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= 0030.0088.p (526 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... 1038 0.0 gi|300313916|ref|YP_003778008.1| two component response regulato... 264 1e-71 gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein... 251 8e-68 gi|300313867|ref|YP_003777959.1| phenol-degradative gene regulat... 248 7e-67 gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcrip... 244 1e-65 >gi|300311822|ref|YP_003775914.1| sigma-54 dependent transcription regulator [Herbaspirillum seropedicae SmR1] Length = 526 Score = 1038 bits (2685), Expect = 0.0, Method: Compositional matrix adjust. Identities = 524/526 (99%), Positives = 526/526 (100%) Query: 1 MTSRTLLDALVPLVADLSREIDDRERYRRLLQTLRTLFPCDAAALLRLEGDVLVPLAIDG 60 MTSRTLLDALVPLVADLSREIDDRERYRRLLQTLRTLFPCDAAALLRLEGDVLVPLAIDG Sbjct: 1 MTSRTLLDALVPLVADLSREIDDRERYRRLLQTLRTLFPCDAAALLRLEGDVLVPLAIDG 60 Query: 61 LSSDTLGRRFRITEHPRFGILLGNAAPTRFAADSPLPDPYDGLVDGLNDQHSGELEVHDC 120 LSSDTLGRRFRITEHPRFGILLGNAAPTRFAADSPLPDPYDGLVDGLNDQHSGELEVHDC Sbjct: 61 LSSDTLGRRFRITEHPRFGILLGNAAPTRFAADSPLPDPYDGLVDGLNDQHSGELEVHDC 120 Query: 121 MGCALTVNGRAWGLMTLDALGRGRFDRVDMDSLQAFAALAAATVNVAERISDLAQAGQQA 180 MGCALTVNGRAWGLMTLDALGRGRFDRVDMDSLQAFAALAAATVNVAERISDLAQAGQQA Sbjct: 121 MGCALTVNGRAWGLMTLDALGRGRFDRVDMDSLQAFAALAAATVNVAERISDLAQAGQQA 180 Query: 181 QQRAEAYRLGLEQSQGQRELMGQSPAHRQLMQEIGMAAPSDMTVLVAGETGTGKELVAHA 240 QQRAEAYRLGLEQSQGQREL+GQSPAHRQLMQEIGMAAPSDMTVLVAGETGTGKELVAHA Sbjct: 181 QQRAEAYRLGLEQSQGQRELIGQSPAHRQLMQEIGMAAPSDMTVLVAGETGTGKELVAHA 240 Query: 241 LHAASPRAHKPMISLNCAALPDTLVESELFGHVRGAFSGAVADRRGKFEMADGGTLFLDE 300 LHAASPRAHKPMISLNCAALPDTLVESELFGHVRGAFSGAVADRRGKFEMADGGTLFLDE Sbjct: 241 LHAASPRAHKPMISLNCAALPDTLVESELFGHVRGAFSGAVADRRGKFEMADGGTLFLDE 300 Query: 301 VGELPLAVQAKLLRVLQSGQLQRVGSDREHRVDVRLIAATNRDLADEVKRGHFRADFYHR 360 VGELPLAVQAKLLRVLQSGQLQRVGSDREHRVDVRLIAATNRDLADEVKRGHFRADFYHR Sbjct: 301 VGELPLAVQAKLLRVLQSGQLQRVGSDREHRVDVRLIAATNRDLADEVKRGHFRADFYHR 360 Query: 361 LSVFPIRVPPLRERGRDVLLLAGYFLEQNRARLGLSSLRLSADAQRALLDYAWPGNIREL 420 LSVFPIRVPPLRERGRDVLLLAGYFLEQNRARLGLSSLRLSADAQRALLDYAWPGNIREL Sbjct: 361 LSVFPIRVPPLRERGRDVLLLAGYFLEQNRARLGLSSLRLSADAQRALLDYAWPGNIREL 420 Query: 421 EHLIGRSALRSLATHRTRPSILTLDAAALELPAPSLATVAAAEPSLPAESTPAQASGSLR 480 EHLIGRSALRSLATHRTRP+ILTLDAAALELPAPSLATVAAAEPSLPAESTPAQASGSLR Sbjct: 421 EHLIGRSALRSLATHRTRPTILTLDAAALELPAPSLATVAAAEPSLPAESTPAQASGSLR 480 Query: 481 DALERYERQLVSAALQRHGGNLAATARELGVDRANLNRLAKRLGLR 526 DALERYERQLVSAALQRHGGNLAATARELGVDRANLNRLAKRLGLR Sbjct: 481 DALERYERQLVSAALQRHGGNLAATARELGVDRANLNRLAKRLGLR 526 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 264 bits (675), Expect = 1e-71, Method: Compositional matrix adjust. Identities = 154/320 (48%), Positives = 201/320 (62%), Gaps = 16/320 (5%) Query: 199 ELMGQSPAHRQLMQEIGMAAPSDMTVLVAGETGTGKELVAHALHAASPRAHKPMISLNCA 258 +L+G+S A RQ+ ++IG AA SD TVLV GETGTGKELVA ALH RA +P +++NCA Sbjct: 135 QLVGESEAMRQVFKQIGRAATSDATVLVLGETGTGKELVARALHRNGARAARPFVAVNCA 194 Query: 259 ALPDTLVESELFGHVRGAFSGAVADRRGKFEMADGGTLFLDEVGELPLAVQAKLLRVLQS 318 A+P L+ESELFGHV+GAFSGA + R G+F+ ADGGTLFLDE+G++ LA QAK+LRVLQ Sbjct: 195 AIPAELIESELFGHVKGAFSGATSPRLGRFQEADGGTLFLDEIGDMELATQAKILRVLQE 254 Query: 319 GQLQRVGSDREHRVDVRLIAATNRDLADEVKRGHFRADFYHRLSVFPIRVPPLRERGRDV 378 +L VG ++ RVDVR+IAAT+RDL E+ +G FR D ++RL V I VP LRER D+ Sbjct: 255 RELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWYRLQVLTIMVPALRERPGDI 314 Query: 379 LLLAGYFLEQNRARLGLSSLRLSADAQRALLDYAWPGNIRELEHLIGRSALRSLATHRTR 438 L +A +FL Q G + R+S A R LL +AWPGN+REL + + R+A+ S Sbjct: 315 LTIAEHFLRQLG---GDAPKRISPAAARLLLQHAWPGNVRELRNTMERAAVMS------- 364 Query: 439 PSILTLDAAALELPAPSLATVAAAEPSLPAESTPAQASGSLRDALERYERQLVSAALQRH 498 +E L+ A + A + G L AL ER ++ ALQ Sbjct: 365 ------HGLCIEAEDIGLSARPPAGAASAASAPAIDWDGPLAVALAEVERVMIERALQGA 418 Query: 499 GGNLAATARELGVDRANLNR 518 GN A AR LG+ R L R Sbjct: 419 AGNRAEAARRLGISRQQLYR 438 >gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein [Herbaspirillum seropedicae SmR1] Length = 542 Score = 251 bits (642), Expect = 8e-68, Method: Compositional matrix adjust. Identities = 143/347 (41%), Positives = 205/347 (59%), Gaps = 18/347 (5%) Query: 181 QQRAEAYRLGLEQSQGQREL---MGQSPAHRQLMQEIGMAAPSDMTVLVAGETGTGKELV 237 QQ E R Q QG+ +L +G S A +++ ++ +APS T+L+ GE+GTGKE++ Sbjct: 181 QQLQEEKRQLSRQLQGKYKLDNVIGISKAMQEVFAQVHQSAPSRSTMLLRGESGTGKEVI 240 Query: 238 AHALHAASPRAHKPMISLNCAALPDTLVESELFGHVRGAFSGAVADRRGKFEMADGGTLF 297 A A+H SPR P I +NCAAL +TL+ESELFGH +GAF+GA +R+G+FE+A GGTLF Sbjct: 241 ARAIHYLSPRKDGPFIKVNCAALSETLLESELFGHEKGAFTGAQGERKGRFELAHGGTLF 300 Query: 298 LDEVGELPLAVQAKLLRVLQSGQLQRVGSDREHRVDVRLIAATNRDLADEVKRGHFRADF 357 LDE+GE+ A QAKLLRVLQ + +RVG R +VDVRL+ ATNRDL V +G FRAD Sbjct: 301 LDEIGEISPAFQAKLLRVLQEREFERVGGSRSIKVDVRLVTATNRDLEKAVAKGEFRADL 360 Query: 358 YHRLSVFPIRVPPLRERGRDVLLLAGYFLEQNRARLGLSSLRLSADAQRALLDYAWPGNI 417 Y+R++V I +PPLRER D+ L +FLE+ R + + +S A + +++ WPGN+ Sbjct: 361 YYRINVVSIFIPPLRERREDIPYLVEHFLEKFRVENQRAMVAMSPQAMKVMMNCYWPGNV 420 Query: 418 RELEHLIGRSA-------LRSLATHRTRPSILTLDAAALELPAPSLATVAAAEPSLPAES 470 RELE+ + R+A + + + LT L P V + A + Sbjct: 421 RELENCVERTATMMRGDLITEVHFSCQQNKCLT---KVLHEPGQQQPVVVVPLERISAHT 477 Query: 471 TPAQASGSLRD-----ALERYERQLVSAALQRHGGNLAATARELGVD 512 P+ SG +D A ER+ + A+++ G A AR L + Sbjct: 478 APSSPSGMAKDKPLAAAPPTSERERLIWAMEQCGWVQAKAARALNIS 524 >gi|300313867|ref|YP_003777959.1| phenol-degradative gene regulator transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 