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= 0017.0120.p (485 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312655|ref|YP_003776747.1| C4-dicarboxylate transport sens... 343 2e-95 gi|300312654|ref|YP_003776746.1| C4-dicarboxylate transport resp... 187 1e-48 gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein... 124 2e-29 gi|300312042|ref|YP_003776134.1| response regulatory protein [He... 121 1e-28 gi|300310282|ref|YP_003774374.1| sigma-54 dependent transcriptio... 119 7e-28 >gi|300312655|ref|YP_003776747.1| C4-dicarboxylate transport sensor kinase transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 600 Score = 343 bits (879), Expect = 2e-95, Method: Compositional matrix adjust. Identities = 176/251 (70%), Positives = 205/251 (81%), Gaps = 3/251 (1%) Query: 12 YQRRRRLQERLESRDALRRAAQELDATIAVRTQELRVANQALEGKYVTLQQTESLLRSTQ 71 YQ RRRL+ER+ SRDALRRAA EL+ IA RT +L ANQALE +Y LQQTESLLR+TQ Sbjct: 308 YQHRRRLEERMASRDALRRAAAELEQRIAERTGQLTAANQALEARYEKLQQTESLLRTTQ 367 Query: 72 NELVQAGKLAMLGQMAAGVTHELNQPLAAIRAFADNAVQFMRRGQLPQVEENLEHISGAS 131 NELVQAGKLAMLGQMAAGVTHELNQPL AIRAFADNAV+F+ RGQ Q ENLE+IS AS Sbjct: 368 NELVQAGKLAMLGQMAAGVTHELNQPLTAIRAFADNAVKFLARGQSAQAVENLEYISSAS 427 Query: 132 AHMGKIIAQLKGFARKSGDAIAVVDVAQTVEAAVLLLRNEFRQQAVSIEIDVRSPVQVMG 191 A MGKIIAQLKGFARKSG+A+A VD++Q +EA+ LLL +E ++ +I ID+R+ V G Sbjct: 428 ATMGKIIAQLKGFARKSGEAVACVDLSQAIEASSLLLASECQKLGATISIDIRAAACVTG 487 Query: 192 DVVRTEQVLINLLRNAIDAVETVEYVADKRVTVIVEHEAGEAVIRIRDSGPGIPDEVAPH 251 DVVRTEQVL+NLLRNA+DAVE E+ KR+ V++E G A++RIRDSG GI DEVAPH Sbjct: 488 DVVRTEQVLVNLLRNALDAVEEAEH---KRIAVVLEVAGGYALVRIRDSGGGIADEVAPH 544 Query: 252 LFEPFFTTKPS 262 LFEPFFTTK S Sbjct: 545 LFEPFFTTKSS 555 >gi|300312654|ref|YP_003776746.1| C4-dicarboxylate transport response regulator transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 445 Score = 187 bits (475), Expect = 1e-48, Method: Compositional matrix adjust. Identities = 105/155 (67%), Positives = 123/155 (79%), Gaps = 10/155 (6%) Query: 338 ADADLPVIVVTGHG-DVMAD--HGGAG--GALVDVDRHALAQ-LQRSQIXG----AFTGA 387 AD D+ + TG G +V+A H +G G V ++ AL + + S+I G AFTGA Sbjct: 168 ADVDVLINGQTGTGKEVVARQLHAASGRKGPFVALNCGALPETVFESEIFGHEPGAFTGA 227 Query: 388 QKRRIGKLEYANGGTLFLDEIESMPMALQVKLLRVLQERRLERLGGNESIVIDCRVIAAS 447 QKRRIGKLEYANGGTLFLDEIESMP+ALQVKLLRVLQERRLERLGGNES+ IDCRV+AAS Sbjct: 228 QKRRIGKLEYANGGTLFLDEIESMPLALQVKLLRVLQERRLERLGGNESVAIDCRVVAAS 287 Query: 448 KADLLQLSAQGLFREDLYYRIGVVSIDLPRLRERR 482 KADLL+L+A+G FREDLYYRIGVV+IDLP L +RR Sbjct: 288 KADLLKLAAEGQFREDLYYRIGVVAIDLPALNQRR 322 Score = 124 bits (311), Expect = 2e-29, Method: Compositional matrix adjust. Identities = 64/94 (68%), Positives = 73/94 (77%), Gaps = 5/94 (5%) Query: 260 KPSGXPNAPNALAILIEDEQSVRKATTQTLELGGFSVQACADAEQALPLLHAGFAGIVVT 