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= 0001.2384.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|300310151|ref|YP_003774243.1| twitching mobility PilT protein... 609 e-175 gi|300313098|ref|YP_003777190.1| Tfp pilus assembly protein, pil... 166 2e-42 gi|300309699|ref|YP_003773791.1| ATPase PilB [Herbaspirillum ser... 100 2e-22 gi|300310145|ref|YP_003774237.1| general secretion pathway prote... 86 4e-18 >gi|300310151|ref|YP_003774243.1| twitching mobility PilT protein [Herbaspirillum seropedicae SmR1] Length = 365 Score = 609 bits (1571), Expect = e-175, Method: Compositional matrix adjust. Identities = 282/364 (77%), Positives = 329/364 (90%) Query: 1 MANNSSFARDLQQELLLLLNNPKTFSDIHIEQDEPVMLKTPRGWQSYGDVPVALDEMQPL 60 M+N+ ARDLQ+ELL L+N+ +TFSDIHIEQD+P+MLKTPRGWQ D+PV ++++ PL Sbjct: 1 MSNDLFLARDLQRELLALVNSSQTFSDIHIEQDQPLMLKTPRGWQPVHDMPVVIEQLAPL 60 Query: 61 LNAIDEDWEDKIIDKAIDSPFILDRWRLRCNVFRMARGTRVAISIRRFPLEPMPLESTGL 120 L+AIDEDWEDKIID A+D P++L WRLRCN++RMARG++VA+SIRRFPLEP+ LE TGL Sbjct: 61 LSAIDEDWEDKIIDGALDCPYVLGEWRLRCNIYRMARGSKVAVSIRRFPLEPLALERTGL 120 Query: 121 PPYIKTILDVTKGLILITGPTGAGKTTTMASMLEYINTTRHAHIVTIEEPIEYELQRKQS 180 P Y+KT+L+ TKG+IL+TGPTGAGKTTT+ASML+YIN +R HI+TIEEPIEYELQRKQS Sbjct: 121 PSYVKTVLEATKGIILVTGPTGAGKTTTIASMLDYINASRRGHIITIEEPIEYELQRKQS 180 Query: 181 IISQKEVPTDTASFSSGLREALRQKPDVLMVGEIRDFETADTVLHAGESGHLVLATLHTS 240 +ISQKEVPTDT SFSSGLREALRQKPDVLMVGEIRDF+TADTVLHAGESGHLVLATLHTS Sbjct: 181 MISQKEVPTDTESFSSGLREALRQKPDVLMVGEIRDFDTADTVLHAGESGHLVLATLHTS 240 Query: 241 SAVRAITKLLSFFPPDQRTQRAASLADSLIGVIFQSLLPSEDGEQHVMASEMVFNNNQQI 300 SAVRAITKLL FFP +QR QRAA+LA+SL+GVIFQSLLPSEDGE HVMASEMVFNNNQQI Sbjct: 241 SAVRAITKLLGFFPQEQRAQRAATLAESLVGVIFQSLLPSEDGEHHVMASEMVFNNNQQI 300 Query: 301 APFIMDPEKLPLIGDFMKRKEDNMSRTLNDVLIQLIAKKRINPRDALRIAYNRIELHEML 360 A FI DP KL LIGDFMKRKEDNMSR+LN+VL+QL+ KK ++ RDALR+AYNR+ELHEML Sbjct: 301 AAFISDPAKLHLIGDFMKRKEDNMSRSLNEVLLQLVHKKSVSARDALRVAYNRLELHEML 360 Query: 361 TSKR 364 S + Sbjct: 361 NSAK 364 >gi|300313098|ref|YP_003777190.1| Tfp pilus assembly protein, pilus retraction ATPase PilT protein [Herbaspirillum seropedicae SmR1] Length = 351 Score = 166 bits (420), Expect = 2e-42, Method: Compositional matrix adjust. Identities = 94/208 (45%), Positives = 133/208 (63%), Gaps = 2/208 (0%) Query: 87 RLRCNVFRMARGTRVAISIRRFPLEPMPLESTGLPPYIKTILDVTKGLILITGPTGAGKT 146 R R + F G A++IR EP L G PP + + GL+L+TGPTGAGK+ Sbjct: 80 RFRVHAFLRQGGP--AVAIRHLGREPPTLAQLGAPPLCAELAERAGGLVLVTGPTGAGKS 137 Query: 147 