sbjct: 420 VLPAAVLARVRQAVSPSLDGVCVTGPGCEHCAGQGTVGRTVVAEIIIPDDHFF 472 >gi|300309699|ref|YP_003773791.1| ATPase PilB [Herbaspirillum seropedicae SmR1] Length = 377 Score = 130 bits (326), Expect = 3e-31, Method: Compositional matrix adjust. Identities = 88/259 (33%), Positives = 137/259 (52%), Gaps = 37/259 (14%) Query: 206 RIATVPTNEGSVMVLRLLYNDAGENTDLRPLGFSDAHAAALQHLKEQPVGINIISGPTGS 265 R++T+PT G +VLR+L + L LG+ A ALQ +P G+ +++GPTGS Sbjct: 101 RVSTLPTQFGEKIVLRILDTEQA-TLALEQLGYEPAQLQALQQAIARPHGMVLMTGPTGS 159 Query: 266 GKSTTLQRILTGEIIEAGGKMHVLTIEDPVEYPIEGAVQTAVTNAGTEEERSRL-FAAAI 324 GK+ +L L + + G +++ T EDPVE + G Q ++ ER+ L FA A+ Sbjct: 160 GKTVSLYACL--QRLNRPG-INIATAEDPVEINLPGINQVSI------NERAGLNFAVAL 210 Query: 325 SNAMRLDPDTIMIGEVRDKASAQNALRASMTGHQVWTTVHANSALAIMDRLTDLGLPP-N 383 +R DPD +M+GE+RD +A A++A+ TGH V +T+H N A A + RL ++G+P N Sbjct: 211 RAFLRQDPDVLMVGEIRDLDTADIAIKAAQTGHLVLSTLHTNDAPATLTRLLNMGVPAYN 270 Query: 384 LTADYTVVTGLISQRLVKTLCQDCRLPLATHQDQLPPAVLARVKQAVSPALEGVCILGPG 443 + A +++ ++QRLV+ LC CR P P G Sbjct: 271 IAASVSLI---VAQRLVRRLC-SCRRPARDASGSFVPH---------------------G 305 Query: 444 CPTCGHHGTIGRTVVAEII 462 CP C H G GRT + +++ Sbjct: 306 CPACSHTGYRGRTGIYQVM 324 >gi|300310151|ref|YP_003774243.1| twitching mobility PilT protein [Herbaspirillum seropedicae SmR1] Length = 365 Score = 83.2 bits (204), Expect = 5e-17, Method: Compositional matrix adjust. Identities = 45/129 (34%), Positives = 79/129 (61%), Gaps = 6/129 (4%) Query: 255 GINIISGPTGSGKSTTLQRILTGEIIEAGGKMHVLTIEDPVEYPIEGAVQTAVTNAGTEE 314 GI +++GPTG+GK+TT+ +L + I A + H++TIE+P+EY ++ Q+ ++ Sbjct: 133 GIILVTGPTGAGKTTTIASML--DYINASRRGHIITIEEPIEYELQRK-QSMISQKEVPT 189 Query: 315 ERSRLFAAAISNAMRLDPDTIMIGEVRDKASAQNALRASMTGHQVWTTVHANSALAIMDR 374 + + F++ + A+R PD +M+GE+RD +A L A +GH V T+H +SA+ + + Sbjct: 190 D-TESFSSGLREALRQKPDVLMVGEIRDFDTADTVLHAGESGHLVLATLHTSSAVRAITK 248 Query: 375 LTDLGLPPN 383 L LG P Sbjct: 249 L--LGFFPQ 255 >gi|300313098|ref|YP_003777190.1| Tfp pilus assembly protein, pilus retraction ATPase PilT protein [Herbaspirillum seropedicae SmR1] Length = 351 Score = 68.9 bits (167), Expect = 9e-13, Method: Compositional matrix adjust. Identities = 58/172 (33%), Positives = 95/172 (55%), Gaps = 12/172 (6%) Query: 249 LKEQPVGINIISGPTGSGKSTTLQRILTGEIIEAGGKMHVLTIEDPVEYPIEGAVQTAVT 308 L E+ G+ +++GPTG+GKS+TL ++ + +H+LTIEDP+E+ Q A+ Sbjct: 118 LAERAGGLVLVTGPTGAGKSSTLAAMI--RHLNETRALHILTIEDPIEF--IHTPQRALI 173 Query: 309 NAGTEEERSRLFAAAISNAMRLDPDTIMIGEVRDKASAQNALRASMTGHQVWTTVHANSA 368 + + AA+ A+R DPD +++GE+RD + + AL A+ TGH V T+HA SA Sbjct: 174 SQRELGTHTADLPAALRAALRADPDVLLVGELRDADTIRLALTAAETGHLVLGTLHAASA 233 Query: 369 LAIMDRLTDLGLP-----PNLTADYTVVTGLISQRLVKTLCQDCRLPLATHQ 415 ++R+ D+ P P + G+I+Q L+ T D R +A H+ Sbjct: 234 ARTVERMLDV-FPAGEKEPARAMLAESLQGVIAQTLLPT--ADGRARVAAHE 282 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 0.317 0.132 0.381 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: 1,489,333 Number of extensions: 61259 Number of successful extensions: 317 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 309 Number of HSP's successfully gapped: 4 Length of query: 485 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 396 Effective length of database: 1,198,455 Effective search space: 474588180 Effective search space used: 474588180 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 (21.7 bits) S2: 132 (55.5 bits)