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= 0001.0878.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|300310416|ref|YP_003774508.1| MocR family transcription regul... 985 0.0 gi|300311134|ref|YP_003775226.1| transcription regulator protein... 134 3e-32 gi|300311139|ref|YP_003775231.1| MocR family transcription regul... 128 1e-30 gi|300313928|ref|YP_003778020.1| GntR family transcription regul... 122 5e-29 gi|300312337|ref|YP_003776429.1| transcription regulator protein... 122 5e-29 >gi|300310416|ref|YP_003774508.1| MocR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 516 Score = 985 bits (2546), Expect = 0.0, Method: Compositional matrix adjust. Identities = 493/523 (94%), Positives = 503/523 (96%), Gaps = 7/523 (1%) Query: 1 LKLASLSDYLLLRINRPPAKAAPGKGKAASARESSAAKITKTAKTFGVSTPVNRQIYQLI 60 +K+ASLSDYLLLRINRP AKAAPGK KA SA ES AAK TPVNRQIYQLI Sbjct: 1 MKIASLSDYLLLRINRPAAKAAPGKAKAGSAPESGAAKPAP-------RTPVNRQIYQLI 53 Query: 61 REAILAHTLPAGMQLPSSRDLALELGTSRNTVTYAYEQLLAEGYLESRTGAGTFVADTAP 120 REAILAHTLPAGMQLPSSRDLALELG+SRNTVTYAYEQLLAEGYLESR GAGTFVADTAP Sbjct: 54 REAILAHTLPAGMQLPSSRDLALELGSSRNTVTYAYEQLLAEGYLESRPGAGTFVADTAP 113 Query: 121 DQIPEAVERVEPLTDPSGKSELSARGALLTRQAGVGERQWGAFMPGVPDVTCVPHKIWGR 180 DQIPEAVER EPLTDPSGKSELSARGA+LTRQAGVGERQWGAFMPGVPDVTCVP+KIWGR Sbjct: 114 DQIPEAVERPEPLTDPSGKSELSARGAMLTRQAGVGERQWGAFMPGVPDVTCVPYKIWGR 173 Query: 181 LQNKHWRRSNSDLLTYGPGAGYTGLREQIAEYLRVARSVNCTPSQVLITTGIHQSIDIVV 240 LQNKHWRRSN+DLLTYGPGAGY GLREQIAEYLRVARSVNCTPSQVLITTGIHQS+DIVV Sbjct: 174 LQNKHWRRSNADLLTYGPGAGYAGLREQIAEYLRVARSVNCTPSQVLITTGIHQSLDIVV 233 Query: 241 KLLGEHGDTAWVEDPCYWGTRSVLNSLGIQSVPIAVDQEGMRMRLANLRRPPRFICTTPS 300 KLLGEHGD+AWVEDPCYWGTRSVLNSLGIQSVPIAVDQEGMRMRLANLRRPPRFICTTPS Sbjct: 234 KLLGEHGDSAWVEDPCYWGTRSVLNSLGIQSVPIAVDQEGMRMRLANLRRPPRFICTTPS 293 Query: 301 HQYPLGMVMSLSRRRMLLEYAATHKVWIIEDDYDSEFRYGGRPLASLQGMDTQDRVLYMG 360 HQYPLGMVMSLSRRRMLLEYAATHKVWIIEDDYDSEFRYGGRPLASLQGMDTQDRVLYMG Sbjct: 294 HQYPLGMVMSLSRRRMLLEYAATHKVWIIEDDYDSEFRYGGRPLASLQGMDTQDRVLYMG 353 Query: 361 TFSKIMFPGLRIGFLVVPESLAQAFATGIAELYRNGQVFLQATLADFMAEGHFASHIRKM 420 TFSKIMFPGLRIGFLVVPESLA+AF+TGIAELYRNGQVFLQATLADFMAEGHFASHIRKM Sbjct: 354 TFSKIMFPGLRIGFLVVPESLARAFSTGIAELYRNGQVFLQATLADFMAEGHFASHIRKM 413 Query: 421 RVLYAERLQLLQQSINRHFGEKMTITGGEAGLHLVLGLPQECDDVLICEQALQAGIVVRP 480 RVLYAERLQLLQQSINRHFGEKMTITGGEAGLHLVLGLPQECDDVLICEQAL AGIVVRP Sbjct: 414 RVLYAERLQLLQQSINRHFGEKMTITGGEAGLHLVLGLPQECDDVLICEQALAAGIVVRP 473 Query: 481 LSRYYMHARGARRGLLLGYASVPNDEIARAFDKLAAVIKPHLA 523 LSRYYMHARGARRGLLLGYASVPNDEIARAFDKLAAVIKPHLA Sbjct: 474 LSRYYMHARGARRGLLLGYASVPNDEIARAFDKLAAVIKPHLA 516 >gi|300311134|ref|YP_003775226.