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= 0001.0018.p (619 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 ... 1092 0.0 gi|300313446|ref|YP_003777538.1| cytochrome c oxidase polypeptid... 395 e-111 gi|300311626|ref|YP_003775718.1| cytochrome c oxidase polypeptid... 358 e-100 >gi|300311778|ref|YP_003775870.1| cytochrome o ubiquinol oxidase subunit I protein [Herbaspirillum seropedicae SmR1] Length = 667 Score = 1092 bits (2823), Expect = 0.0, Method: Compositional matrix adjust. Identities = 538/619 (86%), Positives = 570/619 (92%), Gaps = 5/619 (0%) Query: 1 LWRDWITSIDHKKIGIMYVILGIVMLLRGFADALMMRAQQALSFGDSAGFLPPHHYDQVF 60 LWRDW TSIDHK+IGIMY++L IVMLLRGFADA+MMRAQQA++FGD+AGFLPPHHYDQVF Sbjct: 54 LWRDWFTSIDHKRIGIMYIVLAIVMLLRGFADAVMMRAQQAIAFGDNAGFLPPHHYDQVF 113 Query: 61 TAHGVIMIFFVAMPLVTGLMNYVVPLQIGARDVAFPFLNNFSFWMTTFGAGLVMASLFVG 120 TAHGVIMIFFVAMPLVTGLMNYVVPLQIGARDVAFPFLNNFSFWMTTFGA LVMASLFVG Sbjct: 114 TAHGVIMIFFVAMPLVTGLMNYVVPLQIGARDVAFPFLNNFSFWMTTFGALLVMASLFVG 173 Query: 121 EFARTGWLAYPPLSGILGSPDVGVDYYIWSLQIAGVGTLLSGINLIATIVKMRAPGMNMM 180 EFARTGWLAYPPLSGIL SPDVGVDYYIW+LQ+AGVGTLLSGINL+ TIVKMRAPGMNMM Sbjct: 174 EFARTGWLAYPPLSGILYSPDVGVDYYIWALQVAGVGTLLSGINLVVTIVKMRAPGMNMM 233 Query: 181 KMPVFTWTALCTNVLIVAAFPILTAVLGMLSLDRMFGTNFFTNDLGGNAMMYVNLIWIWG 240 KMPVFTWT+LCTNVLIVAAFP+LTAVL MLSLDR+FGTNFFTND+GGNAMMYVNLIWIWG Sbjct: 234 KMPVFTWTSLCTNVLIVAAFPVLTAVLAMLSLDRVFGTNFFTNDMGGNAMMYVNLIWIWG 293 Query: 241 HPEVYILILPAFGIFSEIVSTFSGKRLFGYTSMVYATVVITILSYLVWLHHFFTMGSGAS 300 HPEVYIL+LPAFGIFSEIVSTFSGKRLFGYTSMVYATVVITILSYLVWLHHFFTMGSGAS Sbjct: 294 HPEVYILVLPAFGIFSEIVSTFSGKRLFGYTSMVYATVVITILSYLVWLHHFFTMGSGAS 353 Query: 301 VNSFFGITTMIISIPTGAKIFNWLFTMYRGRIRFEVPMLWTIGFMITFVIGGMTGVMLAV 360 VNSFFGITTMIISIPTGAKIFNWLFTMYRGRIRFEVPMLWTIGFM+TFVIGGMTGV+LAV Sbjct: 354 VNSFFGITTMIISIPTGAKIFNWLFTMYRGRIRFEVPMLWTIGFMVTFVIGGMTGVLLAV 413 Query: 361 PPADFVLHNSLFLIAHFHNVIIGGVVFGMFAGINFWFPKAFGYKLDDFWGRCSFWFWCIG 420 PPADFVLHNSLFLIAHFHNVIIGGVVFGMFAGINFWFPKAFG+KL++FWG+CSFWFW +G Sbjct: 414 PPADFVLHNSLFLIAHFHNVIIGGVVFGMFAGINFWFPKAFGFKLNEFWGKCSFWFWLVG 473 Query: 421 FWVAFTPLYVLGFMGVTRRMSHFEDPSLQIWFQIAAFGALLIAAGIGSFIIQLVVSYLRR 480 F++AF PLYVLG MGVTRRMSHF+DPSLQIWF +AA GA LIA GIGSFIIQ+ VS R Sbjct: 474 FYLAFMPLYVLGLMGVTRRMSHFDDPSLQIWFVVAAIGAGLIALGIGSFIIQIAVSIRDR 533 Query: 481 DKLRDTTGDPWGARTLEWSTSSPPPDYNFAFTPRVHDNDAWADMKANGYTRPQDGFVPIH 540 KL D TGDPW RTLEWSTSSPPP YNFAFTP VHDNDAWADMK N Y RP FV IH Sbjct: 534 KKLADVTGDPWNGRTLEWSTSSPPPAYNFAFTPVVHDNDAWADMKKNKYQRPLGDFVEIH 