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= 0001.2410.p (459 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... 783 0.0 gi|300311372|ref|YP_003775464.1| flagellum-specific ATP synthase... 317 1e-87 gi|300313646|ref|YP_003777738.1| F0F1-type ATP synthase subunit ... 141 1e-34 gi|300313648|ref|YP_003777740.1| F0F1-type ATP synthase subunit ... 112 5e-26 gi|300310193|ref|YP_003774285.1| transcription termination facto... 65 1e-11 >gi|300310125|ref|YP_003774217.1| type III secretion ATP synthase [Herbaspirillum seropedicae SmR1] Length = 460 Score = 783 bits (2023), Expect = 0.0, Method: Compositional matrix adjust. Identities = 387/447 (86%), Positives = 415/447 (92%) Query: 11 LELKLQYMRRQLGAWRQSLNPRPGFVSFGKVSQVLGTLVEAHMPPVQIGELCHLRDPHVE 70 LE +L +R +L AW+ +L RPGF S G+V+QVLGTL+EAHMPPVQIGELC+L +P Sbjct: 12 LEGQLAALRARLPAWQAALPLRPGFSSQGRVAQVLGTLIEAHMPPVQIGELCNLFNPEQP 71 Query: 71 GPPILAEVVGFTDKAAILSALSPLEGVSSSTIIEPLRRAHSIEVGDHLFGCVLDGFGRWM 130 G +LAEVVGFTDKA+ILSALSPLEGVS+ T+IEPLRR+HSIEVGDHLFGCVLDGFGRWM Sbjct: 72 GKTMLAEVVGFTDKASILSALSPLEGVSTRTVIEPLRRSHSIEVGDHLFGCVLDGFGRWM 131 Query: 131 FRAPAAAENVATWRAMSPVMRDAPKATDRPRISVPLATGVRAIDGLLTMGTGQRIGVFAG 190 FRAPAA ENVATWRAMSPV+RDAP AT RPRI+ PL TGVRAIDGLLTMG GQRIGVFAG Sbjct: 132 FRAPAAQENVATWRAMSPVIRDAPPATSRPRIATPLPTGVRAIDGLLTMGMGQRIGVFAG 191 Query: 191 PGCGKTTLMAAIARGCEAQAIVFGLIGERGRELNEFLEHELDAELIRKTVVVCATSDRTS 250 PGCGKTTLMAAIARGC+A+AIVFGLIGERGRELNEFL+HELDAELIRKTVVVCATSDRTS Sbjct: 192 PGCGKTTLMAAIARGCQAEAIVFGLIGERGRELNEFLDHELDAELIRKTVVVCATSDRTS 251 Query: 251 MERARAAFTATAIAEAFRDRGMKVLLLVDSLTRFARAQREIGLAAGEPPARGGFTPSVYT 310 MER+RAAFTATAIAE FRDRGMKVLLLVDSLTRFARAQREIGLAAGEPPARGGFTPSVYT Sbjct: 252 MERSRAAFTATAIAEGFRDRGMKVLLLVDSLTRFARAQREIGLAAGEPPARGGFTPSVYT 311 Query: 311 MLPRLIERAGGTPQGSITAMYTVLVDGESVSDPIGDEAKSLLDGHILLTRKLAEQGHYPA 370 MLPRLIERAGGTPQGSITAMYTVLVDGES SDPIGDEAKSLLDGHILLTRKLAEQGHYPA Sbjct: 312 MLPRLIERAGGTPQGSITAMYTVLVDGESSSDPIGDEAKSLLDGHILLTRKLAEQGHYPA 371 Query: 371 IDVLASISRVMSNVTTREHRKAASHFRELMARYQEMELLIRLGEYKSGTDPVADRAVKLR 430 IDVLASISRVMSNVT+REHR+AAS FREL+ARYQEMELLIRLGEYKSG DPVADRA++LR Sbjct: 372 IDVLASISRVMSNVTSREHRRAASRFRELLARYQEMELLIRLGEYKSGADPVADRAMELR 