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= 0019.0057.p (525 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311822|ref|YP_003775914.1| sigma-54 dependent transcriptio... 851 0.0 gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein... 253 2e-68 gi|300313867|ref|YP_003777959.1| phenol-degradative gene regulat... 252 6e-68 gi|300313916|ref|YP_003778008.1| two component response regulato... 250 2e-67 gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcrip... 243 3e-65 >gi|300311822|ref|YP_003775914.1| sigma-54 dependent transcription regulator [Herbaspirillum seropedicae SmR1] Length = 526 Score = 851 bits (2198), Expect = 0.0, Method: Compositional matrix adjust. Identities = 452/526 (85%), Positives = 485/526 (92%), Gaps = 1/526 (0%) Query: 1 MTSKVLLDALLPLVADLSRQIDDRERYRRLLQTLRTLFPCDAAALLRLEGELLVPLAIDG 60 MTS+ LLDAL+PLVADLSR+IDDRERYRRLLQTLRTLFPCDAAALLRLEG++LVPLAIDG Sbjct: 1 MTSRTLLDALVPLVADLSREIDDRERYRRLLQTLRTLFPCDAAALLRLEGDVLVPLAIDG 60 Query: 61 LSSDTLGRRFRIADHPRFGVLLANLGPTRFPADSSLPDPYDGLVDGLNDAHSGALEVHDC 120 LSSDTLGRRFRI +HPRFG+LL N PTRF ADS LPDPYDGLVDGLND HSG LEVHDC Sbjct: 61 LSSDTLGRRFRITEHPRFGILLGNAAPTRFAADSPLPDPYDGLVDGLNDQHSGELEVHDC 120 Query: 121 MGCALSVNGRPWGLVTLDALGAGRFDGVDMASLQAFAALAAATVHVAERIDDLAAAGERA 180 MGCAL+VNGR WGL+TLDALG GRFD VDM SLQAFAALAAATV+VAERI DLA AG++A Sbjct: 121 MGCALTVNGRAWGLMTLDALGRGRFDRVDMDSLQAFAALAAATVNVAERISDLAQAGQQA 180 Query: 181 RQRAEAYRLGLEESQGKRELIGQSPAQQQLLEEIRMAAPSDMTVLVTGETGTGKELVAHA 240 +QRAEAYRLGLE+SQG+RELIGQSPA +QL++EI MAAPSDMTVLV GETGTGKELVAHA Sbjct: 181 QQRAEAYRLGLEQSQGQRELIGQSPAHRQLMQEIGMAAPSDMTVLVAGETGTGKELVAHA 240 Query: 241 LHAASPRAHKPMISLNCAALPDTLVESELFGHVRGAFSGAVADRRGKFEMADGGTLFLDE 300 LHAASPRAHKPMISLNCAALPDTLVESELFGHVRGAFSGAVADRRGKFEMADGGTLFLDE Sbjct: 241 LHAASPRAHKPMISLNCAALPDTLVESELFGHVRGAFSGAVADRRGKFEMADGGTLFLDE 300 Query: 301 VGELPLAVQAKLLRVLQSGQLQRVGSDREHRVDVRLIAATNRDLAEEVKRGHFRADFYHR 360 VGELPLAVQAKLLRVLQSGQLQRVGSDREHRVDVRLIAATNRDLA+EVKRGHFRADFYHR Sbjct: 301 VGELPLAVQAKLLRVLQSGQLQRVGSDREHRVDVRLIAATNRDLADEVKRGHFRADFYHR 360 Query: 361 LSVFPIRVPPLRERGRDVLLLAGYFLEQNRARLGLSSLRLAADAQRALLDYAWPGNIREL 420 LSVFPIRVPPLRERGRDVLLLAGYFLEQNRARLGLSSLRL+ADAQRALLDYAWPGNIREL Sbjct: 361 LSVFPIRVPPLRERGRDVLLLAGYFLEQNRARLGLSSLRLSADAQRALLDYAWPGNIREL 420 Query: 421 EHLIGRSALRALASQPKRSAILTLDAAALEL-GHSARPLASPDTAANAQAEPAQPGEGLR 479 EHLIGRSALR+LA+ R ILTLDAAALEL S +A+ + + A++ PAQ LR Sbjct: 421 EHLIGRSALRSLATHRTRPTILTLDAAALELPAPSLATVAAAEPSLPAESTPAQASGSLR 480 Query: 480 AAVERFERKLVSDCLERHGGNLAATARELGVDRANLNRLARRLGLR 525 A+ER+ER+LVS L+RHGGNLAATARELGVDRANLNRLA+RLGLR Sbjct: 481 DALERYERQLVSAALQRHGGNLAATARELGVDRANLNRLAKRLGLR 526 >gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein [Herbaspirillum seropedicae SmR1] Length = 542 Score = 253 bits (647), Expect = 2e-68, Method: Compositional matrix adjust. Identities = 126/258 (48%), Positives = 179/258 (69%), Gaps = 4/258 (1%) Query: 174 AAAGERARQRAEAYRLGLEESQGKREL---IGQSPAQQQLLEEIRMAAPSDMTVLVTGET 230 + A ER + + E +L + QGK +L IG S A Q++ ++ +APS T+L+ GE+ Sbjct: 175 SVAAERQQLQEEKRQLS-RQLQGKYKLDNVIGISKAMQEVFAQVHQSAPSRSTMLLRGES 233 Query: 231 GTGKELVAHALHAASPRAHKPMISLNCAALPDTLVESELFGHVRGAFSGAVADRRGKFEM 290 GTGKE++A A+H SPR P I +NCAAL +TL+ESELFGH +GAF+GA +R+G+FE+ Sbjct: 234 GTGKEVIARAIHYLSPRKDGPFIKVNCAALSETLLESELFGHEKGAFTGAQGERKGRFEL 293 Query: 291 ADGGTLFLDEVGELPLAVQAKLLRVLQSGQLQRVGSDREHRVDVRLIAATNRDLAEEVKR 350 A GGTLFLDE+GE+ A QAKLLRVLQ + +RVG R +VDVRL+ ATNRDL + V + Sbjct: 294 AHGGTLFLDEIGEISPAFQAKLLRVLQEREFERVGGSRSIKVDVRLVTATNRDLEKAVAK 353 Query: 351 GHFRADFYHRLSVFPIRVPPLRERGRDVLLLAGYFLEQNRARLGLSSLRLAADAQRALLD 410 G FRAD Y+R++V I +PPLRER D+ L +FLE+ R + + ++ A + +++ Sbjct: 354 GEFRADLYYRINVVSIFIPPLRERREDIPYLVEHFLEKFRVENQRAMVAMSPQAMKVMMN 413 Query: 411 YAWPGNIRELEHLIGRSA 428 WPGN+RELE+ + R+A Sbjct: 414 CYWPGNVRELENCVERTA 431 >gi|300313867|ref|YP_003777959.1| phenol-degradative gene regulator transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 611 Score = 252 bits (643), Expect = 6e-68, Method: Compositional matrix adjust. Identities = 148/339 (43%), Positives = 197/339 (58%), Gaps = 23/339 (6%) Query: 200 LIGQSPAQQQLLEEIRMAAPSDMTVLVTGETGTGKELVAHALHAASPRAHKPMISLNCAA 259 L+G S A + A +D TVL TGE+G GKE A LH RA + I++NCAA Sbjct: 264 LVGTSSAFNAACHLLNRVAATDATVLFTGESGVGKERFARMLHQIGKRAKRACIAINCAA 323 Query: 260 LPDTLVESELFGHVRGAFSGAVADRRGKFEMADGGTLFLDEVGELPLAVQAKLLRVLQSG 319 +P+TL+E+ELFG RGA++GA R G+FE+ADGGTLFLDEVG L L Q KLLRVLQ G Sbjct: 324 IPETLIEAELFGVERGAYTGATQSRAGRFELADGGTLFLDEVGTLSLVAQGKLLRVLQEG 383 Query: 320 QLQRVGSDREHRVDVRLIAATNRDLAEEVKRGHFRADFYHRLSVFPIRVPPLRERGRDVL 379 + +RVGS R +VDVR++AATN DLA+ V+ G FR D + RL+VFPI +PPLRER D+ Sbjct: 384 EFERVGSARPVKVDVRVVAATNEDLAQAVREGRFRQDLFFRLNVFPIHLPPLRERRDDIP 443 Query: 380 LLAGYFLEQNRARLGLSSLRLAADAQRALLDYAWPGNIRELEHLIGRSALRA------LA 433 LL +FL+ R G++ A +ALL+Y++PGNIREL++LI R + A L Sbjct: 444 LLMNHFLKLYGQRHGIAVRGFTQRAIQALLNYSFPGNIRELQNLIERGVILAQGHPLDLP 503 Query: 434 SQPKRSAILTLDAAALELGHSARPLASPDTAANAQAEPAQP-----------------GE 476 L + +L L LA + + A P GE Sbjct: 504 HMFISGERLNDEVLSLALQGETGMLAGKSVEKSVEKSVAHPTAQGLLDVLRQWRQEAAGE 563 Query: 477 GLRAAVERFERKLVSDCLERHGGNLAATARELGVDRANL 515 + ER+L+++ +ER GNL+A AR LG+ RA L Sbjct: 564 AAALTLPEMERRLIAEAIERAEGNLSAAARLLGISRAQL 602 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 250 bits (639), Expect = 2e-67, Method: Compositional matrix adjust. Identities = 148/321 (46%), Positives = 202/321 (62%), Gaps = 15/321 (4%) Query: 197 