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= 0035.0004.p (364 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... 457 e-130 gi|300310145|ref|YP_003774237.1| general secretion pathway prote... 112 6e-26 gi|300310151|ref|YP_003774243.1| twitching mobility PilT protein... 94 1e-20 gi|300313098|ref|YP_003777190.1| Tfp pilus assembly protein, pil... 76 4e-15 >gi|300309699|ref|YP_003773791.1| ATPase PilB [Herbaspirillum seropedicae SmR1] Length = 377 Score = 457 bits (1175), Expect = e-130, Method: Compositional matrix adjust. Identities = 227/372 (61%), Positives = 275/372 (73%), Gaps = 30/372 (8%) Query: 20 PDFDDASAVNYLQKILLDAINLGASDLHFEPFEKHCRIRFRIDGQLRDIVEPPLSMKDKL 79 P DD V L K+L DA+++GASDLHFEPFE +CR+R RIDG L ++ +PPLS+KDKL Sbjct: 7 PLADDVPVVRLLYKLLADAVSMGASDLHFEPFEHYCRVRLRIDGILHELAQPPLSLKDKL 66 Query: 80 ASHIKIISGLDIAEKRMPQDGRMKLSLSSTRAIDFRVSTLPTLFGEKIVMRILDASHSQL 139 A+ +KI++ LDIAEKR+PQDG+M+L+L TR +DFRVSTLPT FGEKIV+RILD + L Sbjct: 67 ATRLKILARLDIAEKRLPQDGKMRLALE-TRTVDFRVSTLPTQFGEKIVLRILDTEQATL 125 Query: 140 GIDALGYNDAQKDLLLQAIRRPYGMVLMTGPTGSGKTVSLYSCLSLLNQPGTNISTVEDP 199 ++ LGY AQ L QAI RP+GMVLMTGPTGSGKTVSLY+CL LN+PG NI+T EDP Sbjct: 126 ALEQLGYEPAQLQALQQAIARPHGMVLMTGPTGSGKTVSLYACLQRLNRPGINIATAEDP 185 Query: 200 AEISLPGINQVNVNQRAGLTFPIALRAFLRQDPDVIMVGEIRDPETADIAVKAAQTGHLV 259 EI+LPGINQV++N+RAGL F +ALRAFLRQDPDV+MVGEIRD +TADIA+KAAQTGHLV Sbjct: 186 VEINLPGINQVSINERAGLNFAVALRAFLRQDPDVLMVGEIRDLDTADIAIKAAQTGHLV 245 Query: 260 FSTLHTNDAPSTLTRLMNMGVPAFNVASAA-----------------------------G 290 STLHTNDAP+TLTRL+NMGVPA+N+A++ G Sbjct: 246 LSTLHTNDAPATLTRLLNMGVPAYNIAASVSLIVAQRLVRRLCSCRRPARDASGSFVPHG 305 Query: 291 CRRCGDTGYKGRVGIYQVMPISEAIEGLILAHAPAPDIEAQAVREGVLTLRQAGLQKVRE 350 C C TGY+GR GIYQVMP+S ++ LI A A DI QA EGV+ LR+AGL K Sbjct: 306 CPACSHTGYRGRTGIYQVMPVSATMQSLIQAQAGTQDIARQARAEGVIDLRRAGLLKALR 365 Query: 351 GLTSLEEILACT 362 G TSL E+LA T Sbjct: 366 GDTSLGEVLAST 377 >gi|300310145|ref|YP_003774237.1| general secretion pathway protein E [Herbaspirillum seropedicae SmR1] Length = 541 Score = 112 bits (279), Expect = 6e-26, Method: Compositional matrix adjust. Identities = 65/185 (35%), Positives = 109/185 (58%), Gaps = 9/185 (4%) Query: 114 FRVSTLPTLFGEKIVMRIL-DASHSQLGIDALGYNDAQKDLLLQAIRRPYGMVLMTGPTG 172 R++T+PT G +V+R+L + + + + LG+++A L + +P GM +++GPTG Sbjct: 208 VRIATVPTSEGSVMVLRLLYNDAGDNIDLRPLGFSEAHASALQKLKEQPVGMNIISGPTG 267 Query: 173 