431 Query: 431 AEQLAFLRQDTSTSAPFQPTLDKLMEL 457 EQL+FLRQDTS SA FQ TLD LME+ Sbjct: 432 PEQLSFLRQDTSGSADFQETLDTLMEM 458 >gi|300311372|ref|YP_003775464.1| flagellum-specific ATP synthase [Herbaspirillum seropedicae SmR1] Length = 468 Score = 317 bits (812), Expect = 1e-87, Method: Compositional matrix adjust. Identities = 197/444 (44%), Positives = 269/444 (60%), Gaps = 35/444 (7%) Query: 39 GKVSQVLGTLVEAHMPPVQIGELCHLRDPHVEGPPILAEVVGFTDKAAILSALSPLEGVS 98 G++++V G ++EA + +G C++ P+ G I AEVVGF D L S +EG+ Sbjct: 33 GRITRVAGLVMEAVGLKLPVGSPCNVPLPN--GTMIEAEVVGFQDDRLFLMPQSDVEGIV 90 Query: 99 SSTIIE------------PL----RRA--HS--IEVGDHLFGCVLDGFGRWMFR-APAAA 137 T + P+ RRA HS + VG+ L G VLDG GR + P Sbjct: 91 PGTRVYPVEPVRPPPRTGPISFTPRRADEHSRRLPVGEELLGRVLDGAGRPLDNLGPLHT 150 Query: 138 ENVATW--RAMSPVMRDAPKATDRPRISVPLATGVRAIDGLLTMGTGQRIGVFAGPGCGK 195 E A RA +P+ R AP I L TG+RAI+ +LT+G GQR+G+FAG G GK Sbjct: 151 ERSAPLAVRAANPLGR-AP-------IRDILDTGIRAINSMLTVGRGQRMGLFAGSGVGK 202 Query: 196 TTLMAAIARGCEAQAIVFGLIGERGRELNEFLEHELDAELIRKTVVVCATSDRTSMERAR 255 + L+ +AR A IV GLIGERGRE+ EF+E L AE + ++VVV A +D + R + Sbjct: 203 SVLLGMMARYTSADVIVVGLIGERGREVKEFIEQILGAEGLARSVVVAAPADTPPLMRLQ 262 Query: 256 AAFTATAIAEAFRDRGMKVLLLVDSLTRFARAQREIGLAAGEPPARGGFTPSVYTMLPRL 315 A T+IAE FRD+G VLL++DSLTR+A AQREI LA GEPPA G+ PSV+ LP L Sbjct: 263 GAAYCTSIAEYFRDQGKDVLLIMDSLTRYAMAQREIALAIGEPPATKGYPPSVFAKLPAL 322 Query: 316 IERAGGTPQ--GSITAMYTVLVDGESVSDPIGDEAKSLLDGHILLTRKLAEQGHYPAIDV 373 +ERAG + GSITA YTVL +G+ DPI D A+++LDGHI+L R+LAE GHYPAID+ Sbjct: 323 VERAGNGDEGGGSITAFYTVLTEGDDQQDPIADAARAILDGHIVLNRQLAEAGHYPAIDI 382 Query: 374 LASISRVMSNVTTREHRKAASHFRELMARYQEMELLIRLGEYKSGTDPVADRAVKLRAEQ 433 SISR M ++T EH++++ H ++L +R+Q LI +G Y +G+DP+ D A+ L Sbjct: 383 EQSISRAMHSITDAEHQRSSRHLKQLYSRFQRNRDLISVGAYAAGSDPILDEAIALLPRM 442 Query: 434 LAFLRQDTSTSAPFQPTLDKLMEL 457 AFL+Q A +L +L L Sbjct: 443 EAFLQQGIHEQADVSESLRQLTAL 466 >gi|300313646|ref|YP_003777738.1| F0F1-type ATP synthase subunit beta [Herbaspirillum seropedicae SmR1] Length = 466 Score = 141 bits (355), Expect = 1e-34, Method: Compositional matrix adjust. Identities = 123/436 (28%), Positives = 199/436 (45%), Gaps = 28/436 (6%) Query: 39 GKVSQVLGTLVEAHMPPVQIGELCHLRDPHVEGPPILAEVVG-FTDKAAILSALSPLEGV 97 GK+ Q +G +V+ P + ++ +EG + EV D AL +G+ Sbjct: 4 GKIVQCIGAVVDVEFPRDAMPKVYDAL--KLEGSDLTLEVQQQLGDGVVRTIALGSSDGL 61 Query: 98 SSSTIIEPLRRAHSIEVGDHLFGCVLDGFGRWMFR-APAAAENVATWRAMSPVMRDAPKA 156 I + ++ VG G ++D G + P + E A+ + R AP Sbjct: 62 RRGLTISNTGKPITVPVGTATLGRIMDVLGNPIDECGPVSHEQTAS------IHRKAPAY 115 Query: 157 TDRPRISVPLATGVRAIDGLLTMGTGQRIGVFAGPGCGKT-TLMAAIARGCEAQA--IVF 213 + L TG++ ID + G ++G+F G G GKT +M I +A + VF Sbjct: 116 DELSPSQELLETGIKVIDLVCPFAKGGKVGLFGGAGVGKTVNMMELINNIAKAHSGLSVF 175 Query: 214 GLIGERGRELNEFLEHELDAELI-------RKTVVVCATSDRTSMERARAAFTATAIAEA 266 +GER RE N+F +A+++ K +V + R R A T IAE Sbjct: 176 AGVGERTREGNDFYHEMAEAKVVDLENPTNSKVAMVYGQMNEPPGNRLRVALTGLTIAEG 235 Query: 267 FRDRGMKVLLLVDSLTRFARAQREIGLAAGEPPARGGFTPSVYTMLPRLIERAGGTPQGS 326 FRD G VL VD++ R+ A E+ G P+ G+ P++ + RL ER T GS Sbjct: 236 FRDEGKDVLFFVDNIYRYTLAGTEVSALLGRMPSAVGYQPTLAEEMGRLQERITSTKTGS 295 Query: 327 ITAMYTVLVDGESVSDPIGDEAKSLLDGHILLTRKLAEQGHYPAIDVLASISRVMS-NVT 385 IT++ V V + ++DP + LD ++L+R +A G YPA+D L S SR + V Sbjct: 296 ITSIQAVYVPADDLTDPSPATTFAHLDSTVVLSRDIASLGIYPAVDPLDSTSRQLDPQVV 355 Query: 386 TREHRKAASHFRELMARYQEMELLIRLGEYKSGTDPVA--DRAVKLRAEQLA-FLRQDTS 442 +EH + A + + RY+E+ +I + G D +A D+ + RA ++ FL Q Sbjct: 356 GQEHYETARAVQGTLQRYKELRDIIAI----LGMDELAPEDKLIVARARKMQRFLSQPFH 411 Query: 443 TSAPFQPTLDKLMELQ 458 + F + K + L+ Sbjct: 412 VAEVFTGSPGKYVSLK 427 >gi|300313648|ref|YP_003777740.1| F0F1-type ATP synthase subunit alpha [Herbaspirillum seropedicae SmR1] Length = 513 Score = 112 bits (281), Expect = 5e-26, Method: Compositional matrix adjust. Identities = 85/333 (25%), Positives = 151/333 (45%), Gaps = 22/333 (6%) Query: 91 LSPLEGVSSSTIIEPLRRAHSIEVGDHLFGCVLDGFGRWMFRAPAAAENVATWRAMSPVM 150 L E +S +++ R + +G L G V++ G+ P + + +P+ Sbjct: 76 LGEYEHISEGDVVKCTGRILEVPIGPELKGRVVNALGQ-----PIDGKGPINAKLTAPIE 130 Query: 151 RDAPKATDRPRISVPLATGVRAIDGLLTMGTGQRIGVFAGPGCGKTTLM--AAIARGCEA 208 + AP R +S P+ TG+++ID ++ +G GQR + GKT + A I + + Sbjct: 131 KIAPGVIARQSVSQPMQTGLKSIDSMVPVGRGQRELIIGDRQTGKTAVAIDAIINQKGQN 190 Query: 209 