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= 0001.1764.p (680 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311223|ref|YP_003775315.1| sigma-54 dependent transcriptio... 1156 0.0 gi|300313101|ref|YP_003777193.1| sigma54-dependent transcription... 253 5e-68 gi|300312042|ref|YP_003776134.1| response regulatory protein [He... 216 6e-57 gi|300313916|ref|YP_003778008.1| two component response regulato... 205 1e-53 gi|300312421|ref|YP_003776513.1| propionate catabolism operon re... 199 7e-52 >gi|300311223|ref|YP_003775315.1| sigma-54 dependent transcription activator protein [Herbaspirillum seropedicae SmR1] Length = 675 Score = 1156 bits (2991), Expect = 0.0, Method: Compositional matrix adjust. Identities = 587/680 (86%), Positives = 607/680 (89%), Gaps = 5/680 (0%) Query: 1 MQYQANRPGAGALLGAAPLVQAATDGVLDLQAIERSHQRSSSYGITRGQQPDLPVLSRAD 60 MQYQANRP AGALLG +PLVQA+TDGV DLQAIERSHQRSSSYGI RGQ+PDL LSRAD Sbjct: 1 MQYQANRPSAGALLGTSPLVQASTDGVPDLQAIERSHQRSSSYGIMRGQRPDLDSLSRAD 60 Query: 61 LAQALEANQTLSGHARPVMETLYDQIRNTHSMVILSDAEGTIIHTLGDSDFLAKADRVAL 120 LAQ LEANQTLSGHARPVMETLYDQIRNTHSMVILSDAEGTI+HTLGDSDFLAKADRVAL Sbjct: 61 LAQTLEANQTLSGHARPVMETLYDQIRNTHSMVILSDAEGTILHTLGDSDFLAKADRVAL 120 Query: 121 GSGARWSEQLRGTNAIGTALYEQKPTTVHAQQHYLDANRFLTCSAAPIFDHRGQVLGVLD 180 G G RWSEQLRGTNAIGTAL+EQKPTTVHAQQHYLDANRFLTCSAAPIFDHRGQVLGVLD Sbjct: 121 GPGGRWSEQLRGTNAIGTALFEQKPTTVHAQQHYLDANRFLTCSAAPIFDHRGQVLGVLD 180 Query: 181 VSGECGSFHKHTMALVRMSAQMIENHLLAGSFPDGITLHFHSRAEFVGTLVEGIVSFTPG 240 VSGECGSFHKHTMALVRMSAQMIENHLLAGSFPD ITLHFHSRAEFVGTLVEGIVSFTPG Sbjct: 181 VSGECGSFHKHTMALVRMSAQMIENHLLAGSFPDCITLHFHSRAEFVGTLVEGIVSFTPG 240 Query: 241 GRFLAANRSAQFQLGLTLSALQSHTFASLFGVPLSLLFEHHRKATPGLLELCLHNGIRIH 300 GRFLAANRSAQFQLGLTL+ALQSHTFASLFGVPLSLLFEHHRKA PGLLELCLHNGIRIH Sbjct: 241 GRFLAANRSAQFQLGLTLAALQSHTFASLFGVPLSLLFEHHRKAAPGLLELCLHNGIRIH 300 Query: 301 GRAELRLRNQHFQNAREAAIDTPELMHPMPSAPATPSAPLAPQRRVHPGQVRPDLQALDT 360 GRAELRLR+QHFQ AREA ID P L+ P TP QR H Q RPDLQALDT Sbjct: 301 GRAELRLRDQHFQAAREAVIDAPGLL-PPAPNTTTPPPSPPQQRARH--QRRPDLQALDT 357 Query: 361 GDARMSAIIGKLRKVIDRDIAVLITGETGTGKEWLAQAIHRESARFRATQTRGGAAPFVA 420 GD RMSAII KLR+VIDRDI +LITGETGTGKEWLAQAIH +SARF A Q R GAAPFVA Sbjct: 358 GDVRMSAIIAKLRRVIDRDIPILITGETGTGKEWLAQAIHGDSARFGARQNRAGAAPFVA 417 Query: 421 