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= 0037.0093.p (675 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... 1355 0.0 gi|300313101|ref|YP_003777193.1| sigma54-dependent transcription... 250 3e-67 gi|300312042|ref|YP_003776134.1| response regulatory protein [He... 209 6e-55 gi|300313916|ref|YP_003778008.1| two component response regulato... 207 2e-54 gi|300312421|ref|YP_003776513.1| propionate catabolism operon re... 192 9e-50 >gi|300311223|ref|YP_003775315.1| sigma-54 dependent transcription activator protein [Herbaspirillum seropedicae SmR1] Length = 675 Score = 1355 bits (3506), Expect = 0.0, Method: Compositional matrix adjust. Identities = 667/675 (98%), Positives = 669/675 (99%) Query: 1 MQYQANRPSAGALLGASPLVQASTDGVPDLQAIERSHQRSSSYGIMRGQRPDLDSLSRAD 60 MQYQANRPSAGALLG SPLVQASTDGVPDLQAIERSHQRSSSYGIMRGQRPDLDSLSRAD Sbjct: 1 MQYQANRPSAGALLGTSPLVQASTDGVPDLQAIERSHQRSSSYGIMRGQRPDLDSLSRAD 60 Query: 61 LAQTLEANLALSGHARPVMETLYDQIRNTHSMVILSDAEGTILHTLGDSDFLAKADRVAL 120 LAQTLEAN LSGHARPVMETLYDQIRNTHSMVILSDAEGTILHTLGDSDFLAKADRVAL Sbjct: 61 LAQTLEANQTLSGHARPVMETLYDQIRNTHSMVILSDAEGTILHTLGDSDFLAKADRVAL 120 Query: 121 GPGGRWSEQLRGTNAIGTALFEQKPTTVHAQQHYLDANRFLTCSAAPIFDHRGQVLGVLD 180 GPGGRWSEQLRGTNAIGTALFEQKPTTVHAQQHYLDANRFLTCSAAPIFDHRGQVLGVLD Sbjct: 121 GPGGRWSEQLRGTNAIGTALFEQKPTTVHAQQHYLDANRFLTCSAAPIFDHRGQVLGVLD 180 Query: 181 VSGECGSFHKHTMALVRMSAQMIENHLLAGSFPDCITLHFHSRAEFVGTLVEGIVSFTPG 240 VSGECGSFHKHTMALVRMSAQMIENHLLAGSFPDCITLHFHSRAEFVGTLVEGIVSFTPG Sbjct: 181 VSGECGSFHKHTMALVRMSAQMIENHLLAGSFPDCITLHFHSRAEFVGTLVEGIVSFTPG 240 Query: 241 GRFLAANRSAQFQLGLTLAALQSHTFASLFGVPLSLLFEHHRKAAPGLLELCLHNGIRIH 300 GRFLAANRSAQFQLGLTLAALQSHTFASLFGVPLSLLFEHHRKAAPGLLELCLHNGIRIH Sbjct: 241 GRFLAANRSAQFQLGLTLAALQSHTFASLFGVPLSLLFEHHRKAAPGLLELCLHNGIRIH 300 Query: 301 GRAELRLRDQHFQAAREAVIDAPGLLPPAPDTANPPPSPPQQRARHQRRPDLQALDTGDV 360 GRAELRLRDQHFQAAREAVIDAPGLLPPAP+T PPPSPPQQRARHQRRPDLQALDTGDV Sbjct: 301 GRAELRLRDQHFQAAREAVIDAPGLLPPAPNTTTPPPSPPQQRARHQRRPDLQALDTGDV 360 Query: 361 RMSAIIAKLRRVIDRDIPILITGETGTGKEWLAQAIHGDSARFGARQNRAGAAPFVAVNC 420 RMSAIIAKLRRVIDRDIPILITGETGTGKEWLAQAIHGDSARFGARQNRAGAAPFVAVNC Sbjct: 361 RMSAIIAKLRRVIDRDIPILITGETGTGKEWLAQAIHGDSARFGARQNRAGAAPFVAVNC 420 Query: 421 SAIPENLIEAELFGYEDGAFTGARRKGALGKIAQAHGGTLFLDEIGDMPLALQGRLLRVL 