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= 0028.0259.p (696 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311106|ref|YP_003775198.1| transmembrane NADH dehydrogenas... 1405 0.0 gi|300311634|ref|YP_003775726.1| NADH:ubiquinone oxidoreductase ... 106 7e-24 gi|300311108|ref|YP_003775200.1| NADH-ubiquinone oxidoreductase ... 88 3e-18 gi|300311107|ref|YP_003775199.1| transmembrane NADH dehydrogenas... 74 4e-14 >gi|300311106|ref|YP_003775198.1| transmembrane NADH dehydrogenase I subunit L [Herbaspirillum seropedicae SmR1] Length = 696 Score = 1405 bits (3636), Expect = 0.0, Method: Compositional matrix adjust. Identities = 692/696 (99%), Positives = 696/696 (100%) Query: 1 MAGQLNPHLLLAVPLAPLAGSAIAGLLGTKFFGNVVGRKVSHTATILGVLIAAIISIQTL 60 MAGQLNPHLLLAVPLAPLAGSAIAGLLGTKFFGNVVGRKVSHTATILGVLIAAIIS+QTL Sbjct: 1 MAGQLNPHLLLAVPLAPLAGSAIAGLLGTKFFGNVVGRKVSHTATILGVLIAAIISLQTL 60 Query: 61 LAVLDGATYNGTLYNWMTVAGLKLEIGFMVDSLTAMMMCVVTFVSLMVHIYTIGYMAEDE 120 LAVLDGATYNGTLYNWMTVAGLKLEIGFMVDSLTAMMMCVVTFVSLMVHIYTIGYMAEDE Sbjct: 61 LAVLDGATYNGTLYNWMTVAGLKLEIGFMVDSLTAMMMCVVTFVSLMVHIYTIGYMAEDE 120 Query: 121 GYNRFFSYISLFTFSMLMLVMSNNFLQLFFGWEAVGLVSYLLIGFWYTRPTAIKANMKAF 180 GYNRFFSYISLFTFSMLMLVMSNNFLQLFFGWEAVGLVSYLLIGFWYTRPTAIKANMKAF Sbjct: 121 GYNRFFSYISLFTFSMLMLVMSNNFLQLFFGWEAVGLVSYLLIGFWYTRPTAIKANMKAF 180 Query: 181 LVNRVGDFGFILGIGLLLAYAGSMNYTEVFDKRAELAQLTLPGTDWMLLTVACICLFVGA 240 LVNRVGDFGFILGIGLLLAYAGSMNYTEVFDKRAELAQLTLPGTDWMLLTVACICLFVGA Sbjct: 181 LVNRVGDFGFILGIGLLLAYAGSMNYTEVFDKRAELAQLTLPGTDWMLLTVACICLFVGA 240 Query: 241 MGKSAQFPLHVWLPDSMEGPTPISALIHAATMVTAGIFMVTRMSPLFELSDTALSFILVI 300 MGKSAQFPLHVWLPDSMEGPTPISALIHAATMVTAGIFMVTRMSPLFELSDTALSFILVI Sbjct: 241 MGKSAQFPLHVWLPDSMEGPTPISALIHAATMVTAGIFMVTRMSPLFELSDTALSFILVI 300 Query: 301 GAITALFMGFLGTMQNDIKRVVAYSTLSQLGYMTVALGASAYSVAVFHLMTHAFFKALLF 360 GAITALFMGFLGTMQNDIKRVVAYSTLSQLGYMTVALGASAYSVAVFHLMTHAFFKALLF Sbjct: 301 GAITALFMGFLGTMQNDIKRVVAYSTLSQLGYMTVALGASAYSVAVFHLMTHAFFKALLF 360 Query: 361 LGAGSVIIGMHHDQDMRNMGGLRKYMPITWITSLLGSLALIGTPFFSGFYSKDSIIEAAA 420 LGAGSVIIGMHHDQDMRNMGGLRKYMPITWITSLLGSLALIGTPFFSGFYSKDSIIEAAA Sbjct: 361 LGAGSVIIGMHHDQDMRNMGGLRKYMPITWITSLLGSLALIGTPFFSGFYSKDSIIEAAA 420 Query: 421 ESHLAGSGFAYFAVLASVFVTAFYSFRMYFMVFHGKQRFGQAHGHDDHHAPAAAHGVHDD 480 ESHLAGSGFAYFAVLASVFVTAFYSFRMYFMVFHGK+RFGQAHGHDDHHAPAAAHGVHDD Sbjct: 421 ESHLAGSGFAYFAVLASVFVTAFYSFRMYFMVFHGKERFGQAHGHDDHHAPAAAHGVHDD 480 Query: 481 HAHDAHDDHGHDEHHHGLAPGQKPHESPLVVTLPLILLAIPSVIVGFFAISPMLYGDFFK 