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= 0028.0112.p (210 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... 319 1e-88 gi|300313101|ref|YP_003777193.1| sigma54-dependent transcription... 135 3e-33 gi|300312042|ref|YP_003776134.1| response regulatory protein [He... 125 2e-30 gi|300313916|ref|YP_003778008.1| two component response regulato... 110 9e-26 gi|300313867|ref|YP_003777959.1| phenol-degradative gene regulat... 108 3e-25 >gi|300311223|ref|YP_003775315.1| sigma-54 dependent transcription activator protein [Herbaspirillum seropedicae SmR1] Length = 675 Score = 319 bits (817), Expect = 1e-88, Method: Compositional matrix adjust. Identities = 167/211 (79%), Positives = 179/211 (84%), Gaps = 4/211 (1%) Query: 1 MPLALQGRLLRVLQERAVTPLGSQRVIPVDFALVCATNQPLREMAARHAFREDLYYRING 60 MPLALQGRLLRVLQERAVTPLGSQRVIPVDFALVCATNQPLREMAARHAFREDLYYRING Sbjct: 468 MPLALQGRLLRVLQERAVTPLGSQRVIPVDFALVCATNQPLREMAARHAFREDLYYRING 527 Query: 61 LQVKLPALRERSDLSALIDRILEQEGGRHAPRFDAKALALLQSSRWPGNLRQLSNLIRTA 120 LQVKLPALR+RSDL LI+RILE EGG HAPRFDA+A ALL +S WPGNLRQL+NL+RT+ Sbjct: 528 LQVKLPALRDRSDLPQLIERILEDEGGPHAPRFDAQAQALLLASHWPGNLRQLANLVRTS 587 Query: 121 LAMADGEAWIGVEHLPDDFLDEA-APLQAGCGMPAPAAHEETDEKPLSMHDSEWAAIERA 179 LAMA+GE IG HLPDDFL+EA AP GM A LS+ D+EWAAIERA Sbjct: 588 LAMAEGEEAIGPHHLPDDFLEEAGAPGALHDGMHTMHA---VRSDCLSIQDNEWAAIERA 644 Query: 180 LRTHDGNVSAAAKALGVSRNTLYRRFKSRGH 210 LRTH GNVSAAAKALGVSRNT+YRR KSRGH Sbjct: 645 LRTHAGNVSAAAKALGVSRNTIYRRLKSRGH 675 >gi|300313101|ref|YP_003777193.1| sigma54-dependent transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 437 Score = 135 bits (339), Expect = 3e-33, Method: Compositional matrix adjust. Identities = 89/222 (40%), Positives = 125/222 (56%), Gaps = 20/222 (9%) Query: 1 MPLALQGRLLRVLQERAVTPLGSQRVIPVDFALVCATNQPLREMAARHAFREDLYYRING 60 MPLALQ RLLRVL ER V PLG++ +PVD L+CAT+Q L+ + A FREDLYYR+ G Sbjct: 199 MPLALQTRLLRVLSEREVIPLGARHPVPVDVQLICATHQDLKTLIAEGRFREDLYYRVAG 258 Query: 61 LQVKLPALRERSDLSALIDRILEQEGGRHA--PRFDAKALALLQSSRWPGNLRQLSNLIR 118 ++LPALRERSD L+ +++ +E GR A +A AL L + WPGNLRQ+ +IR Sbjct: 259 GVLRLPALRERSDRRRLVMQMITEELGRPADDSVIEAAALQRLLAYPWPGNLRQMHAVIR 318 Query: 119 TALAMADGEAWIGVEHLPDDF-------LDEAAPLQAGCGM-------PAPAAHEETDEK 164 + A+ +G I V LP++ L E P+ + A E + Sbjct: 319 YSCAVMNG-GRIEVRDLPEELMQFQPATLAEVHPITRTAQIRPFTSRAEGEAGRERSSGD 377 Query: 165 PLSMHDSEWAAIERALRTHDGNVSAAAKALGVSRNTLYRRFK 206 P + E + AL N+SAA++ LG+ R +LYR+ + Sbjct: 378 P---YRDERTRVIDALNGSRWNISAASRQLGMCRASLYRKLR 416 >gi|300312042|ref|YP_003776134.1| response regulatory protein [Herbaspirillum seropedicae SmR1] Length = 450 Score = 125 bits (315), Expect = 2e-30, Method: Compositional matrix adjust. Identities = 78/210 (37%), Positives = 116/210 (55%), Gaps = 28/210 (13%) Query: 1 MPLALQGRLLRVLQERAVTPLGSQRVIPVDFALVCATNQPLREMAARHAFREDLYYRING 60 +P+ LQ +LLR LQER + +G IPVD ++CAT+Q L+E+ A FREDLYYR+ Sbjct: 252 LPMPLQAKLLRFLQERVIERVGGHTEIPVDVRVICATHQNLKELTASGGFREDLYYRLCE 311 Query: 61 LQVKLPALRERSDLSALIDRILEQ----EGGRHAPRFDAKALALLQSSRWPGNLRQLSNL 116 + +K+PAL+ER + L+ R Q + GR A+A ++ WPGN+R++ N Sbjct: 312 IIIKIPALKERHGDAVLLARHFVQKFCAKEGRATLHLSQDAVAAIERYEWPGNVREMENC 371 Query: 117 IRTALAMADGEAWIGVEHLPDDFLDEAAPLQAGCGMPAPAAHEETDEKPLSMH----DSE 172 + A+ MADG+ I E L G+ E + +PL++ ++E Sbjct: 372 VMRAVIMADGQ-QITAEDL---------------GLSV----EGREAEPLNLRQVRDEAE 411 Query: 173 WAAIERALRTHDGNVSAAAKALGVSRNTLY 202 A+ +AL DGN+ AA+ LGVSR TLY Sbjct: 412 RKAVVKALTRMDGNILKAAELLGVSRPTLY 441 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 110 bits (275), Expect = 9e-26, Method: Compositional matrix adjust. Identities = 78/213 (36%), Positives = 114/213 (53%), Gaps = 12/213 (5%) Query: 1 MPLALQGRLLRVLQERAVTPLGSQRVIPVDFALVCATNQPLREMAARHAFREDLYYRING 60 M LA Q ++LRVLQER +TP+G + + VD ++ AT++ L+ + FREDL+YR+ Sbjct: 240 MELATQAKILRVLQERELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWYRLQV 299 Query: 61 LQVKLPALRER-SDLSALIDRILEQEGGRHAPRFDAKALALLQSSRWPGNLRQLSNLIRT 119 L + +PALRER D+ + + L Q GG R A LL WPGN+R+L N + Sbjct: 300 LTIMVPALRERPGDILTIAEHFLRQLGGDAPKRISPAAARLLLQHAWPGNVRELRNTMER 359 Query: 120 ALAMADGEAWIGVEHLPDDFLDEAAPLQAGCGMPAPAAHEETD-EKPL--SMHDSEWAAI 176 A M+ G L + D + G + A+ D + PL ++ + E I Sbjct: 360 AAVMSHG--------LCIEAEDIGLSARPPAGAASAASAPAIDWDGPLAVALAEVERVMI 411 Query: 177 ERALRTHDGNVSAAAKALGVSRNTLYRRFKSRG 209 ERAL+ GN + AA+ LG+SR LYRR + G Sbjct: 412 ERALQGAAGNRAEAARRLGISRQQLYRRLEEAG 444 >gi|300313867|ref|YP_003777959.1| phenol-degradative gene regulator transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 611 Score = 108 bits (271), Expect = 3e-25, Method: Compositional matrix adjust. Identities = 84/246 (34%), Positives = 123/246 (50%), Gaps = 39/246 (15%) Query: 1 MPLALQGRLLRVLQERAVTPLGSQRVIPVDFALVCATNQPLREMAARHAFREDLYYRING 60 + L QG+LLRVLQE +GS R + VD +V ATN+ L + FR+DL++R+N Sbjct: 368 LSLVAQGKLLRVLQEGEFERVGSARPVKVDVRVVAATNEDLAQAVREGRFRQDLFFRLNV 427 Query: 61 LQVKLPALRE-RSDLSALIDRILEQEGGRHAPR---FDAKALALLQSSRWPGNLRQLSNL 116 + LP LRE R D+ L++ L+ G RH F +A+ L + +PGN+R+L NL Sbjct: 428 FPIHLPPLRERRDDIPLLMNHFLKLYGQRHGIAVRGFTQRAIQALLNYSFPGNIRELQNL 487 Query: 117 IRTALAMADG------EAWIGVEHLPDDFLDEAAPLQAGCGMPAPAAHEETDEKP----- 165 I + +A G +I E L D+ L A LQ GM A + E++ EK Sbjct: 488 IERGVILAQGHPLDLPHMFISGERLNDEVLSLA--LQGETGMLAGKSVEKSVEKSVAHPT 545 Query: 166 ---------------------LSMHDSEWAAIERALRTHDGNVSAAAKALGVSRNTL-YR 203 L++ + E I A+ +GN+SAAA+ LG+SR L YR Sbjct: 546 AQGLLDVLRQWRQEAAGEAAALTLPEMERRLIAEAIERAEGNLSAAARLLGISRAQLAYR 605 Query: 204 RFKSRG 209 + K +G Sbjct: 606 QQKGQG 611 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 0.134 0.399 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: 705,468 Number of extensions: 30400 Number of successful extensions: 129 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 110 Number of HSP's successfully gapped: 12 Length of query: 210 Length of database: 1,619,870 Length adjustment: 81 Effective length of query: 129 Effective length of database: 1,236,335 Effective search space: 159487215 Effective search space used: 159487215 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: 128 (53.9 bits)