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= 0054.0001.p (467 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312337|ref|YP_003776429.1| transcription regulator protein... 741 0.0 gi|300311134|ref|YP_003775226.1| transcription regulator protein... 332 3e-92 gi|300313928|ref|YP_003778020.1| GntR family transcription regul... 302 4e-83 gi|300312133|ref|YP_003776225.1| transcription regulator protein... 256 2e-69 gi|300311016|ref|YP_003775108.1| MocR family transcription regul... 135 6e-33 >gi|300312337|ref|YP_003776429.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 469 Score = 741 bits (1914), Expect = 0.0, Method: Compositional matrix adjust. Identities = 357/452 (78%), Positives = 395/452 (87%), Gaps = 2/452 (0%) Query: 12 STLTQRLVQLIRRQISEGVYAPGTRLPSIRDMAKTHDCAKNTIVNAFDYLTALGVLEPRR 71 +TLT LVQLIRRQI+EGVYAPG+RLPSIR+MA H CAKNTIVN FD LTALG+ EPRR Sbjct: 6 TTLTSTLVQLIRRQIAEGVYAPGSRLPSIREMAARHGCAKNTIVNVFDELTALGLAEPRR 65 Query: 72 GSGFFVCAAAPAIKDDDEASSLSRAMDVVWLMREQLKSDPEHLRLGDGFPPVDWLNEVRL 131 G+GFFVC A P K+D+E + LSRAMDVVWLMREQLK DP LRLGDGFPPV+WL++VRL Sbjct: 66 GAGFFVCVAPPRPKEDEEGN-LSRAMDVVWLMREQLKHDPGQLRLGDGFPPVEWLHDVRL 124 Query: 132 DKFHQKVVRTGLGALFGYGSRFGYQPLRQHLVHRLANHGIEASASQIVLTHGANQALDIV 191 DKFHQKVVRTG+GALFGYGSRFGY PLRQHLVH+LA HGIEA QIVLTHGANQALDIV Sbjct: 125 DKFHQKVVRTGIGALFGYGSRFGYLPLRQHLVHKLAQHGIEAGTGQIVLTHGANQALDIV 184 Query: 192 IRNFVKPGDRVLVDEPGYYMLFGKLKLGGARIVGIPRLADGPDLEALEREL-KIGKPCLF 250 IR+F++PGDRVLVDEPGYYML+GKLKL GARI+GIPRL DGPD+ LEREL + GKP LF Sbjct: 185 IRHFIRPGDRVLVDEPGYYMLYGKLKLSGARIIGIPRLPDGPDVAVLERELHRPGKPPLF 244 Query: 251 FTQTLAHNPTGSDTSPHKAHKILQLADRYNAIIVENDTFADFKPNAAPRISTLDQLRRTI 310 FTQ+LAHNPT SDTSPHKAH+ILQLADRY AIIVEND FADFKP APRI+TLDQLRRT+ Sbjct: 245 FTQSLAHNPTASDTSPHKAHRILQLADRYQAIIVENDAFADFKPATAPRIATLDQLRRTV 304 Query: 311 YVGSFSKSVSAALRVGFLACHRDLASDLADIKMLVHVSSSEYCERTLDVILSEGHYSRHA 370 YVGSFSKSVSAALRVGF+ACHRDLASDLADIKMLVH+SSSEYCERTLDVILS+GH+SRH Sbjct: 305 YVGSFSKSVSAALRVGFIACHRDLASDLADIKMLVHMSSSEYCERTLDVILSDGHFSRHT 364 Query: 371 ARLRDRLTHATESARRLLENMGAELFCAPAQSMYLWAAMPGYPDSKTLAQALMRQNIVTA 430 ARLR+RL ATE AR LE +GAELFCAP Q+MYLWA P + D+K LAQ LM++ IV A Sbjct: 365 ARLRERLAQATEQARAQLEGLGAELFCAPQQAMYLWARFPWFEDAKRLAQRLMQRQIVLA 424 Query: 431 PGSIFHIDTEAPSRWSRYNVGLLGDPRFAAAM 462 PGSIFH+DTE WSR+NVGLL D RFA AM Sbjct: 425 PGSIFHVDTEQTQPWSRFNVGLLADARFADAM 456 >gi|300311134|ref|YP_003775226.