KRELIGQSPAQQQLLEEIRMAAPSDMTVLVTGETGTGKELVAHALHAASPRAHKPMISLN 256 + +L+G+S A +Q+ ++I AA SD TVLV GETGTGKELVA ALH RA +P +++N Sbjct: 133 RNQLVGESEAMRQVFKQIGRAATSDATVLVLGETGTGKELVARALHRNGARAARPFVAVN 192 Query: 257 CAALPDTLVESELFGHVRGAFSGAVADRRGKFEMADGGTLFLDEVGELPLAVQAKLLRVL 316 CAA+P L+ESELFGHV+GAFSGA + R G+F+ ADGGTLFLDE+G++ LA QAK+LRVL Sbjct: 193 CAAIPAELIESELFGHVKGAFSGATSPRLGRFQEADGGTLFLDEIGDMELATQAKILRVL 252 Query: 317 QSGQLQRVGSDREHRVDVRLIAATNRDLAEEVKRGHFRADFYHRLSVFPIRVPPLRERGR 376 Q +L VG ++ RVDVR+IAAT+RDL E+ +G FR D ++RL V I VP LRER Sbjct: 253 QERELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWYRLQVLTIMVPALRERPG 312 Query: 377 DVLLLAGYFLEQNRARLGLSSLRLAADAQRALLDYAWPGNIRELEHLIGRSALRALASQP 436 D+L +A +FL Q G + R++ A R LL +AWPGN+REL + + R+A+ Sbjct: 313 DILTIAEHFLRQLG---GDAPKRISPAAARLLLQHAWPGNVRELRNTMERAAV------- 362 Query: 437 KRSAILTLDAAALELGHSARPLASPDTAANAQAEPAQPGEGLRAAVERFERKLVSDCLER 496 S L ++A + L + A+ + P L A+ ER ++ L+ Sbjct: 363 -MSHGLCIEAEDIGLSARPP-AGAASAASAPAIDWDGP---LAVALAEVERVMIERALQG 417 Query: 497 HGGNLAATARELGVDRANLNR 517 GN A AR LG+ R L R Sbjct: 418 AAGNRAEAARRLGISRQQLYR 438 >gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcription activator protein [Herbaspirillum seropedicae SmR1] Length = 500 Score = 243 bits (620), Expect = 3e-65, Method: Compositional matrix adjust. Identities = 119/225 (52%), Positives = 166/225 (73%) Query: 199 ELIGQSPAQQQLLEEIRMAAPSDMTVLVTGETGTGKELVAHALHAASPRAHKPMISLNCA 258 E++GQ+PA Q + I + S++TVL+TGE+G+GKELVA ALH SPRA +P ++LN A Sbjct: 135 EILGQAPAMQDVFRAIGRLSQSNVTVLITGESGSGKELVARALHKHSPRASQPFVALNTA 194 Query: 259 ALPDTLVESELFGHVRGAFSGAVADRRGKFEMADGGTLFLDEVGELPLAVQAKLLRVLQS 318 A+P L+ESELFGH RGAF+GA A RRG+FE A+GGTLFLDE+G++PL +Q +LLRVL Sbjct: 195 AIPKDLLESELFGHERGAFTGAQAMRRGRFEQAEGGTLFLDEIGDMPLDLQTRLLRVLSD 254 Query: 319 GQLQRVGSDREHRVDVRLIAATNRDLAEEVKRGHFRADFYHRLSVFPIRVPPLRERGRDV 378 G RVG + + +VR+IAAT+++L + V+ G FR D YHRL+V +R+P LRER D+ Sbjct: 255 GHFYRVGGHQSLKANVRVIAATHQNLEQRVREGLFREDLYHRLNVIRLRLPSLRERSEDI 314 Query: 379 LLLAGYFLEQNRARLGLSSLRLAADAQRALLDYAWPGNIRELEHL 423 +LA YFL Q+ +LG+ + RL+ A + L +PGN+R+LE+L Sbjct: 315 PILARYFLAQSARQLGVEAKRLSPQAMQFLSQLEFPGNVRQLENL 359 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 0.392 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: 1,377,193 Number of extensions: 57547 Number of successful extensions: 298 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 280 Number of HSP's successfully gapped: 12 Length of query: 525 Length of database: 1,619,870 Length adjustment: 90 Effective length of query: 435 Effective length of database: 1,193,720 Effective search space: 519268200 Effective search space used: 519268200 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: 133 (55.8 bits)