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= 0028.0257.p (499 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 ... 978 0.0 gi|300311106|ref|YP_003775198.1| transmembrane NADH dehydrogenas... 88 1e-18 gi|300311107|ref|YP_003775199.1| transmembrane NADH dehydrogenas... 67 3e-12 >gi|300311108|ref|YP_003775200.1| NADH-ubiquinone oxidoreductase subunit N [Herbaspirillum seropedicae SmR1] Length = 502 Score = 978 bits (2528), Expect = 0.0, Method: Compositional matrix adjust. Identities = 493/499 (98%), Positives = 496/499 (99%) Query: 1 MNLIPVYPEIFLLIATSAILLIDMFLPESKRVITYLLSLAALVVCAVLTFADLNTGATVY 60 MNLIPVYPEIFLLIATSAILLIDMFLPESKRVITYLLSLAALVVCAVLTFADLN+GATVY Sbjct: 4 MNLIPVYPEIFLLIATSAILLIDMFLPESKRVITYLLSLAALVVCAVLTFADLNSGATVY 63 Query: 61 TFNNMFVSDPLANLLKLFTYLGVGVTLIYSRQYNTARGITGGPLGGEYYALALFALLGQM 120 TFNNMFVSDPLANLLKLFTYLGVGVTLIYSRQYNTARGITGG LGGEYYALALFALLGQM Sbjct: 64 TFNNMFVSDPLANLLKLFTYLGVGVTLIYSRQYNTARGITGGMLGGEYYALALFALLGQM 123 Query: 121 VMISGNSFLSIYLGLELMSLSLYALVALRRDHAASTEAGMKYFILGALASGFLLYGMSML 180 VMISGNSFLSIYLGLELMSLSLYALVALRRDHAASTEAGMKYFILGALASGFLLYGMSML Sbjct: 124 VMISGNSFLSIYLGLELMSLSLYALVALRRDHAASTEAGMKYFILGALASGFLLYGMSML 183 Query: 181 YGATGGALELNEVFRAIVSGTVDRTPLVFGIVFVVAGLAFKLGAVPFHMWVPDVYQGSPT 240 YGATGGALELNEVFRAIVSGTVDRTPLVFGIVFVVAGLAFKLGAVPFHMWVPDVYQGSPT Sbjct: 184 YGATGGALELNEVFRAIVSGTVDRTPLVFGIVFVVAGLAFKLGAVPFHMWVPDVYQGSPT 243 Query: 241 PVTLLLGAAPKLATFAITFRLLVEGMLPLAVDWQQMLMVLAVLSIILGNVTAIAQTNIKR 300 PVTLLLGAAPKLATFAITFRLLVEGMLPLAVDWQQMLMVLAVLSIILGNVTAIAQTNIKR Sbjct: 244 PVTLLLGAAPKLATFAITFRLLVEGMLPLAVDWQQMLMVLAVLSIILGNVTAIAQTNIKR 303 Query: 301 MLAYSTISHMGFMLLGMMSGVVDGNLFSAVNAYSSSLFYAVTYVITTLGSFGVIILLSRS 360 MLAYSTISHMGFMLLGMMSGVVDGNLFSAVNAYSSSLFYAVTYVITTLGSFGVIILLSRS Sbjct: 304 MLAYSTISHMGFMLLGMMSGVVDGNLFSAVNAYSSSLFYAVTYVITTLGSFGVIILLSRS 363 Query: 361 GFEADTLDDFKGLNQRSPWFAAVMMIMMFSLAGIPPLVGFYAKLSVLQAAMATGQIWLPV 420 GFEADTLDDFKGLNQRSPWFAAVMMIMMFSLAGIPPLVGFYAKLSVLQAAMATGQIWLPV Sbjct: 364 GFEADTLDDFKGLNQRSPWFAAVMMIMMFSLAGIPPLVGFYAKLSVLQAAMATGQIWLPV 423 Query: 421 LAVVFSLIGAFYYIRVVKVMYFDEPTDTSKIVATPEMRVVLSLNGIAALAIGLWPGHLMD 480 LAV+FSLIGAFYYIRVVKVMYFDEP D SKIVATPEMRVVLSLNGIAALAIGLWPGHLMD Sbjct: 424 LAVIFSLIGAFYYIRVVKVMYFDEPADNSKIVATPEMRVVLSLNGIAALAIGLWPGHLMD 483 Query: 481 ACTNAIVSTLATFLSKVVA 499 ACTNAIV+TLATFLSKVVA Sbjct: 484 ACTNAIVTTLATFLSKVVA 502 >gi|300311106|ref|YP_003775198.1| transmembrane NADH dehydrogenase I subunit L [Herbaspirillum seropedicae SmR1] Length = 696 Score = 88.2 bits (217), Expect = 1e-18, Method: Compositional matrix adjust. Identities = 97/353 (27%), Positives = 167/353 (47%), Gaps = 46/353 (13%) Query: 107 EYYALALFALLGQMVMISGNSFLSIYLGLELMSLSLYALVALRRDHAASTEAGMKYFILG 166 Y +L F++L +++ N+FL ++ G E + L Y L+ + +A MK F++ Sbjct: 127 SYISLFTFSML---MLVMSNNFLQLFFGWEAVGLVSYLLIGFWYTRPTAIKANMKAFLVN 183 Query: 167 