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 500 Score = 332 bits (852), Expect = 3e-92, Method: Compositional matrix adjust. Identities = 185/464 (39%), Positives = 271/464 (58%), Gaps = 16/464 (3%) Query: 13 TLTQRLVQLIRRQISEGVYAPGTRLPSIRDMAKTHDCAKNTIVNAFDYLTALGVLEPRRG 72 +L +++V+ IR +I + + G R+PSIR A T+ ++ T+V A+D L A G LE RRG Sbjct: 39 SLVEQIVRGIRARIDDKLLRSGMRMPSIRQFADTNQISRFTVVEAYDRLVAQGYLESRRG 98 Query: 73 SGFFVCAAAP-----AIKDDDEASSLSRAMDVVWLMREQLKSDPEHLRLGDGFPPVDWLN 127 SGF+V AP + + R +DVVWL+R + P G G P DWL+ Sbjct: 99 SGFYVKERAPLGGSYGAAQAELDTEPGRGLDVVWLVRNMFRQMPPAKMPGGGLLPPDWLD 158 Query: 128 EVRLDKFHQKVVRTGLGALFGYGSRFGYQPLRQHLVHRLANHGIEASASQIVLTHGANQA 187 + + V R L GYG+ G+ PLRQ L +LA I A+ QIVLT G Q Sbjct: 159 GELIANALRAVSRDNPQLLLGYGTPQGFLPLRQQLQLKLAELEIAAAPEQIVLTTGVTQG 218 Query: 188 LDIVIRNFVKPGDRVLVDEPGYYMLFGKLKLGGARIVGIPRLADGPDLEALERELKIGKP 247 LD V R+F++PGD + VD+P ++++FG GA++VGIPRL DGPD+ L + KP Sbjct: 219 LDTVARHFLRPGDVIFVDDPAWFLMFGSFAALGAKVVGIPRLGDGPDIARLRELAAVHKP 278 Query: 248 CLFFTQTLAHNPTGSDTSPHKAHKILQLADRYNAIIVENDTFADFKPNA----APRISTL 303 L+ ++ HNPT + S KA ++L++A+ ++ +IVE+D + D P + A RI+ L Sbjct: 279 KLYVINSVLHNPTSTSLSAAKAFQVLRIAEEHDFVIVEDDIYCDMHPGSAVQPATRIAAL 338 Query: 304 DQLRRTIYVGSFSKSVSAALRVGFLACHRDLASDLADIKMLVHVSSSEYCERTLDVILSE 363 DQL+R IY+G FSK++SA LRVG++A +LA LAD K+L +++ E ER +LSE Sbjct: 339 DQLQRVIYLGGFSKTLSANLRVGYIATSAELARSLADRKLLSTLTTGEIGERVAYKVLSE 398 Query: 364 GHYSRHAARLRDRLTHATESARRLLENMGAELFCAPAQSMYLWAAMPGYPDSKTLAQALM 423 GHY +HA R+R RL A + R LE +G ++ AP M+LW D+ + +A M Sbjct: 399 GHYRKHAERVRARLNGARDKVMRQLERLGMDVVEAPPCGMFLWVDTGR--DTNVMTEAAM 456 Query: 424 RQNIVTAPGSIFHIDTEAPSRWSRYNVGLLGDP---RF-AAAMQ 463 ++ + APGS+F + PS + R NV + DP RF A AM+ Sbjct: 457 QEGFLLAPGSLFS-PAQLPSTYMRINVASMADPGIWRFLAQAME 499 >gi|300313928|ref|YP_003778020.1| GntR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 472 Score = 302 bits (773), Expect = 4e-83, Method: Compositional matrix adjust. Identities = 161/442 (36%), Positives = 246/442 (55%), Gaps = 4/442 (0%) Query: 26 ISEGVYAPGTRLPSIRDMAKTHDCAKNTIVNAFDYLTALGVLEPRRGSGFFVCAAAPAIK 85 I G G RLPS+R A+ HD +T+V A++ L A G+L+ RRG+GFFV A A Sbjct: 33 IETGELRSGERLPSVRQFAQHHDIGSSTVVEAYEQLVARGMLQARRGAGFFVAARAGQSG 92 Query: 86 DDDEASSLSRAMDVVWLMREQLKSDPEHLRLGDGFPPVDWLNEVRLDKFHQKVVRTGLGA 145 +D WL+ E + ++ G G+ P WLN+ L + ++++R+ Sbjct: 93 QHAVFVPPEPVIDSAWLLSEMFADERVPIKAGCGWLPGKWLNDEGLHQAERRIIRSPGAQ 152 Query: 146 LFGYGSRFGYQPLRQHLVHRLANHGIEASASQIVLTHGANQALDIVIRNFVKPGDRVLVD 205 GYG +GY PLRQ + L + +E Q++ THGA QALD+VIR +PGD VL+D Sbjct: 153 