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 500 Score = 134 bits (336), Expect = 3e-32, Method: Compositional matrix adjust. Identities = 122/443 (27%), Positives = 206/443 (46%), Gaps = 30/443 (6%) Query: 55 QIYQLIREAILAHTLPAGMQLPSSRDLALELGTSRNTVTYAYEQLLAEGYLESRTGAGTF 114 QI + IR I L +GM++PS R A SR TV AY++L+A+GYLESR G+G + Sbjct: 43 QIVRGIRARIDDKLLRSGMRMPSIRQFADTNQISRFTVVEAYDRLVAQGYLESRRGSGFY 102 Query: 115 VADTAPDQIPEAVERVEPLTDPSGKSELSARGALLTRQAGVGERQWGAFMPGVPDVTCVP 174 V + AP + E T+P ++ + RQ + G +P P Sbjct: 103 VKERAPLGGSYGAAQAELDTEPGRGLDVVWLVRNMFRQMPPAKMPGGGLLP--------P 154 Query: 175 HKIWGRLQNKHWRRSNSD----LLTYGPGAGYTGLREQIAEYLRVAR-SVNCTPSQVLIT 229 + G L R + D LL YG G+ LR+Q+ L++A + P Q+++T Sbjct: 155 DWLDGELIANALRAVSRDNPQLLLGYGTPQGFLPLRQQLQ--LKLAELEIAAAPEQIVLT 212 Query: 230 TGIHQSIDIVVKLLGEHGDTAWVEDPCYWGTRSVLNSLGIQSVPIAVDQEG---MRMR-L 285 TG+ Q +D V + GD +V+DP ++ +LG + V I +G R+R L Sbjct: 213 TGVTQGLDTVARHFLRPGDVIFVDDPAWFLMFGSFAALGAKVVGIPRLGDGPDIARLREL 272 Query: 286 ANLRRPPRFICTTPSHQYPLGMVMSLSRRRMLLEYAATHKVWIIEDDYDSEFRYGG--RP 343 A + +P ++ + H P +S ++ +L A H I+EDD + G +P Sbjct: 273 AAVHKPKLYVINSVLHN-PTSTSLSAAKAFQVLRIAEEHDFVIVEDDIYCDMHPGSAVQP 331 Query: 344 LASLQGMDTQDRVLYMGTFSKIMFPGLRIGFLVVPESLAQAFAT-GIAELYRNGQVFLQA 402 + +D RV+Y+G FSK + LR+G++ LA++ A + G++ + Sbjct: 332 ATRIAALDQLQRVIYLGGFSKTLSANLRVGYIATSAELARSLADRKLLSTLTTGEIG-ER 390 Query: 403 TLADFMAEGHFASHIRKMRVLYAERLQLLQQSINRHFGEKMTITGGEA-GLHLVLGLPQE 461 ++EGH+ H ++R RL + + R E++ + EA + L + Sbjct: 391 VAYKVLSEGHYRKHAERVRA----RLNGARDKVMRQL-ERLGMDVVEAPPCGMFLWVDTG 445 Query: 462 CDDVLICEQALQAGIVVRPLSRY 484 D ++ E A+Q G ++ P S + Sbjct: 446 RDTNVMTEAAMQEGFLLAPGSLF 468 >gi|300311139|ref|YP_003775231.1| MocR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 398 Score = 128 bits (321), Expect = 1e-30, Method: Compositional matrix adjust. Identities = 91/363 (25%), Positives = 162/363 (44%), Gaps = 5/363 (1%) Query: 162 AFMPGVPDVTCVPHKIWGRLQNKHWRRSNSDLLTYGPGAGYTGLREQIAEYLRVARSVNC 221 +F G+P P + ++ + L YGP GY LRE IA L Sbjct: 39 SFAGGLPSPLTFPVEHMKTAFDRVLSQQGKMALQYGPTDGYLPLREWIAASLST-NGAQI 97 Query: 222 