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= 0009.0269.p (346 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313098|ref|YP_003777190.1| Tfp pilus assembly protein, pil... 368 e-103 gi|300310151|ref|YP_003774243.1| twitching mobility PilT protein... 186 3e-48 gi|300309699|ref|YP_003773791.1| ATPase PilB [Herbaspirillum ser... 107 1e-24 gi|300310145|ref|YP_003774237.1| general secretion pathway prote... 91 2e-19 >gi|300313098|ref|YP_003777190.1| Tfp pilus assembly protein, pilus retraction ATPase PilT protein [Herbaspirillum seropedicae SmR1] Length = 351 Score = 368 bits (945), Expect = e-103, Method: Compositional matrix adjust. Identities = 192/336 (57%), Positives = 246/336 (73%) Query: 1 MDIPDLLAFSVKNQASDLHLSTGLPPMLRLRGDMRRVNLPVLLAQDVDDMLNAIMEPAQA 60 MDI LLAF+V+NQASDLHL G+PP+LR+ G +RRVNL + L A+M A Sbjct: 1 MDIAVLLAFAVRNQASDLHLCAGMPPLLRVHGALRRVNLQAPTGPQLQQWLQALMPAALH 60 Query: 61 EAYRRDLECDFAIDIAGLARFRINAFQQARGPAAVIRTIPHSIRSLADLDAPPVLVELAL 120 Y + ECDFAI++A L RFR++AF + GPA IR + +LA L APP+ ELA Sbjct: 61 PRYAQGRECDFAIELAALGRFRVHAFLRQGGPAVAIRHLGREPPTLAQLGAPPLCAELAE 120 Query: 121 RRQGLILVTGPTGSGKSTTLAAMIRHINEQRPAHILTIEDPIEFIHAPDKSLISQRAVGA 180 R GL+LVTGPTG+GKS+TLAAMIRH+NE R HILTIEDPIEFIH P ++LISQR +G Sbjct: 121 RAGGLVLVTGPTGAGKSSTLAAMIRHLNETRALHILTIEDPIEFIHTPQRALISQRELGT 180 Query: 181 HTHSFANALRSALREDPDVILIGELRDLDSIRLALTAAETGHLVLATLHTSSAAKSIDRI 240 HT ALR+ALR DPDV+L+GELRD D+IRLALTAAETGHLVL TLH +SAA++++R+ Sbjct: 181 HTADLPAALRAALRADPDVLLVGELRDADTIRLALTAAETGHLVLGTLHAASAARTVERM 240 Query: 241 IDVFPGDEKDMVRSMLSESLSAVVSQILLKTKAGDDRIAAHEIMLGTPAIRNLIREGKVA 300 +DVFP EK+ R+ML+ESL V++Q LL T G R+AAHE+++ TPA+RNLIREG+ A Sbjct: 241 LDVFPAGEKEPARAMLAESLQGVIAQTLLPTADGRARVAAHELLVATPAVRNLIREGRSA 300 Query: 301 QMVSVMQTSGGAGMQTLDHCLGDLLRRDLITTETAR 336 Q++S+MQ GMQTL+ L L ++ I+ +T R Sbjct: 301 QLLSLMQAGAAQGMQTLEAALQRLHQQGRISAQTLR 336 >gi|300310151|ref|YP_003774243.1| twitching mobility PilT protein [Herbaspirillum seropedicae SmR1] Length = 365 Score = 186 bits (471), Expect = 3e-48, Method: Compositional matrix adjust. Identities = 111/287 (38%), Positives = 173/287 (60%), Gaps = 8/287 (2%) Query: 5 DLLAFSVKNQA-SDLHLSTGLPPMLRL-RGDMRRVNLPVLLAQDVDDMLNAIMEPAQAEA 62 +LLA +Q SD+H+ P ML+ RG ++PV++ Q + +L+AI E + + Sbjct: 14 ELLALVNSSQTFSDIHIEQDQPLMLKTPRGWQPVHDMPVVIEQ-LAPLLSAIDEDWEDKI 72 Query: 63 YRRDLECDFAIDIAGLARFRINAFQQARGP--AAVIRTIPHSIRSLADLDAPPVLVELAL 120 L+C + + G R R N ++ ARG A IR P +L P + + Sbjct: 73 IDGALDCPYVL---GEWRLRCNIYRMARGSKVAVSIRRFPLEPLALERTGLPSYVKTVLE 129 Query: 121 RRQGLILVTGPTGSGKSTTLAAMIRHINEQRPAHILTIEDPIEFIHAPDKSLISQRAVGA 180 +G+ILVTGPTG+GK+TT+A+M+ +IN R HI+TIE+PIE+ +S+ISQ+ V Sbjct: 130 ATKGIILVTGPTGAGKTTTIASMLDYINASRRGHIITIEEPIEYELQRKQSMISQKEVPT 189 Query: 