QAIVFGLIGERGRELNEFLEHELDAELIRKTVVVCATSDRTSMERARAAFTATAIAEAFR 268 ++ IG++ + + + T+VV AT+ ++ + +A++ A+ E FR Sbjct: 191 MTCIYVAIGQKASSVKNVVRALEAHGAMEYTIVVAATASESAAMQYVSAYSGCAMGEYFR 250 Query: 269 DRGMKVLLLVDSLTRFARAQREIGLAAGEPPARGGFTPSVYTMLPRLIERAGGT------ 322 DRG L++ D L++ A A R++ L PP R + V+ + RL+ERA Sbjct: 251 DRGQDALIVYDDLSKQAVAYRQVSLLLRRPPGREAYPGDVFYLHSRLLERAARVNADYVE 310 Query: 323 ---------PQGSITAMYTVLVDGESVSDPIGDEAKSLLDGHILLTRKLAEQGHYPAIDV 373 GS+TA+ + VS + S+ DG I L L G PAI+ Sbjct: 311 KFTNGEVKGQTGSLTALPIIETQAGDVSAFVPTNVISITDGQIFLETSLFNAGIRPAINA 370 Query: 374 LASISRVMSNVTTREHRKAASHFRELMARYQEM 406 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 = 65.1 bits (157), Expect = 1e-11, Method: Compositional matrix adjust. Identities = 67/243 (27%), Positives = 111/243 (45%), Gaps = 14/243 (5%) Query: 171 RAIDGLLTMGTGQRIGVFAGPGCGKTTLMAAIARGCEAQ----AIVFGLIGERGRELNEF 226 R ID + +G GQR + A P GK+ ++ IA ++ LI ER E+ E Sbjct: 160 RIIDLIAPVGRGQRGLLVASPKSGKSVMLQHIAHAITTNHPDTVMIVLLIDERPEEVTE- 218 Query: 227 LEHELDAELIRKTVVVCATSDRTSMERARAAFTATAIAEAFRDRGMKVLLLVDSLTRFAR 286 ++ + E VV +T D + + A A+ + V++L+DS+TR AR Sbjct: 219 MQRSVRGE------VVASTFDEPATRHVQVAEMVLEKAKRLVEMKKDVVILLDSITRLAR 272 Query: 287 AQREIGLAAGEPPARGGFTPSVYTMLPRLIERAGGTPQ-GSITAMYTVLVD-GESVSDPI 344 A + A+G+ GG + R A + GS+T + T L++ G + D I Sbjct: 273 AYNTVIPASGKVLT-GGVDANALQRPKRFFGAARNVEEGGSLTIIATALIETGSRMDDVI 331 Query: 345 GDEAKSLLDGHILLTRKLAEQGHYPAIDVLASISRVMSNVTTREHRKAASHFRELMARYQ 404 +E K + + L R+LAE+ YPAI++ S +R + + + R+LM Sbjct: 332 YEEFKGTGNMEVHLERRLAEKRVYPAINLSKSGTRREELLIKPDQLQKIWVLRKLMYDMD 391 Query: 405 EME 407 E+E Sbjct: 392 EIE 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 0.321 0.135 0.393 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: 1,431,499 Number of extensions: 61662 Number of successful extensions: 301 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 292 Number of HSP's successfully gapped: 5 Length of query: 459 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 371 Effective length of database: 1,203,190 Effective search space: 446383490 Effective search space used: 446383490 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)