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= 0001.1639.p (502 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311108|ref|YP_003775200.1| NADH-ubiquinone oxidoreductase ... 962 0.0 gi|300311106|ref|YP_003775198.1| transmembrane NADH dehydrogenas... 92 1e-19 gi|300311107|ref|YP_003775199.1| transmembrane NADH dehydrogenas... 66 7e-12 >gi|300311108|ref|YP_003775200.1| NADH-ubiquinone oxidoreductase subunit N [Herbaspirillum seropedicae SmR1] Length = 502 Score = 962 bits (2486), Expect = 0.0, Method: Compositional matrix adjust. Identities = 482/502 (96%), Positives = 489/502 (97%) Query: 1 MNNMNLIPVYPEIFLLIATSAILLIDMFLPEAKRVITYLLSLAALVVCAVLTFGDLNSGA 60 MNNMNLIPVYPEIFLLIATSAILLIDMFLPE+KRVITYLLSLAALVVCAVLTF DLNSGA Sbjct: 1 MNNMNLIPVYPEIFLLIATSAILLIDMFLPESKRVITYLLSLAALVVCAVLTFADLNSGA 60 Query: 61 TVYTFNNMFVSDPLANLLKLFTYLGVGVTLIYSRQYNTARGITGGALGGEYYVLALFALL 120 TVYTFNNMFVSDPLANLLKLFTYLGVGVTLIYSRQYNTARGITGG LGGEYY LALFALL Sbjct: 61 TVYTFNNMFVSDPLANLLKLFTYLGVGVTLIYSRQYNTARGITGGMLGGEYYALALFALL 120 Query: 121 GQMVMISGNSFLSIYLGLELMSLSLYALVALRRDHAASTEAGMKYFILGALASGFLLYGM 180 GQMVMISGNSFLSIYLGLELMSLSLYALVALRRDHAASTEAGMKYFILGALASGFLLYGM Sbjct: 121 GQMVMISGNSFLSIYLGLELMSLSLYALVALRRDHAASTEAGMKYFILGALASGFLLYGM 180 Query: 181 SMLYGATGGALELNEVFRAIASGTVDRTALVFGIVFVVAGLAFKLGAVPFHMWVPDVYQG 240 SMLYGATGGALELNEVFRAI SGTVDRT LVFGIVFVVAGLAFKLGAVPFHMWVPDVYQG Sbjct: 181 SMLYGATGGALELNEVFRAIVSGTVDRTPLVFGIVFVVAGLAFKLGAVPFHMWVPDVYQG 240 Query: 241 SPTPVTLLLGAAPKLAAFAIIFRLLVEGMLPLAEQWQQMLMVLAVLSIILGNVTAIAQTN 300 SPTPVTLLLGAAPKLA FAI FRLLVEGMLPLA WQQMLMVLAVLSIILGNVTAIAQTN Sbjct: 241 SPTPVTLLLGAAPKLATFAITFRLLVEGMLPLAVDWQQMLMVLAVLSIILGNVTAIAQTN 300 Query: 301 IKRMLAYSTISHMGFMLLGMMSGVIDSNLFSAVNAYSSSLFYAITYVITTLGSFGVIILL 360 IKRMLAYSTISHMGFMLLGMMSGV+D NLFSAVNAYSSSLFYA+TYVITTLGSFGVIILL Sbjct: 301 IKRMLAYSTISHMGFMLLGMMSGVVDGNLFSAVNAYSSSLFYAVTYVITTLGSFGVIILL 360 Query: 361 SRSGFEADTLDDFKGLNQRSPWFAAVMMIMMFSLAGIPPLVGFYAKLSVLQAAMATGQLW 420 SRSGFEADTLDDFKGLNQRSPWFAAVMMIMMFSLAGIPPLVGFYAKLSVLQAAMATGQ+W Sbjct: 361 SRSGFEADTLDDFKGLNQRSPWFAAVMMIMMFSLAGIPPLVGFYAKLSVLQAAMATGQIW 420 Query: 421 LPVLAVIFSLIGAFYYIRVVKVMYFDEPTDTSKIVATPEMRVVLSFNGIAAVALGLWPGH 480 LPVLAVIFSLIGAFYYIRVVKVMYFDEP D SKIVATPEMRVVLS NGIAA+A+GLWPGH Sbjct: 421 LPVLAVIFSLIGAFYYIRVVKVMYFDEPADNSKIVATPEMRVVLSLNGIAALAIGLWPGH 480 Query: 481 LMDACTNAIVTTLATFLSKVVS 502 LMDACTNAIVTTLATFLSKVV+ Sbjct: 481 LMDACTNAIVTTLATFLSKVVA 502 >gi|300311106|ref|YP_003775198.1| transmembrane NADH dehydrogenase I subunit L [Herbaspirillum seropedicae SmR1] Length = 696 Score = 91.7 bits (226), Expect = 1e-19, Method: Compositional matrix adjust. Identities = 91/340 (26%), Positives = 159/340 (46%), Gaps = 43/340 (12%) Query: 123 MVMISGNSFLSIYLGLELMSLSLYALVALRRDHAASTEAGMKYFILGALAS-GFLLYGMS 181 ++++ N+FL ++ G E + L Y L+ + +A MK F++ + GF+L G+ Sbjct: 137 LMLVMSNNFLQLFFGWEAVGLVSYLLIGFWYTRPTAIKANMKAFLVNRVGDFGFIL-GIG 