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= 0011.0339.p (633 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... 1244 0.0 gi|300313446|ref|YP_003777538.1| cytochrome c oxidase polypeptid... 426 e-120 gi|300311778|ref|YP_003775870.1| cytochrome o ubiquinol oxidase ... 368 e-103 >gi|300311626|ref|YP_003775718.1| cytochrome c oxidase polypeptide I transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 633 Score = 1244 bits (3219), Expect = 0.0, Method: Compositional matrix adjust. Identities = 626/633 (98%), Positives = 628/633 (99%) Query: 1 MTPDPRAEEARRLEQTWSDPPGLWGWLCAVNHKAIARRFMVTTFVFFLLGGLLALAMRLQ 60 MTPDPRAEEARRLEQTWSDPPGLWGWLCAVNHKAIARRFMVTTFVFFLLGG+LALAMRLQ Sbjct: 1 MTPDPRAEEARRLEQTWSDPPGLWGWLCAVNHKAIARRFMVTTFVFFLLGGMLALAMRLQ 60 Query: 61 LARPDAELIGARLYNQLFTMHGTTMMFLFAVPVMQAVAAYLLPLMIGARSVAFPRLNAFA 120 LARPDAELIGARLYNQLFTMHGTTMMFLFAVPVMQAVAAYLLPLMIGARSVAFPRLNAFA Sbjct: 61 LARPDAELIGARLYNQLFTMHGTTMMFLFAVPVMQAVAAYLLPLMIGARSVAFPRLNAFA 120 Query: 121 YWIFLFGGLLLYGAFFAGSGPDVGWFAYVPLALNPYASGKGVDIWAQMITFTELSALIEA 180 YWIFLFGGLLLYGAF AGSGPDVGWFAYVPLALNPYASGKGVDIWAQMITFTELSALIEA Sbjct: 121 YWIFLFGGLLLYGAFLAGSGPDVGWFAYVPLALNPYASGKGVDIWAQMITFTELSALIEA 180 Query: 181 IVIITTVMKLRAPGMSLRRMPLFAWAMLVTSVMVLFAMPAVMLASTGLITDRLVNTQFYS 240 IVIITTVMKLRAPGMSLRRMPLFAWAMLVTSVMVLFAMPAVMLASTGLITDRLVNTQFYS Sbjct: 181 IVIITTVMKLRAPGMSLRRMPLFAWAMLVTSVMVLFAMPAVMLASTGLITDRLVNTQFYS 240 Query: 241 HQNGGDVLLWQHLFWFFGHPEVYLIFLPPLGMISTIIPTFARRSMVGYPAMVLALIATAF 300 HQNGGD LLWQHLFWFFGHPEVYLIFLPPLGMISTIIPTFARRSMVGYPAMVLALIATAF Sbjct: 241 HQNGGDALLWQHLFWFFGHPEVYLIFLPPLGMISTIIPTFARRSMVGYPAMVLALIATAF 300 Query: 301 LAFGLWVHHMFATTLPEAGKLFFTAASLLIALPTALQIFCWISTIWLGRPVFKTPLLFVL 360 LAFGLWVHHMFATTLPEAGKLFFTAASLLIALPTALQIFCWISTIWLGRPVFKTPLLFVL Sbjct: 301 LAFGLWVHHMFATTLPEAGKLFFTAASLLIALPTALQIFCWISTIWLGRPVFKTPLLFVL 360 Query: 361 AFFFILVMGGLTGLMLASVPLDLQLHDTYFVVAHLHYVLLGGAIFPLFGGFYYWFPKFTG 420 AFFFILVMGGLTGLMLASVPLDLQLHDTYFVVAHLHYVLLGGAIFPLFGGFYYWFPKFTG Sbjct: 361 AFFFILVMGGLTGLMLASVPLDLQLHDTYFVVAHLHYVLLGGAIFPLFGGFYYWFPKFTG 420 Query: 421 RMLDERLGRWNFWLFFVGFNVCFFPMHVLGLQGMTRRVYTYAAQMGWEGLNLTATIGAFL 480 RMLDERLGRWNFWLFFVGFNVCFFPMHVLGLQGMTRRVYTYAAQMGWEGLNLTATIGAFL Sbjct: 421 RMLDERLGRWNFWLFFVGFNVCFFPMHVLGLQGMTRRVYTYAAQMGWEGLNLTATIGAFL 480 Query: 481 IGLSVLLFLLNVAHSLWRGAAAGDNPWGAATLEWSLPSPPPAGNFLEVPVVHAADPLWQA 540 IGLSVLLFLLNV HSLWRGAAAGDNPWGAATLEWSLPSPPPAGNFLEVPVVHAADPLWQA Sbjct: 481 IGLSVLLFLLNVVHSLWRGAAAGDNPWGAATLEWSLPSPPPAGNFLEVPVVHAADPLWQA 540 Query: 