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= 0001.1913.p (468 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311372|ref|YP_003775464.1| flagellum-specific ATP synthase... 926 0.0 gi|300310125|ref|YP_003774217.1| type III secretion ATP synthase... 325 5e-90 gi|300313646|ref|YP_003777738.1| F0F1-type ATP synthase subunit ... 166 4e-42 gi|300313648|ref|YP_003777740.1| F0F1-type ATP synthase subunit ... 134 2e-32 gi|300310193|ref|YP_003774285.1| transcription termination facto... 80 3e-16 >gi|300311372|ref|YP_003775464.1| flagellum-specific ATP synthase [Herbaspirillum seropedicae SmR1] Length = 468 Score = 926 bits (2393), Expect = 0.0, Method: Compositional matrix adjust. Identities = 460/468 (98%), Positives = 464/468 (99%) Query: 1 MNSPMPSHSSLWQAYLHNCRSLVAMAEPTRTAGRITRVAGLVMEAVGLKLPVGSPCNVPL 60 MNSPMPSHSSLWQAYLHNCRSLVAMAEPT TAGRITRVAGLVMEAVGLKLPVGSPCNVPL Sbjct: 1 MNSPMPSHSSLWQAYLHNCRSLVAMAEPTMTAGRITRVAGLVMEAVGLKLPVGSPCNVPL 60 Query: 61 PNGMMIEAEVVGFQDERLFLMPQSDVEGIVPGTRVYPVEPVRPPPRTGPISFTPRRADEH 120 PNG MIEAEVVGFQD+RLFLMPQSDVEGIVPGTRVYPVEPVRPPPRTGPISFTPRRADEH Sbjct: 61 PNGTMIEAEVVGFQDDRLFLMPQSDVEGIVPGTRVYPVEPVRPPPRTGPISFTPRRADEH 120 Query: 121 SRRLPVGDELLGRVLDGAGRPLDNLGPLHTERSAPLAVRAANPLGRAPIRDILDTGIRAI 180 SRRLPVG+ELLGRVLDGAGRPLDNLGPLHTERSAPLAVRAANPLGRAPIRDILDTGIRAI Sbjct: 121 SRRLPVGEELLGRVLDGAGRPLDNLGPLHTERSAPLAVRAANPLGRAPIRDILDTGIRAI 180 Query: 181 NSMLTVGRGQRMGLFAGSGVGKSVLLGMMARYTSADVIVVGLIGERGREVKEFIEQILGA 240 NSMLTVGRGQRMGLFAGSGVGKSVLLGMMARYTSADVIVVGLIGERGREVKEFIEQILGA Sbjct: 181 NSMLTVGRGQRMGLFAGSGVGKSVLLGMMARYTSADVIVVGLIGERGREVKEFIEQILGA 240 Query: 241 EGLARSVVVAAPADTPPLMRLQGAAYCTSIAEYFRDQGKDVLLIMDSLTRYAMAQREIAL 300 EGLARSVVVAAPADTPPLMRLQGAAYCTSIAEYFRDQGKDVLLIMDSLTRYAMAQREIAL Sbjct: 241 EGLARSVVVAAPADTPPLMRLQGAAYCTSIAEYFRDQGKDVLLIMDSLTRYAMAQREIAL 300 Query: 301 AIGEPPATKGYPPSVFAKLPALVERAGNGDEGGGSITAFYTVLTEGDDQQDPIADAARAI 360 AIGEPPATKGYPPSVFAKLPALVERAGNGDEGGGSITAFYTVLTEGDDQQDPIADAARAI Sbjct: 301 AIGEPPATKGYPPSVFAKLPALVERAGNGDEGGGSITAFYTVLTEGDDQQDPIADAARAI 360 Query: 361 LDGHIVLNRQLAEAGHYPAIDIEQSISRAMHSITDADHQRRSRHLKQLYSRFQRNRDLIS 420 LDGHIVLNRQLAEAGHYPAIDIEQSISRAMHSITDA+HQR