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= 0013.0106.p (643 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311626|ref|YP_003775718.1| cytochrome c oxidase polypeptid... 979 0.0 gi|300313446|ref|YP_003777538.1| cytochrome c oxidase polypeptid... 424 e-120 gi|300311778|ref|YP_003775870.1| cytochrome o ubiquinol oxidase ... 385 e-108 gi|300312501|ref|YP_003776593.1| cbb3-type cytochrome c oxidase ... 69 2e-12 >gi|300311626|ref|YP_003775718.1| cytochrome c oxidase polypeptide I transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 633 Score = 979 bits (2532), Expect = 0.0, Method: Compositional matrix adjust. Identities = 479/628 (76%), Positives = 536/628 (85%) Query: 16 EASQADALEATWRDPPGWRGWICAVNHKTISRRFMIATFVFFLLGGVLALMIRLQLAQPA 75 A +A LE TW DPPG GW+CAVNHK I+RRFM+ TFVFFLLGG+LAL +RLQLA+P Sbjct: 6 RAEEARRLEQTWSDPPGLWGWLCAVNHKAIARRFMVTTFVFFLLGGMLALAMRLQLARPD 65 Query: 76 NTVIGPSLYNQLFTMHGTTMMFLFAVPVMQAIAIYLIPLMIGARSVAFPLLNAFAYWIFV 135 +IG LYNQLFTMHGTTMMFLFAVPVMQA+A YL+PLMIGARSVAFP LNAFAYWIF+ Sbjct: 66 AELIGARLYNQLFTMHGTTMMFLFAVPVMQAVAAYLLPLMIGARSVAFPRLNAFAYWIFL 125 Query: 136 FGGMMLYAAFIVGSGPDVGWFAYVPLSLTSYSSGKGVDFWAQMITFTELSGLIEAIVIIT 195 FGG++LY AF+ GSGPDVGWFAYVPL+L Y+SGKGVD WAQMITFTELS LIEAIVIIT Sbjct: 126 FGGLLLYGAFLAGSGPDVGWFAYVPLALNPYASGKGVDIWAQMITFTELSALIEAIVIIT 185 Query: 196 TILKMRAPGMSLRRMPLFVWAMLVTSFMVLFAMPAVMFGSTALITDRLVGTQFYSSGDGG 255 T++K+RAPGMSLRRMPLF WAMLVTS MVLFAMPAVM ST LITDRLV TQFYS +GG Sbjct: 186 TVMKLRAPGMSLRRMPLFAWAMLVTSVMVLFAMPAVMLASTGLITDRLVNTQFYSHQNGG 245 Query: 256 DALLWQHLFWFFGHPEVYLIFIPPLGFLSQIIATFSRRPIVGYPLMVLALIATGFLAFGL 315 DALLWQHLFWFFGHPEVYLIF+PPLG +S II TF+RR +VGYP MVLALIAT FLAFGL Sbjct: 246 DALLWQHLFWFFGHPEVYLIFLPPLGMISTIIPTFARRSMVGYPAMVLALIATAFLAFGL 305 Query: 316 WVHHMFATNLPEIGKAFFTAASLLIALPTASQIFCWLATLWSGRLSLRTPLLFVLAFFVI 375 WVHHMFAT LPE GK FFTAASLLIALPTA QIFCW++T+W GR +TPLLFVLAFF I Sbjct: 306 WVHHMFATTLPEAGKLFFTAASLLIALPTALQIFCWISTIWLGRPVFKTPLLFVLAFFFI 365 Query: 376 LLLGGLTGIMLALVPLDLQLHDTFFVVAHLHYVLLGGAVFPLFGAIYYWFPKFTGRLLGE 435 L++GGLTG+MLA VPLDLQLHDT+FVVAHLHYVLLGGA+FPLFG YYWFPKFTGR+L E Sbjct: 366 LVMGGLTGLMLASVPLDLQLHDTYFVVAHLHYVLLGGAIFPLFGGFYYWFPKFTGRMLDE 425 Query: 436 RLGRWQFWLFFIGFNVSFFPMHMLGLQGMPRRVYTYPVQMGWGALNFLSTIGAMMIAASV 495 RLGRW FWLFF+GFNV FFPMH+LGLQGM RRVYTY QMGW LN +TIGA +I SV Sbjct: 426 RLGRWNFWLFFVGFNVCFFPMHVLGLQGMTRRVYTYAAQMGWEGLNLTATIGAFLIGLSV 