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= 0001.2361.p (542 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein... 1104 0.0 gi|300313867|ref|YP_003777959.1| phenol-degradative gene regulat... 253 3e-68 gi|300314016|ref|YP_003778108.1| two component transcription reg... 252 7e-68 gi|300312042|ref|YP_003776134.1| response regulatory protein [He... 251 8e-68 gi|300313916|ref|YP_003778008.1| two component response regulato... 251 1e-67 >gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein [Herbaspirillum seropedicae SmR1] Length = 542 Score = 1104 bits (2856), Expect = 0.0, Method: Compositional matrix adjust. Identities = 537/542 (99%), Positives = 539/542 (99%) Query: 1 MATILDDRSVNLELVTIYEISKILGSSLDLSKTLREVLNVLSAHLETKRVLLSLMQDSGE 60 MATILDDRSVNLELVTIYEISKILGSSLDLSKTLREVLNVLSAHLETKRVLLSLMQDSGE Sbjct: 1 MATILDDRSVNLELVTIYEISKILGSSLDLSKTLREVLNVLSAHLETKRVLLSLMQDSGE 60 Query: 61 LQLVSAIGLSYEEFQSGRYRVGEGITGKIFQTETPIVVRDLAQEPLFLARTSPRQSQDGE 120 LQLVSAIGLSYEEFQSGRYRVGEGITGKIFQTETPIVVRDLAQEPLFLARTSPRQSQDGE Sbjct: 61 LQLVSAIGLSYEEFQSGRYRVGEGITGKIFQTETPIVVRDLAQEPLFLARTSPRQSQDGE 120 Query: 121 VLSFVGVPIKAAREMLGVLCVFRDGQSPSRSVDHEVRLLTMVANLIGQTVRLYRSVAAER 180 V+SFVGVPIKAAREMLGVLCVFRDGQSPSRSVDHEVRLLTMVANLIGQTVRLYRSVAAER Sbjct: 121 VISFVGVPIKAAREMLGVLCVFRDGQSPSRSVDHEVRLLTMVANLIGQTVRLYRSVAAER 180 Query: 181 QQLQEEKRQLSRQLQGKYKLDNVIGISKAMQEVFAQVHQSAPSRSTMLLRGESGTGKEVI 240 QQLQEEKRQLSRQLQGKYKLDNVIGISKAMQEVFAQVHQSAPSRSTMLLRGESGTGKEVI Sbjct: 181 QQLQEEKRQLSRQLQGKYKLDNVIGISKAMQEVFAQVHQSAPSRSTMLLRGESGTGKEVI 240 Query: 241 ARAIHYLSPRKDGPFIKVNCAALSETLLESELFGHEKGAFTGAQGERKGRFELAHGGTLF 300 ARAIHYLSPRKDGPFIKVNCAALSETLLESELFGHEKGAFTGAQGERKGRFELAHGGTLF Sbjct: 241 ARAIHYLSPRKDGPFIKVNCAALSETLLESELFGHEKGAFTGAQGERKGRFELAHGGTLF 300 Query: 301 LDEIGEISPAFQAKLLRVLQEREFERVGGSRSIKVDVRLVTATNRDLEKAVAKGEFRADL 360 LDEIGEISPAFQAKLLRVLQEREFERVGGSRSIKVDVRLVTATNRDLEKAVAKGEFRADL Sbjct: 301 LDEIGEISPAFQAKLLRVLQEREFERVGGSRSIKVDVRLVTATNRDLEKAVAKGEFRADL 360 Query: 361 YYRINVVSIFIPPLRERREDIPYLVEHFLEKFRVENQRAMVAMSPQAMKVMINCYWPGNV 420 YYRINVVSIFIPPLRERREDIPYLVEHFLEKFRVENQRAMVAMSPQAMKVM+NCYWPGNV Sbjct: 361 YYRINVVSIFIPPLRERREDIPYLVEHFLEKFRVENQRAMVAMSPQAMKVMMNCYWPGNV 420 Query: 421 RELENCVERTATMMRGDLITEVHFSCQQNKCLTKVLHEPGQQQPVVVVPLERISAHTLPS 480 RELENCVERTATMMRGDLITEVHFSCQQNKCLTKVLHEPGQQQPVVVVPLERISAHT PS Sbjct: 421 RELENCVERTATMMRGDLITEVHFSCQQNKCLTKVLHEPGQQQPVVVVPLERISAHTAPS 480 Query: 481 SPSGMVKDKPLAATPPTSERERLIWAMEQCGWVQAKAARALNISPRQMGYALQKFNIEVK 540 SPSGM KDKPLAA PPTSERERLIWAMEQCGWVQAKAARALNISPRQMGYALQKFNIEVK Sbjct: 481 SPSGMAKDKPLAAAPPTSERERLIWAMEQCGWVQAKAARALNISPRQMGYALQKFNIEVK 540 Query: 541 KF 542 KF Sbjct: 541 KF 542 >gi|300313867|ref|YP_003777959.1| phenol-degradative gene regulator transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 