480 SAIPENLIEAELFGYEDGAFTGARRKGALGKIAQAHGGTLFLDEIGDMPLALQGRLLRVL Sbjct: 421 SAIPENLIEAELFGYEDGAFTGARRKGALGKIAQAHGGTLFLDEIGDMPLALQGRLLRVL 480 Query: 481 QERAVTPLGSQRVIPVDFALVCATNQPLREMAARHAFREDLYYRINGLQVKLPALRDRSD 540 QERAVTPLGSQRVIPVDFALVCATNQPLREMAARHAFREDLYYRINGLQVKLPALRDRSD Sbjct: 481 QERAVTPLGSQRVIPVDFALVCATNQPLREMAARHAFREDLYYRINGLQVKLPALRDRSD 540 Query: 541 LPQLIERILEDEGGPHAPRFDAQAQALLLASHWPGNLRQLANLVRTSLAMAEGEEAIGPH 600 LPQLIERILEDEGGPHAPRFDAQAQALLLASHWPGNLRQLANLVRTSLAMAEGEEAIGPH Sbjct: 541 LPQLIERILEDEGGPHAPRFDAQAQALLLASHWPGNLRQLANLVRTSLAMAEGEEAIGPH 600 Query: 601 HLPDDFLEEAGAPGVLHDGMHTMHALRSDCLSIQDNEWAAIERALRTHAGNVSAAAKALG 660 HLPDDFLEEAGAPG LHDGMHTMHA+RSDCLSIQDNEWAAIERALRTHAGNVSAAAKALG Sbjct: 601 HLPDDFLEEAGAPGALHDGMHTMHAVRSDCLSIQDNEWAAIERALRTHAGNVSAAAKALG 660 Query: 661 VSRNTIYRRLKSRGH 675 VSRNTIYRRLKSRGH Sbjct: 661 VSRNTIYRRLKSRGH 675 >gi|300313101|ref|YP_003777193.1| sigma54-dependent transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 437 Score = 250 bits (638), Expect = 3e-67, Method: Compositional matrix adjust. Identities = 151/337 (44%), Positives = 207/337 (61%), Gaps = 26/337 (7%) Query: 351 DLQALDTGDVRMSAIIAKLRRVIDRDIPILITGETGTGKEWLAQAIHGDSARFGARQNRA 410 D+ L GD M +I + +R+IDR IP+LI GETGTGKE+L++A+H SAR Sbjct: 90 DIDQLAAGDACMHDLIERGKRLIDRGIPVLILGETGTGKEYLSRALHDYSARR------- 142 Query: 411 GAAPFVAVNCSAIPENLIEAELFGYEDGAFTGARRKGALGKIAQAHGGTLFLDEIGDMPL 470 A ++AVNC++IPE+L E+ELFGY GAF+GA G GK+ QA GGTLFLDEIGDMPL Sbjct: 143 -RASWIAVNCASIPESLAESELFGYCKGAFSGALPGGMKGKVQQADGGTLFLDEIGDMPL 201 Query: 471 ALQGRLLRVLQERAVTPLGSQRVIPVDFALVCATNQPLREMAARHAFREDLYYRINGLQV 530 ALQ RLLRVL ER V PLG++ +PVD L+CAT+Q L+ + A FREDLYYR+ G + Sbjct: 202 ALQTRLLRVLSEREVIPLGARHPVPVDVQLICATHQDLKTLIAEGRFREDLYYRVAGGVL 261 Query: 531 KLPALRDRSDLPQLIERILEDEGGPHAPRFDAQAQAL--LLASHWPGNLRQLANLVRTSL 588 +LPALR+RSD +L+ +++ +E G A +A AL LLA WPGNLRQ+ ++R S Sbjct: 262 RLPALRERSDRRRLVMQMITEELGRPADDSVIEAAALQRLLAYPWPGNLRQMHAVIRYSC 321 Query: 589 AMAEGEEAIGPHHLPDDFLE-EAGAPGVLHDGMHTMHAL-------------RSDCLSIQ 634 A+ G I LP++ ++ + +H T RS + Sbjct: 322 AVMNGGR-IEVRDLPEELMQFQPATLAEVHPITRTAQIRPFTSRAEGEAGRERSSGDPYR 380 Query: 635 DNEWAAIERALRTHAGNVSAAAKALGVSRNTIYRRLK 671 D I+ AL N+SAA++ LG+ R ++YR+L+ Sbjct: 381 DERTRVID-ALNGSRWNISAASRQLGMCRASLYRKLR 416 >gi|300312042|ref|YP_003776134.1| response regulatory protein [Herbaspirillum seropedicae SmR1] Length = 450 Score = 209 bits (532), Expect = 6e-55, Method: Compositional matrix adjust. Identities = 125/324 (38%), Positives = 185/324 (57%), Gaps = 35/324 (10%) Query: 352 LQALDTGDVRMSAIIAKLRRVIDRDIPILITGETGTGKEWLAQAIHGDSARFGARQNRAG 411 L L T D M A+ + +V +++ G +GTGKE LA+A+H S R G R Sbjct: 145 LGGLITRDAGMLAVCRSIEKVAPSSASVMLLGSSGTGKEVLARALHQLSPRSGRR----- 199 Query: 412 AAPFVAVNCSAIPENLIEAELFGYEDGAFTGARRKGALGKIAQAHGGTLFLDEIGDMPLA 471 F+A+NC+AIPENL+E+ELFGYE GAFTGA ++ +GK+ AHGGT FLDE+GD+P+ Sbjct: 200 ---FMAINCAAIPENLLESELFGYEKGAFTGAAKQ-TIGKVELAHGGTFFLDEVGDLPMP 255 Query: 472 LQGRLLRVLQERAVTPLGSQRVIPVDFALVCATNQPLREMAARHAFREDLYYRINGLQVK 531 LQ +LLR LQER + +G IPVD ++CAT+Q L+E+ A FREDLYYR+ + +K Sbjct: 256 LQAKLLRFLQERVIERVGGHTEIPVDVRVICATHQNLKELTASGGFREDLYYRLCEIIIK 315 Query: 532 LPALRDRSDLPQLIERILEDEGGPHAPR----FDAQAQALLLASHWPGNLRQLANLVRTS 587 +PAL++R L+ R + R A A + WPGN+R++ N V + Sbjct: 316 IPALKERHGDAVLLARHFVQKFCAKEGRATLHLSQDAVAAIERYEWPGNVREMENCVMRA 375 Query: 588 LAMAEGEEAIGPHHLPDDFLEEAGAPGVLHDGMHTMHALRSDCLSIQ----DNEWAAIER 643 + MA+G++ E+ G ++ ++ L+++ + E A+ + Sbjct: 376 VIMADGQQITA---------EDLGL---------SVEGREAEPLNLRQVRDEAERKAVVK 417 Query: 644 ALRTHAGNVSAAAKALGVSRNTIY 667 AL GN+ AA+ LGVSR T+Y Sbjct: 418 ALTRMDGNILKAAELLGVSRPTLY 441 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 207 bits (528), Expect = 2e-54, Method: Compositional matrix adjust. Identities = 134/319 (42%), Positives = 184/319 (57%), Gaps = 23/319 (7%) Query: 362 MSAIIAKLRRVIDRDIPILITGETGTGKEWLAQAIHGDSARFGARQNRAGAAPFVAVNCS 421 M + ++ R D +L+ GETGTGKE +A+A+H R GAR R PFVAVNC+ Sbjct: 143 MRQVFKQIGRAATSDATVLVLGETGTGKELVARALH----RNGARAAR----PFVAVNCA 194 Query: 422 AIPENLIEAELFGYEDGAFTGARRKGALGKIAQAHGGTLFLDEIGDMPLALQGRLLRVLQ 481 AIP LIE+ELFG+ GAF+GA LG+ +A GGTLFLDEIGDM LA Q ++LRVLQ Sbjct: 195 AIPAELIESELFGHVKGAFSGATSP-RLGRFQEADGGTLFLDEIGDMELATQAKILRVLQ 253 Query: 482 ERAVTPLGSQRVIPVDFALVCATNQPLREMAARHAFREDLYYRINGLQVKLPALRDR-SD 540 ER +TP+G + + VD ++ AT++ L+ + FREDL+YR+ L + +PALR+R D Sbjct: 254 ERELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWYRLQVLTIMVPALRERPGD 313 Query: 541 LPQLIERILEDEGGPHAPRFDAQAQALLLASHWPGNLRQLANLVRTSLAMAEG----EEA 596 + + E L GG R A LLL