181 HTHSFANALRSALREDPDVILIGELRDLDSIRLALTAAETGHLVLATLHTSSAAKSIDRI 240 T SF++ LR ALR+ PDV+++GE+RD D+ L A E+GHLVLATLHTSSA ++I ++ Sbjct: 190 DTESFSSGLREALRQKPDVLMVGEIRDFDTADTVLHAGESGHLVLATLHTSSAVRAITKL 249 Query: 241 IDVFPGDEKDMVRSMLSESLSAVVSQILLKTKAGDDRIAAHEIMLGT 287 + FP +++ + L+ESL V+ Q LL ++ G+ + A E++ Sbjct: 250 LGFFPQEQRAQRAATLAESLVGVIFQSLLPSEDGEHHVMASEMVFNN 296 >gi|300309699|ref|YP_003773791.1| ATPase PilB [Herbaspirillum seropedicae SmR1] Length = 377 Score = 107 bits (267), Expect = 1e-24, Method: Compositional matrix adjust. Identities = 87/251 (34%), Positives = 140/251 (55%), Gaps = 31/251 (12%) Query: 81 FRINAFQQARGPAAVIRTI--PHSIRSLADLDAPPV----LVELALRRQGLILVTGPTGS 134 FR++ G V+R + + +L L P L + R G++L+TGPTGS Sbjct: 100 FRVSTLPTQFGEKIVLRILDTEQATLALEQLGYEPAQLQALQQAIARPHGMVLMTGPTGS 159 Query: 135 GKSTTLAAMIRHINEQRPA-HILTIEDPIEFIHAP--DKSLISQRAVGAHTHSFANALRS 191 GK+ +L A ++ +N RP +I T EDP+E I+ P ++ I++RA +FA ALR+ Sbjct: 160 GKTVSLYACLQRLN--RPGINIATAEDPVE-INLPGINQVSINERA----GLNFAVALRA 212 Query: 192 ALREDPDVILIGELRDLDSIRLALTAAETGHLVLATLHTSSAAKSIDRIIDV-FPGDEKD 250 LR+DPDV+++GE+RDLD+ +A+ AA+TGHLVL+TLHT+ A ++ R++++ P Sbjct: 213 FLRQDPDVLMVGEIRDLDTADIAIKAAQTGHLVLSTLHTNDAPATLTRLLNMGVPAYN-- 270 Query: 251 MVRSMLSESLSAVVSQILLKTKAGDDRIA----AHEIMLGTPAIRNLIREGKVAQMVSVM 306 ++ S+S +V+Q L++ R A + G PA + G+ + VM Sbjct: 271 -----IAASVSLIVAQRLVRRLCSCRRPARDASGSFVPHGCPACSHTGYRGRTG-IYQVM 324 Query: 307 QTSGGAGMQTL 317 S A MQ+L Sbjct: 325 PVS--ATMQSL 333 >gi|300310145|ref|YP_003774237.1| general secretion pathway protein E [Herbaspirillum seropedicae SmR1] Length = 541 Score = 90.5 bits (223), Expect = 2e-19, Method: Compositional matrix adjust. Identities = 51/124 (41%), Positives = 80/124 (64%), Gaps = 4/124 (3%) Query: 124 GLILVTGPTGSGKSTTLAAMIRH--INEQRPAHILTIEDPIEFI--HAPDKSLISQRAVG 179 G+ +++GPTGSGKSTTL ++ I + H+LTIEDP+E+ A ++ + + Sbjct: 258 GMNIISGPTGSGKSTTLQRVLTGEIIEAEGKLHVLTIEDPVEYPIDGAVQTAVTNAGSEE 317 Query: 180 AHTHSFANALRSALREDPDVILIGELRDLDSIRLALTAAETGHLVLATLHTSSAAKSIDR 239 + +FA A+ +A+R DPD I+IGE+RD + + AL A+ TGH V T+H +SA IDR Sbjct: 318 ERSRAFAAAISNAMRLDPDTIMIGEVRDRATAQNALRASMTGHQVWTTVHANSALAIIDR 377 Query: 240 IIDV 243 ++D+ Sbjct: 378 LLDL 381 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 0.135 0.377 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: 1,018,934 Number of extensions: 40509 Number of successful extensions: 308 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 304 Number of HSP's successfully gapped: 4 Length of query: 346 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 260 Effective length of database: 1,212,660 Effective search space: 315291600 Effective search space used: 315291600 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)