593 Query: 541 MPKNTGAGPXGAGFIIAALSAVIGFGLIWQMWLLAGAGFIALMAAIITHTFNYKRDYYIS 600 MPKNT GAGFIIAALSAV+GF LIW MWL A A F+ L+AA I HTFNY RDYYI Sbjct: 594 MPKNT-----GAGFIIAALSAVLGFTLIWHMWLPAVATFVVLVAATIIHTFNYNRDYYIP 648 Query: 601 ADDVVLTEANRTRLLDSHV 619 AD+VV EA RTRLL+SHV Sbjct: 649 ADEVVRVEAERTRLLNSHV 667 >gi|300313446|ref|YP_003777538.1| cytochrome c oxidase polypeptide I transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 539 Score = 395 bits (1015), Expect = e-111, Method: Compositional matrix adjust. Identities = 217/516 (42%), Positives = 312/516 (60%), Gaps = 11/516 (2%) Query: 2 WRDWITSIDHKKIGIMYVILGIVMLLRGFADALMMRAQQALSFGDSAGFLPPHHYDQVFT 61 WR W+ + +HK IG +Y+ MLL G AL++RA+ F F P ++Q+ T Sbjct: 32 WRRWLFATNHKDIGTLYLWFSFTMLLSGGVLALLIRAEL---FQPGLQFFRPEFFNQLTT 88 Query: 62 AHGVIMIFFVAMPLVTGLMNYVVPLQIGARDVAFPFLNNFSFWMTTFGAGLVMASLFV-G 120 HG++M+F MP G N+++PLQIGA D+AF +NNFSFW+ A L+ S V G Sbjct: 89 MHGLVMVFGAIMPAFVGFANWMIPLQIGASDMAFARMNNFSFWLLPPAALLLAGSFLVPG 148 Query: 121 EFARTGWLAYPPLSGILGSPDVGVDYYIWSLQIAGVGTLLSGINLIATIVKMRAPGMNMM 180 GW Y PLS +G G+D I+++ I G +++ IN+I TI+ MRAPGM +M Sbjct: 149 GATAAGWTLYAPLSTQMGP---GMDMGIFAMHIMGASSIMGSINIIVTILNMRAPGMTLM 205 Query: 181 KMPVFTWTALCTNVLIVAAFPILTAVLGMLSLDRMFGTNFFTNDLGGNAMMYVNLIWIWG 240 KMP+F WT L T L++A P+L + M DR FGT+FF GG+ +MY ++ W +G Sbjct: 206 KMPMFCWTWLITAYLLIAVMPVLAGAITMTLTDRHFGTSFFNAAGGGDPVMYQHIFWFFG 265 Query: 241 HPEVYILILPAFGIFSEIVSTFSGKRLFGYTSMVYATVVITILSYLVWLHHFFTMGSGAS 300 HPEVYI+ILPAFGI S+I+ F+ K LFGY SMVYAT I ILS++VW HH FT G + Sbjct: 266 HPEVYIMILPAFGIVSQIIPAFARKPLFGYASMVYATASIAILSFIVWAHHMFTTGMPVT 325 Query: 301 VNSFFGITTMIISIPTGAKIFNWLFTMYRGRIRFEVPMLWTIGFMITFVIGGMTGVMLAV 360 FF TM+I++PTG KIFNW+ TM+RG + FE PML+++GF+ F +GG TG++LAV Sbjct: 326 AQLFFMYATMLIAVPTGVKIFNWIATMWRGSMTFETPMLFSVGFIFVFTMGGFTGLILAV 385 Query: 361 PPADFVLHNSLFLIAHFHNVIIGGVVFGMFAGINFWFPKAFGYKLDDFWGRCSFWFWCIG 420 P D + ++ +++AHFH V++ G +F +FAG +W PK G+ +++ G+ FW I Sbjct: 386 TPIDIQMQDTYYVVAHFHYVLVAGSLFALFAGYYYWGPKWTGFMYNEWRGKFHFWASLIT 445 Query: 421 FWVAFTPLYVLGFMGVTRRMSHFEDPSLQIWFQIAAFGALLIAAGIGSFIIQLVVSYLRR 480 F + F P++ LG G+ RR + + + IA+ GA F+ +V+ ++ Sbjct: 446 FNITFFPMHFLGLAGMPRRYADYPA-QFTDFNMIASIGAFGFGLSQVYFLFFVVIPSIKG 504 Query: 481 DKLRDTTGDPW-GARTLEWSTSSPPPDYNFAFTPRV 515 K + PW GA LEW+ SP P + F P V Sbjct: 505 GKQAE--AKPWEGAEGLEWTVPSPAPFHTFEEPPVV 538 >gi|300311626|ref|YP_003775718.1| cytochrome c oxidase polypeptide I transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 633 Score = 