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= 0001.0745.p (374 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310282|ref|YP_003774374.1| sigma-54 dependent transcriptio... 656 0.0 gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein... 239 2e-64 gi|300313916|ref|YP_003778008.1| two component response regulato... 235 4e-63 gi|300311822|ref|YP_003775914.1| sigma-54 dependent transcriptio... 234 6e-63 gi|300312042|ref|YP_003776134.1| response regulatory protein [He... 233 2e-62 >gi|300310282|ref|YP_003774374.1| sigma-54 dependent transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 380 Score = 656 bits (1693), Expect = 0.0, Method: Compositional matrix adjust. Identities = 334/380 (87%), Positives = 342/380 (90%), Gaps = 6/380 (1%) Query: 1 MNASNRSAHLYALPSSTE-----AARTATPLLTLPHARKLGTSIRATAQVFHDPVSVALL 55 M+AS+RSAHLYALPSS E AAR + PLLTLPHARKLGTSIRATAQVFHDPVS+ALL Sbjct: 1 MHASHRSAHLYALPSSPEGHGDLAARASPPLLTLPHARKLGTSIRATAQVFHDPVSLALL 60 Query: 56 ERVQMVAPSDANVVIIGATGTGKELIARHVHELSTRRNGPFVAVNCGAFSENLAESELFG 115 ERVQ VAPSDANVVIIGATGTGKELIARHVHELS RR+ PFVAVNCGAFSE+LAESELFG Sbjct: 61 ERVQRVAPSDANVVIIGATGTGKELIARHVHELSQRRDAPFVAVNCGAFSESLAESELFG 120 Query: 116 HEKGAFTGAIAHKAGWFEAANGGTLFLDEIGDLPLAIQVKLLRVLQEREVVRLGSRRSIP 175 HEKGAFTGAI HK GWFEAANGGTLFLDEIGDLPLAIQVKLLRVLQEREVVRLGSRRSIP Sbjct: 121 HEKGAFTGAITHKPGWFEAANGGTLFLDEIGDLPLAIQVKLLRVLQEREVVRLGSRRSIP 180 Query: 176 IDVRIIAATNVRLQDAVAAGHFRQDLYYRLQVVQLTIPRLRERPEDILPLAYHFLDEYRQ 235 IDVRIIAATNVRLQDAVAAGHFRQDLYYRLQVVQL IPRLRERP DILPLAYHFL EYRQ Sbjct: 181 IDVRIIAATNVRLQDAVAAGHFRQDLYYRLQVVQLAIPRLRERPLDILPLAYHFLHEYRQ 240 Query: 236 RLGYGARGIDAEGERKLRSHDWPGNIRELENAIHHALLICQDEQLRAEHLHLSHVE-RLG 294 RLGYGA ID EGERKLR HDWPGNIRELENAIHHALLICQD+ LRAEH HLSHVE RL Sbjct: 241 RLGYGAARIDGEGERKLRQHDWPGNIRELENAIHHALLICQDDCLRAEHFHLSHVERRLD 300 Query: 295 AAQPVVGSHADDPLQALEQVLQSLFNQSQAGLFEKIEDTVFRTAFEFCERNQVQAARLLD 354 A +DPL ALEQ LQ LFNQSQ GLFEKIEDTVFRTAFEFCERNQVQAARLLD Sbjct: 301 YAVAAADERGNDPLHALEQALQGLFNQSQEGLFEKIEDTVFRTAFEFCERNQVQAARLLD 360 Query: 355 ISRNVLRARLIRTGQISALK 374 ISRNVLRARLIR GQISALK Sbjct: 361 ISRNVLRARLIRNGQISALK 380 >gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein [Herbaspirillum seropedicae SmR1] Length = 542 Score = 239 bits (610), Expect = 2e-64, Method: Compositional matrix adjust. Identities = 138/316 (43%), Positives = 183/316 (57%), Gaps = 23/316 (7%) Query: 57 RVQMVAPSDANVVIIGATGTGKELIARHVHELSTRRNGPFVAVNCGAFSENLAESELFGH 116 +V APS + +++ G +GTGKE+IAR +H LS R++GPF+ VNC A SE L ESELFGH Sbjct: 216 QVHQSAPSRSTMLLRGESGTGKEVIARAIHYLSPRKDGPFIKVNCAALSETLLESELFGH 275 Query: 117 EKGAFTGAIAHKAGWFEAANGGTLFLDEIGDLPLAIQVKLLRVLQEREVVRLGSRRSIPI 176 EKGAFTGA + G FE A+GGTLFLDEIG++ A Q KLLRVLQERE R+G RSI + Sbjct: 276 EKGAFTGAQGERKGRFELAHGGTLFLDEIGEISPAFQAKLLRVLQEREFERVGGSRSIKV 335 Query: 177 DVRIIAATNVRLQDAVAAGHFRQDLYYRLQVVQLTIPRLRERPEDILPLAYHFLDEYRQR 236 DVR++ ATN L+ AVA G FR DLYYR+ VV + IP LRER EDI L HFL+++R Sbjct: 336 DVRLVTATNRDLEKAVAKGEFRADLYYRINVVSIFIPPLRERREDIPYLVEHFLEKFRVE 395 Query: 237 LGYGARGIDAEGERKLRSHDWPGNIRELENAIHHALLICQDEQLRAEHLHLSHVERL--- 293 + + + + + WPGN+RELEN + + + + + H + L Sbjct: 396 NQRAMVAMSPQAMKVMMNCYWPGNVRELENCVERTATMMRGDLITEVHFSCQQNKCLTKV 455 Query: 294 ----GAAQPVVGSHADDPLQALEQVLQSLFNQSQAGLFE---------KIEDTVFRTAFE 340 G QPVV + LE++ S +G+ + E A E Sbjct: 456 LHEPGQQQPVV-------VVPLERISAHTAPSSPSGMAKDKPLAAAPPTSERERLIWAME 508 Query: 341 FCERNQVQAARLLDIS 356 C Q +AAR L+IS Sbjct: 509 QCGWVQAKAARALNIS 524 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 235 bits (600), Expect = 4e-63, Method: Compositional matrix adjust. Identities = 138/316 (43%), Positives = 184/316 (58%), Gaps = 16/316 (5%) Query: 54 LLERVQMVAPSDANVVIIGATGTGKELIARHVHELSTRRNGPFVAVNCGAFSENLAESEL 113 + +++ A SDA V+++G TGTGKEL+AR +H R PFVAVNC A L ESEL Sbjct: 146 VFKQIGRAATSDATVLVLGETGTGKELVARALHRNGARAARPFVAVNCAAIPAELIESEL 205 Query: 114 FGHEKGAFTGAIAHKAGWFEAANGGTLFLDEIGDLPLAIQVKLLRVLQEREVVRLGSRRS 173 FGH KGAF+GA + + G F+ A+GGTLFLDEIGD+ LA Q K+LRVLQERE+ +G +S Sbjct: 206 FGHVKGAFSGATSPRLGRFQEADGGTLFLDEIGDMELATQAKILRVLQERELTPVGGNQS 265 Query: 174 IPIDVRIIAATNVRLQDAVAAGHFRQDLYYRLQVVQLTIPRLRERPEDILPLAYHFLDEY 233 + +DVR+IAAT+ LQ + G FR+DL+YRLQV+ + +P LRERP DIL +A HFL Sbjct: 266 VRVDVRVIAATHRDLQHEITQGRFREDLWYRLQVLTIMVPALRERPGDILTIAEHFL--- 322 Query: 234 RQRLGYGARGIDAEGERKLRSHDWPGNIRELENAIHHALLICQDEQLRAEHLHLSHVERL 293 RQ G + I R L H WPGN+REL N + A ++ + AE + LS Sbjct: 323 RQLGGDAPKRISPAAARLLLQHAWPGNVRELRNTMERAAVMSHGLCIEAEDIGLSARPPA 382 Query: 294 GAAQPVVGSHADDPLQALEQVLQSLFNQSQAGLFEKIEDTVFRTAFEFCERNQVQAARLL 353 GAA D ++ A ++E + A + N+ +AAR L Sbjct: 383 GAASAASAPAID-------------WDGPLAVALAEVERVMIERALQGAAGNRAEAARRL 429 Query: 354 DISRNVLRARLIRTGQ 369 ISR L RL G+ Sbjct: 430 GISRQQLYRRLEEAGK 445 >gi|300311822|ref|YP_003775914.1| sigma-54 dependent transcription regulator [Herbaspirillum seropedicae SmR1] Length = 526 Score = 234 bits (598), Expect = 6e-63, Method: Compositional matrix adjust. Identities = 116/229 (50%), Positives = 156/229 (68%) Query: 45 VFHDPVSVALLERVQMVAPSDANVVIIGATGTGKELIARHVHELSTRRNGPFVAVNCGAF 104 + P L++ + M APSD V++ G TGTGKEL+A +H S R + P +++NC A Sbjct: 201 IGQSPAHRQLMQEIGMAAPSDMTVLVAGETGTGKELVAHALHAASPRAHKPMISLNCAAL 260 Query: 105 SENLAESELFGHEKGAFTGAIAHKAGWFEAANGGTLFLDEIGDLPLAIQVKLLRVLQERE 164 + L ESELFGH +GAF+GA+A + G FE A+GGTLFLDE+G+LPLA+Q KLLRVLQ + Sbjct: 261 PDTLVESELFGHVRGAFSGAVADRRGKFEMADGGTLFLDEVGELPLAVQAKLLRVLQSGQ 320 Query: 165 VVRLGSRRSIPIDVRIIAATNVRLQDAVAAGHFRQDLYYRLQVVQLTIPRLRERPEDILP 224 + R+GS R +DVR+IAATN L D V GHFR D Y+RL V + +P LRER D+L Sbjct: 321 LQRVGSDREHRVDVRLIAATNRDLADEVKRGHFRADFYHRLSVFPIRVPPLRERGRDVLL 380 Query: 225 LAYHFLDEYRQRLGYGARGIDAEGERKLRSHDWPGNIRELENAIHHALL 273 LA +FL++ R RLG + + A+ +R L + WPGNIRELE+ I + L Sbjct: 381 LAGYFLEQNRARLGLSSLRLSADAQRALLDYAWPGNIRELEHLIGRSAL 429 >gi|300312042|ref|YP_003776134.1| response regulatory protein [Herbaspirillum seropedicae SmR1] Length = 450 Score = 233 bits (593), Expect = 2e-62, Method: Compositional matrix adjust. Identities = 112/244 (45%), Positives = 164/244 (67%) Query: 45 VFHDPVSVALLERVQMVAPSDANVVIIGATGTGKELIARHVHELSTRRNGPFVAVNCGAF 104 + D +A+ ++ VAPS A+V+++G++GTGKE++AR +H+LS R F+A+NC A Sbjct: 149 ITRDAGMLAVCRSIEKVAPSSASVMLLGSSGTGKEVLARALHQLSPRSGRRFMAINCAAI 208 Query: 105 SENLAESELFGHEKGAFTGAIAHKAGWFEAANGGTLFLDEIGDLPLAIQVKLLRVLQERE 164 ENL ESELFG+EKGAFTGA G E A+GGT FLDE+GDLP+ +Q KLLR LQER Sbjct: 209 PENLLESELFGYEKGAFTGAAKQTIGKVELAHGGTFFLDEVGDLPMPLQAKLLRFLQERV 268 Query: 165 VVRLGSRRSIPIDVRIIAATNVRLQDAVAAGHFRQDLYYRLQVVQLTIPRLRERPEDILP 224 + R+G IP+DVR+I AT+ L++ A+G FR+DLYYRL + + IP L+ER D + Sbjct: 269 IERVGGHTEIPVDVRVICATHQNLKELTASGGFREDLYYRLCEIIIKIPALKERHGDAVL 328 Query: 225 LAYHFLDEYRQRLGYGARGIDAEGERKLRSHDWPGNIRELENAIHHALLICQDEQLRAEH 284 LA HF+ ++ + G + + + ++WPGN+RE+EN + A+++ +Q+ AE Sbjct: 329 LARHFVQKFCAKEGRATLHLSQDAVAAIERYEWPGNVREMENCVMRAVIMADGQQITAED 388 Query: 285 LHLS 288 L LS Sbjct: 389 LGLS 392 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 0.322 0.136 0.390 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: 1,141,979 Number of extensions: 48794 Number of successful extensions: 210 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 195 Number of HSP's successfully gapped: 12 Length of query: 374 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 287 Effective length of database: 1,207,925 Effective search space: 346674475 Effective search space used: 346674475 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)