611 Score = 248 bits (634), Expect = 7e-67, Method: Compositional matrix adjust. Identities = 150/344 (43%), Positives = 204/344 (59%), Gaps = 32/344 (9%) Query: 200 LMGQSPAHRQLMQEIGMAAPSDMTVLVAGETGTGKELVAHALHAASPRAHKPMISLNCAA 259 L+G S A + A +D TVL GE+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 QLQRVGSDREHRVDVRLIAATNRDLADEVKRGHFRADFYHRLSVFPIRVPPLRERGRDVL 379 + +RVGS R +VDVR++AATN DLA V+ G FR D + RL+VFPI +PPLRER D+ Sbjct: 384 EFERVGSARPVKVDVRVVAATNEDLAQAVREGRFRQDLFFRLNVFPIHLPPLRERRDDIP 443 Query: 380 LLAGYFLEQNRARLGLSSLRLSADAQRALLDYAWPGNIRELEHLIGRSALRS-------- 431 LL +FL+ R G++ + A +ALL+Y++PGNIREL++LI R + + Sbjct: 444 LLMNHFLKLYGQRHGIAVRGFTQRAIQALLNYSFPGNIRELQNLIERGVILAQGHPLDLP 503 Query: 432 ---LATHRTRPSILTLDAAALELPAPSLATVAAAEPSLPAESTPAQASGSLRDALERY-- 486 ++ R +L+L AL+ LA + E S+ A G L D L ++ Sbjct: 504 HMFISGERLNDEVLSL---ALQGETGMLAG-KSVEKSVEKSVAHPTAQG-LLDVLRQWRQ 558 Query: 487 --------------ERQLVSAALQRHGGNLAATARELGVDRANL 516 ER+L++ A++R GNL+A AR LG+ RA L Sbjct: 559 EAAGEAAALTLPEMERRLIAEAIERAEGNLSAAARLLGISRAQL 602 >gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcription activator protein [Herbaspirillum seropedicae SmR1] Length = 500 Score = 244 bits (623), Expect = 1e-65, Method: Compositional matrix adjust. Identities = 122/234 (52%), Positives = 170/234 (72%), Gaps = 1/234 (0%) Query: 191 LEQSQGQR-ELMGQSPAHRQLMQEIGMAAPSDMTVLVAGETGTGKELVAHALHAASPRAH 249 +EQ Q E++GQ+PA + + + IG + S++TVL+ GE+G+GKELVA ALH SPRA Sbjct: 126 IEQGAAQTPEILGQAPAMQDVFRAIGRLSQSNVTVLITGESGSGKELVARALHKHSPRAS 185 Query: 250 KPMISLNCAALPDTLVESELFGHVRGAFSGAVADRRGKFEMADGGTLFLDEVGELPLAVQ 309 +P ++LN AA+P L+ESELFGH RGAF+GA A RRG+FE A+GGTLFLDE+G++PL +Q Sbjct: 186 QPFVALNTAAIPKDLLESELFGHERGAFTGAQAMRRGRFEQAEGGTLFLDEIGDMPLDLQ 245 Query: 310 AKLLRVLQSGQLQRVGSDREHRVDVRLIAATNRDLADEVKRGHFRADFYHRLSVFPIRVP 369 +LLRVL G RVG + + +VR+IAAT+++L V+ G FR D YHRL+V +R+P Sbjct: 246 TRLLRVLSDGHFYRVGGHQSLKANVRVIAATHQNLEQRVREGLFREDLYHRLNVIRLRLP 305 Query: 370 PLRERGRDVLLLAGYFLEQNRARLGLSSLRLSADAQRALLDYAWPGNIRELEHL 423 LRER D+ +LA YFL Q+ +LG+ + RLS A + L +PGN+R+LE+L Sbjct: 306 SLRERSEDIPILARYFLAQSARQLGVEAKRLSPQAMQFLSQLEFPGNVRQLENL 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 0.135 0.386 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: 1,484,327 Number of extensions: 62234 Number of successful extensions: 307 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 289 Number of HSP's successfully gapped: 12 Length of query: 526 Length of database: 1,619,870 Length adjustment: 90 Effective length of query: 436 Effective length of database: 1,193,720 Effective search space: 520461920 Effective search space used: 520461920 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: 133 (55.8 bits)