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= 0036.0001.p (351 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... 677 0.0 gi|300310151|ref|YP_003774243.1| twitching mobility PilT protein... 179 2e-46 gi|300309699|ref|YP_003773791.1| ATPase PilB [Herbaspirillum ser... 110 2e-25 gi|300310145|ref|YP_003774237.1| general secretion pathway prote... 91 1e-19 >gi|300313098|ref|YP_003777190.1| Tfp pilus assembly protein, pilus retraction ATPase PilT protein [Herbaspirillum seropedicae SmR1] Length = 351 Score = 677 bits (1747), Expect = 0.0, Method: Compositional matrix adjust. Identities = 349/351 (99%), Positives = 349/351 (99%) Query: 1 MDIAVLLAFAVRNQASDLHLCAGMPPLLRVHGALRRVNLQAPTGPQLQQWLQALMPAALH 60 MDIAVLLAFAVRNQASDLHLCAGMPPLLRVHGALRRVNLQAPTGPQLQQWLQALMPAALH Sbjct: 1 MDIAVLLAFAVRNQASDLHLCAGMPPLLRVHGALRRVNLQAPTGPQLQQWLQALMPAALH 60 Query: 61 PRYAQGRECDFAIELAALGRFRVHAFLRQGGPAAAIRHLGREPPTLAQLGAPPLCAELAE 120 PRYAQGRECDFAIELAALGRFRVHAFLRQGGPA AIRHLGREPPTLAQLGAPPLCAELAE Sbjct: 61 PRYAQGRECDFAIELAALGRFRVHAFLRQGGPAVAIRHLGREPPTLAQLGAPPLCAELAE 120 Query: 121 RAGGLVLVTGPTGAGKSSTLAAMIRHLNETRALHILTIEDPIEFIHTPQRALISQRELGT 180 RAGGLVLVTGPTGAGKSSTLAAMIRHLNETRALHILTIEDPIEFIHTPQRALISQRELGT Sbjct: 121 RAGGLVLVTGPTGAGKSSTLAAMIRHLNETRALHILTIEDPIEFIHTPQRALISQRELGT 180 Query: 181 HTTDLPAALRAALRADPDVLLVGELRDADTIRLALTAAETGHLVLGTLHAASAARTVERM 240 HT DLPAALRAALRADPDVLLVGELRDADTIRLALTAAETGHLVLGTLHAASAARTVERM Sbjct: 181 HTADLPAALRAALRADPDVLLVGELRDADTIRLALTAAETGHLVLGTLHAASAARTVERM 240 Query: 241 LDVFPAGEKEPARAMLAESLQGVIAQTLLPTADGRARVAAHELLVATPAVRNLIREGRSA 300 LDVFPAGEKEPARAMLAESLQGVIAQTLLPTADGRARVAAHELLVATPAVRNLIREGRSA Sbjct: 241 LDVFPAGEKEPARAMLAESLQGVIAQTLLPTADGRARVAAHELLVATPAVRNLIREGRSA 300 Query: 301 QLLSLMQAGAAQGMQTLEAALQRLHQQGRISAQTLRQHLGQEPQAGPGMAV 351 QLLSLMQAGAAQGMQTLEAALQRLHQQGRISAQTLRQHLGQEPQAGPGMAV Sbjct: 301 QLLSLMQAGAAQGMQTLEAALQRLHQQGRISAQTLRQHLGQEPQAGPGMAV 351 >gi|300310151|ref|YP_003774243.1| twitching mobility PilT protein [Herbaspirillum seropedicae SmR1] Length = 365 Score = 179 bits (455), Expect = 2e-46, Method: Compositional matrix adjust. Identities = 110/289 (38%), Positives = 161/289 (55%), Gaps = 18/289 (6%) Query: 6 LLAFAVRNQA-SDLHLCAGMPPLLR-------VHGALRRVNLQAPTGPQLQQ-WLQALMP 56 LLA +Q SD+H+ P +L+ VH + AP + + W ++ Sbjct: 15 LLALVNSSQTFSDIHIEQDQPLMLKTPRGWQPVHDMPVVIEQLAPLLSAIDEDWEDKIID 74 Query: 57 AALHPRYAQGRECDFAIELAALGRFRVHAFLRQGGPAAAIRHLGREPPTLAQLGAPPLCA 116 AL +C + + L R ++ R A +IR EP L + G P Sbjct: 75 GAL--------DCPYVLGEWRL-RCNIYRMARGSKVAVSIRRFPLEPLALERTGLPSYVK 125 Query: 117 ELAERAGGLVLVTGPTGAGKSSTLAAMIRHLNETRALHILTIEDPIEFIHTPQRALISQR 176 + E G++LVTGPTGAGK++T+A+M+ ++N +R HI+TIE+PIE+ ++++ISQ+ Sbjct: 126 TVLEATKGIILVTGPTGAGKTTTIASMLDYINASRRGHIITIEEPIEYELQRKQSMISQK 185 Query: 177 ELGTHTTDLPAALRAALRADPDVLLVGELRDADTIRLALTAAETGHLVLGTLHAASAART 236 E+ T T + LR ALR PDVL+VGE+RD DT L A E+GHLVL TLH +SA R Sbjct: 186 EVPTDTESFSSGLREALRQKPDVLMVGEIRDFDTADTVLHAGESGHLVLATLHTSSAVRA 245 Query: 237 VERMLDVFPAGEKEPARAMLAESLQGVIAQTLLPTADGRARVAAHELLV 285 + ++L FP ++ A LAESL GVI Q+LLP+ DG V A E++ Sbjct: 246 