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= 0012.0017.p (518 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313806|ref|YP_003777898.1| PAS/PAC HisKA ATPase_c domains ... 722 0.0 gi|300310177|ref|YP_003774269.1| C4-dicarboxylate transport sens... 160 2e-40 gi|300310677|ref|YP_003774769.1| two component transmembrane sen... 136 4e-33 gi|300313027|ref|YP_003777119.1| two component transmembrane sen... 110 3e-25 gi|300312655|ref|YP_003776747.1| C4-dicarboxylate transport sens... 106 5e-24 >gi|300313806|ref|YP_003777898.1| PAS/PAC HisKA ATPase_c domains containing sensor signal transduction histidine kinase [Herbaspirillum seropedicae SmR1] Length = 524 Score = 722 bits (1864), Expect = 0.0, Method: Compositional matrix adjust. Identities = 378/519 (72%), Positives = 425/519 (81%), Gaps = 2/519 (0%) Query: 1 LPSDPCPADDDA-LLHALRELSALLDPVLLKPALTRALCQLAGARRCLLVRHEAGLTLIE 59 LP+ P DD LL ALRELSALLDP+ LKPA+ RA C + GAR CLLVR LIE Sbjct: 7 LPAGPADPDDSTRLLQALRELSALLDPLRLKPAIARAACAVTGARHCLLVRTTPEGLLIE 66 Query: 60 AEARRDGMAVCNNKDHCIAGPDDLHTATLTLRLSHRGQARGELLLYYDAPPAAAMTRCAH 119 AEA ++ + + + D+L L L L H QA G L L ++A A Sbjct: 67 AEALCQDQSILDARRNRAVAEDELQ-GLLALPLMHGQQALGTLYLQWEAALPERTRALAA 125 Query: 120 HLAAHAAVALANAADHAQALLEKEQLLCAERELRTSQELLKQGERFNHAGSMRYLVREDL 179 A +AAVALANA HA L E EQL CAE+ELRTSQELLKQGERFNH GSMRYLVREDL Sbjct: 126 QFADYAAVALANALAHAHLLQENEQLTCAEKELRTSQELLKQGERFNHTGSMRYLVREDL 185 Query: 180 MFCSDELCRIYGLPPGRNCITYDEFASIMHPDDRQEVIETVNAAVAMGGTIRVEHRICRQ 239 M+CSDELCRIYGL PGRNCITY+EFA+IMHPDDRQEV+ETVNAAVAMGGTIRVEHRICRQ Sbjct: 186 MYCSDELCRIYGLAPGRNCITYEEFAAIMHPDDRQEVVETVNAAVAMGGTIRVEHRICRQ 245 Query: 240 DTGEVRYLSGIGKPVWVDGTFTEYVGTATDITVRRQAEYAIRAAQVDMERVSRANTVGQL 299 DTGEVRYLSGIGKP+W DGTFTEYVGTATDITVRRQ EYAIRAAQ+DMERVSRANTVGQL Sbjct: 246 DTGEVRYLSGIGKPIWRDGTFTEYVGTATDITVRRQNEYAIRAAQIDMERVSRANTVGQL 305 Query: 300 TASIAHEINQPLMSIVSNAGASLRWLNRPVPELEHARAGLRDIISEGQRAGGIISSLQNL 359 TASIAHEINQPLMSIV+NAGASLRWL+RPVP+LEHAR GLRDII+EGQRAGGIIS L++L Sbjct: 306 TASIAHEINQPLMSIVANAGASLRWLDRPVPDLEHARTGLRDIIAEGQRAGGIISGLRDL 365 Query: 360 TRNRAPQFERLNLAALIRHTLTLSRSELEQREVHLSLSLPPAEVHVLGDTVQLQQVLLNL 419 TRN AP ER+NL A+IRH LTLSRSELE+REV L LSL