SRHLKQLYSRFQRNRDLIS Sbjct: 361 LDGHIVLNRQLAEAGHYPAIDIEQSISRAMHSITDAEHQRSSRHLKQLYSRFQRNRDLIS 420 Query: 421 VGAYAAGSDPILDEAIALLPRMEAFLQQGIHEQSDVSESLGQLTALFG 468 VGAYAAGSDPILDEAIALLPRMEAFLQQGIHEQ+DVSESL QLTALFG Sbjct: 421 VGAYAAGSDPILDEAIALLPRMEAFLQQGIHEQADVSESLRQLTALFG 468 >gi|300310125|ref|YP_003774217.1| type III secretion ATP synthase [Herbaspirillum seropedicae SmR1] Length = 460 Score = 325 bits (833), Expect = 5e-90, Method: Compositional matrix adjust. Identities = 194/443 (43%), Positives = 268/443 (60%), Gaps = 35/443 (7%) Query: 31 TAGRITRVAGLVMEAVGLKLPVGSPCNVPLPN--GMMIEAEVVGFQDERLFLMPQSDVEG 88 + GR+ +V G ++EA + +G CN+ P G + AEVVGF D+ L S +EG Sbjct: 38 SQGRVAQVLGTLIEAHMPPVQIGELCNLFNPEQPGKTMLAEVVGFTDKASILSALSPLEG 97 Query: 89 IVPGTRVYPVEPVRPPPRTGPISFTPRRADEHSRRLPVGDELLGRVLDGAGRPL------ 142 + TR +EP+R S + VGD L G VLDG GR + Sbjct: 98 V--STRTV-IEPLR-----------------RSHSIEVGDHLFGCVLDGFGRWMFRAPAA 137 Query: 143 -DNLGPLHTERSAPLAVRAANPLGRAP-IRDILDTGIRAINSMLTVGRGQRMGLFAGSGV 200 +N+ T R+ +R A P P I L TG+RAI+ +LT+G GQR+G+FAG G Sbjct: 138 QENVA---TWRAMSPVIRDAPPATSRPRIATPLPTGVRAIDGLLTMGMGQRIGVFAGPGC 194 Query: 201 GKSVLLGMMARYTSADVIVVGLIGERGREVKEFIEQILGAEGLARSVVVAAPADTPPLMR 260 GK+ L+ +AR A+ IV GLIGERGRE+ EF++ L AE + ++VVV A +D + R Sbjct: 195 GKTTLMAAIARGCQAEAIVFGLIGERGRELNEFLDHELDAELIRKTVVVCATSDRTSMER 254 Query: 261 LQGAAYCTSIAEYFRDQGKDVLLIMDSLTRYAMAQREIALAIGEPPATKGYPPSVFAKLP 320 + A T+IAE FRD+G VLL++DSLTR+A AQREI LA GEPPA G+ PSV+ LP Sbjct: 255 SRAAFTATAIAEGFRDRGMKVLLLVDSLTRFARAQREIGLAAGEPPARGGFTPSVYTMLP 314 Query: 321 ALVERAGNGDEGGGSITAFYTVLTEGDDQQDPIADAARAILDGHIVLNRQLAEAGHYPAI 380 L+ERAG + GSITA YTVL +G+ DPI D A+++LDGHI+L R+LAE GHYPAI Sbjct: 315 RLIERAGGTPQ--GSITAMYTVLVDGESSSDPIGDEAKSLLDGHILLTRKLAEQGHYPAI 372 Query: 381 DIEQSISRAMHSITDADHQRRSRHLKQLYSRFQRNRDLISVGAYAAGSDPILDEAIALLP 440 D+ SISR M ++T +H+R + ++L +R+Q LI +G Y +G+DP+ D A+ L P Sbjct: 373 DVLASISRVMSNVTSREHRRAASRFRELLARYQEMELLIRLGEYKSGADPVADRAMELRP 432 Query: 441 RMEAFLQQGIHEQSDVSESLGQL 463 +FL+Q +D E+L L Sbjct: 433 EQLSFLRQDTSGSADFQETLDTL 455 >gi|300313646|ref|YP_003777738.1| F0F1-type ATP synthase subunit beta [Herbaspirillum seropedicae