QVGYGHPYGYAPLRQLITQFLGHWSLELGIEQVLTTHGATQALDLVIRTMTQPGDTVLID 212 Query: 206 EPGYYMLFGKLKLGGARIVGIPRLADGPDLEALERELKIGKPCLFFTQTLAHNPTGSDTS 265 +PGY L L+L G ++G+PR G D + LE + P +FFT ++ NPTG+ + Sbjct: 213 DPGYCNLIAMLRLAGLNVIGVPRTPGGVDTDVLETLARTHHPKMFFTTSVLQNPTGTSYT 272 Query: 266 PHKAHKILQLADRYNAIIVENDTFADFKPNAAPRISTLDQLRRTIYVGSFSKSVSAALRV 325 P A ++LQ A+R+ +VE+D F + P ++ LD L+R IYVGS+SK+++ +LRV Sbjct: 273 PACAMRVLQAAERHGFWVVEDDIFRELGQATDPMLAALDGLQRVIYVGSYSKTIAPSLRV 332 Query: 326 GFLACHRDLASDLADIKMLVHVSSSEYCERTLDVILSEGHYSRHAARLRDRLTHATESAR 385 G++AC R+LA + KM++ +++SE ER + +L+EGH+ RH L L A + Sbjct: 333 GYIACQRELARQIVHTKMVLTLTNSEINERLVHNVLTEGHHRRHVQTLNATLLSAQATLN 392 Query: 386 RLLENMGAELFCAPAQSMYLWAAMPGYP-DSKTLAQALMRQNIVTAPGSIFHIDTEAPSR 444 L +G F A M+ WA + G ++ +A ++ I APG FH+ AP + Sbjct: 393 AKLSEVGLTPFTAARGGMFSWATIEGCELSAREIADRARQKGIWLAPGDFFHLS--APHQ 450 Query: 445 WS-RYNVGLLGDPRFAAAMQGL 465 S R+NVG P ++GL Sbjct: 451 TSFRFNVGYADVPELFDFLRGL 472 >gi|300312133|ref|YP_003776225.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 491 Score = 256 bits (655), Expect = 2e-69, Method: Compositional matrix adjust. Identities = 157/446 (35%), Positives = 247/446 (55%), Gaps = 20/446 (4%) Query: 18 LVQLIRRQISEGV----YAPGTRLPSIRDMAKTHDCAKNTIVNAFDYLTALGVLEPRRGS 73 LV I + EGV A G +LPS+R +A++ +++T+ A++ L A G + R G+ Sbjct: 32 LVDRIFTAVLEGVRTRRLAHGDKLPSLRVVAESAQVSRDTVARAYEKLVAHGHVYTRPGA 91 Query: 74 GFFVCAAAPAIKDDDEASSLSRAMDVVWLMR-EQLKSDPE---HLRLGDGFPPVDWLNEV 129 GFFV D+ A++ ++ L Q DP H LG G P +W+N Sbjct: 92 GFFVRV------DNQVANAQTQTAPAPLLTNWRQRLLDPRTLLHRGLGSGDLPAEWINVP 145 Query: 130 RLDKFHQKVVRTGLGALFGYGSRFGYQPLRQHLVHRLANHGIEASASQIVLTHGANQALD 189 +L + V R+ + GYG GY PLRQ L +LA+ G++ + Q++ T GA A++ Sbjct: 146 QLAAALRAVSRSNINWAAGYGDAQGYLPLRQQLQRKLADIGVDVTPPQVLTTLGATDAIN 205 Query: 190 IVIRNFVK-PGDRVLVDEPGYYMLFGKLKLGGARIVGIPRLADGPDLEALERELKIGKPC 248 +++ ++++ PG VLVD+PG ++L +L G IVG+ R ADGPD+ AL+ + P Sbjct: 206 LIVMSYLRQPGMTVLVDDPGSFLLMERLLASGMHIVGVARDADGPDITALQNACEQHGPT 265 Query: 249 LFFTQTLAHNPTGSDTSPHKAHKILQLADRYNAIIVENDTFADFKPNA----APRISTLD 304 +F Q+L H+P + SP +A +IL+LA+R+N IVE+DT+ D P A R+++LD Sbjct: 266 FYFCQSLLHSPGYTGLSPQRAFQILRLAERFNFTIVEDDTYGDLAPAHRSPHATRLASLD 325 Query: 305 QLRRTIYVGSFSKSVSAALRVGFLACHRDLASDLADIKMLVHVSSSEYCERTLDVILSEG 364 QL+ +YVGSFSK++ A +R GF+A + L K++ S+ ER + +LSEG Sbjct: 326 QLQHVLYVGSFSKTLGAGMRAGFIAGNPQQIEWLLLYKLVSRASNGSLAERAIYRLLSEG 385 Query: 365 HYSRHAARLRDRLTHATESARRLLENMGAELFCAPAQSMYLWAAMPGYPDSKTLAQALMR 424 Y RH +LR