PA+ VLGD VQLQQV+LNL Sbjct: 366 TRNAAPVCERVNLHAVIRHILTLSRSELERREVSLLLSLTPADAFVLGDQVQLQQVMLNL 425 Query: 420 VVNAIDAMAAVPENARTLNIGVSCCNEQRVKVEIQDSGEGIAADAMPHIFDAFYTTKENG 479 VVNAI+AM+++PE+AR L+I S C+EQR++V++QDSGEGIA +AM +FDAFYTTK++G Sbjct: 426 VVNAIEAMSSMPEHARVLSITASSCDEQRIEVKVQDSGEGIAPEAMRRVFDAFYTTKDSG 485 Query: 480 MGMGLAICRSIIETHRGRLRVEAAQPQGTVFSFDLPRVP 518 MGMGLAICRSIIE HRGRLRV AAQP G +FSFDLPRVP Sbjct: 486 MGMGLAICRSIIENHRGRLRVAAAQPHGALFSFDLPRVP 524 >gi|300310177|ref|YP_003774269.1| C4-dicarboxylate transport sensor histidine kinase [Herbaspirillum seropedicae SmR1] Length = 674 Score = 160 bits (406), Expect = 2e-40, Method: Compositional matrix adjust. Identities = 104/310 (33%), Positives = 158/310 (50%), Gaps = 4/310 (1%) Query: 210 PDDRQEVIETVNAAVAMGGTIRVEHRICRQDTGEVRYLSGIGKPVWVDGTFTEYVGTATD 269 P+ E E + +A T + E R+D L V DG T ++G+ D Sbjct: 359 PEAMDEYQERFSNVLAGRATPQFETIFQRRDGERFPVLIFESPLVDQDGKQTGWMGSILD 418 Query: 270 ITVRRQAEYAIRAAQVDMERVSRANTVGQLTASIAHEINQPLMSIVSNAGASLRWLNRPV 329 I+ R++AE R + ++ +R ++G++ +++AHE+NQPL +I S +L + + Sbjct: 419 ISERKRAEDLNRTQEEKLQASARLASMGEIASTLAHELNQPLAAISSYTTGALNLMQQGQ 478 Query: 330 PELEHARAGLRDIISEGQRAGGIISSLQNLTRNRAPQFERLNLAALIRHTLTLSRSELEQ 389 + + + L I ++ QRAG +I S+ + R P +R+ + LI + L + +Q Sbjct: 479 ADPKALQPALEKIHAQAQRAGHVIRSVHQFVKKREPARQRVQMRQLIDNVAPLIELQAQQ 538 Query: 390 REVHLSLSLPPAEVHVLGDTVQLQQVLLNLVVNAIDAMAAVPENARTLNIGVSCC-NE-- 446 V L L +P + VLGD + L+QV+LNL N I AMAAVP R L + NE Sbjct: 539 FFVVLQLQVPRSLPPVLGDQILLEQVILNLTRNGIQAMAAVPSARRILRVAAEVTRNEDG 598 Query: 447 -QRVKVEIQDSGEGIAADAMPHIFDAFYTTKENGMGMGLAICRSIIETHRGRLRVEAAQP 505 + V V + D G GI D +F F++TK GMGMGL ICR+ IE H G L Sbjct: 599 AESVTVSVTDQGHGIPDDVAARLFSPFFSTKAEGMGMGLNICRTTIEFHGGTLTYTDNPA 658 Query: 506 QGTVFSFDLP 515 GT+F F LP Sbjct: 659 GGTIFRFSLP 668 >gi|300310677|ref|YP_003774769.1| two component transmembrane sensor histidine kinase [Herbaspirillum seropedicae SmR1] Length = 508 Score = 136 bits (343), Expect = 4e-33, Method: Compositional matrix adjust. Identities = 104/344 (30%), Positives = 176/344 (51%), Gaps = 15/344 (4%) Query: 181 FCSDELCRIYGLPPGRNCITYDEFASIMHPDDRQEVIETVNAAVAMGGTIRVEHRICRQD 240 + SD ++ G+ PG+N F PD ++E+ E + A+ + + +RI R+D Sbjct: 169 YLSDAGRKLLGVRPGQN--PPKNFVEQCLPDSQEELQELLTLALPDAISFPLRYRIARKD 226 Query: 241 TGEVRYLSGIGKPVWVDGTFTEYVGTATDITVRRQAEYAIRAAQVDMERVSRANTVGQLT 300 G VR+ + + + ++ ++ DIT + +AE A R Q +E ++R N +G++ Sbjct: 227 -GLVRWHHAVCRYIEIENDLKGHLLHFHDITDQVEAEEARRRDQAALEYLARHNAMGEMA 285 Query: 301 ASIAHEINQPLMSIVSNAGASLRWLNRPVPELEHARAGLRDIISEGQR---AGGIISSLQ 357 +IAHE++QPL +I + S+ LN E A + + S G++ A II S+ Sbjct: 286 TAIAHELSQPLAAIRNFLEGSVLRLNHSEALREQAGQIIWGLESAGRQVDHAAAIIKSV- 344 Query: 358 NLTRNRAPQFERLNLAALIRHTLTLSRSELEQR----EVHLSLSLPPAEVHVLGDTVQLQ 413 R + E+ + L R +E R V L + + V + V + Sbjct: 345 ---REYVVKLEQSEGLIDLNEVLAEVRWFIEMRAAEGRVQLEVQASEEALVVSCEKVLIG 401 Query: 414 QVLLNLVVNAIDAMAAVPENARTLNIGVSCCNEQRVKVEIQDSGEGIAADAMPHIFDAFY 473 QV+LNL NAI+ M+ PEN R + I ++ ++Q + + + D G GI A +FD F+ Sbjct: 402 QVILNLAFNAIEEMSHFPENQRRVCISLARKDQQAL-LTVADEGRGIDAGHRERLFDGFF 460 Query: 474 TTKENGMGMGLAICRSIIETHRGRLRVEAAQPQGTVFSFDLPRV 517 ++K +G G+GLA+C++II HRG + + AQ +GT F F LP V Sbjct: 461 SSKVSGNGIGLALCKNIIARHRGDIWAQPAQVRGTRFCFTLPLV 504 >gi|300313027|ref|YP_003777119.1| two component transmembrane sensor histidine kinase [Herbaspirillum seropedicae SmR1] Length = 454 Score = 110 bits (275), Expect = 3e-25, Method: Compositional matrix adjust. Identities = 109/407 (26%), Positives = 182/407 (44%), Gaps = 93/407 (22%) Query: 179 LMFCSDELCRIYGLPPGRNCITYDEFASIMHPDDRQEVIETVNAAVAMGGTIRVEHRICR 238 L F S+ R+ G P + + + +HPDD ++ +++AM + VE Sbjct: 57 LTFVSENASRVLGYEPCEMLDDPNFWFNHIHPDDTAQIF----SSLAM---LFVED---- 105 Query: 239 QDTGEVRYLSGIGKPVWV----------DGTFTEYVGTATDITVR--------RQAEYA- 279 Q E R+ + G +W+ DGT E +G TDIT R RQAE Sbjct: 106 QKIYEYRFRTSNGSYLWMHDTLRLIRDPDGTPQEVIGLMTDITGRKEMEDTLQRQAEEQR 165 Query: 280 -----IRAAQVDMERVSRANTVGQLTASIAHEINQPLMSIVSN----------------- 317 ++ AQ + + + ++GQL A +AHEIN P+ + +N Sbjct: 166 KLIEQLKMAQAQLMQSEKLASIGQLAAGVAHEINNPIGFVSANLNTLGNYVATLLEGIQL 225 Query: 318 ----------------------AGASLRWLNRPVPEL-EHARAGLRDIISEGQRAGGIIS 354 A A L +L+ V EL + GL QR I+ Sbjct: 226 HQCLQGGALPAAMAQEQLRSFEARADLAFLSEDVTELLAESNEGL-------QRVRNIVQ 278 Query: 355 SLQNLTRNRAPQFERLNLAALIRHTLTLSRSELEQREVHLSLSLPPAEVHVLGDTV-QLQ 413 SL++ +R ++ +L + TL ++ +EL+ + +S+ E+ ++ +L Sbjct: 279 SLKDFSRIGESNWQMTDLHRGLDSTLNIANNELKYK---VSIVKQYGELPLVKCLASELN 335 Query: 414 QVLLNLVVNAIDAMAAVPENARTLNIGVSCCNEQRVKVEIQDSGEGIAADAMPHIFDAFY 473 QV +NL+VNA A++ T+ I + + +V V I D+G GIA + + IF+ F+ Sbjct: 336 QVFMNLLVNAAQAIS----ERGTVTICTARAGD-KVSVSISDTGHGIAPENLNRIFEPFF 390 Query: 474 TTKE--NGMGMGLAICRSIIETHRGRLRVEAAQPQGTVFSFDLPRVP 518 TTK +G G+GL++ I++ H G +RV +A GT F+ +LP P Sbjct: 391 TTKPVGSGTGLGLSLSYGIVKKHGGDIRVSSAPGCGTTFTIELPIDP 437 >gi|300312655|ref|YP_003776747.1| C4-dicarboxylate transport sensor kinase transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 600 Score = 106 bits (264), Expect = 5e-24, Method: Compositional matrix adjust. Identities = 79/245 (32%), Positives = 125/245 (51%), Gaps = 10/245 (4%) Query: 274 RQAEYAIRAAQVDMERVSRANTVGQLTASIAHEINQPLMSIVSNAGASLRWLNRPVPELE 333 +Q E +R Q ++ + + +GQ+ A + HE+NQPL +I + A ++++L R + Sbjct: 357 QQTESLLRTTQNELVQAGKLAMLGQMAAGVTHELNQPLTAIRAFADNAVKFLARG--QSA 414 Query: 334 HARAGLRDIISEGQRAGGIISSLQNLTRNRAPQFERLNLAALIRHTLTLSRSELEQREVH 393 A L I S G II+ L+ R ++L+ I + L SE ++ Sbjct: 415 QAVENLEYISSASATMGKIIAQLKGFARKSGEAVACVDLSQAIEASSLLLASECQKLGAT 474 Query: 394 LSLSLPPAEVHVLGDTVQLQQVLLNLVVNAIDAMAAVPENARTLNIGVSC-CNEQRVKVE 452 +S+ + A V GD V+ +QVL+NL+ NA+DA+ E A I V V Sbjct: 475 ISIDIRAAAC-VTGDVVRTEQVLVNLLRNALDAV----EEAEHKRIAVVLEVAGGYALVR 529 Query: 453 IQDSGEGIAADAMPHIFDAFYTTKEN--GMGMGLAICRSIIETHRGRLRVEAAQPQGTVF 510 I+DSG GIA + PH+F+ F+TTK + G+G+GLAI SI++ G+L + G F Sbjct: 530 IRDSGGGIADEVAPHLFEPFFTTKSSSKGLGLGLAISSSIVQAMNGQLSAHNHEEGGAEF 589 Query: 511 SFDLP 515 LP Sbjct: 590 VVRLP 594 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 0.321 0.134 0.394 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: 1,428,479 Number of extensions: 55593 Number of successful extensions: 306 Number of sequences better than 1.0e-08: 28 Number of HSP's gapped: 292 Number of HSP's successfully gapped: 28 Length of query: 518 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 429 Effective length of database: 1,198,455 Effective search space: 514137195 Effective search space used: 514137195 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 (21.9 bits) S2: 133 (55.8 bits)