541 PRLPSHVSGLDNGQREVLITSAIEAHPQHRFWLPTPSPWPLLSALATTVLFIGSIFSPWA 600 PRLPSHVSGLDNGQREVLITS IEAHPQHRFWLPTPSPWPLLSALATT LFIGSIFSPWA Sbjct: 541 PRLPSHVSGLDNGQREVLITSVIEAHPQHRFWLPTPSPWPLLSALATTALFIGSIFSPWA 600 Query: 601 VVWGALPVGLATAIWFWPRRQRSRARIASEVRP 633 VVWGALPVGLATAIWFWPRRQRS+ARIASEVRP Sbjct: 601 VVWGALPVGLATAIWFWPRRQRSQARIASEVRP 633 >gi|300313446|ref|YP_003777538.1| cytochrome c oxidase polypeptide I transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 539 Score = 426 bits (1096), Expect = e-120, Method: Compositional matrix adjust. Identities = 229/510 (44%), Positives = 322/510 (63%), Gaps = 8/510 (1%) Query: 26 WLCAVNHKAIARRFMVTTFVFFLLGGLLALAMRLQLARPDAELIGARLYNQLFTMHGTTM 85 WL A NHK I ++ +F L GG+LAL +R +L +P + +NQL TMHG M Sbjct: 35 WLFATNHKDIGTLYLWFSFTMLLSGGVLALLIRAELFQPGLQFFRPEFFNQLTTMHGLVM 94 Query: 86 MFLFAVPVMQAVAAYLLPLMIGARSVAFPRLNAFAYWIFLFGGLLLYGAFFA-GSGPDVG 144 +F +P A +++PL IGA +AF R+N F++W+ LLL G+F G G Sbjct: 95 VFGAIMPAFVGFANWMIPLQIGASDMAFARMNNFSFWLLPPAALLLAGSFLVPGGATAAG 154 Query: 145 WFAYVPLALNPYASGKGVDIWAQMITFTELSALIEAIVIITTVMKLRAPGMSLRRMPLFA 204 W Y PL+ G G+D+ + S+++ +I II T++ +RAPGM+L +MP+F Sbjct: 155 WTLYAPLSTQ---MGPGMDMGIFAMHIMGASSIMGSINIIVTILNMRAPGMTLMKMPMFC 211 Query: 205 WAMLVTSVMVLFAMPAVMLASTGLITDRLVNTQFYSHQNGGDVLLWQHLFWFFGHPEVYL 264 W L+T+ +++ MP + A T +TDR T F++ GGD +++QH+FWFFGHPEVY+ Sbjct: 212 WTWLITAYLLIAVMPVLAGAITMTLTDRHFGTSFFNAAGGGDPVMYQHIFWFFGHPEVYI 271 Query: 265 IFLPPLGMISTIIPTFARRSMVGYPAMVLALIATAFLAFGLWVHHMFATTLPEAGKLFFT 324 + LP G++S IIP FAR+ + GY +MV A + A L+F +W HHMF T +P +LFF Sbjct: 272 MILPAFGIVSQIIPAFARKPLFGYASMVYATASIAILSFIVWAHHMFTTGMPVTAQLFFM 331 Query: 325 AASLLIALPTALQIFCWISTIWLGRPVFKTPLLFVLAFFFILVMGGLTGLMLASVPLDLQ 384 A++LIA+PT ++IF WI+T+W G F+TP+LF + F F+ MGG TGL+LA P+D+Q Sbjct: 332 YATMLIAVPTGVKIFNWIATMWRGSMTFETPMLFSVGFIFVFTMGGFTGLILAVTPIDIQ 391 Query: 385 LHDTYFVVAHLHYVLLGGAIFPLFGGFYYWFPKFTGRMLDERLGRWNFWLFFVGFNVCFF 444 + DTY+VVAH HYVL+ G++F LF G+YYW PK+TG M +E G+++FW + FN+ FF Sbjct: 392 MQDTYYVVAHFHYVLVAGSLFALFAGYYYWGPKWTGFMYNEWRGKFHFWASLITFNITFF 451 Query: 445 PMHVLGLQGMTRRVYTYAAQMGWEGLNLTATIGAFLIGLSVLLFLLNVA-HSLWRGAAAG 503 PMH LGL GM RR Y AQ + N+ A+IGAF GLS + FL V S+ G A Sbjct: 452 PMHFLGLAGMPRRYADYPAQ--FTDFNMIASIGAFGFGLSQVYFLFFVVIPSIKGGKQAE 509 Query: 504 DNPW-GAATLEWSLPSPPPAGNFLEVPVVH 532 PW GA LEW++PSP P F E PVV Sbjct: 510 AKPWEGAEGLEWTVPSPAPFHTFEEPPVVK 539 >gi|300311778|ref|YP_003775870.1| cytochrome o ubiquinol oxidase subunit I protein [Herbaspirillum seropedicae