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= 0104.0009.p (462 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310125|ref|YP_003774217.1| type III secretion ATP synthase... 782 0.0 gi|300311372|ref|YP_003775464.1| flagellum-specific ATP synthase... 314 9e-87 gi|300313646|ref|YP_003777738.1| F0F1-type ATP synthase subunit ... 140 2e-34 gi|300313648|ref|YP_003777740.1| F0F1-type ATP synthase subunit ... 106 5e-24 gi|300310193|ref|YP_003774285.1| transcription termination facto... 67 2e-12 >gi|300310125|ref|YP_003774217.1| type III secretion ATP synthase [Herbaspirillum seropedicae SmR1] Length = 460 Score = 782 bits (2020), Expect = 0.0, Method: Compositional matrix adjust. Identities = 380/447 (85%), Positives = 415/447 (92%) Query: 14 IDDRLTRLRQRLPEWLERLPAKPGFTSHGKVSQVLGTLIEAHMPPVQIGELCNLINPDVS 73 ++ +L LR RLP W LP +PGF+S G+V+QVLGTLIEAHMPPVQIGELCNL NP+ Sbjct: 12 LEGQLAALRARLPAWQAALPLRPGFSSQGRVAQVLGTLIEAHMPPVQIGELCNLFNPEQP 71 Query: 74 GKDMLAEVVGFTDKAAILSALSPLEGVSTRTVIEPLRRAHSIEVGDHLFGCVLDGFGRWM 133 GK MLAEVVGFTDKA+ILSALSPLEGVSTRTVIEPLRR+HSIEVGDHLFGCVLDGFGRWM Sbjct: 72 GKTMLAEVVGFTDKASILSALSPLEGVSTRTVIEPLRRSHSIEVGDHLFGCVLDGFGRWM 131 Query: 134 FRAPAARDNQSTWRAVAPVMRDAPKATDRPRIATPLATGVRAIDGLLSMGVGQRIGVFAG 193 FRAPAA++N +TWRA++PV+RDAP AT RPRIATPL TGVRAIDGLL+MG+GQRIGVFAG Sbjct: 132 FRAPAAQENVATWRAMSPVIRDAPPATSRPRIATPLPTGVRAIDGLLTMGMGQRIGVFAG 191 Query: 194 PGCGKTTLMAAIARGCEAEAIVFGLIGERGRELNEFLEHELDADLIRKTVVVCATSDRTS 253 PGCGKTTLMAAIARGC+AEAIVFGLIGERGRELNEFL+HELDA+LIRKTVVVCATSDRTS Sbjct: 192 PGCGKTTLMAAIARGCQAEAIVFGLIGERGRELNEFLDHELDAELIRKTVVVCATSDRTS 251 Query: 254 MERSRARITATAIAESFRERGKSVLLLIDSLTRFARAQREIGLAAGEPPARGGFTPSVYT 313 MERSRA TATAIAE FR+RG VLLL+DSLTRFARAQREIGLAAGEPPARGGFTPSVYT Sbjct: 252 MERSRAAFTATAIAEGFRDRGMKVLLLVDSLTRFARAQREIGLAAGEPPARGGFTPSVYT 311 Query: 314 MLPRLIERAGATREGSITAMYTVLVDGESASDPIGDEAKSLLDGHILLTRKLAEQGHYPA 373 MLPRLIERAG T +GSITAMYTVLVDGES+SDPIGDEAKSLLDGHILLTRKLAEQGHYPA Sbjct: 312 MLPRLIERAGGTPQGSITAMYTVLVDGESSSDPIGDEAKSLLDGHILLTRKLAEQGHYPA 371 Query: 374 IDVLASISRVMSNVTTREHRQAASSFRELMARYQEMELLIRLGEYKEGADPVADRAMQMR 433 IDVLASISRVMSNVT+REHR+AAS FREL+ARYQEMELLIRLGEYK GADPVADRAM++R Sbjct: 372 