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= 0009.0323.p (472 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... 827 0.0 gi|300311108|ref|YP_003775200.1| NADH-ubiquinone oxidoreductase ... 75 1e-14 gi|300311106|ref|YP_003775198.1| transmembrane NADH dehydrogenas... 73 4e-14 >gi|300311107|ref|YP_003775199.1| transmembrane NADH dehydrogenase I subunit M [Herbaspirillum seropedicae SmR1] Length = 496 Score = 827 bits (2135), Expect = 0.0, Method: Compositional matrix adjust. Identities = 417/471 (88%), Positives = 442/471 (93%) Query: 1 VGRDDNPSVARWLALLGAVVSLLVTIPLVLHFDAAAHGYQFVEKTPWIDRFNISYFLGID 60 +GRD NP +ARWLAL G++V L+VT PL+ HFD AHGYQFVEKTPWIDRFNISYFLG+D Sbjct: 26 LGRDSNPGLARWLALFGSLVGLVVTFPLIQHFDPLAHGYQFVEKTPWIDRFNISYFLGLD 85 Query: 61 GLSLWFIPLTAFITVIVVLAGWEVIQKRVGQYMGAFLILSGLMIGVFSALDGMLFYVFFE 120 G+SLWF+PLTAFITVIVVLAGW VIQKRV QYMGAFLILSG+M+GVFSALD MLFY FFE Sbjct: 86 GISLWFVPLTAFITVIVVLAGWVVIQKRVAQYMGAFLILSGIMVGVFSALDAMLFYAFFE 145 Query: 121 ATLIPMFIIVGVWGGANRVYAAFKFFLYTLLGSLLMLIALIYLYIVSGGSFEIPTWHQLP 180 ATLIPMFIIVGVWGG NRVYAAFK FLYTLLGSLLMLIALIYLY VSGGSFEIPTWHQ+P Sbjct: 146 ATLIPMFIIVGVWGGDNRVYAAFKLFLYTLLGSLLMLIALIYLYYVSGGSFEIPTWHQVP 205 Query: 181 LSMIEQKLLFFAFLMAFAVKVPMWPVHTWLPDAHVEAPTGGSIVLAAIMLKLGAYGFLRF 240 LSM+EQK+LFFAFL AFAVKVPMWPVHTWLPDAHV+APTGGSIVLAAIMLKLGAYGFLRF Sbjct: 206 LSMLEQKILFFAFLAAFAVKVPMWPVHTWLPDAHVQAPTGGSIVLAAIMLKLGAYGFLRF 265 Query: 241 SLPIAPDASHALSGFMITLSLVAVIYIGLVALVQQDMKKLVAYSSIAHMGFVTLGFFMFN 300 SLPI PDASHALSGFMI LSLVAVIYIGLVALVQQDMKKLVAYSSIAHMGFVTLGFFMFN Sbjct: 266 SLPILPDASHALSGFMIFLSLVAVIYIGLVALVQQDMKKLVAYSSIAHMGFVTLGFFMFN 325 Query: 301 DMAVQGGIAQMISHGFVSGAMFMCIGVLYDRMHTREIAQYGGVVNKMPRFAAFFILFSLA 360 DMAVQGGI QMISHGFVSGAMFMCIGVLYD+MHTREI+QYGGVVNKMPRFA FFILFSLA Sbjct: 326 DMAVQGGIVQMISHGFVSGAMFMCIGVLYDQMHTREISQYGGVVNKMPRFAFFFILFSLA 385 Query: 361 NCGLPATSGFVGEFMVILGAVKFNFWIGLLSATALILGAAYSLWLTKRVIFGAVTNHHVE 420 NCGLPATSGFVGEFMVILGAVKFNFWIGLL+ATALILGAAYSLWL KRVIFGAVTNHHV Sbjct: 386 NCGLPATSGFVGEFMVILGAVKFNFWIGLLAATALILGAAYSLWLAKRVIFGAVTNHHVA 445 Query: 421 ELTDVNKREFFILGLLAIAVLVMGLYPAPVTDTMQTSVSDLLKHVSVSKIG 471 EL D+N REF ILGLLAIA LVMG+YP +TD++QTSV+DLLKHV+VSKI Sbjct: 446 ELVDLNGREFLILGLLAIATLVMGVYPGIITDSIQTSVTDLLKHVAVSKIN 496 >gi|300311108|ref|YP_003775200.1| NADH-ubiquinone oxidoreductase subunit N [Herbaspirillum seropedicae SmR1] Length = 502 Score = 75.1 bits (183), Expect = 1e-14, Method: Compositional matrix adjust. Identities = 86/352 (24%), Positives = 160/352 (45%), Gaps = 47/352 (13%) Query: 136 ANRVYAAFKFFLYTLLGSLLMLIALIYLYIVSGGSFEIPTWHQLPLS-MIEQKLLFFA-- 