ITKLLGFFPQEQRAQRAATLAESLVGVIFQSLLPSEDGEHHVMASEMVF 294 >gi|300309699|ref|YP_003773791.1| ATPase PilB [Herbaspirillum seropedicae SmR1] Length = 377 Score = 110 bits (274), Expect = 2e-25, Method: Compositional matrix adjust. Identities = 117/349 (33%), Positives = 164/349 (46%), Gaps = 46/349 (13%) Query: 6 LLAFAVRNQASDLHLCAGMPPL-------LRVHGALRRVNLQAPTG--PQLQQWLQALMP 56 LLA AV ASDLH P LR+ G L + Q P +L L+ L Sbjct: 21 LLADAVSMGASDLHF----EPFEHYCRVRLRIDGILHELA-QPPLSLKDKLATRLKILAR 75 Query: 57 AAL-HPRYAQGRECDFAIELAALGRFRVHAFLRQGGPAAAIRHLGREPPTLA--QLGAPP 113 + R Q + A+E + FRV Q G +R L E TLA QLG P Sbjct: 76 LDIAEKRLPQDGKMRLALETRTVD-FRVSTLPTQFGEKIVLRILDTEQATLALEQLGYEP 134 Query: 114 LCAELAERA----GGLVLVTGPTGAGKSSTLAAMIRHLNETRALHILTIEDPIEFIHTPQ 169 + ++A G+VL+TGPTG+GK+ +L A ++ LN ++I T EDP+E I+ P Sbjct: 135 AQLQALQQAIARPHGMVLMTGPTGSGKTVSLYACLQRLNRP-GINIATAEDPVE-INLPG 192 Query: 170 RALISQRELGTHTTDLPAALRAALRADPDVLLVGELRDADTIRLALTAAETGHLVLGTLH 229 +S E + ALRA LR DPDVL+VGE+RD DT +A+ AA+TGHLVL TLH Sbjct: 193 INQVSINERAG--LNFAVALRAFLRQDPDVLMVGEIRDLDTADIAIKAAQTGHLVLSTLH 250 Query: 230 AASAARTVERMLDV-FPAGEKEPARAMLAESLQGVIAQTLL--------PTADGRARVAA 280 A T+ R+L++ PA +A S+ ++AQ L+ P D Sbjct: 251 TNDAPATLTRLLNMGVPAYN-------IAASVSLIVAQRLVRRLCSCRRPARDASGSFVP 303 Query: 281 HELLVATPAVRNLIREGRSAQLLSLMQAGAAQGMQTLEAALQRLHQQGR 329 H PA + GR+ + + Q + +A Q + +Q R Sbjct: 304 H----GCPACSHTGYRGRTGIYQVMPVSATMQSLIQAQAGTQDIARQAR 348 >gi|300310145|ref|YP_003774237.1| general secretion pathway protein E [Herbaspirillum seropedicae SmR1] Length = 541 Score = 90.9 bits (224), Expect = 1e-19, Method: Compositional matrix adjust. Identities = 82/261 (31%), Positives = 125/261 (47%), Gaps = 26/261 (9%) Query: 6 LLAFAVRNQASDLHL-----CAGMPPLLRVHGALRRVNLQA-PTGPQLQQWLQALMPAAL 59 LL A R++ASD+HL C + R+H L +V Q G +L L M + Sbjct: 124 LLNKACRSRASDIHLRVRKNCTEI--YFRIHNDLVQVGGQTREYGERLLATLYGAMTSVS 181 Query: 60 HPRYAQGRECDFAIEL-----AALGRFRVHAFLRQGGPAAAIRHLGRE--------PPTL 106 Y D AI AL R+ G +R L + P Sbjct: 182 DSSYKPTERQDAAIADRDKLPPALYGVRIATVPTSEGSVMVLRLLYNDAGDNIDLRPLGF 241 Query: 107 AQLGAPPLCAELAERAGGLVLVTGPTGAGKSSTLAAMI--RHLNETRALHILTIEDPIEF 164 ++ A L +L E+ G+ +++GPTG+GKS+TL ++ + LH+LTIEDP+E+ Sbjct: 242 SEAHASAL-QKLKEQPVGMNIISGPTGSGKSTTLQRVLTGEIIEAEGKLHVLTIEDPVEY 300 Query: 165 --IHTPQRALISQRELGTHTTDLPAALRAALRADPDVLLVGELRDADTIRLALTAAETGH 222 Q A+ + + AA+ A+R DPD +++GE+RD T + AL A+ TGH Sbjct: 301 PIDGAVQTAVTNAGSEEERSRAFAAAISNAMRLDPDTIMIGEVRDRATAQNALRASMTGH 360 Query: 223 LVLGTLHAASAARTVERMLDV 243 V T+HA SA ++R+LD+ Sbjct: 361 QVWTTVHANSALAIIDRLLDL 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 0.322 0.134 0.386 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: 1,103,278 Number of extensions: 46654 Number of successful extensions: 321 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 317 Number of HSP's successfully gapped: 4 Length of query: 351 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 265 Effective length of database: 1,212,660 Effective search space: 321354900 Effective search space used: 321354900 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)