611 Score = 253 bits (646), Expect = 3e-68, Method: Compositional matrix adjust. Identities = 161/442 (36%), Positives = 236/442 (53%), Gaps = 40/442 (9%) Query: 125 VGVPIKAAREMLGVLCVFRDGQSPSRSVDHEVRLLTMVANLIGQTVRLYRSVAAERQQLQ 184 VG I +LG L +FR+ Q + H +IG++ L+ + + L Sbjct: 175 VGYAIGYVSTLLGHLVIFREVQCRAMGTAH--------CRVIGRSAELWSDAEEDLRYLN 226 Query: 185 EEKRQLSRQL------------QGKYKLDN-------VIGISKAMQEVFAQVHQSAPSRS 225 + S L QG + D+ ++G S A +++ A + + Sbjct: 227 AQDFVGSGMLASEADASAEDGAQGAGEQDDDTDLVTALVGTSSAFNAACHLLNRVAATDA 286 Query: 226 TMLLRGESGTGKEVIARAIHYLSPRKDGPFIKVNCAALSETLLESELFGHEKGAFTGAQG 285 T+L GESG GKE AR +H + R I +NCAA+ ETL+E+ELFG E+GA+TGA Sbjct: 287 TVLFTGESGVGKERFARMLHQIGKRAKRACIAINCAAIPETLIEAELFGVERGAYTGATQ 346 Query: 286 ERKGRFELAHGGTLFLDEIGEISPAFQAKLLRVLQEREFERVGGSRSIKVDVRLVTATNR 345 R GRFELA GGTLFLDE+G +S Q KLLRVLQE EFERVG +R +KVDVR+V ATN Sbjct: 347 SRAGRFELADGGTLFLDEVGTLSLVAQGKLLRVLQEGEFERVGSARPVKVDVRVVAATNE 406 Query: 346 DLEKAVAKGEFRADLYYRINVVSIFIPPLRERREDIPYLVEHFLEKFRVENQRAMVAMSP 405 DL +AV +G FR DL++R+NV I +PPLRERR+DIP L+ HFL+ + + A+ + Sbjct: 407 DLAQAVREGRFRQDLFFRLNVFPIHLPPLRERRDDIPLLMNHFLKLYGQRHGIAVRGFTQ 466 Query: 406 QAMKVMINCYWPGNVRELENCVERTATMMRGDLITEVHFSCQQNKCLTKVLHEPGQQQPV 465 +A++ ++N +PGN+REL+N +ER + +G + H + +VL Q + Sbjct: 467 RAIQALLNYSFPGNIRELQNLIERGVILAQGHPLDLPHMFISGERLNDEVLSLALQGETG 526 Query: 466 VVV------PLERISAHTLPSSPSGMVKD-------KPLAATPPTSERERLIWAMEQCGW 512 ++ +E+ AH +++ + A T P ER + A+E+ Sbjct: 527 MLAGKSVEKSVEKSVAHPTAQGLLDVLRQWRQEAAGEAAALTLPEMERRLIAEAIERAEG 586 Query: 513 VQAKAARALNISPRQMGYALQK 534 + AAR L IS Q+ Y QK Sbjct: 587 NLSAAARLLGISRAQLAYRQQK 608 >gi|300314016|ref|YP_003778108.1| two component transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 466 Score = 252 bits (643), Expect = 7e-68, Method: Compositional matrix adjust. Identities = 119/238 (50%), Positives = 169/238 (71%) Query: 202 NVIGISKAMQEVFAQVHQSAPSRSTMLLRGESGTGKEVIARAIHYLSPRKDGPFIKVNCA 261 +++ S+ + E+ A+ A S +++L+RG+SGTGKE++ARAIH S R + PFI VNC Sbjct: 143 DILSRSQRVAELLAEARLVAASDASILIRGDSGTGKELLARAIHRASARAEQPFIAVNCG 202 Query: 262 ALSETLLESELFGHEKGAFTGAQGERKGRFELAHGGTLFLDEIGEISPAFQAKLLRVLQE 321 A+ E LLESELFGH KGAFTGA R+G F+ AHGGTLFLDEIG++ Q KLLRVLQE Sbjct: 203 AIPEQLLESELFGHVKGAFTGAVEHREGLFQAAHGGTLFLDEIGDMPLPLQVKLLRVLQE 262 Query: 322 REFERVGGSRSIKVDVRLVTATNRDLEKAVAKGEFRADLYYRINVVSIFIPPLRERREDI 381 + +VG +++ +VDVR+++AT+RDLE A+ +G+FR DLYYR+NVV++ +P L ERREDI Sbjct: 263 KTVRQVGANQAGEVDVRIISATHRDLEAAMREGQFREDLYYRLNVVTLHLPALEERREDI 322 Query: 382 PYLVEHFLEKFRVENQRAMVAMSPQAMKVMINCYWPGNVRELENCVERTATMMRGDLI 439 L HFL+ + + + +P A++++ +WPGNVR+L N VE+ + LI Sbjct: 323 ALLANHFLKTIAAKYPKRLTGFAPDALEILSLAHWPGNVRQLYNVVEQVCALSTAPLI 380 >gi|300312042|ref|YP_003776134.1| response regulatory protein [Herbaspirillum