SmR1] Length = 667 Score = 368 bits (945), Expect = e-103, Method: Compositional matrix adjust. Identities = 197/524 (37%), Positives = 308/524 (58%), Gaps = 12/524 (2%) Query: 23 LWG-----WLCAVNHKAIARRFMVTTFVFFLLGGLLALAMRLQLA---RPDAELIGARLY 74 LWG W +++HK I ++V V L G A+ MR Q A +A + Y Sbjct: 50 LWGMLWRDWFTSIDHKRIGIMYIVLAIVMLLRGFADAVMMRAQQAIAFGDNAGFLPPHHY 109 Query: 75 NQLFTMHGTTMMFLFAVPVMQAVAAYLLPLMIGARSVAFPRLNAFAYWIFLFGGLLLYGA 134 +Q+FT HG M+F A+P++ + Y++PL IGAR VAFP LN F++W+ FG LL+ + Sbjct: 110 DQVFTAHGVIMIFFVAMPLVTGLMNYVVPLQIGARDVAFPFLNNFSFWMTTFGALLVMAS 169 Query: 135 FFAGSGPDVGWFAYVPLALNPYASGKGVDIWAQMITFTELSALIEAIVIITTVMKLRAPG 194 F G GW AY PL+ Y+ GVD + + + L+ I ++ T++K+RAPG Sbjct: 170 LFVGEFARTGWLAYPPLSGILYSPDVGVDYYIWALQVAGVGTLLSGINLVVTIVKMRAPG 229 Query: 195 MSLRRMPLFAWAMLVTSVMVLFAMPAVMLASTGLITDRLVNTQFYSHQNGGDVLLWQHLF 254 M++ +MP+F W L T+V+++ A P + L DR+ T F+++ GG+ +++ +L Sbjct: 230 MNMMKMPVFTWTSLCTNVLIVAAFPVLTAVLAMLSLDRVFGTNFFTNDMGGNAMMYVNLI 289 Query: 255 WFFGHPEVYLIFLPPLGMISTIIPTFARRSMVGYPAMVLALIATAFLAFGLWVHHMFATT 314 W +GHPEVY++ LP G+ S I+ TF+ + + GY +MV A + L++ +W+HH F Sbjct: 290 WIWGHPEVYILVLPAFGIFSEIVSTFSGKRLFGYTSMVYATVVITILSYLVWLHHFFTMG 349 Query: 315 LPEAGKLFFTAASLLIALPTALQIFCWISTIWLGRPVFKTPLLFVLAFFFILVMGGLTGL 374 + FF +++I++PT +IF W+ T++ GR F+ P+L+ + F V+GG+TG+ Sbjct: 350 SGASVNSFFGITTMIISIPTGAKIFNWLFTMYRGRIRFEVPMLWTIGFMVTFVIGGMTGV 409 Query: 375 MLASVPLDLQLHDTYFVVAHLHYVLLGGAIFPLFGGFYYWFPKFTGRMLDERLGRWNFWL 434 +LA P D LH++ F++AH H V++GG +F +F G +WFPK G L+E G+ +FW Sbjct: 410 LLAVPPADFVLHNSLFLIAHFHNVIIGGVVFGMFAGINFWFPKAFGFKLNEFWGKCSFWF 469 Query: 435 FFVGFNVCFFPMHVLGLQGMTRRVYTYAAQMGWEGLNLTATIGAFLIGLSVLLFLLNVAH 494 + VGF + F P++VLGL G+TRR+ ++ + + A IGA LI L + F++ +A Sbjct: 470 WLVGFYLAFMPLYVLGLMGVTRRM-SHFDDPSLQIWFVVAAIGAGLIALGIGSFIIQIAV 528 Query: 495 SLWRGAAAGD---NPWGAATLEWSLPSPPPAGNFLEVPVVHAAD 535 S+ D +PW TLEWS SPPPA NF PVVH D Sbjct: 529 SIRDRKKLADVTGDPWNGRTLEWSTSSPPPAYNFAFTPVVHDND 572 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 0.143 0.479 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: 1,947,211 Number of extensions: 76782 Number of successful extensions: 359 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: 633 Length of database: 1,619,870 Length adjustment: 91 Effective length of query: 542 Effective length of database: 1,188,985 Effective search space: 644429870 Effective search space used: 644429870 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 (21.9 bits) S2: 133 (55.8 bits)