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= 0003.0076.p (375 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... 626 0.0 gi|300311223|ref|YP_003775315.1| sigma-54 dependent transcriptio... 259 4e-70 gi|300313916|ref|YP_003778008.1| two component response regulato... 210 2e-55 gi|300312042|ref|YP_003776134.1| response regulatory protein [He... 205 6e-54 gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcrip... 195 5e-51 >gi|300313101|ref|YP_003777193.1| sigma54-dependent transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 437 Score = 626 bits (1615), Expect = 0.0, Method: Compositional matrix adjust. Identities = 315/385 (81%), Positives = 337/385 (87%), Gaps = 10/385 (2%) Query: 1 MPTTPVAQPLP----DSDVCLTPVPPSASPRHAPRYRDIGQLAAGDELMRDLVERGKRLI 56 MPTTPV QPL DSDV + SAS RHAPRYRDI QLAAGD M DL+ERGKRLI Sbjct: 53 MPTTPVEQPLAEAEADSDVRTSTAARSASSRHAPRYRDIDQLAAGDACMHDLIERGKRLI 112 Query: 57 DRGIPVLILGETGTGKEYLARALHDYSARRRASWIAINCASIPESLAESELFGYCKGAFS 116 DRGIPVLILGETGTGKEYL+RALHDYSARRRASWIA+NCASIPESLAESELFGYCKGAFS Sbjct: 113 DRGIPVLILGETGTGKEYLSRALHDYSARRRASWIAVNCASIPESLAESELFGYCKGAFS 172 Query: 117 GALPGGMKGKVQQADGGTLFLDEIGDMPFALQTRLLRVLSEREVIPLGALRPVPVDVQLI 176 GALPGGMKGKVQQADGGTLFLDEIGDMP ALQTRLLRVLSEREVIPLGA PVPVDVQLI Sbjct: 173 GALPGGMKGKVQQADGGTLFLDEIGDMPLALQTRLLRVLSEREVIPLGARHPVPVDVQLI 232 Query: 177 CATHQDLKTLVAEGRFREDLYYRIAGGVLRLPALRDRSDRPALVMQMIADELGHPADESM 236 CATHQDLKTL+AEGRFREDLYYR+AGGVLRLPALR+RSDR LVMQMI +ELG PAD+S+ Sbjct: 233 CATHQDLKTLIAEGRFREDLYYRVAGGVLRLPALRERSDRRRLVMQMITEELGRPADDSV 292 Query: 237 LDPVALQRLLAYPWPGNLRQLHAVIRYSCAVMNDGRITLRDLPEELMQFQPVTLAQVLPL 296 ++ ALQRLLAYPWPGNLRQ+HAVIRYSCAVMN GRI +RDLPEELMQFQP TLA+V P+ Sbjct: 293 IEAAALQRLLAYPWPGNLRQMHAVIRYSCAVMNGGRIEVRDLPEELMQFQPATLAEVHPI 352 Query: 297 HRPA------SRMAAEGSSQANAADPGRDERTRVIEALNGSRWNISAASRQLGMCRASLY 350 R A SR E + ++ DP RDERTRVI+ALNGSRWNISAASRQLGMCRASLY Sbjct: 353 TRTAQIRPFTSRAEGEAGRERSSGDPYRDERTRVIDALNGSRWNISAASRQLGMCRASLY 412 Query: 351 RKLRQLEIPHVRDQAMPAHAAYAVA 375 RKLRQL+IPHVRDQAMPA+ AYAVA Sbjct: 413 RKLRQLDIPHVRDQAMPAYPAYAVA 437 >gi|300311223|ref|YP_003775315.1| sigma-54 dependent transcription activator protein [Herbaspirillum seropedicae SmR1] Length = 675 Score = 259 bits (661), Expect = 4e-70, Method: Compositional matrix adjust. Identities = 158/331 (47%), Positives = 207/331 (62%), Gaps = 20/331 (6%) Query: 34 DIGQLAAGDELMRDLVERGKRLIDRGIPVLILGETGTGKEYLARALHDYSAR-----RRA 88 D+ L GD M ++ + +R+IDR IP+LI GETGTGKE+LA+A+H SAR RA Sbjct: 351 DLQALDTGDVRMSAIIAKLRRVIDRDIPILITGETGTGKEWLAQAIHGDSARFGARQNRA 410 Query: 89 