SmR1] Length = 466 Score = 166 bits (420), Expect = 4e-42, Method: Compositional matrix adjust. Identities = 114/358 (31%), Positives = 189/358 (52%), Gaps = 22/358 (6%) Query: 124 LPVGDELLGRVLDGAGRPLDNLGPLHTERSAPLAVRAANPLGRAPIRDILDTGIRAINSM 183 +PVG LGR++D G P+D GP+ E++A + +A +P +++L+TGI+ I+ + Sbjct: 76 VPVGTATLGRIMDVLGNPIDECGPVSHEQTASIHRKAPAYDELSPSQELLETGIKVIDLV 135 Query: 184 LTVGRGQRMGLFAGSGVGKSV----LLGMMARYTSADVIVVGLIGERGREVKEFIEQILG 239 +G ++GLF G+GVGK+V L+ +A+ S + G +GER RE +F ++ Sbjct: 136 CPFAKGGKVGLFGGAGVGKTVNMMELINNIAKAHSGLSVFAG-VGERTREGNDFYHEMAE 194 Query: 240 AEGL-------ARSVVVAAPADTPPLMRLQGAAYCTSIAEYFRDQGKDVLLIMDSLTRYA 292 A+ + ++ +V + PP RL+ A +IAE FRD+GKDVL +D++ RY Sbjct: 195 AKVVDLENPTNSKVAMVYGQMNEPPGNRLRVALTGLTIAEGFRDEGKDVLFFVDNIYRYT 254 Query: 293 MAQREIALAIGEPPATKGYPPSVFAKLPALVERAGNGDEGGGSITAFYTVLTEGDDQQDP 352 +A E++ +G P+ GY P++ ++ L ER + GSIT+ V DD DP Sbjct: 255 LAGTEVSALLGRMPSAVGYQPTLAEEMGRLQERITSTKT--GSITSIQAVYVPADDLTDP 312 Query: 353 IADAARAILDGHIVLNRQLAEAGHYPAIDIEQSISRAMH-SITDADHQRRSRHLKQLYSR 411 A LD +VL+R +A G YPA+D S SR + + +H +R ++ R Sbjct: 313 SPATTFAHLDSTVVLSRDIASLGIYPAVDPLDSTSRQLDPQVVGQEHYETARAVQGTLQR 372 Query: 412 FQRNRDLISVGAYAAGSDPILDEAIALLPR---MEAFLQQGIHEQSDVSESLGQLTAL 466 ++ RD+I++ G D + E ++ R M+ FL Q H + S G+ +L Sbjct: 373 YKELRDIIAI----LGMDELAPEDKLIVARARKMQRFLSQPFHVAEVFTGSPGKYVSL 426 >gi|300313648|ref|YP_003777740.1| F0F1-type ATP synthase subunit alpha [Herbaspirillum seropedicae SmR1] Length = 513 Score = 134 bits (337), Expect = 2e-32, Method: Compositional matrix adjust. Identities = 88/280 (31%), Positives = 146/280 (52%), Gaps = 15/280 (5%) Query: 124 LPVGDELLGRVLDGAGRPLDNLGPLHTERSAPLAVRAANPLGRAPIRDILDTGIRAINSM 183 +P+G EL GRV++ G+P+D GP++ + +AP+ A + R + + TG+++I+SM Sbjct: 97 VPIGPELKGRVVNALGQPIDGKGPINAKLTAPIEKIAPGVIARQSVSQPMQTGLKSIDSM 156 Query: 184 LTVGRGQRMGLFAGSGVGKS-VLLGMMARYTSADVIVVGL-IGERGREVKEFIEQILGAE 241 + VGRGQR + GK+ V + + ++ + + IG++ VK + + Sbjct: 157 VPVGRGQRELIIGDRQTGKTAVAIDAIINQKGQNMTCIYVAIGQKASSVKNVVRALEAHG 216 Query: 242 GLARSVVVAAPADTPPLMRLQGAAYCTSIAEYFRDQGKDVLLIMDSLTRYAMAQREIALA 301 + ++VVAA A M+ A ++ EYFRD+G+D L++ D L++ A+A R+++L