358 bits (920), Expect = e-100, Method: Compositional matrix adjust. Identities = 195/520 (37%), Positives = 307/520 (59%), Gaps = 15/520 (2%) Query: 5 WITSIDHKKIGIMYVILGIVMLLRGFADALMMRAQQALSFGDSAGFLPPHHYDQVFTAHG 64 W+ +++HK I +++ V L G AL MR Q A + G Y+Q+FT HG Sbjct: 26 WLCAVNHKAIARRFMVTTFVFFLLGGMLALAMRLQLARPDAELIG---ARLYNQLFTMHG 82 Query: 65 VIMIFFVAMPLVTGLMNYVVPLQIGARDVAFPFLNNFSFWMTTFGAGLVMASLFVGEFAR 124 M+F A+P++ + Y++PL IGAR VAFP LN F++W+ FG L+ + G Sbjct: 83 TTMMFLFAVPVMQAVAAYLLPLMIGARSVAFPRLNAFAYWIFLFGGLLLYGAFLAGSGPD 142 Query: 125 TGWLAYPPLSGILGSPDVGVDYYIWSLQIAGVGTLLSGINLIATIVKMRAPGMNMMKMPV 184 GW AY PL+ + GVD + + + L+ I +I T++K+RAPGM++ +MP+ Sbjct: 143 VGWFAYVPLALNPYASGKGVDIWAQMITFTELSALIEAIVIITTVMKLRAPGMSLRRMPL 202 Query: 185 FTWTALCTNVLIVAAFP-ILTAVLGMLSLDRMFGTNFFTNDLGGNAMMYVNLIWIWGHPE 243 F W L T+V+++ A P ++ A G+++ DR+ T F+++ GG+A+++ +L W +GHPE Sbjct: 203 FAWAMLVTSVMVLFAMPAVMLASTGLIT-DRLVNTQFYSHQNGGDALLWQHLFWFFGHPE 261 Query: 244 VYILILPAFGIFSEIVSTFSGKRLFGYTSMVYATVVITILSYLVWLHHFFTMGSGASVNS 303 VY++ LP G+ S I+ TF+ + + GY +MV A + L++ +W+HH F + Sbjct: 262 VYLIFLPPLGMISTIIPTFARRSMVGYPAMVLALIATAFLAFGLWVHHMFATTLPEAGKL 321 Query: 304 FFGITTMIISIPTGAKIFNWLFTMYRGRIRFEVPMLWTIGFMITFVIGGMTGVMLAVPPA 363 FF +++I++PT +IF W+ T++ GR F+ P+L+ + F V+GG+TG+MLA P Sbjct: 322 FFTAASLLIALPTALQIFCWISTIWLGRPVFKTPLLFVLAFFFILVMGGLTGLMLASVPL 381 Query: 364 DFVLHNSLFLIAHFHNVIIGGVVFGMFAGINFWFPKAFGYKLDDFWGRCSFWFWCIGFWV 423 D LH++ F++AH H V++GG +F +F G +WFPK G LD+ GR +FW + +GF V Sbjct: 382 DLQLHDTYFVVAHLHYVLLGGAIFPLFGGFYYWFPKFTGRMLDERLGRWNFWLFFVGFNV 441 Query: 424 AFTPLYVLGFMGVTRRMSHFEDPSLQIWFQ----IAAFGALLIAAGIGSFIIQLVVSYLR 479 F P++VLG G+TRR+ + + Q+ ++ A GA LI + F++ +V S R Sbjct: 442 CFFPMHVLGLQGMTRRVYTY---AAQMGWEGLNLTATIGAFLIGLSVLLFLLNVVHSLWR 498 Query: 480 RDKLRDTTGDPWGARTLEWSTSSPPPDYNFAFTPRVHDND 519 D +PWGA TLEWS SPPP NF P VH D Sbjct: 499 GAAAGD---NPWGAATLEWSLPSPPPAGNFLEVPVVHAAD 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 0.331 0.144 0.478 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: 2,013,237 Number of extensions: 85696 Number of successful extensions: 327 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 312 Number of HSP's successfully gapped: 3 Length of query: 619 Length of database: 1,619,870 Length adjustment: 91 Effective length of query: 528 Effective length of database: 1,188,985 Effective search space: 627784080 Effective search space used: 627784080 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 133 (55.8 bits)