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= 0001.2463.p (472 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... 224 1e-59 gi|300314016|ref|YP_003778108.1| two component transcription reg... 221 1e-58 gi|300313867|ref|YP_003777959.1| phenol-degradative gene regulat... 218 8e-58 gi|300313916|ref|YP_003778008.1| two component response regulato... 218 1e-57 gi|300312042|ref|YP_003776134.1| response regulatory protein [He... 214 1e-56 >gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein [Herbaspirillum seropedicae SmR1] Length = 542 Score = 224 bits (571), Expect = 1e-59, Method: Compositional matrix adjust. Identities = 126/296 (42%), Positives = 173/296 (58%), Gaps = 24/296 (8%) Query: 142 IDEQHRVVGFVERL--QTVR-HASVQASRQGL--------------------VGKSAAFN 178 +D + R++ V L QTVR + SV A RQ L +G S A Sbjct: 152 VDHEVRLLTMVANLIGQTVRLYRSVAAERQQLQEEKRQLSRQLQGKYKLDNVIGISKAMQ 211 Query: 179 RALGELQRVAASELPVLLLGESGTGKELFARALHEASAHARGPFVVLDCSGLTETLFESE 238 ++ + A S +LL GESGTGKE+ ARA+H S GPF+ ++C+ L+ETL ESE Sbjct: 212 EVFAQVHQSAPSRSTMLLRGESGTGKEVIARAIHYLSPRKDGPFIKVNCAALSETLLESE 271 Query: 239 LFGYEKGAFTGAHVRKAGLVETAKGGTLFLDEIGDVPLGMQVKLLRLIESGTYRRVGAVD 298 LFG+EKGAFTGA + G E A GGTLFLDEIG++ Q KLLR+++ + RVG Sbjct: 272 LFGHEKGAFTGAQGERKGRFELAHGGTLFLDEIGEISPAFQAKLLRVLQEREFERVGGSR 331 Query: 299 TQQADFRLVAATHKPLQKMVANAQFRQDLYYRISAFPIHLPALRERRDDIALLVQSLLQR 358 + + D RLV AT++ L+K VA +FR DLYYRI+ I +P LRERR+DI LV+ L++ Sbjct: 332 SIKVDVRLVTATNRDLEKAVAKGEFRADLYYRINVVSIFIPPLRERREDIPYLVEHFLEK 391 Query: 359 GNGAPQQRL-QVSPQAMASLLNYDWPGNIRELRNVLERARLFADDGVIKPEHLALE 413 Q+ + +SPQAM ++N WPGN+REL N +ER +I H + + Sbjct: 392 FRVENQRAMVAMSPQAMKVMMNCYWPGNVRELENCVERTATMMRGDLITEVHFSCQ 447 >gi|300314016|ref|YP_003778108.1| two component transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 466 Score = 221 bits (563), Expect = 1e-58, Method: Compositional matrix adjust. Identities = 132/312 (42%), Positives = 184/312 (58%), Gaps = 8/312 (2%) Query: 164 QASRQGLVGKSAAFNRALGELQRVAASELPVLLLGESGTGKELFARALHEASAHARGPFV 223 Q+ R ++ +S L E + VAAS+ +L+ G+SGTGKEL ARA+H ASA A PF+ Sbjct: 138 QSWRADILSRSQRVAELLAEARLVAASDASILIRGDSGTGKELLARAIHRASARAEQPFI 197 Query: 224 VLDCSGLTETLFESELFGYEKGAFTGAHVRKAGLVETAKGGTLFLDEIGDVPLGMQVKLL 283 ++C + E L ESELFG+ KGAFTGA + GL + A GGTLFLDEIGD+PL +QVKLL Sbjct: 198 AVNCGAIPEQLLESELFGHVKGAFTGAVEHREGLFQAAHGGTLFLDEIGDMPLPLQVKLL 257 Query: 284 RLIESGTYRRVGAVDTQQADFRLVAATHKPLQKMVANAQFRQDLYYRISAFPIHLPALRE 343 R+++ T R+VGA + D R+++ATH+ L+ + QFR+DLYYR++ +HLPAL E Sbjct: 258 RVLQEKTVRQVGANQAGEVDVRIISATHRDLEAAMREGQFREDLYYRLNVVTLHLPALEE 317 Query: 344 RRDDIALLVQSLLQRGNGAPQQRLQ-VSPQAMASLLNYDWPGNIRELRNVLERARLFADD 402 RR+DIALL L+ +RL +P A+ L WPGN+R+L NV+E+ + Sbjct: 318 RREDIALLANHFLKTIAAKYPKRLTGFAPDALEILSLAHWPGNVRQLYNVVEQVCALSTA 377 Query: 403 GVIKPEHL---ALEPPLAIPVRSLQAGRSSHRSDLADLADIVRQFHGTRKELARSLGWSE 459 +I P L AL P +R +A + R L L + G + AR + Sbjct: 378 PLI-PASLVQRALRTPTLDLLRYAEAKQKFERDYLIRLLKLT---DGNVSDAARLADRNR 433 Query: 460 RTLYRRLKAVGL 471 YR L+ GL Sbjct: 434 TEFYRLLQKNGL 445 >gi|300313867|ref|YP_003777959.1| phenol-degradative gene regulator transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 611 Score = 218 bits (555), Expect = 8e-58, Method: Compositional matrix adjust. Identities = 117/235 (49%), Positives = 158/235 (67%), Gaps = 7/235 (2%) Query: 170 LVGKSAAFNRALGELQRVAASELPVLLLGESGTGKELFARALHEASAHARGPFVVLDCSG 229 LVG S+AFN A L RVAA++ VL GESG GKE FAR LH+ A+ + ++C+ Sbjct: 264 LVGTSSAFNAACHLLNRVAATDATVLFTGESGVGKERFARMLHQIGKRAKRACIAINCAA 323 Query: 230 LTETLFESELFGYEKGAFTGAHVRKAGLVETAKGGTLFLDEIGDVPLGMQVKLLRLIESG 289 + ETL E+ELFG E+GA+TGA +AG E A GGTLFLDE+G + L Q KLLR+++ G Sbjct: 324 IPETLIEAELFGVERGAYTGATQSRAGRFELADGGTLFLDEVGTLSLVAQGKLLRVLQEG 383 Query: 290 TYRRVGAVDTQQADFRLVAATHKPLQKMVANAQFRQDLYYRISAFPIHLPALRERRDDIA 349 + RVG+ + D R+VAAT++ L + V +FRQDL++R++ FPIHLP LRERRDDI Sbjct: 384 EFERVGSARPVKVDVRVVAATNEDLAQAVREGRFRQDLFFRLNVFPIHLPPLRERRDDIP 443 Query: 350 LLVQSLL----QRGNGAPQQRLQVSPQAMASLLNYDWPGNIRELRNVLERARLFA 400 LL+ L QR A + Q +A+ +LLNY +PGNIREL+N++ER + A Sbjct: 444 LLMNHFLKLYGQRHGIAVRGFTQ---RAIQALLNYSFPGNIRELQNLIERGVILA 495 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 218 bits (554), Expect = 1e-57, Method: Compositional matrix adjust. Identities = 132/324 (40%), Positives = 182/324 (56%), Gaps = 32/324 (9%) Query: 167 RQGLVGKSAAFNRALGELQRVAASELPVLLLGESGTGKELFARALHEASAHARGPFVVLD 226 R LVG+S A + ++ R A S+ VL+LGE+GTGKEL ARALH A A PFV ++ Sbjct: 133 RNQLVGESEAMRQVFKQIGRAATSDATVLVLGETGTGKELVARALHRNGARAARPFVAVN 192 Query: 227 CSGLTETLFESELFGYEKGAFTGAHVRKAGLVETAKGGTLFLDEIGDVPLGMQVKLLRLI 286 C+ + L ESELFG+ KGAF+GA + G + A GGTLFLDEIGD+ L Q K+LR++ Sbjct: 193 CAAIPAELIESELFGHVKGAFSGATSPRLGRFQEADGGTLFLDEIGDMELATQAKILRVL 252 Query: 287 ESGTYRRVGAVDTQQADFRLVAATHKPLQKMVANAQFRQDLYYRISAFPIHLPALRERRD 346 + VG + + D R++AATH+ LQ + +FR+DL+YR+ I +PALRER Sbjct: 253 QERELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWYRLQVLTIMVPALRERPG 312 Query: 347 DIALLVQSLL-QRGNGAPQQRLQVSPQAMASLLNYDWPGNIRELRNVLERARLFADDGVI 405 DI + + L Q G AP+ ++SP A LL + WPGN+RELRN +ERA + + I Sbjct: 313 DILTIAEHFLRQLGGDAPK---RISPAAARLLLQHAWPGNVRELRNTMERAAVMSHGLCI 369 Query: 406 KPEHLAL-------------------EPPLAIPVRSLQAGRSSHRSDLADLADIVRQFHG 446 + E + L + PLA+ + ++ R L A G Sbjct: 370 EAEDIGLSARPPAGAASAASAPAIDWDGPLAVALAEVE--RVMIERALQGAA-------G 420 Query: 447 TRKELARSLGWSERTLYRRLKAVG 470 R E AR LG S + LYRRL+ G Sbjct: 421 NRAEAARRLGISRQQLYRRLEEAG 444 >gi|300312042|ref|YP_003776134.1| response regulatory protein [Herbaspirillum seropedicae SmR1] Length = 450 Score = 214 bits (545), Expect = 1e-56, Method: Compositional matrix adjust. Identities = 131/342 (38%), Positives = 188/342 (54%), Gaps = 18/342 (5%) Query: 135 DVELRPIIDEQHRVVGFVERL----------QTVRHASVQASRQGLVGKSAAFNRALGEL 184 D +P IDE R+V V+R Q ++ A + GL+ + A + Sbjct: 105 DFHQKPCIDETLRLV--VQRAFYLHALQRENQRMQQAGGHTALGGLITRDAGMLAVCRSI 162 Query: 185 QRVAASELPVLLLGESGTGKELFARALHEASAHARGPFVVLDCSGLTETLFESELFGYEK 244 ++VA S V+LLG SGTGKE+ ARALH+ S + F+ ++C+ + E L ESELFGYEK Sbjct: 163 EKVAPSSASVMLLGSSGTGKEVLARALHQLSPRSGRRFMAINCAAIPENLLESELFGYEK 222 Query: 245 GAFTGAHVRKAGLVETAKGGTLFLDEIGDVPLGMQVKLLRLIESGTYRRVGAVDTQQADF 304 GAFTGA + G VE A GGT FLDE+GD+P+ +Q KLLR ++ RVG D Sbjct: 223 GAFTGAAKQTIGKVELAHGGTFFLDEVGDLPMPLQAKLLRFLQERVIERVGGHTEIPVDV 282 Query: 305 RLVAATHKPLQKMVANAQFRQDLYYRISAFPIHLPALRERRDDIALLVQSLLQRGNGAP- 363 R++ ATH+ L+++ A+ FR+DLYYR+ I +PAL+ER D LL + +Q+ Sbjct: 283 RVICATHQNLKELTASGGFREDLYYRLCEIIIKIPALKERHGDAVLLARHFVQKFCAKEG 342 Query: 364 QQRLQVSPQAMASLLNYDWPGNIRELRNVLERARLFADDGVIKPEHLAL--EPPLAIPVR 421 + L +S A+A++ Y+WPGN+RE+ N + RA + AD I E L L E A P+ Sbjct: 343 RATLHLSQDAVAAIERYEWPGNVREMENCVMRAVIMADGQQITAEDLGLSVEGREAEPLN 402 Query: 422 SLQAGRSSHRSDLADLADIVRQFHGTRKELARSLGWSERTLY 463 Q + R + + + G + A LG S TLY Sbjct: 403 LRQVRDEAERK---AVVKALTRMDGNILKAAELLGVSRPTLY 441 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 0.136 0.395 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: 1,437,167 Number of extensions: 61502 Number of successful extensions: 258 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 237 Number of HSP's successfully gapped: 12 Length of query: 472 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 383 Effective length of database: 1,198,455 Effective search space: 459008265 Effective search space used: 459008265 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: 132 (55.5 bits)