195 Query: 182 MLYGATGGALELNEVFRAIAS-------GTVDRTALVFGIVFVVAGLAFKLGAVPFHMWV 234 +L A G++ EVF A GT D L + + G K P H+W+ Sbjct: 196 LLL-AYAGSMNYTEVFDKRAELAQLTLPGT-DWMLLTVACICLFVGAMGKSAQFPLHVWL 253 Query: 235 PDVYQGSPTPVTLLLGAAPKLAAFAIIFRLLVEGMLPLAEQWQQMLMVLAVLSIILGNVT 294 PD +G PTP++ L+ AA + A I + + L++ ++V+ ++ + Sbjct: 254 PDSMEG-PTPISALIHAATMVTA-GIFMVTRMSPLFELSDTALSFILVIGAITALFMGFL 311 Query: 295 AIAQTNIKRMLAYSTISHMGFMLLGMMSGVIDSNLFSAVNAYSSSLFYAITYVITT---- 350 Q +IKR++AYST+S +G+M + + +AYS ++F+ +T+ Sbjct: 312 GTMQNDIKRVVAYSTLSQLGYMTVAL-----------GASAYSVAVFHLMTHAFFKALLF 360 Query: 351 LGSFGVIILLSRSGFEADTLDDFKGLNQRSPWFAAVMMIMMFSLAGIPPLVGFYAKLSVL 410 LG+ VII + + + GL + P ++ +L G P GFY+K S++ Sbjct: 361 LGAGSVIIGMHHD----QDMRNMGGLRKYMPITWITSLLGSLALIGTPFFSGFYSKDSII 416 Query: 411 QAA-----MATGQLWLPVLAVIFSLIGAFYYIRVVKVMYF 445 +AA +G + VLA +F + AFY R MYF Sbjct: 417 EAAAESHLAGSGFAYFAVLASVF--VTAFYSFR----MYF 450 >gi|300311107|ref|YP_003775199.1| transmembrane NADH dehydrogenase I subunit M [Herbaspirillum seropedicae SmR1] Length = 496 Score = 65.9 bits (159), Expect = 7e-12, Method: Compositional matrix adjust. Identities = 84/341 (24%), Positives = 158/341 (46%), Gaps = 27/341 (7%) Query: 161 AGMKYFILGALASGFLLYGMSMLYGATGGALELNEVFRAIASGTVDRTALVFGIVFVVAG 220 A K F+ L S +L + LY +GG+ E+ + S + + Sbjct: 166 AAFKLFLYTLLGSLLMLIALIYLYYVSGGSFEIPTWHQVPLSMLEQKILFFAFLAAFAV- 224 Query: 221 LAFKLGAVPFHMWVPDVYQGSPTPVTLLLGAAP-KLAAFAII-FRLLVEGMLPLAEQWQQ 278 K+ P H W+PD + +PT +++L A KL A+ + F L + LP A Sbjct: 225 ---KVPMWPVHTWLPDAHVQAPTGGSIVLAAIMLKLGAYGFLRFSLPI---LPDASHALS 278 Query: 279 MLMV-LAVLSIILGNVTAIAQTNIKRMLAYSTISHMGFMLLGMMSGVIDSNLFSAVNAYS 337 M+ L+++++I + A+ Q ++K+++AYS+I+HMGF+ LG +F+ + A Sbjct: 279 GFMIFLSLVAVIYIGLVALVQQDMKKLVAYSSIAHMGFVTLGFF-------MFNDM-AVQ 330 Query: 338 SSLFYAITYVITTLGSFGVIILLSRSGFEADTLDDFKGLNQRSPWFAAVMMIMMFSLA-- 395 + I++ + F I +L + + G+ + P FA ++FSLA Sbjct: 331 GGIVQMISHGFVSGAMFMCIGVLYDQ-MHTREISQYGGVVNKMPRFA--FFFILFSLANC 387 Query: 396 GIPPLVGFYAKLSVLQAAMATGQLWLPVLAVIFSLIGAFYYIRVVKVMYFDEPTD--TSK 453 G+P GF + V+ A+ W+ +LA ++GA Y + + K + F T+ ++ Sbjct: 388 GLPATSGFVGEFMVILGAVKF-NFWIGLLAATALILGAAYSLWLAKRVIFGAVTNHHVAE 446 Query: 454 IVATPEMR-VVLSFNGIAAVALGLWPGHLMDACTNAIVTTL 493 +V ++L IA + +G++PG + D+ ++ L Sbjct: 447 LVDLNGREFLILGLLAIATLVMGVYPGIITDSIQTSVTDLL 487 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 0.328 0.140 0.407 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: 1,439,909 Number of extensions: 59457 Number of successful extensions: 279 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 274 Number of HSP's successfully gapped: 4 Length of query: 502 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 413 Effective length of database: 1,198,455 Effective search space: 494961915 Effective search space used: 494961915 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 (21.7 bits) S2: 133 (55.8 bits)