RL A LE +G L P +YLW +PG ++ +A+ ++ Sbjct: 386 GYRRHCEQLRTRLDQARPRLMAALEALGIVLPHRPDAGLYLWGKLPGDLNAMEVAERMLA 445 Query: 425 QNIVTAPGSIFHIDTEAPSRWSRYNV 450 +TAPG +F +A + R+NV Sbjct: 446 NGYLTAPGPVFS-SGQAARSYMRFNV 470 >gi|300311016|ref|YP_003775108.1| MocR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 480 Score = 135 bits (341), Expect = 6e-33, Method: Compositional matrix adjust. Identities = 111/443 (25%), Positives = 206/443 (46%), Gaps = 29/443 (6%) Query: 26 ISEGVYAPGTRLPSIRDMAKTHDCAKNTIVNAFDYLTALGVLEPRRGSGFFV-----CAA 80 I +GV PG R+ S+R ++ H + T+V A++ L + G++E + SG+FV Sbjct: 18 IRDGVLRPGERIASVRIASQQHKVSVTTVVRAYELLESRGIIESQPQSGYFVREQPEAPP 77 Query: 81 APAIK----DDDEASSLSRAMDVVWLMREQLKSDPEH--LRLGDGFPPVDWLNEVRLDKF 134 PA++ +D A S +DV L+ LK+ + + LG +P RL ++ Sbjct: 78 KPALRTTSREDHPAWQESTEVDVSRLVLATLKTIQQDGTVPLGSPYPNPALFPSHRLAQY 137 Query: 135 HQKVVRTGLGALFGYGSRFGYQPLRQHLVHRLANHGIEASASQIVLTHGANQALDIVIRN 194 ++ R + G+ L + + R +G++ +IV+T GA +A+++ ++ Sbjct: 138 AGRIARHASQSSVFDDLPPGHPELLRQIARRYLENGLKVDPEEIVITVGATEAINLCLQA 197 Query: 195 FVKPGDRVLVDEPGYYMLFGKLKLGGARIVGIPRLAD-GPDLEALERELKIGKPCLFFTQ 253 +PGD + V+ P +Y + ++ G R + IP G D+ ALE +K Sbjct: 198 VARPGDTIAVETPTFYAMLHAIERLGMRALEIPTDPQRGIDVGALEERMKTQAIAACMVM 257 Query: 254 TLAHNPTGSDTSPHKAHKILQLADRYNAIIVENDTFAD-FKPNAAP-RISTLDQLRRTIY 311 NP G + ++++LA+++ ++EN +++ + NA P + D+ ++ Sbjct: 258 PNFQNPLGFQMPDSEKERLVRLAEQHQMPVIENAVYSELYYGNAHPSSLKNYDRDGLVLH 317 Query: 312 VGSFSKSVSAALRVGFLACHRDLASDLADIKMLVHVSSSEYCERTLDVILSEGHYSRHAA 371 SFSKS+++A R+G+ R A + +K L +++ +R + L++G Y RH Sbjct: 318 CSSFSKSLTSAYRIGWAMPGRYRA-QVEKLKFLNTLATPTAPQRAIAEYLTQGGYERHLR 376 Query: 372 RLRDRLTHATESARRLLENMGAELFCA------PAQSMYLWAAMPGYPDSKTLAQALMRQ 425 R+R A R ++ + F A P LW +P D+ L + + Sbjct: 377 RVR----RAFAQQRDMMRHFVLRFFPAGTQVSEPQGGYVLWVELPQGVDAMELYRRSLAL 432 Query: 426 NIVTAPGSIFHIDTEAPSRWSRY 448 I APG IF A +R+S + Sbjct: 433 GITVAPGRIF----AATNRYSHF 451 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 0.322 0.136 0.407 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: 1,495,571 Number of extensions: 63396 Number of successful extensions: 240 Number of sequences better than 1.0e-08: 10 Number of HSP's gapped: 222 Number of HSP's successfully gapped: 10 Length of query: 467 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 378 Effective length of database: 1,198,455 Effective search space: 453015990 Effective search space used: 453015990 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)