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= 0034.0078.p (471 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311778|ref|YP_003775870.1| cytochrome o ubiquinol oxidase ... 927 0.0 gi|300313446|ref|YP_003777538.1| cytochrome c oxidase polypeptid... 317 1e-87 gi|300311626|ref|YP_003775718.1| cytochrome c oxidase polypeptid... 277 2e-75 >gi|300311778|ref|YP_003775870.1| cytochrome o ubiquinol oxidase subunit I protein [Herbaspirillum seropedicae SmR1] Length = 667 Score = 927 bits (2395), Expect = 0.0, Method: Compositional matrix adjust. Identities = 455/471 (96%), Positives = 463/471 (98%) Query: 1 VDYYIWALQVAGVGTLLSGINLVVTIVKMRAPGMNMMKMPVFTWTSLCTNVLIVAAFPVL 60 VDYYIWALQVAGVGTLLSGINLVVTIVKMRAPGMNMMKMPVFTWTSLCTNVLIVAAFPVL Sbjct: 197 VDYYIWALQVAGVGTLLSGINLVVTIVKMRAPGMNMMKMPVFTWTSLCTNVLIVAAFPVL 256 Query: 61 TAVLGMLSLDRIFGTNFFTNDMGGNAMMYVNLIWIWGHPEVYILILPAFGVFSEIVSTFS 120 TAVL MLSLDR+FGTNFFTNDMGGNAMMYVNLIWIWGHPEVYIL+LPAFG+FSEIVSTFS Sbjct: 257 TAVLAMLSLDRVFGTNFFTNDMGGNAMMYVNLIWIWGHPEVYILVLPAFGIFSEIVSTFS 316 Query: 121 GKRLFGYTSMVHATVVITILSYLVWLHHFFTMGSGASVNSFFGITTMIISIPTGAKIFNW 180 GKRLFGYTSMV+ATVVITILSYLVWLHHFFTMGSGASVNSFFGITTMIISIPTGAKIFNW Sbjct: 317 GKRLFGYTSMVYATVVITILSYLVWLHHFFTMGSGASVNSFFGITTMIISIPTGAKIFNW 376 Query: 181 LFTMYRGRIRFEVPMLWTIGFMVTFVIGGMTGVLLAVPPADFVLHNSLFLIAHFHNVIIG 240 LFTMYRGRIRFEVPMLWTIGFMVTFVIGGMTGVLLAVPPADFVLHNSLFLIAHFHNVIIG Sbjct: 377 LFTMYRGRIRFEVPMLWTIGFMVTFVIGGMTGVLLAVPPADFVLHNSLFLIAHFHNVIIG 436 Query: 241 GVVFGMFAGINFWFPKAFGFKLNEFWGKCSFWFWLVGFYLAFMPLYVLGLMGVTRRMSHF 300 GVVFGMFAGINFWFPKAFGFKLNEFWGKCSFWFWLVGFYLAFMPLYVLGLMGVTRRMSHF Sbjct: 437 GVVFGMFAGINFWFPKAFGFKLNEFWGKCSFWFWLVGFYLAFMPLYVLGLMGVTRRMSHF 496 Query: 301 DDPSLQIWFVVAALGAGLIALGIGSFIIQIAVSIRDRKKLADVTGDPWNGRTLEWSTSSP 360 DDPSLQIWFVVAA+GAGLIALGIGSFIIQIAVSIRDRKKLADVTGDPWNGRTLEWSTSSP Sbjct: 497 DDPSLQIWFVVAAIGAGLIALGIGSFIIQIAVSIRDRKKLADVTGDPWNGRTLEWSTSSP 556 Query: 361 PPAYNFAFTPVVHDNDAWADMKKNNYQRPLGDFVEIHMPKNTGAGFIIAALSAAVGFAMI 420 PPAYNFAFTPVVHDNDAWADMKKN YQRPLGDFVEIHMPKNTGAGFIIAALSA +GF +I Sbjct: 557 PPAYNFAFTPVVHDNDAWADMKKNKYQRPLGDFVEIHMPKNTGAGFIIAALSAVLGFTLI 616 Query: 421 WHMWLPAVAGFVALCVATIVHTFNYNRDYYIPADEVVRVEAERTRLLNSHV 471 WHMWLPAVA FV L ATI+HTFNYNRDYYIPADEVVRVEAERTRLLNSHV Sbjct: 617 WHMWLPAVATFVVLVAATIIHTFNYNRDYYIPADEVVRVEAERTRLLNSHV 667 >gi|300313446|ref|YP_003777538.1| cytochrome c oxidase polypeptide I transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 539 Score = 317 bits (813), Expect = 1e-87, Method: Compositional matrix adjust. Identities = 167/374 (44%), Positives = 236/374 (63%), Gaps = 6/374 (1%) Query: 1 VDYYIWALQVAGVGTLLSGINLVVTIVKMRAPGMNMMKMPVFTWTSLCTNVLIVAAFPVL 60 +D I+A+ + G +++ IN++VTI+ MRAPGM +MKMP+F WT L T L++A PVL Sbjct: 169 MDMGIFAMHIMGASSIMGSINIIVTILNMRAPGMTLMKMPMFCWTWLITAYLLIAVMPVL 228 Query: 61 TAVLGMLSLDRIFGTNFFTNDMGGNAMMYVNLIWIWGHPEVYILILPAFGVFSEIVSTFS 120 + M DR FGT+FF GG+ +MY ++ W +GHPEVYI+ILPAFG+ S+I+ F+ Sbjct: 229 AGAITMTLTDRHFGTSFFNAAGGGDPVMYQHIFWFFGHPEVYIMILPAFGIVSQIIPAFA 288 Query: 121 