IDVLASISRVMSNVTSREHRRAASRFRELLARYQEMELLIRLGEYKSGADPVADRAMELR 431 Query: 434 PEQLDFLRQDTSTSSDYRQTLARIQEM 460 PEQL FLRQDTS S+D+++TL + EM Sbjct: 432 PEQLSFLRQDTSGSADFQETLDTLMEM 458 >gi|300311372|ref|YP_003775464.1| flagellum-specific ATP synthase [Herbaspirillum seropedicae SmR1] Length = 468 Score = 314 bits (805), Expect = 9e-87, Method: Compositional matrix adjust. Identities = 191/448 (42%), Positives = 270/448 (60%), Gaps = 34/448 (7%) Query: 34 AKPGFTSHGKVSQVLGTLIEAHMPPVQIGELCNLINPDVSGKDMLAEVVGFTDKAAILSA 93 A+P T+ G++++V G ++EA + +G CN+ P+ G + AEVVGF D L Sbjct: 26 AEPTMTA-GRITRVAGLVMEAVGLKLPVGSPCNVPLPN--GTMIEAEVVGFQDDRLFLMP 82 Query: 94 LSPLEGVSTRTVIE------------PL----RRA--HS--IEVGDHLFGCVLDGFGRWM 133 S +EG+ T + P+ RRA HS + VG+ L G VLDG GR + Sbjct: 83 QSDVEGIVPGTRVYPVEPVRPPPRTGPISFTPRRADEHSRRLPVGEELLGRVLDGAGRPL 142 Query: 134 FRAPAARDNQSTWRA--VAPVMRDAPKATDRPRIATPLATGVRAIDGLLSMGVGQRIGVF 191 DN AP+ A R I L TG+RAI+ +L++G GQR+G+F Sbjct: 143 -------DNLGPLHTERSAPLAVRAANPLGRAPIRDILDTGIRAINSMLTVGRGQRMGLF 195 Query: 192 AGPGCGKTTLMAAIARGCEAEAIVFGLIGERGRELNEFLEHELDADLIRKTVVVCATSDR 251 AG G GK+ L+ +AR A+ IV GLIGERGRE+ EF+E L A+ + ++VVV A +D Sbjct: 196 AGSGVGKSVLLGMMARYTSADVIVVGLIGERGREVKEFIEQILGAEGLARSVVVAAPADT 255 Query: 252 TSMERSRARITATAIAESFRERGKSVLLLIDSLTRFARAQREIGLAAGEPPARGGFTPSV 311 + R + T+IAE FR++GK VLL++DSLTR+A AQREI LA GEPPA G+ PSV Sbjct: 256 PPLMRLQGAAYCTSIAEYFRDQGKDVLLIMDSLTRYAMAQREIALAIGEPPATKGYPPSV 315 Query: 312 YTMLPRLIERAGATRE--GSITAMYTVLVDGESASDPIGDEAKSLLDGHILLTRKLAEQG 369 + LP L+ERAG E GSITA YTVL +G+ DPI D A+++LDGHI+L R+LAE G Sbjct: 316 FAKLPALVERAGNGDEGGGSITAFYTVLTEGDDQQDPIADAARAILDGHIVLNRQLAEAG 375 Query: 370 HYPAIDVLASISRVMSNVTTREHRQAASSFRELMARYQEMELLIRLGEYKEGADPVADRA 429 HYPAID+ SISR M ++T EH++++ ++L +R+Q LI +G Y G+DP+ D A Sbjct: 376 HYPAIDIEQSISRAMHSITDAEHQRSSRHLKQLYSRFQRNRDLISVGAYAAGSDPILDEA 435 Query: 430 MQMRPEQLDFLRQDTSTSSDYRQTLARI 457 + + P FL+Q +D ++L ++ Sbjct: 436 IALLPRMEAFLQQGIHEQADVSESLRQL 463 >gi|300313646|ref|YP_003777738.1| F0F1-type ATP synthase subunit beta [Herbaspirillum seropedicae SmR1] Length = 466 Score = 140 bits (354), Expect = 2e-34, Method: Compositional matrix adjust. Identities = 