WPGN+R+L N + + M+ G E Sbjct: 314 ILTIAEHFLRQLGGDAPKRISPAAARLLLQHAWPGNVRELRNTMERAAVMSHGLCIEAED 373 Query: 597 IGPHHLPDDFLEEAGAPGVLH-DGMHTMHALRSDCLSIQDNEWAAIERALRTHAGNVSAA 655 IG P A + + DG +++ + E IERAL+ AGN + A Sbjct: 374 IGLSARPPAGAASAASAPAIDWDG--------PLAVALAEVERVMIERALQGAAGNRAEA 425 Query: 656 AKALGVSRNTIYRRLKSRG 674 A+ LG+SR +YRRL+ G Sbjct: 426 ARRLGISRQQLYRRLEEAG 444 >gi|300312421|ref|YP_003776513.1| propionate catabolism operon regulatory protein [Herbaspirillum seropedicae SmR1] Length = 544 Score = 192 bits (487), Expect = 9e-50, Method: Compositional matrix adjust. Identities = 132/310 (42%), Positives = 177/310 (57%), Gaps = 28/310 (9%) Query: 379 ILITGETGTGKEWLAQAIHGDSARFGARQNRAGAAPFVAVNCSAIPENLIEAELFGYEDG 438 +LI GETGTGKE AQAIH + A PFVA+NC A+ E+L+E+ELFGYE+G Sbjct: 247 VLIQGETGTGKELAAQAIHRAHPLMQGKTQ--AAHPFVAINCGALAESLLESELFGYEEG 304 Query: 439 AFTGARRKGALGKIAQAHGGTLFLDEIGDMPLALQGRLLRVLQERAVTPLGSQRVIPVDF 498 AFTG+RR G G AH GTL LDEIG+MPL LQ RLLRVL+ER V +G R IPV Sbjct: 305 AFTGSRRGGRAGVFEAAHRGTLLLDEIGEMPLPLQTRLLRVLEEREVVRVGGTRPIPVQV 364 Query: 499 ALVCATNQPLREMAARHAFREDLYYRINGLQVKLPALRD-RSDLPQLIERILED-----E 552 ++ AT+ L+ FR DLYYR++ L ++LP LR+ R D+ L E L+ + Sbjct: 365 RIISATHCDLQARVREGRFRADLYYRLSVLCLQLPPLRERRDDIAALAEWHLKHALAALD 424 Query: 553 GGPHAPRFDAQ---AQALLLASHWPGNLRQLANLV-RTSLAM-AEGEEAIGP---HHLPD 604 PHA A+ LL WPGN+R+L NL+ R +L + AE +A+ P + Sbjct: 425 VRPHA-NLGAEIVRCAPLLCRYDWPGNVRELRNLMERLALFLAAEPLQALTPALIQRVAP 483 Query: 605 DFLEEAGAPGVLHDGMHTMHALRSDCLSIQDNEWAAIERALRTHAGNVSAAAKALGVSRN 664 + + +P + + DN A+I ALR GN +AAA+ LG+SR Sbjct: 484 ELGQAPPSPAAPDEAQENI---------TPDN--ASIAAALRRFRGNRAAAARYLGMSRT 532 Query: 665 TIYRRLKSRG 674 T++R+LK G Sbjct: 533 TLWRKLKESG 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 0.136 0.402 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: 2,150,524 Number of extensions: 93431 Number of successful extensions: 380 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 343 Number of HSP's successfully gapped: 12 Length of query: 675 Length of database: 1,619,870 Length adjustment: 92 Effective length of query: 583 Effective length of database: 1,184,250 Effective search space: 690417750 Effective search space used: 690417750 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)