S---WIAINCASIPESLAESELFGYCKGAFSGALPGGMKGKVQQADGGTLFLDEIGDMPF 145 ++A+NC++IPE+L E+ELFGY GAF+GA G GK+ QA GGTLFLDEIGDMP Sbjct: 411 GAAPFVAVNCSAIPENLIEAELFGYEDGAFTGARRKGALGKIAQAHGGTLFLDEIGDMPL 470 Query: 146 ALQTRLLRVLSEREVIPLGALRPVPVDVQLICATHQDLKTLVAEGRFREDLYYRIAGGVL 205 ALQ RLLRVL ER V PLG+ R +PVD L+CAT+Q L+ + A FREDLYYRI G + Sbjct: 471 ALQGRLLRVLQERAVTPLGSQRVIPVDFALVCATNQPLREMAARHAFREDLYYRINGLQV 530 Query: 206 RLPALRDRSDRPALVMQMIADELGHPADESMLDPVALQRLLAYPWPGNLRQLHAVIRYSC 265 +LPALRDRSD P L+ +++ DE G A D A LLA WPGNLRQL ++R S Sbjct: 531 KLPALRDRSDLPQLIERILEDEGGPHAPR--FDAQAQALLLASHWPGNLRQLANLVRTSL 588 Query: 266 AVMNDGR--ITLRDLPEELMQFQPVTLAQVLPLHRPASRMAAEGSSQANAADPGRDERTR 323 A M +G I LP++ ++ A LH M A S + D +E Sbjct: 589 A-MAEGEEAIGPHHLPDDFLEEAGAPGA----LHDGMHTMHAVRSDCLSIQD---NEWAA 640 Query: 324 VIEALNGSRWNISAASRQLGMCRASLYRKLR 354 + AL N+SAA++ LG+ R ++YR+L+ Sbjct: 641 IERALRTHAGNVSAAAKALGVSRNTIYRRLK 671 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 210 bits (534), Expect = 2e-55, Method: Compositional matrix adjust. Identities = 134/328 (40%), Positives = 186/328 (56%), Gaps = 19/328 (5%) Query: 37 QLAAGDELMRDLVERGKRLIDRGIPVLILGETGTGKEYLARALHDYSARRRASWIAINCA 96 QL E MR + ++ R VL+LGETGTGKE +ARALH AR ++A+NCA Sbjct: 135 QLVGESEAMRQVFKQIGRAATSDATVLVLGETGTGKELVARALHRNGARAARPFVAVNCA 194 Query: 97 SIPESLAESELFGYCKGAFSGALPGGMKGKVQQADGGTLFLDEIGDMPFALQTRLLRVLS 156 +IP L ESELFG+ KGAFSGA + G+ Q+ADGGTLFLDEIGDM A Q ++LRVL Sbjct: 195 AIPAELIESELFGHVKGAFSGATSPRL-GRFQEADGGTLFLDEIGDMELATQAKILRVLQ 253 Query: 157 EREVIPLGALRPVPVDVQLICATHQDLKTLVAEGRFREDLYYRIAGGVLRLPALRDRSDR 216 ERE+ P+G + V VDV++I ATH+DL+ + +GRFREDL+YR+ + +PALR+R Sbjct: 254 ERELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWYRLQVLTIMVPALRERPGD 313 Query: 217 PALVMQMIADELGHPADESMLDPVALQRLLAYPWPGNLRQLHAVIRYSCAVMNDGR-ITL 275 + + +LG A + + P A + LL + WPGN+R+L + + AVM+ G I Sbjct: 314 ILTIAEHFLRQLGGDAPKR-ISPAAARLLLQHAWPGNVRELRNTMERA-AVMSHGLCIEA 371 Query: 276 RDL---PEELMQFQPVTLAQVLPLHRPASRMAAEGSSQANAADPGRDERTRVIEALNGSR 332 D+ A + P + AE ER + AL G+ Sbjct: 372 EDIGLSARPPAGAASAASAPAIDWDGPLAVALAE------------VERVMIERALQGAA 419 Query: 333 WNISAASRQLGMCRASLYRKLRQLEIPH 360 N + A+R+LG+ R LYR+L + H Sbjct: 420 GNRAEAARRLGISRQQLYRRLEEAGKSH 447 >gi|300312042|ref|YP_003776134.1| response regulatory protein [Herbaspirillum seropedicae SmR1] Length = 450 Score = 205 bits (521), Expect = 6e-54, Method: Compositional matrix adjust. Identities = 126/306 (41%), Positives = 176/306 (57%), Gaps = 37/306 (12%) Query: 62 VLILGETGTGKEYLARALHDYSARRRASWIAINCASIPESLAESELFGYCKGAFSGALPG 121 V++LG +GTGKE LARALH S R ++AINCA+IPE+L ESELFGY