540 HAHDAHDDHGHDEHHHGLAPGQKPHESPLVVTLPLILLAIPSVI+GFFAISPMLYGDFFK Sbjct: 481 HAHDAHDDHGHDEHHHGLAPGQKPHESPLVVTLPLILLAIPSVIIGFFAISPMLYGDFFK 540 Query: 541 GVIFFGENHKVMEELAHEYHGPVAMVLHAFTSAPLWLAIAGVVVAYYCYMINPRVPAWFK 600 GVIFFGENHKVMEELAHEYHGPVAMVLHAFTSAPLWLAIAGVVVAYYCYMINPRVPAWFK Sbjct: 541 GVIFFGENHKVMEELAHEYHGPVAMVLHAFTSAPLWLAIAGVVVAYYCYMINPRVPAWFK 600 Query: 601 EKFSIIYTILDNKYYMDKFNEVVFAGGARLLGSGLSTVGDRGIIDGLFVNGSAKVVGWFS 660 EKFSIIYTILDNKYYMDKFNEVVFAGGARLLGSGLSTVGDRG+IDGLFVNGSAKVVGWFS Sbjct: 601 EKFSIIYTILDNKYYMDKFNEVVFAGGARLLGSGLSTVGDRGLIDGLFVNGSAKVVGWFS 660 Query: 661 KFTRLWQSGYIYHYAFVMIIGVLGFLVWFMPFPFAK 696 KFTRLWQSGYIYHYAFVMIIGVLGFLVWFMPFPFAK Sbjct: 661 KFTRLWQSGYIYHYAFVMIIGVLGFLVWFMPFPFAK 696 >gi|300311634|ref|YP_003775726.1| NADH:ubiquinone oxidoreductase subunit L/Multisubunit Na+/H+ antiporter MnhA subunit [Herbaspirillum seropedicae SmR1] Length = 536 Score = 106 bits (264), Expect = 7e-24, Method: Compositional matrix adjust. Identities = 76/257 (29%), Positives = 137/257 (53%), Gaps = 8/257 (3%) Query: 111 YTIGYMAEDEGYNRFFSYISLFTFSMLMLVMSNNFLQLFFGWEAVGLVSYLLIGFWYTRP 170 ++ Y+ + G ++ ++ ++ +L++++++L L W AVGL L+ F+ RP Sbjct: 105 FSARYLQGEGGQRQYAVALAAVLTAVHLLLLADHWLVLIAAWAAVGLALEHLLCFYPERP 164 Query: 171 TAIKANMKAFLVNRVGDFGFILGIGLLLAYAGSMNYTEVFDKRAELAQLTLPGTDWMLLT 230 A A K + +R+ D + L + GS + + ++ A A G L Sbjct: 165 FARLAAYKKRIADRLADLLLGVAALLAWSATGSGSLSALWQHLA--AHGMSAG-----LQ 217 Query: 231 VACICLFVGAMGKSAQFPLHVWLPDSMEGPTPISALIHAATMVTAGIFMVTRMSPLFELS 290 V+ +C+ + + ++A P+H WL ME PTP+SAL+HA +V G F++ R +PL + + Sbjct: 218 VSALCVVLAVILRTALLPVHGWLIQVMEAPTPVSALLHAG-VVNLGGFVLIRFAPLLQQA 276 Query: 291 DTALSFILVIGAITALFMGFLGTMQNDIKRVVAYSTLSQLGYMTVALGASAYSVAVFHLM 350 A S +L++ T L G + + IK +A+ST++Q+G+M + A Y+ A HL+ Sbjct: 277 IPARSVLLLMAVATVLLAGMVMLTRISIKVRLAWSTVAQMGFMLLECAAGLYTFAALHLI 336 Query: 351 THAFFKALLFLGAGSVI 367 H+ +KA FL A SV+ Sbjct: 337 GHSLYKAHAFLSASSVV 353 >gi|300311108|ref|YP_003775200.1| NADH-ubiquinone oxidoreductase subunit N [Herbaspirillum seropedicae SmR1] Length = 502 Score = 87.8 bits (216), Expect = 3e-18, Method: Compositional matrix adjust. Identities = 96/353 (27%), Positives = 166/353 (47%), Gaps = 46/353 (13%) Query: 127 SYISLFTFSML---MLVMSNNFLQLFFGWEAVGLVSYLLIGFWYTRPTAIKANMKAFLVN 183 Y +L F++L +++ N+FL ++ G E + L Y L+ + +A MK F++ Sbjct: 110 EYYALALFALLGQMVMISGNSFLSIYLGLELMSLSLYALVALRRDHAASTEAGMKYFILG 169 Query: 184 