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= 0028.0258.p (496 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311107|ref|YP_003775199.1| transmembrane NADH dehydrogenas... 972 0.0 gi|300311106|ref|YP_003775198.1| transmembrane NADH dehydrogenas... 74 2e-14 gi|300311108|ref|YP_003775200.1| NADH-ubiquinone oxidoreductase ... 74 4e-14 >gi|300311107|ref|YP_003775199.1| transmembrane NADH dehydrogenase I subunit M [Herbaspirillum seropedicae SmR1] Length = 496 Score = 972 bits (2514), Expect = 0.0, Method: Compositional matrix adjust. Identities = 488/496 (98%), Positives = 494/496 (99%) Query: 1 MMQSTFPILSLAIWVPIVFGILVLALGRDSNPGLTRWLALFGSLVGLVVTFPLIQHFDPL 60 MMQSTFPILSLAIWVPIVFGILVLALGRDSNPGL RWLALFGSLVGLVVTFPLIQHFDPL Sbjct: 1 MMQSTFPILSLAIWVPIVFGILVLALGRDSNPGLARWLALFGSLVGLVVTFPLIQHFDPL 60 Query: 61 AHGYQFVEKTPWIDRFSISYFLGLDGISLWFVPLTAFITVIVVLAGWVVIQKRVAQYMGA 120 AHGYQFVEKTPWIDRF+ISYFLGLDGISLWFVPLTAFITVIVVLAGWVVIQKRVAQYMGA Sbjct: 61 AHGYQFVEKTPWIDRFNISYFLGLDGISLWFVPLTAFITVIVVLAGWVVIQKRVAQYMGA 120 Query: 121 FLILSGIMIGVFSSLDAMLFYAFFEATLIPMFIIVGVWGGDNRVYAAFKLFLYTLLGSLL 180 FLILSGIM+GVFS+LDAMLFYAFFEATLIPMFIIVGVWGGDNRVYAAFKLFLYTLLGSLL Sbjct: 121 FLILSGIMVGVFSALDAMLFYAFFEATLIPMFIIVGVWGGDNRVYAAFKLFLYTLLGSLL 180 Query: 181 MLIALIYLYYVSGGSFEIPTWHQVPLSMMEQKILFFAFLAAFAVKVPMWPVHTWLPDAHV 240 MLIALIYLYYVSGGSFEIPTWHQVPLSM+EQKILFFAFLAAFAVKVPMWPVHTWLPDAHV Sbjct: 181 MLIALIYLYYVSGGSFEIPTWHQVPLSMLEQKILFFAFLAAFAVKVPMWPVHTWLPDAHV 240 Query: 241 QAPTGGSIVLAAIMLKLGAYGFLRFSLPILPDASHALSGFMIFLSLVAVIYIGLVALVQQ 300 QAPTGGSIVLAAIMLKLGAYGFLRFSLPILPDASHALSGFMIFLSLVAVIYIGLVALVQQ Sbjct: 241 QAPTGGSIVLAAIMLKLGAYGFLRFSLPILPDASHALSGFMIFLSLVAVIYIGLVALVQQ 300 Query: 301 DMKKLVAYSSIAHMGFVTLGFFMFNDMAVQGGIVQMISHGFVSGAMFMCIGVLYDQMHTR 360 DMKKLVAYSSIAHMGFVTLGFFMFNDMAVQGGIVQMISHGFVSGAMFMCIGVLYDQMHTR Sbjct: 301 DMKKLVAYSSIAHMGFVTLGFFMFNDMAVQGGIVQMISHGFVSGAMFMCIGVLYDQMHTR 360 Query: 361 EISQYGGVVNKMPRFAFFFILFSLANCGLPATSGFVGEFMVILGAVKFNFWIGLLAATAL 420 EISQYGGVVNKMPRFAFFFILFSLANCGLPATSGFVGEFMVILGAVKFNFWIGLLAATAL Sbjct: 361 EISQYGGVVNKMPRFAFFFILFSLANCGLPATSGFVGEFMVILGAVKFNFWIGLLAATAL 420 Query: 421 ILGAAYSLWLAKRVIFGAVTNHHVAELVDVNGREFFILGLLAIATLVMGIYPGIITDSIQ 480 ILGAAYSLWLAKRVIFGAVTNHHVAELVD+NGREF ILGLLAIATLVMG+YPGIITDSIQ Sbjct: 421 ILGAAYSLWLAKRVIFGAVTNHHVAELVDLNGREFLILGLLAIATLVMGVYPGIITDSIQ 480 Query: 481 TSVTDLLKHVAVSKIN 496 TSVTDLLKHVAVSKIN Sbjct: 481 TSVTDLLKHVAVSKIN 496 >gi|300311106|ref|YP_003775198.1| transmembrane NADH dehydrogenase I subunit L [Herbaspirillum seropedicae SmR1] Length = 696 Score = 73.9 bits (180), Expect = 2e-14, Method: Compositional matrix adjust. Identities = 52/185 (28%), Positives = 98/185 (52%), Gaps = 8/185 (4%) Query: 225 KVPMWPVHTWLPDAHVQAPTG-GSIVLAAIMLKLGAYGFLRFSLPILPDASHALSGFMIF 283 K +P+H WLPD+ ++ PT +++ AA M+ G + R S P+ + ALS F++ Sbjct: 243 KSAQFPLHVWLPDS-MEGPTPISALIHAATMVTAGIFMVTRMS-PLFELSDTALS-FILV 299 Query: 284 LSLVAVIYIGLVALVQQDMKKLVAYSSIAHMGFVTLGFFMFNDMAVQGGIVQMISHGFVS 343 + + +++G + +Q D+K++VAYS+++ +G++T+ A + +++H F Sbjct: 300 IGAITALFMGFLGTMQNDIKRVVAYSTLSQLGYMTVA---LGASAYSVAVFHLMTHAFFK 356 Query: 344 GAMFMCIG-VLYDQMHTREISQYGGVVNKMPRFAFFFILFSLANCGLPATSGFVGEFMVI 402 +F+ G V+ H +++ GG+ MP +L SLA G P SGF + +I Sbjct: 357 ALLFLGAGSVIIGMHHDQDMRNMGGLRKYMPITWITSLLGSLALIGTPFFSGFYSKDSII 416 Query: 403 LGAVK 407 A + Sbjct: 417 EAAAE 421 >gi|300311108|ref|YP_003775200.1| NADH-ubiquinone oxidoreductase subunit N [Herbaspirillum seropedicae SmR1] Length = 502 Score = 73.6 bits (179), Expect = 4e-14, Method: Compositional matrix adjust. Identities = 88/345 (25%), Positives = 159/345 (46%), Gaps = 35/345 (10%) Query: 166 AAFKLFLYTLLGSLLMLIALIYLYYVSGGSFEIPTWHQVPLS-MMEQKILFFAFL---AA 221 A K F+ L S +L + LY +GG+ E+ + +S +++ L F + A Sbjct: 161 AGMKYFILGALASGFLLYGMSMLYGATGGALELNEVFRAIVSGTVDRTPLVFGIVFVVAG 220 Query: 222 FAVKVPMWPVHTWLPDAHVQAPTGGSIVL-AAIMLKLGAYGFLRFSLPILPDASHALSGF 280 A K+ P H W+PD + +PT +++L AA L A F +LP A Sbjct: 221 LAFKLGAVPFHMWVPDVYQGSPTPVTLLLGAAPKLATFAITFRLLVEGMLPLAVDWQQML 280 Query: 281 MIFLSLVAVIYIGLVALVQQDMKKLVAYSSIAHMGFVTLGFFMFNDMAVQGGIVQMISHG 340 M+ L+++++I + A+ Q ++K+++AYS+I+HMGF+ LG V G + ++ Sbjct: 281 MV-LAVLSIILGNVTAIAQTNIKRMLAYSTISHMGFMLLGMM---SGVVDGNLFSAVNA- 335 Query: 341 FVSGAMFMCI----------GVL----YDQMHTREISQYGGVVNKMPRFA--FFFILFSL 384 S ++F + GV+ + + G+ + P FA ++FSL Sbjct: 336 -YSSSLFYAVTYVITTLGSFGVIILLSRSGFEADTLDDFKGLNQRSPWFAAVMMIMMFSL 394 Query: 385 ANCGLPATSGFVGEFMVILGAVKF-NFWIGLLAATALILGAAYSLWLAKRVIFGA-VTNH 442 A G+P GF + V+ A+ W+ +LA ++GA Y + + K + F N Sbjct: 395 A--GIPPLVGFYAKLSVLQAAMATGQIWLPVLAVIFSLIGAFYYIRVVKVMYFDEPADNS 452 Query: 443 HVAELVDVNGREFFILGLLAIATLVMGIYPGIITDSIQTSVTDLL 487 + ++ +L L IA L +G++PG + D+ ++ L Sbjct: 453 KIVATPEMR----VVLSLNGIAALAIGLWPGHLMDACTNAIVTTL 493 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 0.332 0.145 0.453 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: 1,458,550 Number of extensions: 59077 Number of successful extensions: 232 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 228 Number of HSP's successfully gapped: 4 Length of query: 496 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 407 Effective length of database: 1,198,455 Effective search space: 487771185 Effective search space used: 487771185 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 (22.0 bits) S2: 132 (55.5 bits)