VNCSAIPENLIEAELFGYEDGAFTGARRKGAIGKIAQAQGGTLFLDEIGDMPLALQGRLL 480 VNCSAIPENLIEAELFGYEDGAFTGARRKGA+GKIAQA GGTLFLDEIGDMPLALQGRLL Sbjct: 418 VNCSAIPENLIEAELFGYEDGAFTGARRKGALGKIAQAHGGTLFLDEIGDMPLALQGRLL 477 Query: 481 RVLQERTVTPLGSQRVIPVEFALVCATNQPLREMAARHSFREDLYYRINGLQVKLPALRE 540 RVLQER VTPLGSQRVIPV+FALVCATNQPLREMAARH+FREDLYYRINGLQVKLPALR+ Sbjct: 478 RVLQERAVTPLGSQRVIPVDFALVCATNQPLREMAARHAFREDLYYRINGLQVKLPALRD 537 Query: 541 RSDLAQLIERILIAEGGALAPRFDEQAQALLQASRWPGNLRQLSNLIRTALAMAEGEAWI 600 RSDL QLIERIL EGG APRFD QAQALL AS WPGNLRQL+NL+RT+LAMAEGE I Sbjct: 538 RSDLPQLIERILEDEGGPHAPRFDAQAQALLLASHWPGNLRQLANLVRTSLAMAEGEEAI 597 Query: 601 GVQHLPDDFLEEAGPLQAGCGMAATTVCEEMRSDCLSIHDNEWATIERALRTHAGNVSAA 660 G HLPDDFLEEAG G +RSDCLSI DNEWA IERALRTHAGNVSAA Sbjct: 598 GPHHLPDDFLEEAGA--PGALHDGMHTMHAVRSDCLSIQDNEWAAIERALRTHAGNVSAA 655 Query: 661 AKALGVSRNTLYRRFKSRGH 680 AKALGVSRNT+YRR KSRGH Sbjct: 656 AKALGVSRNTIYRRLKSRGH 675 >gi|300313101|ref|YP_003777193.1| sigma54-dependent transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 437 Score = 253 bits (645), Expect = 5e-68, Method: Compositional matrix adjust. Identities = 154/337 (45%), Positives = 209/337 (62%), Gaps = 24/337 (7%) Query: 354 DLQALDTGDARMSAIIGKLRKVIDRDIAVLITGETGTGKEWLAQAIHRESARFRATQTRG 413 D+ L GDA M +I + +++IDR I VLI GETGTGKE+L++A+H SAR RA+ Sbjct: 90 DIDQLAAGDACMHDLIERGKRLIDRGIPVLILGETGTGKEYLSRALHDYSARRRAS---- 145 Query: 414 GAAPFVAVNCSAIPENLIEAELFGYEDGAFTGARRKGAIGKIAQAQGGTLFLDEIGDMPL 473 ++AVNC++IPE+L E+ELFGY GAF+GA G GK+ QA GGTLFLDEIGDMPL Sbjct: 146 ----WIAVNCASIPESLAESELFGYCKGAFSGALPGGMKGKVQQADGGTLFLDEIGDMPL 201 Query: 474 ALQGRLLRVLQERTVTPLGSQRVIPVEFALVCATNQPLREMAARHSFREDLYYRINGLQV 533 ALQ RLLRVL ER V PLG++ +PV+ L+CAT+Q L+ + A FREDLYYR+ G + Sbjct: 202 ALQTRLLRVLSEREVIPLGARHPVPVDVQLICATHQDLKTLIAEGRFREDLYYRVAGGVL 261 Query: 534 KLPALRERSDLAQLIERILIAEGGALAPRFDEQAQAL--LQASRWPGNLRQLSNLIRTAL 591 +LPALRERSD +L+ +++ E G A +A AL L A WPGNLRQ+ +IR + Sbjct: 262 RLPALRERSDRRRLVMQMITEELGRPADDSVIEAAALQRLLAYPWPGNLRQMHAVIRYSC 321 Query: 592 AMAEGEAWIGVQHLPDDFLE-------EAGPLQAGCGMAATTVCEE-----MRSDCLSIH 639 A+ G I V+ LP++ ++ E P+ + T E RS Sbjct: 322 AVMNG-GRIEVRDLPEELMQFQPATLAEVHPITRTAQIRPFTSRAEGEAGRERSSGDPYR 380 Query: 640 DNEWATIERALRTHAGNVSAAAKALGVSRNTLYRRFK 676 D I+ AL N+SAA++ LG+ R +LYR+ + Sbjct: 381 DERTRVID-ALNGSRWNISAASRQLGMCRASLYRKLR 416 >gi|300312042|ref|YP_003776134.1| response regulatory protein [Herbaspirillum seropedicae SmR1] Length = 450 Score = 216 bits (549), Expect = 6e-57, Method: Compositional matrix adjust. Identities = 130/322 (40%), Positives = 184/322 (57%), Gaps = 29/322 (9%) Query: 355 LQALDTGDARMSAIIGKLRKVIDRDIAVLITGETGTGKEWLAQAIHRESARFRATQTRGG 414 L L T DA M A+ + KV +V++ G +GTGKE LA+A+H+ S R Sbjct: 145 LGGLITRDAGMLAVCRSIEKVAPSSASVMLLGSSGTGKEVLARALHQLSPR--------S 196 Query: 415 AAPFVAVNCSAIPENLIEAELFGYEDGAFTGARRKGAIGKIAQAQGGTLFLDEIGDMPLA 474 F+A+NC+AIPENL+E+ELFGYE GAFTGA ++ IGK+ A GGT FLDE+GD+P+ Sbjct: 197 GRRFMAINCAAIPENLLESELFGYEKGAFTGAAKQ-TIGKVELAHGGTFFLDEVGDLPMP 255 Query: 475 LQGRLLRVLQERTVTPLGSQRVIPVEFALVCATNQPLREMAARHSFREDLYYRINGLQVK 534 LQ +LLR LQER + +G IPV+ ++CAT+Q L+E+ A FREDLYYR+ + +K Sbjct: 256 LQAKLLRFLQERVIERVGGHTEIPVDVRVICATHQNLKELTASGGFREDLYYRLCEIIIK 315 Query: 535 LPALRERSDLAQLIERILI----AEGGALAPRFDEQAQALLQASRWPGNLRQLSNLIRTA 590 +PAL+ER A L+ R + A+ G + A A ++ WPGN+R++ N + A Sbjct: 316 IPALKERHGDAVLLARHFVQKFCAKEGRATLHLSQDAVAAIERYEWPGNVREMENCVMRA 375 Query: 591 LAMAEGEAWIGVQHLPDDFLEEAGPLQAGCGMAATTVCEEMRSDCLSIHDNEWATIERAL 650 + MA+G+ EA PL ++R + E + +AL Sbjct: 376 VIMADGQQITAEDLGLSVEGREAEPLN----------LRQVRDEA------ERKAVVKAL 419 Query: 651 RTHAGNVSAAAKALGVSRNTLY 672 GN+ AA+ LGVSR TLY Sbjct: 420 TRMDGNILKAAELLGVSRPTLY 441 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 205 bits (521), Expect = 1e-53, Method: Compositional matrix adjust. Identities = 132/329 (40%), Positives = 182/329 (55%), Gaps = 41/329 (12%) Query: 365 MSAIIGKLRKVIDRDIAVLITGETGTGKEWLAQAIHRESARFRATQTRGGAAPFVAVNCS 424 M + ++ + D VL+ GETGTGKE +A+A+HR AR A PFVAVNC+ Sbjct: 143 MRQVFKQIGRAATSDATVLVLGETGTGKELVARALHRNGAR--------AARPFVAVNCA 194 Query: 425 AIPENLIEAELFGYEDGAFTGARRKGAIGKIAQAQGGTLFLDEIGDMPLALQGRLLRVLQ 484 AIP LIE+ELFG+ GAF+GA +G+ +A GGTLFLDEIGDM LA Q ++LRVLQ Sbjct: 195 AIPAELIESELFGHVKGAFSGATSP-RLGRFQEADGGTLFLDEIGDMELATQAKILRVLQ 253 Query: 485 ERTVTPLGSQRVIPVEFALVCATNQPLREMAARHSFREDLYYRINGLQVKLPALRER-SD 543 ER +TP+G + + V+ ++ AT++ L+ + FREDL+YR+ L + +PALRER D Sbjct: 254 ERELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWYRLQVLTIMVPALRERPGD 313 Query: 544 LAQLIERILIAEGGALAPRFDEQAQALLQASRWPGNLRQLSNLIRTALAMAEG---EAW- 