GKRLFGYTSMVHATVVITILSYLVWLHHFFTMGSGASVNSFFGITTMIISIPTGAKIFNW 180 K LFGY SMV+AT I ILS++VW HH FT G + FF TM+I++PTG KIFNW Sbjct: 289 RKPLFGYASMVYATASIAILSFIVWAHHMFTTGMPVTAQLFFMYATMLIAVPTGVKIFNW 348 Query: 181 LFTMYRGRIRFEVPMLWTIGFMVTFVIGGMTGVLLAVPPADFVLHNSLFLIAHFHNVIIG 240 + TM+RG + FE PML+++GF+ F +GG TG++LAV P D + ++ +++AHFH V++ Sbjct: 349 IATMWRGSMTFETPMLFSVGFIFVFTMGGFTGLILAVTPIDIQMQDTYYVVAHFHYVLVA 408 Query: 241 GVVFGMFAGINFWFPKAFGFKLNEFWGKCSFWFWLVGFYLAFMPLYVLGLMGVTRRMSHF 300 G +F +FAG +W PK GF NE+ GK FW L+ F + F P++ LGL G+ RR + Sbjct: 409 GSLFALFAGYYYWGPKWTGFMYNEWRGKFHFWASLITFNITFFPMHFLGLAGMPRRYA-- 466 Query: 301 DDPSLQIWF-VVAALGAGLIALGIGSFIIQIAVSIRDRKKLADVTGDPWNG-RTLEWSTS 358 D P+ F ++A++GA G+ V I K PW G LEW+ Sbjct: 467 DYPAQFTDFNMIASIGA--FGFGLSQVYFLFFVVIPSIKGGKQAEAKPWEGAEGLEWTVP 524 Query: 359 SPPPAYNFAFTPVV 372 SP P + F PVV Sbjct: 525 SPAPFHTFEEPPVV 538 >gi|300311626|ref|YP_003775718.1| cytochrome c oxidase polypeptide I transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 633 Score = 277 bits (708), Expect = 2e-75, Method: Compositional matrix adjust. Identities = 142/378 (37%), Positives = 233/378 (61%), Gaps = 6/378 (1%) Query: 1 VDYYIWALQVAGVGTLLSGINLVVTIVKMRAPGMNMMKMPVFTWTSLCTNVLIVAAFP-V 59 VD + + + L+ I ++ T++K+RAPGM++ +MP+F W L T+V+++ A P V Sbjct: 162 VDIWAQMITFTELSALIEAIVIITTVMKLRAPGMSLRRMPLFAWAMLVTSVMVLFAMPAV 221 Query: 60 LTAVLGMLSLDRIFGTNFFTNDMGGNAMMYVNLIWIWGHPEVYILILPAFGVFSEIVSTF 119 + A G+++ DR+ T F+++ GG+A+++ +L W +GHPEVY++ LP G+ S I+ TF Sbjct: 222 MLASTGLIT-DRLVNTQFYSHQNGGDALLWQHLFWFFGHPEVYLIFLPPLGMISTIIPTF 280 Query: 120 SGKRLFGYTSMVHATVVITILSYLVWLHHFFTMGSGASVNSFFGITTMIISIPTGAKIFN 179 + + + GY +MV A + L++ +W+HH F + FF +++I++PT +IF Sbjct: 281 ARRSMVGYPAMVLALIATAFLAFGLWVHHMFATTLPEAGKLFFTAASLLIALPTALQIFC 340 Query: 180 WLFTMYRGRIRFEVPMLWTIGFMVTFVIGGMTGVLLAVPPADFVLHNSLFLIAHFHNVII 239 W+ T++ GR F+ P+L+ + F V+GG+TG++LA P D LH++ F++AH H V++ Sbjct: 341 WISTIWLGRPVFKTPLLFVLAFFFILVMGGLTGLMLASVPLDLQLHDTYFVVAHLHYVLL 400 Query: 240 GGVVFGMFAGINFWFPKAFGFKLNEFWGKCSFWFWLVGFYLAFMPLYVLGLMGVTRRM-S 298 GG +F +F G +WFPK G L+E G+ +FW + VGF + F P++VLGL G+TRR+ + Sbjct: 401 GGAIFPLFGGFYYWFPKFTGRMLDERLGRWNFWLFFVGFNVCFFPMHVLGLQGMTRRVYT 460 Query: 299 HFDDPSLQIWFVVAALGAGLIALGIGSFIIQIAVSIRDRKKLADVTGDPWNGRTLEWSTS 358 + + + A +GA LI L + F++ + S+ D +PW TLEWS Sbjct: 461 YAAQMGWEGLNLTATIGAFLIGLSVLLFLLNVVHSLWRGAAAGD---NPWGAATLEWSLP 517 Query: 359 SPPPAYNFAFTPVVHDND 376 SPPPA NF PVVH D Sbjct: 518 SPPPAGNFLEVPVVHAAD 535 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 0.472 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: 1,533,334 Number of extensions: 65056 Number of successful extensions: 252 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 246 Number of HSP's successfully gapped: 3 Length of query: 471 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 382 Effective length of database: 1,198,455 Effective search space: 457809810 Effective search space used: 457809810 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: 132 (55.5 bits)