485 Query: 496 LMFLFNVWRSLRRGESAGPDPWGAGTLEWSVPSPPPAGNFVAVPVVHANEPLWSPPAQPS 555 L+FL NV SL RG +AG +PWGA TLEWS+PSPPPAGNF+ VPVVHA +PLW P PS Sbjct: 486 LLFLLNVVHSLWRGAAAGDNPWGAATLEWSLPSPPPAGNFLEVPVVHAADPLWQAPRLPS 545 Query: 556 YVTGLSNTDREVLITSAVEAQPDHRFWLPPPSPWPFLSAVALTVLFIGSIFTPWAVVWGA 615 +V+GL N REVLITS +EA P HRFWLP PSPWP LSA+A T LFIGSIF+PWAVVWGA Sbjct: 546 HVSGLDNGQREVLITSVIEAHPQHRFWLPTPSPWPLLSALATTALFIGSIFSPWAVVWGA 605 Query: 616 IPVAITTTLWFWPRKARTAARTSTEMRP 643 +PV + T +WFWPR+ R+ AR ++E+RP Sbjct: 606 LPVGLATAIWFWPRRQRSQARIASEVRP 633 >gi|300313446|ref|YP_003777538.1| cytochrome c oxidase polypeptide I transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 539 Score = 424 bits (1091), Expect = e-120, Method: Compositional matrix adjust. Identities = 225/512 (43%), Positives = 318/512 (62%), Gaps = 8/512 (1%) Query: 33 WRGWICAVNHKTISRRFMIATFVFFLLGGVLALMIRLQLAQPANTVIGPSLYNQLFTMHG 92 WR W+ A NHK I ++ +F L GGVLAL+IR +L QP P +NQL TMHG Sbjct: 32 WRRWLFATNHKDIGTLYLWFSFTMLLSGGVLALLIRAELFQPGLQFFRPEFFNQLTTMHG 91 Query: 93 TTMMFLFAVPVMQAIAIYLIPLMIGARSVAFPLLNAFAYWIFVFGGMMLYAAFIV-GSGP 151 M+F +P A ++IPL IGA +AF +N F++W+ ++L +F+V G Sbjct: 92 LVMVFGAIMPAFVGFANWMIPLQIGASDMAFARMNNFSFWLLPPAALLLAGSFLVPGGAT 151 Query: 152 DVGWFAYVPLSLTSYSSGKGVDFWAQMITFTELSGLIEAIVIITTILKMRAPGMSLRRMP 211 GW Y PLS G G+D + S ++ +I II TIL MRAPGM+L +MP Sbjct: 152 AAGWTLYAPLST---QMGPGMDMGIFAMHIMGASSIMGSINIIVTILNMRAPGMTLMKMP 208 Query: 212 LFVWAMLVTSFMVLFAMPAVMFGSTALITDRLVGTQFYSSGDGGDALLWQHLFWFFGHPE 271 +F W L+T+++++ MP + T +TDR GT F+++ GGD +++QH+FWFFGHPE Sbjct: 209 MFCWTWLITAYLLIAVMPVLAGAITMTLTDRHFGTSFFNAAGGGDPVMYQHIFWFFGHPE 268 Query: 272 VYLIFIPPLGFLSQIIATFSRRPIVGYPLMVLALIATGFLAFGLWVHHMFATNLPEIGKA 331 VY++ +P G +SQII F+R+P+ GY MV A + L+F +W HHMF T +P + Sbjct: 269 VYIMILPAFGIVSQIIPAFARKPLFGYASMVYATASIAILSFIVWAHHMFTTGMPVTAQL 328 Query: 332 FFTAASLLIALPTASQIFCWLATLWSGRLSLRTPLLFVLAFFVILLLGGLTGIMLALVPL 391 FF A++LIA+PT +IF W+AT+W G ++ TP+LF + F + +GG TG++LA+ P+ Sbjct: 329 FFMYATMLIAVPTGVKIFNWIATMWRGSMTFETPMLFSVGFIFVFTMGGFTGLILAVTPI 388 Query: 392 DLQLHDTFFVVAHLHYVLLGGAVFPLFGAIYYWFPKFTGRLLGERLGRWQFWLFFIGFNV 451 D+Q+ DT++VVAH HYVL+ G++F LF YYW PK+TG + E G++ FW I FN+ Sbjct: 389 DIQMQDTYYVVAHFHYVLVAGSLFALFAGYYYWGPKWTGFMYNEWRGKFHFWASLITFNI 448 Query: 452 SFFPMHMLGLQGMPRRVYTYPVQMGWGALNFLSTIGAMMIAASVLMFL-FNVWRSLRRGE 510 +FFPMH LGL GMPRR YP Q + N +++IGA S + FL F V S++ G+ Sbjct: 449 TFFPMHFLGLAGMPRRYADYPAQ--FTDFNMIASIGAFGFGLSQVYFLFFVVIPSIKGGK 506 Query: 511 SAGPDPW-GAGTLEWSVPSPPPAGNFVAVPVV 541 A PW GA LEW+VPSP P F PVV Sbjct: 507 QAEAKPWEGAEGLEWTVPSPAPFHTFEEPPVV 538 >gi|300311778|ref|YP_003775870.1| cytochrome o ubiquinol oxidase subunit I protein [Herbaspirillum seropedicae SmR1] Length = 667 Score = 385 bits (988), Expect = e-108, Method: Compositional matrix adjust. Identities = 200/532 (37%), Positives = 314/532 (59%), Gaps = 12/532 (2%) Query: 33 WRGWICAVNHKTISRRFMIATFVFFLLGGVLALMIRLQLAQPANTVIG---PSLYNQLFT 89 WR W +++HK I +++ V L G A+M+R Q A G P Y+Q+FT Sbjct: 55 WRDWFTSIDHKRIGIMYIVLAIVMLLRGFADAVMMRAQQAIAFGDNAGFLPPHHYDQVFT 114 Query: 90 MHGTTMMFLFAVPVMQAIAIYLIPLMIGARSVAFPLLNAFAYWIFVFGGMMLYAAFIVGS 149 HG M+F A+P++ + Y++PL IGAR VAFP LN F++W+ FG +++ A+ VG Sbjct: 115 AHGVIMIFFVAMPLVTGLMNYVVPLQIGARDVAFPFLNNFSFWMTTFGALLVMASLFVGE 174 Query: 150 GPDVGWFAYVPLSLTSYSSGKGVDFWAQMITFTELSGLIEAIVIITTILKMRAPGMSLRR 209 GW AY PLS YS GVD++ + + L+ I ++ TI+KMRAPGM++ + Sbjct: 175 FARTGWLAYPPLSGILYSPDVGVDYYIWALQVAGVGTLLSGINLVVTIVKMRAPGMNMMK 234 Query: 210 MPLFVWAMLVTSFMVLFAMPAVMFGSTALITDRLVGTQFYSSGDGGDALLWQHLFWFFGH 269 MP+F W L T+ +++ A P + L DR+ GT F+++ GG+A+++ +L W +GH Sbjct: 235 MPVFTWTSLCTNVLIVAAFPVLTAVLAMLSLDRVFGTNFFTNDMGGNAMMYVNLIWIWGH 294 Query: 270 PEVYLIFIPPLGFLSQIIATFSRRPIVGYPLMVLALIATGFLAFGLWVHHMFATNLPEIG 329 PEVY++ +P G S+I++TFS + + GY MV A + L++ +W+HH F Sbjct: 295 PEVYILVLPAFGIFSEIVSTFSGKRLFGYTSMVYATVVITILSYLVWLHHFFTMGSGASV 354 Query: 330 KAFFTAASLLIALPTASQIFCWLATLWSGRLSLRTPLLFVLAFFVILLLGGLTGIMLALV 389 +FF +++I++PT ++IF WL T++ GR+ P+L+ + F V ++GG+TG++LA+ Sbjct: 355 NSFFGITTMIISIPTGAKIFNWLFTMYRGRIRFEVPMLWTIGFMVTFVIGGMTGVLLAVP 414 Query: 390 PLDLQLHDTFFVVAHLHYVLLGGAVFPLFGAIYYWFPKFTGRLLGERLGRWQFWLFFIGF 449 P D LH++ F++AH H V++GG VF +F I +WFPK G L E G+ FW + +GF Sbjct: 415 PADFVLHNSLFLIAHFHNVIIGGVVFGMFAGINFWFPKAFGFKLNEFWGKCSFWFWLVGF 474 Query: 450 NVSFFPMHMLGLQGMPRRV--YTYPVQMGWGALNFLSTIGAMMIAASVLMFLFNVWRSLR 507 ++F P+++LGL G+ RR+ + P W ++ IGA +IA + F+ + S+R Sbjct: 475 YLAFMPLYVLGLMGVTRRMSHFDDPSLQIWFV---VAAIGAGLIALGIGSFIIQIAVSIR 531 Query: 508 RGESAGP---DPWGAGTLEWSVPSPPPAGNFVAVPVVHANEPLWSPPAQPSY 556 + DPW TLEWS SPPPA NF PVVH N+ W+ + Y Sbjct: 532 DRKKLADVTGDPWNGRTLEWSTSSPPPAYNFAFTPVVHDNDA-WADMKKNKY 582 >gi|300312501|ref|YP_003776593.1| cbb3-type cytochrome c oxidase subunit I transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 