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= 0029.0276.p (377 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313101|ref|YP_003777193.1| sigma54-dependent transcription... 461 e-131 gi|300311223|ref|YP_003775315.1| sigma-54 dependent transcriptio... 213 2e-56 gi|300313916|ref|YP_003778008.1| two component response regulato... 183 2e-47 gi|300312042|ref|YP_003776134.1| response regulatory protein [He... 181 1e-46 gi|300310282|ref|YP_003774374.1| sigma-54 dependent transcriptio... 176 3e-45 >gi|300313101|ref|YP_003777193.1| sigma54-dependent transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 437 Score = 461 bits (1187), Expect = e-131, Method: Compositional matrix adjust. Identities = 227/229 (99%), Positives = 228/229 (99%) Query: 1 MPTTPVEQPLAEAEADSDVRTSTAARSASSRHAPRYRDIDQLAAGDACMHDLVERGKRLI 60 MPTTPVEQPLAEAEADSDVRTSTAARSASSRHAPRYRDIDQLAAGDACMHDL+ERGKRLI Sbjct: 53 MPTTPVEQPLAEAEADSDVRTSTAARSASSRHAPRYRDIDQLAAGDACMHDLIERGKRLI 112 Query: 61 DRGIPVLILGETGTGKEYLSRALHDYSARRRASWIAVNCASIPESLAESELFGYCKGAFS 120 DRGIPVLILGETGTGKEYLSRALHDYSARRRASWIAVNCASIPESLAESELFGYCKGAFS Sbjct: 113 DRGIPVLILGETGTGKEYLSRALHDYSARRRASWIAVNCASIPESLAESELFGYCKGAFS 172 Query: 121 GALPGGMKGKVQQADGGTLFLDEIGDMPLALQTRLLRVLSEREVIPLGARHPVPVDVQLI 180 GALPGGMKGKVQQADGGTLFLDEIGDMPLALQTRLLRVLSEREVIPLGARHPVPVDVQLI Sbjct: 173 GALPGGMKGKVQQADGGTLFLDEIGDMPLALQTRLLRVLSEREVIPLGARHPVPVDVQLI 232 Query: 181 CATHQDLKTLIAEGRFREDLYYRVAGGVLRLPALRERSDRRRLVMQMAT 229 CATHQDLKTLIAEGRFREDLYYRVAGGVLRLPALRERSDRRRLVMQM T Sbjct: 233 CATHQDLKTLIAEGRFREDLYYRVAGGVLRLPALRERSDRRRLVMQMIT 281 >gi|300311223|ref|YP_003775315.1| sigma-54 dependent transcription activator protein [Herbaspirillum seropedicae SmR1] Length = 675 Score = 213 bits (542), Expect = 2e-56, Method: Compositional matrix adjust. Identities = 110/198 (55%), Positives = 142/198 (71%), Gaps = 8/198 (4%) Query: 35 RYRDIDQLAAGDACMHDLVERGKRLIDRGIPVLILGETGTGKEYLSRALHDYSARR---- 90 R D+ L GD M ++ + +R+IDR IP+LI GETGTGKE+L++A+H SAR Sbjct: 348 RRPDLQALDTGDVRMSAIIAKLRRVIDRDIPILITGETGTGKEWLAQAIHGDSARFGARQ 407 Query: 91 ----RASWIAVNCASIPESLAESELFGYCKGAFSGALPGGMKGKVQQADGGTLFLDEIGD 146 A ++AVNC++IPE+L E+ELFGY GAF+GA G GK+ QA GGTLFLDEIGD Sbjct: 408 NRAGAAPFVAVNCSAIPENLIEAELFGYEDGAFTGARRKGALGKIAQAHGGTLFLDEIGD 467 Query: 147 MPLALQTRLLRVLSEREVIPLGARHPVPVDVQLICATHQDLKTLIAEGRFREDLYYRVAG 206 MPLALQ RLLRVL ER V PLG++ +PVD L+CAT+Q L+ + A FREDLYYR+ G Sbjct: 468 MPLALQGRLLRVLQERAVTPLGSQRVIPVDFALVCATNQPLREMAARHAFREDLYYRING 527 Query: 207 GVLRLPALRERSDRRRLV 224 ++LPALR+RSD +L+ Sbjct: 528 LQVKLPALRDRSDLPQLI 545 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 183 bits (464), Expect = 2e-47, Method: Compositional matrix adjust. Identities = 96/178 (53%), Positives = 123/178 (69%), Gaps = 1/178 (0%) Query: 40 