319 KP G A A+LIEDEQ+VR+AT Q LELGGF+V AC AE+ALPL+ FAG+VV+ Sbjct: 3 KPGGA-----ASALLIEDEQTVRRATAQALELGGFAVTACGSAEEALPLITRDFAGVVVS 57 Query: 320 DVRLPGRSGLEVLAHAVAADADLPVIVVTGHGDV 353 DVRLPG SGL+VLA VA D DLPVIVVTGHGDV Sbjct: 58 DVRLPGLSGLDVLARVVAIDHDLPVIVVTGHGDV 91 >gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein [Herbaspirillum seropedicae SmR1] Length = 542 Score = 124 bits (310), Expect = 2e-29, Method: Compositional matrix adjust. Identities = 68/126 (53%), Positives = 86/126 (68%), Gaps = 5/126 (3%) Query: 362 GALVDVDRHALAQ-LQRSQI----XGAFTGAQKRRIGKLEYANGGTLFLDEIESMPMALQ 416 G + V+ AL++ L S++ GAFTGAQ R G+ E A+GGTLFLDEI + A Q Sbjct: 253 GPFIKVNCAALSETLLESELFGHEKGAFTGAQGERKGRFELAHGGTLFLDEIGEISPAFQ 312 Query: 417 VKLLRVLQERRLERLGGNESIVIDCRVIAASKADLLQLSAQGLFREDLYYRIGVVSIDLP 476 KLLRVLQER ER+GG+ SI +D R++ A+ DL + A+G FR DLYYRI VVSI +P Sbjct: 313 AKLLRVLQEREFERVGGSRSIKVDVRLVTATNRDLEKAVAKGEFRADLYYRINVVSIFIP 372 Query: 477 RLRERR 482 LRERR Sbjct: 373 PLRERR 378 >gi|300312042|ref|YP_003776134.1| response regulatory protein [Herbaspirillum seropedicae SmR1] Length = 450 Score = 121 bits (304), Expect = 1e-28, Method: Compositional matrix adjust. Identities = 58/100 (58%), Positives = 75/100 (75%) Query: 382 GAFTGAQKRRIGKLEYANGGTLFLDEIESMPMALQVKLLRVLQERRLERLGGNESIVIDC 441 GAFTGA K+ IGK+E A+GGT FLDE+ +PM LQ KLLR LQER +ER+GG+ I +D Sbjct: 223 GAFTGAAKQTIGKVELAHGGTFFLDEVGDLPMPLQAKLLRFLQERVIERVGGHTEIPVDV 282 Query: 442 RVIAASKADLLQLSAQGLFREDLYYRIGVVSIDLPRLRER 481 RVI A+ +L +L+A G FREDLYYR+ + I +P L+ER Sbjct: 283 RVICATHQNLKELTASGGFREDLYYRLCEIIIKIPALKER 322 >gi|300310282|ref|YP_003774374.1| sigma-54 dependent transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 380 Score = 119 bits (297), Expect = 7e-28, Method: Compositional matrix adjust. Identities = 61/100 (61%), Positives = 72/100 (72%) Query: 382 GAFTGAQKRRIGKLEYANGGTLFLDEIESMPMALQVKLLRVLQERRLERLGGNESIVIDC 441 GAFTGA + G E ANGGTLFLDEI +P+A+QVKLLRVLQER + RLG SI ID Sbjct: 124 GAFTGAITHKPGWFEAANGGTLFLDEIGDLPLAIQVKLLRVLQEREVVRLGSRRSIPIDV 183 Query: 442 RVIAASKADLLQLSAQGLFREDLYYRIGVVSIDLPRLRER 481 R+IAA+ L A G FR+DLYYR+ VV + +PRLRER Sbjct: 184 RIIAATNVRLQDAVAAGHFRQDLYYRLQVVQLAIPRLRER 223 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 0.320 0.135 0.369 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: 1,297,180 Number of extensions: 50667 Number of successful extensions: 378 Number of sequences better than 1.0e-08: 28 Number of HSP's gapped: 391 Number of HSP's successfully gapped: 31 Length of query: 485 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 396 Effective length of database: 1,198,455 Effective search space: 474588180 Effective search space used: 474588180 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 132 (55.5 bits)