seropedicae SmR1] Length = 450 Score = 251 bits (642), Expect = 8e-68, Method: Compositional matrix adjust. Identities = 137/293 (46%), Positives = 182/293 (62%), Gaps = 7/293 (2%) Query: 154 HEVRLLTMVAN------LIGQTVRLYRSVAAERQQLQEEKRQLSRQLQGKYKLDNVIGIS 207 H V+ ++M A I +T+RL A LQ E +++ +Q G L +I Sbjct: 94 HAVKAISMGAYDFHQKPCIDETLRLVVQRAFYLHALQRENQRM-QQAGGHTALGGLITRD 152 Query: 208 KAMQEVFAQVHQSAPSRSTMLLRGESGTGKEVIARAIHYLSPRKDGPFIKVNCAALSETL 267 M V + + APS ++++L G SGTGKEV+ARA+H LSPR F+ +NCAA+ E L Sbjct: 153 AGMLAVCRSIEKVAPSSASVMLLGSSGTGKEVLARALHQLSPRSGRRFMAINCAAIPENL 212 Query: 268 LESELFGHEKGAFTGAQGERKGRFELAHGGTLFLDEIGEISPAFQAKLLRVLQEREFERV 327 LESELFG+EKGAFTGA + G+ ELAHGGT FLDE+G++ QAKLLR LQER ERV Sbjct: 213 LESELFGYEKGAFTGAAKQTIGKVELAHGGTFFLDEVGDLPMPLQAKLLRFLQERVIERV 272 Query: 328 GGSRSIKVDVRLVTATNRDLEKAVAKGEFRADLYYRINVVSIFIPPLRERREDIPYLVEH 387 GG I VDVR++ AT+++L++ A G FR DLYYR+ + I IP L+ER D L H Sbjct: 273 GGHTEIPVDVRVICATHQNLKELTASGGFREDLYYRLCEIIIKIPALKERHGDAVLLARH 332 Query: 388 FLEKFRVENQRAMVAMSPQAMKVMINCYWPGNVRELENCVERTATMMRGDLIT 440 F++KF + RA + +S A+ + WPGNVRE+ENCV R M G IT Sbjct: 333 FVQKFCAKEGRATLHLSQDAVAAIERYEWPGNVREMENCVMRAVIMADGQQIT 385 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 251 bits (641), Expect = 1e-67, Method: Compositional matrix adjust. Identities = 122/236 (51%), Positives = 169/236 (71%), Gaps = 3/236 (1%) Query: 201 DNVIGISKAMQEVFAQVHQSAPSRSTMLLRGESGTGKEVIARAIHYLSPRKDGPFIKVNC 260 + ++G S+AM++VF Q+ ++A S +T+L+ GE+GTGKE++ARA+H R PF+ VNC Sbjct: 134 NQLVGESEAMRQVFKQIGRAATSDATVLVLGETGTGKELVARALHRNGARAARPFVAVNC 193 Query: 261 AALSETLLESELFGHEKGAFTGAQGERKGRFELAHGGTLFLDEIGEISPAFQAKLLRVLQ 320 AA+ L+ESELFGH KGAF+GA R GRF+ A GGTLFLDEIG++ A QAK+LRVLQ Sbjct: 194 AAIPAELIESELFGHVKGAFSGATSPRLGRFQEADGGTLFLDEIGDMELATQAKILRVLQ 253 Query: 321 EREFERVGGSRSIKVDVRLVTATNRDLEKAVAKGEFRADLYYRINVVSIFIPPLRERRED 380 ERE VGG++S++VDVR++ AT+RDL+ + +G FR DL+YR+ V++I +P LRER D Sbjct: 254 ERELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWYRLQVLTIMVPALRERPGD 313 Query: 381 IPYLVEHFLEKFRVENQRAMVAMSPQAMKVMINCYWPGNVRELENCVERTATMMRG 436 I + EHFL + A +SP A ++++ WPGNVREL N +ER A M G Sbjct: 314 ILTIAEHFLRQL---GGDAPKRISPAAARLLLQHAWPGNVRELRNTMERAAVMSHG 366 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 0.319 0.134 0.379 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: 1,430,857 Number of extensions: 53946 Number of successful extensions: 225 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 212 Number of HSP's successfully gapped: 12 Length of query: 542 Length of database: 1,619,870 Length adjustment: 90 Effective length of query: 452 Effective length of database: 1,193,720 Effective search space: 539561440 Effective search space used: 539561440 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)