107/386 (27%), Positives = 179/386 (46%), Gaps = 19/386 (4%) Query: 42 GKVSQVLGTLIEAHMPPVQIGELCNLINPDVSGKDMLAEVVG-FTDKAAILSALSPLEGV 100 GK+ Q +G +++ P + ++ + + + G D+ EV D AL +G+ Sbjct: 4 GKIVQCIGAVVDVEFPRDAMPKVYDALK--LEGSDLTLEVQQQLGDGVVRTIALGSSDGL 61 Query: 101 STRTVIEPLRRAHSIEVGDHLFGCVLDGFGRWMFRAPAARDNQSTWRAVAPVMRDAPKAT 160 I + ++ VG G ++D G P + A + R AP Sbjct: 62 RRGLTISNTGKPITVPVGTATLGRIMDVLGN-----PIDECGPVSHEQTASIHRKAPAYD 116 Query: 161 DRPRIATPLATGVRAIDGLLSMGVGQRIGVFAGPGCGKT-TLMAAIARGCEAEA--IVFG 217 + L TG++ ID + G ++G+F G G GKT +M I +A + VF Sbjct: 117 ELSPSQELLETGIKVIDLVCPFAKGGKVGLFGGAGVGKTVNMMELINNIAKAHSGLSVFA 176 Query: 218 LIGERGRELNEFLEHELDADLI-------RKTVVVCATSDRTSMERSRARITATAIAESF 270 +GER RE N+F +A ++ K +V + R R +T IAE F Sbjct: 177 GVGERTREGNDFYHEMAEAKVVDLENPTNSKVAMVYGQMNEPPGNRLRVALTGLTIAEGF 236 Query: 271 RERGKSVLLLIDSLTRFARAQREIGLAAGEPPARGGFTPSVYTMLPRLIERAGATREGSI 330 R+ GK VL +D++ R+ A E+ G P+ G+ P++ + RL ER +T+ GSI Sbjct: 237 RDEGKDVLFFVDNIYRYTLAGTEVSALLGRMPSAVGYQPTLAEEMGRLQERITSTKTGSI 296 Query: 331 TAMYTVLVDGESASDPIGDEAKSLLDGHILLTRKLAEQGHYPAIDVLASISRVMS-NVTT 389 T++ V V + +DP + LD ++L+R +A G YPA+D L S SR + V Sbjct: 297 TSIQAVYVPADDLTDPSPATTFAHLDSTVVLSRDIASLGIYPAVDPLDSTSRQLDPQVVG 356 Query: 390 REHRQAASSFRELMARYQEMELLIRL 415 +EH + A + + + RY+E+ +I + Sbjct: 357 QEHYETARAVQGTLQRYKELRDIIAI 382 >gi|300313648|ref|YP_003777740.1| F0F1-type ATP synthase subunit alpha [Herbaspirillum seropedicae SmR1] Length = 513 Score = 106 bits (264), Expect = 5e-24, Method: Compositional matrix adjust. Identities = 83/333 (24%), Positives = 149/333 (44%), Gaps = 22/333 (6%) Query: 94 LSPLEGVSTRTVIEPLRRAHSIEVGDHLFGCVLDGFGRWMFRAPAARDNQSTWRAVAPVM 153 L E +S V++ R + +G L G V++ G+ P + AP+ Sbjct: 76 LGEYEHISEGDVVKCTGRILEVPIGPELKGRVVNALGQ-----PIDGKGPINAKLTAPIE 130 Query: 154 RDAPKATDRPRIATPLATGVRAIDGLLSMGVGQRIGVFAGPGCGKTTLM--AAIARGCEA 211 + AP R ++ P+ TG+++ID ++ +G GQR + GKT + A I + + Sbjct: 131 KIAPGVIARQSVSQPMQTGLKSIDSMVPVGRGQRELIIGDRQTGKTAVAIDAIINQKGQN 190 Query: 212 EAIVFGLIGERGRELNEFLEHELDADLIRKTVVVCATSDRTSMERSRARITATAIAESFR 271 ++ IG++ + + + T+VV AT+ ++ + + + A+ E FR Sbjct: 191 MTCIYVAIGQKASSVKNVVRALEAHGAMEYTIVVAATASESAAMQYVSAYSGCAMGEYFR 