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= 0009.0325.p (321 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 ... 561 e-161 gi|300311106|ref|YP_003775198.1| transmembrane NADH dehydrogenas... 73 3e-14 gi|300311107|ref|YP_003775199.1| transmembrane NADH dehydrogenas... 65 6e-12 >gi|300311108|ref|YP_003775200.1| NADH-ubiquinone oxidoreductase subunit N [Herbaspirillum seropedicae SmR1] Length = 502 Score = 561 bits (1445), Expect = e-161, Method: Compositional matrix adjust. Identities = 269/321 (83%), Positives = 303/321 (94%), Gaps = 1/321 (0%) Query: 1 MLYGATG-SLELNDVFRAIVSGTVDRNVLVFGIVFVVAGLAFKLGAVPFHMWVPDVYHGA 59 MLYGATG +LELN+VFRAIVSGTVDR LVFGIVFVVAGLAFKLGAVPFHMWVPDVY G+ Sbjct: 182 MLYGATGGALELNEVFRAIVSGTVDRTPLVFGIVFVVAGLAFKLGAVPFHMWVPDVYQGS 241 Query: 60 PTPMTLLIGGAPKLAAFAMVFRILVEGLLPLAIDWQQMLMVLAVLSIIVGNVTAIAQTNI 119 PTP+TLL+G APKLA FA+ FR+LVEG+LPLA+DWQQMLMVLAVLSII+GNVTAIAQTNI Sbjct: 242 PTPVTLLLGAAPKLATFAITFRLLVEGMLPLAVDWQQMLMVLAVLSIILGNVTAIAQTNI 301 Query: 120 KRMLAYSTISHMGFMLLGMMSGVVDGNLFQAVNAYSSSLFYAITYVLTTLGTFGVILLMA 179 KRMLAYSTISHMGFMLLGMMSGVVDGNLF AVNAYSSSLFYA+TYV+TTLG+FGVI+L++ Sbjct: 302 KRMLAYSTISHMGFMLLGMMSGVVDGNLFSAVNAYSSSLFYAVTYVITTLGSFGVIILLS 361 Query: 180 RSGFEADTLDDFKGLNQRSPWFAGIMLVLMFSLAGIPPMVGFYAKLSVLQAVLGTGQIWL 239 RSGFEADTLDDFKGLNQRSPWFA +M+++MFSLAGIPP+VGFYAKLSVLQA + TGQIWL Sbjct: 362 RSGFEADTLDDFKGLNQRSPWFAAVMMIMMFSLAGIPPLVGFYAKLSVLQAAMATGQIWL 421 Query: 240 AVLAVVFSLVGAFYYLRVIKNMYFDDPADSGKITASFDVRIALSLNGIAALGLGLWPGHL 299 VLAV+FSL+GAFYY+RV+K MYFD+PAD+ KI A+ ++R+ LSLNGIAAL +GLWPGHL Sbjct: 422 PVLAVIFSLIGAFYYIRVVKVMYFDEPADNSKIVATPEMRVVLSLNGIAALAIGLWPGHL 481 Query: 300 MDACTNAIVTTLATFLSKVIA 320 MDACTNAIVTTLATFLSKV+A Sbjct: 482 MDACTNAIVTTLATFLSKVVA 502 >gi|300311106|ref|YP_003775198.1| transmembrane NADH dehydrogenase I subunit L [Herbaspirillum seropedicae SmR1] Length = 696 Score = 73.2 bits (178), Expect = 3e-14, Method: Compositional matrix adjust. Identities = 84/282 (29%), Positives = 132/282 (46%), Gaps = 46/282 (16%) Query: 1 MLYGATGSLELNDVF--RA-----IVSGTVDRNVLVFGIVFVVAGLAFKLGAVPFHMWVP 53 +L GS+ +VF RA + GT D +L + + G K P H+W+P Sbjct: 196 LLLAYAGSMNYTEVFDKRAELAQLTLPGT-DWMLLTVACICLFVGAMGKSAQFPLHVWLP 254 Query: 54 DVYHGAPTPMTLLIGGAPKL-AAFAMVFRILVEGLLPLAIDWQQMLMVLAVLSIIVGNVT 112 D G PTP++ LI A + A MV R+ L L+ ++V+ ++ + Sbjct: 255 DSMEG-PTPISALIHAATMVTAGIFMVTRM--SPLFELSDTALSFILVIGAITALFMGFL 311 Query: 113 AIAQTNIKRMLAYSTISHMGFMLLGMMSGVVDGNLFQAVNAYSSSLFYAITY----VLTT 168 Q +IKR++AYST+S +G+M + + +AYS ++F+ +T+ L Sbjct: 312 GTMQNDIKRVVAYSTLSQLGYMTVAL-----------GASAYSVAVFHLMTHAFFKALLF 360 Query: 169 LGTFGVILLMARSGFEADTLDDFKGLNQRSP--WFAGIMLVLMFSLAGIPPMVGFYAKLS 226 LG VI+ M + + GL + P W ++ L +L G P GFY+K S Sbjct: 361 LGAGSVIIGMHHD----QDMRNMGGLRKYMPITWITSLLGSL--ALIGTPFFSGFYSKDS 414 Query: 227 VLQA-----VLGTGQIWLAVLAVVFSLVGAFYYLRVIKNMYF 263 +++A + G+G + AVLA VF V AFY R MYF Sbjct: 415 IIEAAAESHLAGSGFAYFAVLASVF--VTAFYSFR----MYF 450 >gi|300311107|ref|YP_003775199.1| transmembrane NADH dehydrogenase I subunit M [Herbaspirillum seropedicae SmR1] Length = 496 Score = 65.5 bits (158), Expect = 6e-12, Method: Compositional matrix adjust. Identities = 73/284 (25%), Positives = 131/284 (46%), Gaps = 45/284 (15%) Query: 47 PFHMWVPDVYHGAPTPMTLLIGGAPKLAAFAMVFRILVEGLL----PLAIDWQQML---- 98 P H W+PD + APT GG+ LAA ++ ++ G L P+ D L Sbjct: 230 PVHTWLPDAHVQAPT------GGSIVLAA--IMLKLGAYGFLRFSLPILPDASHALSGFM 281 Query: 99 MVLAVLSIIVGNVTAIAQTNIKRMLAYSTISHMGFMLLGMM---SGVVDGNLFQAVNA-- 153 + L+++++I + A+ Q ++K+++AYS+I+HMGF+ LG V G + Q ++ Sbjct: 282 IFLSLVAVIYIGLVALVQQDMKKLVAYSSIAHMGFVTLGFFMFNDMAVQGGIVQMISHGF 341 Query: 154 YSSSLFYAITYVLTTLGTFGVILLMARSGFEADTLDDFKGLNQRSPWFAGIMLVLMFSLA 213 S ++F I + + T + + G+ + P FA ++FSLA Sbjct: 342 VSGAMFMCIGVLYDQMHT--------------REISQYGGVVNKMPRFA--FFFILFSLA 385 Query: 214 --GIPPMVGFYAKLSVLQAVLGTGQIWLAVLAVVFSLVGAFYYLRVIKNMYFDDPADSGK 271 G+P GF + V+ + W+ +LA ++GA Y L + K + F + Sbjct: 386 NCGLPATSGFVGEFMVILGAVKF-NFWIGLLAATALILGAAYSLWLAKRVIFGAVTNH-H 443 Query: 272 ITASFDVR----IALSLNGIAALGLGLWPGHLMDACTNAIVTTL 311 + D+ + 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 0.329 0.142 0.423 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: 994,813 Number of extensions: 42873 Number of successful extensions: 212 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 207 Number of HSP's successfully gapped: 4 Length of query: 321 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 236 Effective length of database: 1,217,395 Effective search space: 287305220 Effective search space used: 287305220 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: 130 (54.7 bits)