SGKTVSLYSCLS--LLNQPGT-NISTVEDPAEISLPGINQVNVN-----QRAGLTFPIAL 224 SGK+ +L L+ ++ G ++ T+EDP E + G Q V + F A+ Sbjct: 268 SGKSTTLQRVLTGEIIEAEGKLHVLTIEDPVEYPIDGAVQTAVTNAGSEEERSRAFAAAI 327 Query: 225 RAFLRQDPDVIMVGEIRDPETADIAVKAAQTGHLVFSTLHTNDAPSTLTRLMNMGVPAFN 284 +R DPD IM+GE+RD TA A++A+ TGH V++T+H N A + + RL+++G+PA Sbjct: 328 SNAMRLDPDTIMIGEVRDRATAQNALRASMTGHQVWTTVHANSALAIIDRLLDLGLPASL 387 Query: 285 VASAA 289 VA A Sbjct: 388 VADHA 392 >gi|300310151|ref|YP_003774243.1| twitching mobility PilT protein [Herbaspirillum seropedicae SmR1] Length = 365 Score = 94.4 bits (233), Expect = 1e-20, Method: Compositional matrix adjust. Identities = 53/119 (44%), Positives = 76/119 (63%), Gaps = 6/119 (5%) Query: 163 GMVLMTGPTGSGKTVSLYSCLSLLNQPGT-NISTVEDPAEISLPGINQVNVNQRAGLT-- 219 G++L+TGPTG+GKT ++ S L +N +I T+E+P E L Q ++Q+ T Sbjct: 133 GIILVTGPTGAGKTTTIASMLDYINASRRGHIITIEEPIEYELQR-KQSMISQKEVPTDT 191 Query: 220 --FPIALRAFLRQDPDVIMVGEIRDPETADIAVKAAQTGHLVFSTLHTNDAPSTLTRLM 276 F LR LRQ PDV+MVGEIRD +TAD + A ++GHLV +TLHT+ A +T+L+ Sbjct: 192 ESFSSGLREALRQKPDVLMVGEIRDFDTADTVLHAGESGHLVLATLHTSSAVRAITKLL 250 >gi|300313098|ref|YP_003777190.1| Tfp pilus assembly protein, pilus retraction ATPase PilT protein [Herbaspirillum seropedicae SmR1] Length = 351 Score = 75.9 bits (185), Expect = 4e-15, Method: Compositional matrix adjust. Identities = 52/125 (41%), Positives = 77/125 (61%), Gaps = 8/125 (6%) Query: 160 RPYGMVLMTGPTGSGKTVSLYSCLSLLNQP-GTNISTVEDPAE-ISLPGINQVNVNQRAG 217 R G+VL+TGPTG+GK+ +L + + LN+ +I T+EDP E I P + ++QR Sbjct: 121 RAGGLVLVTGPTGAGKSSTLAAMIRHLNETRALHILTIEDPIEFIHTP--QRALISQREL 178 Query: 218 LTFPIALRAFLRQD----PDVIMVGEIRDPETADIAVKAAQTGHLVFSTLHTNDAPSTLT 273 T L A LR PDV++VGE+RD +T +A+ AA+TGHLV TLH A T+ Sbjct: 179 GTHTADLPAALRAALRADPDVLLVGELRDADTIRLALTAAETGHLVLGTLHAASAARTVE 238 Query: 274 RLMNM 278 R++++ Sbjct: 239 RMLDV 243 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 0.319 0.135 0.385 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: 1,059,226 Number of extensions: 44200 Number of successful extensions: 198 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 191 Number of HSP's successfully gapped: 4 Length of query: 364 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 278 Effective length of database: 1,212,660 Effective search space: 337119480 Effective search space used: 337119480 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 (21.8 bits) S2: 131 (55.1 bits)