475 Score = 68.6 bits (166), Expect = 2e-12, Method: Compositional matrix adjust. Identities = 116/494 (23%), Positives = 205/494 (41%), Gaps = 65/494 (13%) Query: 44 TISRRFMIATFVFFLLGGVLALMIRLQLAQPANTVIGPSL-YNQLFTMHGTTMMFLFAVP 102 T+ R+F +AT ++ ++G ++ ++I QLA P + P L + +L +H ++F F Sbjct: 10 TVVRQFTVATILWGVVGMLVGVIIAAQLAWPELNMGVPWLSFGRLRPLHTNAVIFAFGGC 69 Query: 103 VMQAIAIYLIPLMIGARSVAFPLLNAFAYWIFVFGGMMLYAAFIVGSGPDVGWFAYVPLS 162 + A + Y++ R + L AF +W G L IVG+ + PL Sbjct: 70 ALMATSYYVVQRTCQVRLFS-DFLAAFTFW-----GWQL---VIVGAAISL------PLG 114 Query: 163 LTSYSSGKGVDFWAQMITFTELSGLIEAIVIITTILKMRAPGMSLRRMPLFVWAMLVTSF 222 LT ++ W I + + T I + + ++V +F Sbjct: 115 LTRGKEYAELE-WPLTILIAVVWVAYAVVFFGTLIKR--------KVQHIYVANWFYGAF 165 Query: 223 MVLFAMPAVMFGSTALITDRLVGTQFYSSGDGGDALLWQHLFWFFGHPEV-YLIFIPPLG 281 ++ A+ ++ G T T T+ YS G + Q W++GH V + + LG Sbjct: 166 IIAVAILHIVNGMTMPATL----TKSYSMYSGAQDAMIQ---WWYGHNAVGFFLTAGFLG 218 Query: 282 FLSQIIATFSRRPIVGYPLMVLALIATGFLAFGLWVHHMFATNLPEIGKAFFTAASLLIA 341 + I RP+ Y L ++ A F HH+ T LP+ ++ SL++ Sbjct: 219 MMYYFIPKQVNRPVYSYRLSIVHFWALIFTYMWAGPHHLHYTALPDWTQSLGMVFSLILL 278 Query: 342 LPTASQIFCWLATLWSGRLSLRTPLLFVLAFFVILL----LGGLTGIMLALVPLDLQLHD 397 P+ + + TL LRT +L F V+ L + G M+A+ ++ H Sbjct: 279 APSWGGMINGMMTLSGAWHQLRTDP--ILKFLVVSLSFYGMSTFEGPMMAIKTVNALSHY 336 Query: 398 TFFVVAHLHYVLLGGAVFPLFGAIYYWFPKFTGR--LLGERLGRWQFWLFFIGFNVSFFP 455 T + + H+H LG F GA+YY P+ +G+ + + L FW+ IG + Sbjct: 337 TDWTIGHVHSGALGWVGFVTMGAMYYLIPRLSGKTQMWSKDLIEIHFWVATIGIVLYIAA 396 Query: 456 MHMLG-LQGMPRRVY----------------TYPVQMGWGALNFLSTIGAMMIAASVLMF 498 M + G +QG+ R TYP + + +G +M + +L+ Sbjct: 397 MWIAGVMQGLMWRAVNADGTLTYTFVESVKATYPYYV-------IRLMGGLMYLSGMLVM 449 Query: 499 LFNVWRSLRRGESA 512 +N WR++R E A Sbjct: 450 AYNTWRTMRGTELA 463 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 0.330 0.142 0.472 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: 1,994,621 Number of extensions: 83052 Number of successful extensions: 360 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 351 Number of HSP's successfully gapped: 4 Length of query: 643 Length of database: 1,619,870 Length adjustment: 91 Effective length of query: 552 Effective length of database: 1,188,985 Effective search space: 656319720 Effective search space used: 656319720 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 134 (56.2 bits)