TTMASMLEYINTTRHAHIVTIEEPIEYELQRKQSIISQKEVPTDTASFSSGLREALRQKP 206 +T+A+M+ ++N TR HI+TIE+PIE+ ++++ISQ+E+ T TA + LR ALR P Sbjct: 138 STLAAMIRHLNETRALHILTIEDPIEFIHTPQRALISQRELGTHTADLPAALRAALRADP 197 Query: 207 DVLMVGEIRDFETADTVLHAGESGHLVLATLHTSSAVRAITKLLSFFPPDQRTQRAASLA 266 DVL+VGE+RD +T L A E+GHLVL TLH +SA R + ++L FP ++ A LA Sbjct: 198 DVLLVGELRDADTIRLALTAAETGHLVLGTLHAASAARTVERMLDVFPAGEKEPARAMLA 257 Query: 267 DSLIGVIFQSLLPSEDGEQHVMASEMVF 294 +SL GVI Q+LLP+ DG V A E++ Sbjct: 258 ESLQGVIAQTLLPTADGRARVAAHELLV 285 >gi|300309699|ref|YP_003773791.1| ATPase PilB [Herbaspirillum seropedicae SmR1] Length = 377 Score = 100 bits (250), Expect = 2e-22, Method: Compositional matrix adjust. Identities = 66/195 (33%), Positives = 107/195 (54%), Gaps = 14/195 (7%) Query: 92 VFRMARGTRVAISIRRFPLEPMPLESTGLPPYIKTILDVTKGLILITGPTGAGKTTTMAS 151 V R+ + +++ + EP L++ ++ + G++L+TGPTG+GKT ++ + Sbjct: 114 VLRILDTEQATLALEQLGYEPAQLQA------LQQAIARPHGMVLMTGPTGSGKTVSLYA 167 Query: 152 MLEYINTTRHAHIVTIEEPIEYELQR-KQSIISQKEVPTDTASFSSGLREALRQKPDVLM 210 L+ +N +I T E+P+E L Q I+++ +F+ LR LRQ PDVLM Sbjct: 168 CLQRLNRP-GINIATAEDPVEINLPGINQVSINERA----GLNFAVALRAFLRQDPDVLM 222 Query: 211 VGEIRDFETADTVLHAGESGHLVLATLHTSSAVRAITKLLSFFPPDQRTQRAASL--ADS 268 VGEIRD +TAD + A ++GHLVL+TLHT+ A +T+LL+ P + SL A Sbjct: 223 VGEIRDLDTADIAIKAAQTGHLVLSTLHTNDAPATLTRLLNMGVPAYNIAASVSLIVAQR 282 Query: 269 LIGVIFQSLLPSEDG 283 L+ + P+ D Sbjct: 283 LVRRLCSCRRPARDA 297 >gi|300310145|ref|YP_003774237.1| general secretion pathway protein E [Herbaspirillum seropedicae SmR1] Length = 541 Score = 85.9 bits (211), Expect = 4e-18, Method: Compositional matrix adjust. Identities = 52/152 (34%), Positives = 87/152 (57%), Gaps = 12/152 (7%) Query: 133 GLILITGPTGAGKTTTMASML--EYINTTRHAHIVTIEEPIEYELQR--KQSIISQKEVP 188 G+ +I+GPTG+GK+TT+ +L E I H++TIE+P+EY + + ++ + Sbjct: 258 GMNIISGPTGSGKSTTLQRVLTGEIIEAEGKLHVLTIEDPVEYPIDGAVQTAVTNAGSEE 317 Query: 189 TDTASFSSGLREALRQKPDVLMVGEIRDFETADTVLHAGESGHLVLATLHTSSAVRAITK 248 + +F++ + A+R PD +M+GE+RD TA L A +GH V T+H +SA+ I + Sbjct: 318 ERSRAFAAAISNAMRLDPDTIMIGEVRDRATAQNALRASMTGHQVWTTVHANSALAIIDR 377 Query: 249 LLSFFPPDQRTQRAASLADSLI--GVIFQSLL 278 LL P A+ +AD + G+I Q L+ Sbjct: 378 LLDLGLP------ASLVADHAVVTGLISQRLV 403 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 0.384 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: 983,429 Number of extensions: 36606 Number of successful extensions: 229 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 226 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)