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= 0004.0027.p (368 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310488|ref|YP_003774580.1| LacI family transcription regul... 655 0.0 gi|300311238|ref|YP_003775330.1| LacI family transcription regul... 281 4e-77 gi|300310423|ref|YP_003774515.1| GntR family transcription regul... 224 1e-59 gi|300311611|ref|YP_003775703.1| transcription regulator DNA-bin... 131 1e-31 gi|300309932|ref|YP_003774024.1| transcription regulator protein... 121 1e-28 >gi|300310488|ref|YP_003774580.1| LacI family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 365 Score = 655 bits (1691), Expect = 0.0, Method: Compositional matrix adjust. Identities = 330/368 (89%), Positives = 345/368 (93%), Gaps = 3/368 (0%) Query: 1 MSEKRMPPPDSPMQPTSAERDDDSAEPRRRAARKSAGGITLRDVAQLAGVAPITASRALN 60 MSE R+ S P ++ +D D+A PRRR +RKSAGG+TLRDVAQLAGVAPITASRALN Sbjct: 1 MSENRL---SSSEFPAASHQDGDAASPRRRGSRKSAGGVTLRDVAQLAGVAPITASRALN 57 Query: 61 TPSAVSPKVLQKVREAVEKTGYVPNLLAGGLASNKSRLVAVVVPTVIGPVFQEIVHTLTE 120 TPSAVSPKVLQKVREAVEKTGYVPNLLAGGLASNKSRLVAVVVPTVIGPVFQEIVHTLTE Sbjct: 58 TPSAVSPKVLQKVREAVEKTGYVPNLLAGGLASNKSRLVAVVVPTVIGPVFQEIVHTLTE 117 Query: 121 TLAAAGYQVMLGQSGYENSREDALLEAIIGRRPDGVVLTGIMRSAEARKRLLASGIPVVE 180 TLAAAGYQVMLGQSGYENSREDALLEAIIGRRPDGVVLTGIMRSAEARKRLLASGIPVVE Sbjct: 118 TLAAAGYQVMLGQSGYENSREDALLEAIIGRRPDGVVLTGIMRSAEARKRLLASGIPVVE 177 Query: 181 TWDLTPTPIDMLVGFSHEAIGHEVARYLHARGRRKVAVVGGRDERSQRRMNAFAQECAAL 240 TWDLTPTPIDMLVGFSHEAIG EVARYLH RGR+KVAVVGGRDERSQRRMNAFAQEC AL Sbjct: 178 TWDLTPTPIDMLVGFSHEAIGREVARYLHQRGRKKVAVVGGRDERSQRRMNAFAQECVAL 237 Query: 241 GMQQGRGEVPMYHVVAPTTLGQGRQGLAELLQAHPDLDAIFCSSDLLALGVMIEAQSRGI 300 GM +GR +PM+HV APTTLGQGRQGLAELLQA PDLDAIFCSSDLLALGVMIEAQSRGI Sbjct: 238 GMHEGRAPLPMHHVTAPTTLGQGRQGLAELLQAQPDLDAIFCSSDLLALGVMIEAQSRGI 297 Query: 301 AIPGQLAVVGFGDLEFSRDLQPRLTTVRIDGTGIGQRAARFIIERASGSEVSERIVDVGF 360 AIP QLAVVGFGDLEFSRDLQPRLTTVRIDGTGIGQRAARFII+RA+G EV+ER+VDVGF Sbjct: 298 AIPEQLAVVGFGDLEFSRDLQPRLTTVRIDGTGIGQRAARFIIDRAAGIEVAERVVDVGF 357 Query: 361 SIIARDSA 368 SIIARDSA Sbjct: 358 SIIARDSA 365 >gi|300311238|ref|YP_003775330.1| LacI family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 340 Score = 281 bits (720), Expect = 4e-77, Method: Compositional matrix adjust. Identities = 146/331 (44%), Positives = 206/331 (62%), Gaps = 8/331 (2%) Query: 39 ITLRDVAQLAGVAPITASRALNTPSAVSPKVLQKVREAVEKTGYVPNLLAGGLASNKSRL 98 +T DVA+ AGV+ IT SR +N+P VSP ++V + GY+PNLLAGGLAS ++R+ Sbjct: 15 VTKEDVARAAGVSHITVSRVINSPEKVSPATRERVEAFIASMGYIPNLLAGGLASRRTRI 74 Query: 99 VAVVVPTVIGPVFQEIVHTLTETLAAAGYQVMLGQSGYENSREDALLEAIIGRRPDGVVL 158 VA +VPT+ +F E + L+E L GYQ++LGQ+ Y E L+E IGRR DG+VL Sbjct: 75 VAAIVPTISHSIFAETLRGLSEQLCMQGYQLLLGQTNYSEEAETGLVEVFIGRRVDGLVL 