192 A A K+F+ L S +L + LY +GG+ E+ + +S +++ L F Sbjct: 156 AASTEAGMKYFILGALASGFLLYGMSMLYGATGGALELNEVFRAIVSGTVDRTPLVFGIV 215 Query: 193 FLMA-FAVKVPMWPVHTWLPDAHVEAPTGGSIVLAAIMLKLGAYG-----FLRFSLPIAP 246 F++A A K+ P H W+PD + +PT +++L A KL + + LP+A Sbjct: 216 FVVAGLAFKLGAVPFHMWVPDVYQGSPTPVTLLLGAAP-KLATFAITFRLLVEGMLPLAV 274 Query: 247 DASHALSGFMITLSLVAVIYIGLVALVQQDMKKLVAYSSIAHMGFVTLGFFMFNDMAVQG 306 D L + L+++++I + A+ Q ++K+++AYS+I+HMGF+ LG V G Sbjct: 275 DWQQML----MVLAVLSIILGNVTAIAQTNIKRMLAYSTISHMGFMLLGMM---SGVVDG 327 Query: 307 GIAQMISHGFVSGAMFMCIG------------VLYDR--MHTREIAQYGGVVNKMPRFAA 352 + ++ S ++F + +L R + + G+ + P FAA Sbjct: 328 NLFSAVNA--YSSSLFYAVTYVITTLGSFGVIILLSRSGFEADTLDDFKGLNQRSPWFAA 385 Query: 353 FFILFSLANCGLPATSGFVGEFMVILGAVKF-NFWIGLLSATALILGAAYSLWLTKRVIF 411 ++ + G+P GF + V+ A+ W+ +L+ ++GA Y + + K + F Sbjct: 386 VMMIMMFSLAGIPPLVGFYAKLSVLQAAMATGQIWLPVLAVIFSLIGAFYYIRVVKVMYF 445 Query: 412 GAVTNHHVEELTDVNK-----REFFILGLLAIAVLVMGLYPAPVTDTMQTSV 458 +E D +K +L L IA L +GL+P + D ++ Sbjct: 446 --------DEPADNSKIVATPEMRVVLSLNGIAALAIGLWPGHLMDACTNAI 489 >gi|300311106|ref|YP_003775198.1| transmembrane NADH dehydrogenase I subunit L [Herbaspirillum seropedicae SmR1] Length = 696 Score = 73.2 bits (178), Expect = 4e-14, Method: Compositional matrix adjust. Identities = 53/185 (28%), Positives = 98/185 (52%), Gaps = 8/185 (4%) Query: 200 KVPMWPVHTWLPDAHVEAPTG-GSIVLAAIMLKLGAYGFLRFSLPIAPDASHALSGFMIT 258 K +P+H WLPD+ +E PT +++ AA M+ G + R S P+ + ALS F++ Sbjct: 243 KSAQFPLHVWLPDS-MEGPTPISALIHAATMVTAGIFMVTRMS-PLFELSDTALS-FILV 299 Query: 259 LSLVAVIYIGLVALVQQDMKKLVAYSSIAHMGFVTLGFFMFNDMAVQGGIAQMISHGFVS 318 + + +++G + +Q D+K++VAYS+++ +G++T+ A + +++H F Sbjct: 300 IGAITALFMGFLGTMQNDIKRVVAYSTLSQLGYMTVA---LGASAYSVAVFHLMTHAFFK 356 Query: 319 GAMFMCIG-VLYDRMHTREIAQYGGVVNKMPRFAAFFILFSLANCGLPATSGFVGEFMVI 377 +F+ G V+ H +++ GG+ MP +L SLA G P SGF + +I Sbjct: 357 ALLFLGAGSVIIGMHHDQDMRNMGGLRKYMPITWITSLLGSLALIGTPFFSGFYSKDSII 416 Query: 378 LGAVK 382 A + Sbjct: 417 EAAAE 421 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 0.446 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: 1,388,654 Number of extensions: 56916 Number of successful extensions: 241 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 236 Number of HSP's successfully gapped: 4 Length of query: 472 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 383 Effective length of database: 1,198,455 Effective search space: 459008265 Effective search space used: 459008265 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: 132 (55.5 bits)