Sbjct: 217 AMEYTIVVAATASESAAMQYVSAYSGCAMGEYFRDRGQDALIVYDDLSKQAVAYRQVSLL 276 Query: 302 IGEPPATKGYPPSVFAKLPALVERAG-----------NGDEGG--GSITAFYTVLTEGDD 348 + PP + YP VF L+ERA NG+ G GS+TA + T+ D Sbjct: 277 LRRPPGREAYPGDVFYLHSRLLERAARVNADYVEKFTNGEVKGQTGSLTALPIIETQAGD 336 Query: 349 QQDPIADAARAILDGHIVLNRQLAEAGHYPAIDIEQSISR 388 + +I DG I L L AG PAI+ S+SR Sbjct: 337 VSAFVPTNVISITDGQIFLETSLFNAGIRPAINAGISVSR 376 >gi|300310193|ref|YP_003774285.1| transcription termination factor Rho protein [Herbaspirillum seropedicae SmR1] Length = 420 Score = 80.5 bits (197), Expect = 3e-16, Method: Compositional matrix adjust. Identities = 84/272 (30%), Positives = 124/272 (45%), Gaps = 23/272 (8%) Query: 142 LDNLGPLHTERSAPLAVRAANPLGRAPIRDILDTGIRAINSMLTVGRGQRMGLFAGSGVG 201 +NL PLH + L + G I TG R I+ + VGRGQR L A G Sbjct: 133 FENLTPLHPNKLLQLE---RDMRGEENI-----TG-RIIDLIAPVGRGQRGLLVASPKSG 183 Query: 202 KSVLLGMMARYTSAD----VIVVGLIGERGREVKEFIEQILGAEGLARSVVVAAPADTPP 257 KSV+L +A + + V++V LI ER EV E + G VVA+ D P Sbjct: 184 KSVMLQHIAHAITTNHPDTVMIVLLIDERPEEVTEMQRSVRGE-------VVASTFDEPA 236 Query: 258 LMRLQGAAYCTSIAEYFRDQGKDVLLIMDSLTRYAMAQREIALAIGEPPATKGYPPSVFA 317 +Q A A+ + KDV++++DS+TR A A + A G+ T G + Sbjct: 237 TRHVQVAEMVLEKAKRLVEMKKDVVILLDSITRLARAYNTVIPASGK-VLTGGVDANALQ 295 Query: 318 KLPALVERAGNGDEGGGSITAFYTVLTE-GDDQQDPIADAARAILDGHIVLNRQLAEAGH 376 + P A E GGS+T T L E G D I + + + + L R+LAE Sbjct: 296 R-PKRFFGAARNVEEGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLERRLAEKRV 354 Query: 377 YPAIDIEQSISRAMHSITDADHQRRSRHLKQL 408 YPAI++ +S +R + D ++ L++L Sbjct: 355 YPAINLSKSGTRREELLIKPDQLQKIWVLRKL 386 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 0.137 0.397 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: 1,528,174 Number of extensions: 70504 Number of successful extensions: 310 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 300 Number of HSP's successfully gapped: 5 Length of query: 468 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 379 Effective length of database: 1,198,455 Effective search space: 454214445 Effective search space used: 454214445 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)