134 Query: 159 TGIMRSAEARKRLLASGIPVVETWDLTPTPIDMLVGFSHEAIGHEVARYLHARGRRKVAV 218 TG+ S R+RL A+GIPVVETWDLT TPIDML GF + A G + YL+ +G R++A Sbjct: 135 TGVQHSPMTRQRLKAAGIPVVETWDLTDTPIDMLAGFDNHAAGRAMGDYLYQKGYRRMAF 194 Query: 219 VGGRDERSQRRMNAFAQECAALGMQQGRGEVPMYHVVAP--TTLGQGRQGLAELLQAHPD 276 VGG D R R+ + + G H+V P L GR+ + LL HP+ Sbjct: 195 VGGDDPRGMARVAGLRESL------RHHGAAEPVHLVMPMGAFLQAGREAIGRLLTQHPE 248 Query: 277 LDAIFCSSDLLALGVMIEAQSRGIAIPGQLAVVGFGDLEFSRDLQPRLTTVRIDGTGIGQ 336 +DA F S+D++A G +E RGIA+PG++A+ GF +LE + ++ P LTTV+I IG Sbjct: 249 VDAAFFSNDVIAAGAALECARRGIAVPGRIALAGFANLEIATEVLPALTTVQISAHQIGL 308 Query: 337 RAARFIIERASGSEVSERIVDVGFSIIARDS 367 AA ++ R G + + + D+G+SI+ RDS Sbjct: 309 TAAEMLLTRFDGDPLDQAVHDLGYSILERDS 339 >gi|300310423|ref|YP_003774515.1| GntR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 352 Score = 224 bits (570), Expect = 1e-59, Method: Compositional matrix adjust. Identities = 130/358 (36%), Positives = 206/358 (57%), Gaps = 10/358 (2%) Query: 13 MQPTSAERDDDSAEPRRRAARKSAGGITLRDVAQLAGVAPITASRALNTPSAVSPKVLQK 72 M +A + + P R +R + G +T+ DVA AGV+P+T SRAL TP+ V + Q+ Sbjct: 1 MTQRAASKSKPKSPPAVRGSRAT-GRVTIIDVAAEAGVSPMTVSRALKTPALVQEQSRQR 59 Query: 73 VREAVEKTGYVPNLLAGGLASNKSRLVAVVVPTVIGPVFQEIVHTLTETLAAAGYQVMLG 132 + EA++K GYVPN A LAS +S++VAV+VP++ VF E + + + LA+ GYQ ++G Sbjct: 60 ILEAIDKLGYVPNQAAATLASARSQVVAVLVPSLTNAVFIETLSGIRDYLASVGYQFLIG 119 Query: 133 QSGYENSREDALLEAIIGRRPDGVVLTGIMRSAEARKRLLASGIPVVETWDLTPTPIDML 192 ++GY+ +E+ L+ + P G +L+ + + R + IP V +DL + D Sbjct: 120 ETGYDRHKEEELIATYLAHAPAGFLLSSSQQHDILQSRPASRAIPAVRMFDLGRSQQDYS 179 Query: 193 VGFSHEAIGHEVARYLHARGRRKVAVVGGR-DERSQRRMNAFAQECAALGMQQGRGEVPM 251 VGFS GH VAR+L RG R+ A + + D R +R F + G+Q+ G Sbjct: 180 VGFSQTRAGHAVARHLAERGYRRPAFLAAQLDPRMMKRREGFRK-----GLQEA-GLAAD 233 Query: 252 YHVV--APTTLGQGRQGLAELLQAHPDLDAIFCSSDLLALGVMIEAQSRGIAIPGQLAVV 309 V+ PTT+ G Q L +LQ HPD D++FC +D LALG + E Q +GI++P Q+A+ Sbjct: 234 IEVLLPQPTTVDMGAQLLRRVLQDHPDCDSVFCCNDDLALGALFECQRQGISVPRQMAIA 293 Query: 310 GFGDLEFSRDLQPRLTTVRIDGTGIGQRAARFIIERASGSEVSERIVDVGFSIIARDS 367 GF DL ++ P +TTV IG ++A ++ + G E+++ +D+GF + R+S Sbjct: 294 GFNDLSWAACATPSITTVVTPRYDIGYQSAEMLVRQLKGEEIAKGRLDLGFELAVRES 351 >gi|300311611|ref|YP_003775703.1| transcription regulator DNA-binding repressor protein [Herbaspirillum seropedicae SmR1] Length = 337 Score = 131 bits (329), Expect = 1e-31, Method: Compositional matrix adjust. Identities = 99/321 (30%), Positives = 162/321 (50%), Gaps = 13/321 (4%) Query: 40 TLRDVAQLAGVAPITASRALNTPSAVSPKVLQKVREAVEKTGYVPNLLAGGLASNKSRLV 99 T++DVA+LAGV+ T S LN VS ++V AV++ YVP+ LA L S + + Sbjct: 3 TIKDVARLAGVSYTTVSHVLNQTRPVSSDARERVLAAVKELDYVPSALARSLRSKVTGSI 62 Query: 100 