599 + + E L GG R A LL WPGN+R+L N + A M+ G EA Sbjct: 314 ILTIAEHFLRQLGGDAPKRISPAAARLLLQHAWPGNVRELRNTMERAAVMSHGLCIEAED 373 Query: 600 IGVQ---------HLPDDFLEEAGPLQAGCGMAATTVCEEMRSDCLSIHDNEWATIERAL 650 IG+ ++ GPL +++ + E IERAL Sbjct: 374 IGLSARPPAGAASAASAPAIDWDGPL------------------AVALAEVERVMIERAL 415 Query: 651 RTHAGNVSAAAKALGVSRNTLYRRFKSRG 679 + AGN + AA+ LG+SR LYRR + G Sbjct: 416 QGAAGNRAEAARRLGISRQQLYRRLEEAG 444 >gi|300312421|ref|YP_003776513.1| propionate catabolism operon regulatory protein [Herbaspirillum seropedicae SmR1] Length = 544 Score = 199 bits (506), Expect = 7e-52, Method: Compositional matrix adjust. Identities = 137/307 (44%), Positives = 176/307 (57%), Gaps = 20/307 (6%) Query: 382 VLITGETGTGKEWLAQAIHRESARFRATQTRGGAAPFVAVNCSAIPENLIEAELFGYEDG 441 VLI GETGTGKE AQAIHR + A PFVA+NC A+ E+L+E+ELFGYE+G Sbjct: 247 VLIQGETGTGKELAAQAIHRAHPLMQGKTQ--AAHPFVAINCGALAESLLESELFGYEEG 304 Query: 442 AFTGARRKGAIGKIAQAQGGTLFLDEIGDMPLALQGRLLRVLQERTVTPLGSQRVIPVEF 501 AFTG+RR G G A GTL LDEIG+MPL LQ RLLRVL+ER V +G R IPV+ Sbjct: 305 AFTGSRRGGRAGVFEAAHRGTLLLDEIGEMPLPLQTRLLRVLEEREVVRVGGTRPIPVQV 364 Query: 502 ALVCATNQPLREMAARHSFREDLYYRINGLQVKLPALRE-RSDLAQLIERILIAEGGALA 560 ++ AT+ L+ FR DLYYR++ L ++LP LRE R D+A L E L AL Sbjct: 365 RIISATHCDLQARVREGRFRADLYYRLSVLCLQLPPLRERRDDIAALAEWHLKHALAALD 424 Query: 561 PRFDEQAQA-------LLQASRWPGNLRQLSNLI-RTALAMAEGEAWIGVQHLPDDFLEE 612 R A LL WPGN+R+L NL+ R AL +A +Q L ++ Sbjct: 425 VRPHANLGAEIVRCAPLLCRYDWPGNVRELRNLMERLALFLAAEP----LQALTPALIQR 480 Query: 613 AGPLQAGCGMAATTVCEEMRSDCLSIHDNEWATIERALRTHAGNVSAAAKALGVSRNTLY 672 P + G + +E + + DN A+I ALR GN +AAA+ LG+SR TL+ Sbjct: 481 VAP-ELGQAPPSPAAPDEAQENITP--DN--ASIAAALRRFRGNRAAAARYLGMSRTTLW 535 Query: 673 RRFKSRG 679 R+ K G Sbjct: 536 RKLKESG 542 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: 2,018,048 Number of extensions: 82497 Number of successful extensions: 353 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 314 Number of HSP's successfully gapped: 12 Length of query: 680 Length of database: 1,619,870 Length adjustment: 92 Effective length of query: 588 Effective length of database: 1,184,250 Effective search space: 696339000 Effective search space used: 696339000 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: 134 (56.2 bits)