KGAF+GA Sbjct: 172 VMLLGSSGTGKEVLARALHQLSPRSGRRFMAINCAAIPENLLESELFGYEKGAFTGAAKQ 231 Query: 122 GMKGKVQQADGGTLFLDEIGDMPFALQTRLLRVLSEREVIPLGALRPVPVDVQLICATHQ 181 + GKV+ A GGT FLDE+GD+P LQ +LLR L ER + +G +PVDV++ICATHQ Sbjct: 232 TI-GKVELAHGGTFFLDEVGDLPMPLQAKLLRFLQERVIERVGGHTEIPVDVRVICATHQ 290 Query: 182 DLKTLVAEGRFREDLYYRIAGGVLRLPALRDRSDRPALVMQMIADELGHPADESML---- 237 +LK L A G FREDLYYR+ ++++PAL++R L+ + + + L Sbjct: 291 NLKELTASGGFREDLYYRLCEIIIKIPALKERHGDAVLLARHFVQKFCAKEGRATLHLSQ 350 Query: 238 DPV-ALQRLLAYPWPGNLRQLHAVIRYSCAVMNDGRITLRD--LPEELMQFQPVTLAQVL 294 D V A++R Y WPGN+R++ + + + + +IT D L E + +P+ L QV Sbjct: 351 DAVAAIER---YEWPGNVREMENCVMRAVIMADGQQITAEDLGLSVEGREAEPLNLRQV- 406 Query: 295 PLHRPASRMAAEGSSQANAADPGRD--ERTRVIEALNGSRWNISAASRQLGMCRASLYRK 352 RD ER V++AL NI A+ LG+ R +LY Sbjct: 407 -----------------------RDEAERKAVVKALTRMDGNILKAAELLGVSRPTLYDL 443 Query: 353 LRQLEI 358 + + EI Sbjct: 444 MSRHEI 449 >gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcription activator protein [Herbaspirillum seropedicae SmR1] Length = 500 Score = 195 bits (496), Expect = 5e-51, Method: Compositional matrix adjust. Identities = 111/244 (45%), Positives = 158/244 (64%), Gaps = 7/244 (2%) Query: 45 MRDLVERGKRLIDRGIPVLILGETGTGKEYLARALHDYSARRRASWIAINCASIPESLAE 104 M+D+ RL + VLI GE+G+GKE +ARALH +S R ++A+N A+IP+ L E Sbjct: 143 MQDVFRAIGRLSQSNVTVLITGESGSGKELVARALHKHSPRASQPFVALNTAAIPKDLLE 202 Query: 105 SELFGYCKGAFSGALPGGMKGKVQQADGGTLFLDEIGDMPFALQTRLLRVLSEREVIPLG 164 SELFG+ +GAF+GA +G+ +QA+GGTLFLDEIGDMP LQTRLLRVLS+ +G Sbjct: 203 SELFGHERGAFTGA-QAMRRGRFEQAEGGTLFLDEIGDMPLDLQTRLLRVLSDGHFYRVG 261 Query: 165 ALRPVPVDVQLICATHQDLKTLVAEGRFREDLYYRIAGGVLRLPALRDRS-DRPALVMQM 223 + + +V++I ATHQ+L+ V EG FREDLY+R+ LRLP+LR+RS D P L Sbjct: 262 GHQSLKANVRVIAATHQNLEQRVREGLFREDLYHRLNVIRLRLPSLRERSEDIPILARYF 321 Query: 224 IAD---ELGHPADESMLDPVALQRLLAYPWPGNLRQLHAVIRYSCAVMNDGRITLRDLPE 280 +A +LG A L P A+Q L +PGN+RQL + + + + ++DLP+ Sbjct: 322 LAQSARQLGVEAKR--LSPQAMQFLSQLEFPGNVRQLENLCNWITVMAPGQTVEIKDLPQ 379 Query: 281 ELMQ 284 +L++ Sbjct: 380 DLVE 383 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 0.137 0.410 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: 1,299,717 Number of extensions: 58410 Number of successful extensions: 269 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 239 Number of HSP's successfully gapped: 12 Length of query: 375 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 288 Effective length of database: 1,207,925 Effective search space: 347882400 Effective search space used: 347882400 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)