AVVVPTVIGPVFQEIVHTLTETLAAAGYQVMLGQSGYENSREDALLEAIIGRRPDGVVLT 159 +++P P F E+ + + AGY V+L S + ++ L+ + + DG+++ Sbjct: 63 GLIIPNNTNPYFSELARGIEDHCYGAGYSVILCNSDDDPDKQRDYLQVLQTKHCDGLIIA 122 Query: 160 GIMRSAEARKRLLASGIPVVETWDLTPTPIDMLVGFSHEAIGHEV-ARYLHARGRRKVAV 218 + ++ L IP V D P +D+ + + A+G + AR+L R +VA Sbjct: 123 TLNQADLNPAGKL--DIPTV-LLDRAPKELDIDLVSTDNAVGGSLAARHLLDLRRCRVAC 179 Query: 219 VGGRD--ERSQRRMNAFAQECAALGMQQGRGEVPMYHVVAPTTLGQGRQGLAELLQAHP- 275 + G D E S R+ F Q G+ + + H A + G Q LLQ P Sbjct: 180 IAGPDGLELSDERVRGFRQTLEQGGLALADSD--LLH--ADFSGIGGYQAAMRLLQGRPA 235 Query: 276 --DLDAIFCSSDLLALGVMIEAQSRGIAIPGQLAVVGFGDLEFSRDLQPRLTTVRIDGTG 333 DAIFC +D++A+GV+ A I +PG+L+VVGF D+E ++ + P LTTV + Sbjct: 236 DQRPDAIFCCNDMMAIGVLRAAGELQIEVPGELSVVGFDDIELAQFVHPPLTTVAQNTRK 295 Query: 334 IGQRAARFIIERASGSEVSER 354 +G A+F++ER + + R Sbjct: 296 LGNLTAQFLLERIADPSLPAR 316 >gi|300309932|ref|YP_003774024.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 358 Score = 121 bits (303), Expect = 1e-28, Method: Compositional matrix adjust. Identities = 96/317 (30%), Positives = 151/317 (47%), Gaps = 20/317 (6%) Query: 40 TLRDVAQLAGVAPITASRALNTPSAVSPKVLQKVREAVEKTGYVPNLLAGGLASNKSRLV 99 +++ VA LAGV+ T SR LN P +VS + +K+ ++ + G+ PN L + SR V Sbjct: 4 SIKQVAHLAGVSIATVSRLLNKPGSVSAETAEKIHRSIAELGFRPNFTGRNLRAGNSRTV 63 Query: 100 AVVVPTVIGPVFQEIVHTLTETLAAAGYQVMLGQSGYENSREDALLEAIIGRRPDGVVLT 159 VVVPT+ VF + + + A Y VM + Y E A +E ++G R DG++LT Sbjct: 64 GVVVPTLSNTVFAQCLQGIELAARALDYSVMFTTTEYLPEEETAAVELLLGHRVDGMILT 123 Query: 160 GIMRSAEARKRLLA-SGIPVVETW-----DLTPTPIDMLVGFSHEAIGHEVARYLHARGR 213 SA A LL IP V + D T P V + A + +L G Sbjct: 124 VADASANATLDLLERERIPFVLAYNQLGTDQTAAPARASVSVDNRAAACDAVAHLIGLGH 183 Query: 214 RKVAVVGGRDERSQRRMNAFAQECAALGMQQGRGEVPMY------HVVAPTTLGQGRQGL 267 R++ ++ GR S R M + L + G PM H + T +Q + Sbjct: 184 RRIQMLSGRFNASDRAMQRY---YGYLDAMRAAGLAPMAVIEVERHTL--TAAADYQQMM 238 Query: 268 AELLQAHPDLDAIFCSSDLLALGVMIEAQSRGIAIPGQLAVVGFGDLEFSRDLQPRLTTV 327 A+ Q P A+FCS+DLLA+ M + ++ G+ +P ++V+GF + ++P L +V Sbjct: 239 ADPRQ-RP--TALFCSNDLLAMSAMRDLRALGMKVPNDISVMGFDGIPVGALMEPVLASV 295 Query: 328 RIDGTGIGQRAARFIIE 344 IG+ A R ++E Sbjct: 296 VQPSEQIGEVALRVLVE 312 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 0.318 0.134 0.378 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: 1,097,930 Number of extensions: 45040 Number of successful extensions: 222 Number of sequences better than 1.0e-08: 8 Number of HSP's gapped: 215 Number of HSP's successfully gapped: 8 Length of query: 368 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 281 Effective length of database: 1,207,925 Effective search space: 339426925 Effective search space used: 339426925 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 131 (55.1 bits)