TPSQVLITTGIHQSIDIVVKLLGEHGDTAWVEDPCYWGTRSVLNSLGIQSVPIAVDQEGM 281 + QVL+ +G Q +D++ K+L + G VE P Y G G + + D+ G+ Sbjct: 98 SAEQVLMVSGSQQGLDLLGKVLIDEGSKVLVETPSYLGALQAFALYGAKFESVPSDEFGL 157 Query: 282 RMR-LANLRRPPRFICTTPSHQYPLGMVMSLSRRRMLLEYAATHKVWIIEDDYDSEFRYG 340 + + + R + + P+ Q P G + RR L+E A + +IEDD Y Sbjct: 158 QPETIEAIAGGARMLYSLPNFQNPTGRTLPTERRFKLVETCARLGLPLIEDDPYGALSYQ 217 Query: 341 GRPLASLQGMDTQDRVLYMGTFSKIMFPGLRIGFLVVPESLAQAFATGIAELYRNGQVFL 400 PL + M+ V+YMG+FSK++ PG+R+G++V P L + Sbjct: 218 NAPLPKMLSMNPSG-VIYMGSFSKVLTPGIRLGYVVAPRPLILKMEQAKQATDLHTAQLT 276 Query: 401 QATLADFMAEGHFASHIRKMRVLYAERLQLLQQSINRHFGEKMTITGGEAGLHLVLGLPQ 460 Q + + + +G H+ +R LY ++ Q + ++ ++F + + E G+ + + LP+ Sbjct: 277 QMVVYEAIKDGFLDQHVPTIRKLYGDQCQAMLDALQQYFPASCSWSKPEGGMFIWVTLPE 336 Query: 461 ECD-DVLICEQALQAGIVVRPLSRYYMHARGARRGLLLGYASVPNDEIARAFDKLAAVIK 519 D L+ E Q + P + +Y + + L L + +VP ++I ++L +I Sbjct: 337 HIDAGALLNEAVEQEKVAFVPGAPFYANV-AQKNTLRLSFVTVPPEQIRAGVERLGKLIA 395 Query: 520 PHL 522 L Sbjct: 396 SKL 398 >gi|300313928|ref|YP_003778020.1| GntR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 472 Score = 122 bits (307), Expect = 5e-29, Method: Compositional matrix adjust. Identities = 128/449 (28%), Positives = 200/449 (44%), Gaps = 35/449 (7%) Query: 69 LPAGMQLPSSRDLALELGTSRNTVTYAYEQLLAEGYLESRTGAGTFVADTAPDQIPEAV- 127 L +G +LPS R A +TV AYEQL+A G L++R GAG FVA A AV Sbjct: 38 LRSGERLPSVRQFAQHHDIGSSTVVEAYEQLVARGMLQARRGAGFFVAARAGQSGQHAVF 97 Query: 128 ERVEPLTDPSG-KSELSARGALLTRQAGVGERQWGAFMPGVPDVTCVPHKIWGRLQNKHW 186 EP+ D + SE+ A + + AG G ++PG + + + + + Sbjct: 98 VPPEPVIDSAWLLSEMFADERVPIK-AGCG------WLPG----KWLNDEGLHQAERRII 146 Query: 187 RRSNSDLLTYGPGAGYTGLREQIAEYLRVARSVNCTPSQVLITTGIHQSIDIVVKLLGEH 246 R + + YG GY LR+ I ++L S+ QVL T G Q++D+V++ + + Sbjct: 147 RSPGAQQVGYGHPYGYAPLRQLITQFLG-HWSLELGIEQVLTTHGATQALDLVIRTMTQP 205 Query: 247 GDTAWVEDPCYWGTRSV-----LNSLGIQSVPIAVDQEGMRMRLANLRRPPRFICTTPSH 301 GDT ++DP Y ++ LN +G+ P VD + + LA P F TT Sbjct: 206 GDTVLIDDPGYCNLIAMLRLAGLNVIGVPRTPGGVDTDVLET-LARTHHPKMFF-TTSVL 263 Query: 302 QYPLGMVMSLSRRRMLLEYAATHKVWIIEDDYDSEFRYGGRPLASLQGMDTQDRVLYMGT 361 Q P G + + +L+ A H W++EDD E P+ L +D RV+Y+G+ Sbjct: 264 QNPTGTSYTPACAMRVLQAAERHGFWVVEDDIFRELGQATDPM--LAALDGLQRVIYVGS 321 Query: 362 FSKIMFPGLRIGFLVVPESLAQAFATGIAELYRNGQVFLQATLADFMAEGHFASHIRKMR 421 +SK + P LR+G++ LA+ L + + + + EGH H R ++ Sbjct: 322 