RVGDFGFIL-GIGLLL-AYAGSMNYTEVFDKRAELAQLTLPGT-DWMLLTVACICLFVGA 240 + GF+L G+ +L A G++ EVF RA + GT D L + + G Sbjct: 170 ALAS-GFLLYGMSMLYGATGGALELNEVF--RA-----IVSGTVDRTPLVFGIVFVVAGL 221 Query: 241 MGKSAQFPLHVWLPDSMEG-PTPISALIHAA-TMVTAGIFMVTRMSPLFELSDTALSFIL 298 K P H+W+PD +G PTP++ L+ AA + T I + + L+ ++ Sbjct: 222 AFKLGAVPFHMWVPDVYQGSPTPVTLLLGAAPKLATFAITFRLLVEGMLPLAVDWQQMLM 281 Query: 299 VIGAITALFMGFLGTMQNDIKRVVAYSTLSQLGYMTVAL-----------GASAYSVAVF 347 V+ ++ + Q +IKR++AYST+S +G+M + + +AYS ++F Sbjct: 282 VLAVLSIILGNVTAIAQTNIKRMLAYSTISHMGFMLLGMMSGVVDGNLFSAVNAYSSSLF 341 Query: 348 HLMTHAFFKALLFLGAGSVIIGMHHD----QDMRNMGGLRKYMPITWITSLLGSLALIGT 403 + +T+ LG+ VII + + + GL + P ++ +L G Sbjct: 342 YAVTYVITT----LGSFGVIILLSRSGFEADTLDDFKGLNQRSPWFAAVMMIMMFSLAGI 397 Query: 404 PFFSGFYSKDSIIEAAAESHLAGSGFAYFAVLASVF--VTAFYSFR----MYF 450 P GFY+K S+++AA +G + VLA +F + AFY R MYF Sbjct: 398 PPLVGFYAKLSVLQAA-----MATGQIWLPVLAVIFSLIGAFYYIRVVKVMYF 445 >gi|300311107|ref|YP_003775199.1| transmembrane NADH dehydrogenase I subunit M [Herbaspirillum seropedicae SmR1] Length = 496 Score = 73.9 bits (180), Expect = 4e-14, Method: Compositional matrix adjust. Identities = 52/185 (28%), Positives = 98/185 (52%), Gaps = 8/185 (4%) Query: 243 KSAQFPLHVWLPDS-MEGPTPISALIHAATMVTAGIFMVTRMS-PLFELSDTALS-FILV 299 K +P+H WLPD+ ++ PT +++ AA M+ G + R S P+ + ALS F++ Sbjct: 225 KVPMWPVHTWLPDAHVQAPTG-GSIVLAAIMLKLGAYGFLRFSLPILPDASHALSGFMIF 283 Query: 300 IGAITALFMGFLGTMQNDIKRVVAYSTLSQLGYMTVA---LGASAYSVAVFHLMTHAFFK 356 + + +++G + +Q D+K++VAYS+++ +G++T+ A + +++H F Sbjct: 284 LSLVAVIYIGLVALVQQDMKKLVAYSSIAHMGFVTLGFFMFNDMAVQGGIVQMISHGFVS 343 Query: 357 ALLFLGAGSVIIGMHHDQDMRNMGGLRKYMPITWITSLLGSLALIGTPFFSGFYSKDSII 416 +F+ G V+ H +++ GG+ MP +L SLA G P SGF + +I Sbjct: 344 GAMFMCIG-VLYDQMHTREISQYGGVVNKMPRFAFFFILFSLANCGLPATSGFVGEFMVI 402 Query: 417 EAAAE 421 A + Sbjct: 403 LGAVK 407 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 0.329 0.142 0.443 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: 1,912,301 Number of extensions: 74489 Number of successful extensions: 310 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 302 Number of HSP's successfully gapped: 4 Length of query: 696 Length of database: 1,619,870 Length adjustment: 92 Effective length of query: 604 Effective length of database: 1,184,250 Effective search space: 715287000 Effective search space used: 715287000 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 (21.8 bits) S2: 134 (56.2 bits)