250 Query: 272 ERGKSVLLLIDSLTRFARAQREIGLAAGEPPARGGFTPSVYTMLPRLIERAGAT------ 325 +RG+ L++ D L++ A A R++ L PP R + V+ + RL+ERA Sbjct: 251 DRGQDALIVYDDLSKQAVAYRQVSLLLRRPPGREAYPGDVFYLHSRLLERAARVNADYVE 310 Query: 326 ---------REGSITAMYTVLVDGESASDPIGDEAKSLLDGHILLTRKLAEQGHYPAIDV 376 + GS+TA+ + S + S+ DG I L L G PAI+ Sbjct: 311 KFTNGEVKGQTGSLTALPIIETQAGDVSAFVPTNVISITDGQIFLETSLFNAGIRPAINA 370 Query: 377 LASISRVMSNVTTREHRQAASSFRELMARYQEM 409 S+SRV T+ + + R +A+Y+E+ Sbjct: 371 GISVSRVGGAAQTKVIKGLSGGIRTDLAQYREL 403 >gi|300310193|ref|YP_003774285.1| transcription termination factor Rho protein [Herbaspirillum seropedicae SmR1] Length = 420 Score = 67.4 bits (163), Expect = 2e-12, Method: Compositional matrix adjust. Identities = 70/246 (28%), Positives = 111/246 (45%), Gaps = 20/246 (8%) Query: 174 RAIDGLLSMGVGQRIGVFAGPGCGKTTLMAAIARGCEAE----AIVFGLIGERGRELNEF 229 R ID + +G GQR + A P GK+ ++ IA ++ LI ER E+ E Sbjct: 160 RIIDLIAPVGRGQRGLLVASPKSGKSVMLQHIAHAITTNHPDTVMIVLLIDERPEEVTE- 218 Query: 230 LEHELDADLIRKTV---VVCATSDRTSMERSRARITATAIAESFRERGKSVLLLIDSLTR 286 ++++V VV +T D + + A+ E K V++L+DS+TR Sbjct: 219 ---------MQRSVRGEVVASTFDEPATRHVQVAEMVLEKAKRLVEMKKDVVILLDSITR 269 Query: 287 FARAQREIGLAAGEPPARGGFTPSVYTMLPRLIERAGATRE-GSITAMYTVLVD-GESAS 344 ARA + A+G+ GG + R A E GS+T + T L++ G Sbjct: 270 LARAYNTVIPASGKVLT-GGVDANALQRPKRFFGAARNVEEGGSLTIIATALIETGSRMD 328 Query: 345 DPIGDEAKSLLDGHILLTRKLAEQGHYPAIDVLASISRVMSNVTTREHRQAASSFRELMA 404 D I +E K + + L R+LAE+ YPAI++ S +R + + Q R+LM Sbjct: 329 DVIYEEFKGTGNMEVHLERRLAEKRVYPAINLSKSGTRREELLIKPDQLQKIWVLRKLMY 388 Query: 405 RYQEME 410 E+E Sbjct: 389 DMDEIE 394 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 0.320 0.135 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: 1,429,167 Number of extensions: 61679 Number of successful extensions: 342 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 331 Number of HSP's successfully gapped: 5 Length of query: 462 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 373 Effective length of database: 1,198,455 Effective search space: 447023715 Effective search space used: 447023715 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: 132 (55.5 bits)