YSKTIAPSLRVGYIACQRELARQIVHTKMVLTLTNSEINERLVHNVLTEGH---HRRHVQ 378 Query: 422 VLYAERLQLLQQSINRHFGEK-----MTITGGEAGLHLVLGLPQECDDVLICEQALQAGI 476 L A L Q ++N E GG + G E I ++A Q GI Sbjct: 379 TLNATLLS-AQATLNAKLSEVGLTPFTAARGGMFSWATIEGC--ELSAREIADRARQKGI 435 Query: 477 VVRPLSRYYMHA-RGARRGLLLGYASVPN 504 + P +++ A +GYA VP Sbjct: 436 WLAPGDFFHLSAPHQTSFRFNVGYADVPE 464 >gi|300312337|ref|YP_003776429.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 469 Score = 122 bits (307), Expect = 5e-29, Method: Compositional matrix adjust. Identities = 108/443 (24%), Positives = 190/443 (42%), Gaps = 21/443 (4%) Query: 49 STPVNRQIYQLIREAILAHTLPAGMQLPSSRDLALELGTSRNTVTYAYEQLLAEGYLESR 108 ST + + QLIR I G +LPS R++A G ++NT+ +++L A G E R Sbjct: 5 STTLTSTLVQLIRRQIAEGVYAPGSRLPSIREMAARHGCAKNTIVNVFDELTALGLAEPR 64 Query: 109 TGAGTFVADTAPDQIPEAVERVEPLTDPSGKSELSARGALLTRQAGVGERQWGAFMPGVP 168 GAG FV P P D G + L R+ + G P Sbjct: 65 RGAGFFVCVAPP----------RPKEDEEGNLSRAMDVVWLMREQLKHDPGQLRLGDGFP 114 Query: 169 DVTCVPHKIWGRLQNKHWRRSNSDLLTYGPGAGYTGLREQIAEYLRVARSVNCTPSQVLI 228 V + + K R L YG GY LR+ + L + Q+++ Sbjct: 115 PVEWLHDVRLDKFHQKVVRTGIGALFGYGSRFGYLPLRQHLVHKL-AQHGIEAGTGQIVL 173 Query: 229 TTGIHQSIDIVVKLLGEHGDTAWVEDPCYWGTRSVLN-----SLGIQSVPIAVDQEGMRM 283 T G +Q++DIV++ GD V++P Y+ L +GI +P D + Sbjct: 174 THGANQALDIVIRHFIRPGDRVLVDEPGYYMLYGKLKLSGARIIGIPRLPDGPDVAVLER 233 Query: 284 RLANLRRPPRFICTTPSHQYPLGMVMSLSRRRMLLEYAATHKVWIIEDDYDSEFRYGGRP 343 L +PP F + +H P S + +L+ A ++ I+E+D ++F+ P Sbjct: 234 ELHRPGKPPLFFTQSLAHN-PTASDTSPHKAHRILQLADRYQAIIVENDAFADFKPATAP 292 Query: 344 LASLQGMDTQDRVLYMGTFSKIMFPGLRIGFLVVPESLAQAFATGIAELYRNGQVFLQAT 403 + +D R +Y+G+FSK + LR+GF+ LA A ++ + + + T Sbjct: 293 --RIATLDQLRRTVYVGSFSKSVSAALRVGFIACHRDLASDLADIKMLVHMSSSEYCERT 350 Query: 404 LADFMAEGHFASHIRKMRVLYAERLQLLQQSINRHFGEKMTITGGEAGLHLVLGLPQECD 463 L +++GHF+ H ++R A+ + + + G ++ +A ++L P D Sbjct: 351 LDVILSDGHFSRHTARLRERLAQATEQARAQLE-GLGAELFCAPQQA-MYLWARFPWFED 408 Query: 464 DVLICEQALQAGIVVRPLSRYYM 486 + ++ +Q IV+ P S +++ Sbjct: 409 AKRLAQRLMQRQIVLAPGSIFHV 431 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 0.404 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: 1,627,876 Number of extensions: 71750 Number of successful extensions: 257 Number of sequences better than 1.0e-08: 10 Number of HSP's gapped: 236 Number of HSP's successfully gapped: 10 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)