DQLAAGDACMHDLVERGKRLIDRGIPVLILGETGTGKEYLSRALHDYSARRRASWIAVNC 99 +QL M + ++ R VL+LGETGTGKE ++RALH AR ++AVNC Sbjct: 134 NQLVGESEAMRQVFKQIGRAATSDATVLVLGETGTGKELVARALHRNGARAARPFVAVNC 193 Query: 100 ASIPESLAESELFGYCKGAFSGALPGGMKGKVQQADGGTLFLDEIGDMPLALQTRLLRVL 159 A+IP L ESELFG+ KGAFSGA + G+ Q+ADGGTLFLDEIGDM LA Q ++LRVL Sbjct: 194 AAIPAELIESELFGHVKGAFSGATSPRL-GRFQEADGGTLFLDEIGDMELATQAKILRVL 252 Query: 160 SEREVIPLGARHPVPVDVQLICATHQDLKTLIAEGRFREDLYYRVAGGVLRLPALRER 217 ERE+ P+G V VDV++I ATH+DL+ I +GRFREDL+YR+ + +PALRER Sbjct: 253 QERELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWYRLQVLTIMVPALRER 310 >gi|300312042|ref|YP_003776134.1| response regulatory protein [Herbaspirillum seropedicae SmR1] Length = 450 Score = 181 bits (458), Expect = 1e-46, Method: Compositional matrix adjust. Identities = 87/152 (57%), Positives = 115/152 (75%), Gaps = 1/152 (0%) Query: 66 VLILGETGTGKEYLSRALHDYSARRRASWIAVNCASIPESLAESELFGYCKGAFSGALPG 125 V++LG +GTGKE L+RALH S R ++A+NCA+IPE+L ESELFGY KGAF+GA Sbjct: 172 VMLLGSSGTGKEVLARALHQLSPRSGRRFMAINCAAIPENLLESELFGYEKGAFTGAAKQ 231 Query: 126 GMKGKVQQADGGTLFLDEIGDMPLALQTRLLRVLSEREVIPLGARHPVPVDVQLICATHQ 185 + GKV+ A GGT FLDE+GD+P+ LQ +LLR L ER + +G +PVDV++ICATHQ Sbjct: 232 TI-GKVELAHGGTFFLDEVGDLPMPLQAKLLRFLQERVIERVGGHTEIPVDVRVICATHQ 290 Query: 186 DLKTLIAEGRFREDLYYRVAGGVLRLPALRER 217 +LK L A G FREDLYYR+ ++++PAL+ER Sbjct: 291 NLKELTASGGFREDLYYRLCEIIIKIPALKER 322 >gi|300310282|ref|YP_003774374.1| sigma-54 dependent transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 380 Score = 176 bits (446), Expect = 3e-45, Method: Compositional matrix adjust. Identities = 90/166 (54%), Positives = 122/166 (73%), Gaps = 1/166 (0%) Query: 52 LVERGKRLIDRGIPVLILGETGTGKEYLSRALHDYSARRRASWIAVNCASIPESLAESEL 111 L+ER +R+ V+I+G TGTGKE ++R +H+ S RR A ++AVNC + ESLAESEL Sbjct: 59 LLERVQRVAPSDANVVIIGATGTGKELIARHVHELSQRRDAPFVAVNCGAFSESLAESEL 118 Query: 112 FGYCKGAFSGALPGGMKGKVQQADGGTLFLDEIGDMPLALQTRLLRVLSEREVIPLGARH 171 FG+ KGAF+GA+ G + A+GGTLFLDEIGD+PLA+Q +LLRVL EREV+ LG+R Sbjct: 119 FGHEKGAFTGAITH-KPGWFEAANGGTLFLDEIGDLPLAIQVKLLRVLQEREVVRLGSRR 177 Query: 172 PVPVDVQLICATHQDLKTLIAEGRFREDLYYRVAGGVLRLPALRER 217 +P+DV++I AT+ L+ +A G FR+DLYYR+ L +P LRER Sbjct: 178 SIPIDVRIIAATNVRLQDAVAAGHFRQDLYYRLQVVQLAIPRLRER 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 0.323 0.137 0.405 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: 1,051,489 Number of extensions: 40878 Number of successful extensions: 184 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 172 Number of HSP's successfully gapped: 12 Length of query: 377 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 290 Effective length of database: 1,207,925 Effective search space: 350298250 Effective search space used: 350298250 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: 131 (55.1 bits)