ALAS-GFLLYGMSMLYGATGGALELNEVF--RAIVS-----GTVDRTPLVFGIVFVVAGL 218 + GF+L G+ +L A G++ EVF RA ++ GT D L + + G Sbjct: 184 RVGDFGFIL-GIGLLL-AYAGSMNYTEVFDKRAELAQLTLPGT-DWMLLTVACICLFVGA 240 Query: 219 AFKLGAVPFHMWVPDVYQGSPTPVTLLLGAAPKLATFAITFRLLVEGMLPLAVDWQQMLM 278 K P H+W+PD +G PTP++ L+ AA + T I + + L+ ++ Sbjct: 241 MGKSAQFPLHVWLPDSMEG-PTPISALIHAA-TMVTAGIFMVTRMSPLFELSDTALSFIL 298 Query: 279 VLAVLSIILGNVTAIAQTNIKRMLAYSTISHMGFMLLGMMSGVVDGNLFSAVNAYSSSLF 338 V+ ++ + Q +IKR++AYST+S +G+M + + +AYS ++F Sbjct: 299 VIGAITALFMGFLGTMQNDIKRVVAYSTLSQLGYMTVAL-----------GASAYSVAVF 347 Query: 339 YAVTYVITT----LGSFGVIILLSRSGFEADTLDDFKGLNQRSPWFAAVMMIMMFSLAGI 394 + +T+ LG+ VII + + + GL + P ++ +L G Sbjct: 348 HLMTHAFFKALLFLGAGSVIIGMHHD----QDMRNMGGLRKYMPITWITSLLGSLALIGT 403 Query: 395 PPLVGFYAKLSVLQAA-----MATGQIWLPVLAVVFSLIGAFYYIRVVKVMYF 442 P GFY+K S+++AA +G + VLA VF + AFY R MYF Sbjct: 404 PFFSGFYSKDSIIEAAAESHLAGSGFAYFAVLASVF--VTAFYSFR----MYF 450 >gi|300311107|ref|YP_003775199.1| transmembrane NADH dehydrogenase I subunit M [Herbaspirillum seropedicae SmR1] Length = 496 Score = 67.4 bits (163), Expect = 3e-12, Method: Compositional matrix adjust. Identities = 83/344 (24%), Positives = 155/344 (45%), Gaps = 33/344 (9%) Query: 158 AGMKYFILGALASGFLLYGMSMLYGATGGALELNEVFRAIVSGTVDRTPLVFGIVFVVAG 217 A K F+ L S +L + LY +GG+ E+ + +S + + Sbjct: 166 AAFKLFLYTLLGSLLMLIALIYLYYVSGGSFEIPTWHQVPLSMLEQKILFFAFLAAFAV- 224 Query: 218 LAFKLGAVPFHMWVPDVYQGSPTPVTLLLGAAPKLATFAITFRLLVEGMLPLAVDWQQML 277 K+ P H W+PD + +PT +++L AA L A F +LP A Sbjct: 225 ---KVPMWPVHTWLPDAHVQAPTGGSIVL-AAIMLKLGAYGFLRFSLPILPDASHALSGF 280 Query: 278 MV-LAVLSIILGNVTAIAQTNIKRMLAYSTISHMGFMLLGMM---SGVVDGNLFSAVNA- 332 M+ L+++++I + A+ Q ++K+++AYS+I+HMGF+ LG V G + ++ Sbjct: 281 MIFLSLVAVIYIGLVALVQQDMKKLVAYSSIAHMGFVTLGFFMFNDMAVQGGIVQMISHG 340 Query: 333 -YSSSLFYAVTYVITTLGSFGVIILLSRSGFEADTLDDFKGLNQRSPWFAAVMMIMMFSL 391 S ++F + + + + + G+ + P FA ++FSL Sbjct: 341 FVSGAMFMCIGVLYDQM--------------HTREISQYGGVVNKMPRFA--FFFILFSL 384 Query: 392 A--GIPPLVGFYAKLSVLQAAMATGQIWLPVLAVVFSLIGAFYYIRVVKVMYFDEPTD-- 447 A G+P GF + V+ A+ W+ +LA ++GA Y + + K + F T+ Sbjct: 385 ANCGLPATSGFVGEFMVILGAVKF-NFWIGLLAATALILGAAYSLWLAKRVIFGAVTNHH 443 Query: 448 TSKIVA-TPEMRVVLSLNGIAALAIGLWPGHLMDACTNAIVSTL 490 +++V ++L L IA L +G++PG + D+ ++ L Sbjct: 444 VAELVDLNGREFLILGLLAIATLVMGVYPGIITDSIQTSVTDLL 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 0.141 0.409 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: 1,441,693 Number of extensions: 60120 Number of successful extensions: 266 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 261 Number of HSP's successfully gapped: 4 Length of query: 499 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 410 Effective length of database: 1,198,455 Effective search space: 491366550 Effective search space used: 491366550 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: 132 (55.5 bits)