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= 0001.0959.p (371 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... 639 0.0 gi|300311238|ref|YP_003775330.1| LacI family transcription regul... 278 5e-76 gi|300310423|ref|YP_003774515.1| GntR family transcription regul... 217 1e-57 gi|300311611|ref|YP_003775703.1| transcription regulator DNA-bin... 129 4e-31 gi|300309932|ref|YP_003774024.1| transcription regulator protein... 124 1e-29 >gi|300310488|ref|YP_003774580.1| LacI family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 365 Score = 639 bits (1647), Expect = 0.0, Method: Compositional matrix adjust. Identities = 322/358 (89%), Positives = 337/358 (94%) Query: 14 SSPEPNRDLREEDGAEPRRRGPRKSAGGVTLRDVAQLAGVAPITASRALNTPAAVSPKVL 73 SS P ++ D A PRRRG RKSAGGVTLRDVAQLAGVAPITASRALNTP+AVSPKVL Sbjct: 8 SSEFPAASHQDGDAASPRRRGSRKSAGGVTLRDVAQLAGVAPITASRALNTPSAVSPKVL 67 Query: 74 QKVRAAVEKTGYVPNLLAGGLASNKSRLVAVVVPTVIGPVFQEIVHTLTETLAAAGYQVM 133 QKVR AVEKTGYVPNLLAGGLASNKSRLVAVVVPTVIGPVFQEIVHTLTETLAAAGYQVM Sbjct: 68 QKVREAVEKTGYVPNLLAGGLASNKSRLVAVVVPTVIGPVFQEIVHTLTETLAAAGYQVM 127 Query: 134 LGQSGYENSREDALLEAIIGRRPDGVVLTGIMRSPQARKRLLASGIPVVETWDLTASPID 193 LGQSGYENSREDALLEAIIGRRPDGVVLTGIMRS +ARKRLLASGIPVVETWDLT +PID Sbjct: 128 LGQSGYENSREDALLEAIIGRRPDGVVLTGIMRSAEARKRLLASGIPVVETWDLTPTPID 187 Query: 194 MLVGFSHEAIGREVARYLHGRARQRVAVVGGRDERSQRRMNAFAQQAMALGMHQGPAPLA 253 MLVGFSHEAIGREVARYLH R R++VAVVGGRDERSQRRMNAFAQ+ +ALGMH+G APL Sbjct: 188 MLVGFSHEAIGREVARYLHQRGRKKVAVVGGRDERSQRRMNAFAQECVALGMHEGRAPLP 247 Query: 254 MHHVSAPTTLGQGRQGLAELLQRQPDIDAIFCSSDLLALGVMIEAQSRGIAIPRQLAVVG 313 MHHV+APTTLGQGRQGLAELLQ QPD+DAIFCSSDLLALGVMIEAQSRGIAIP QLAVVG Sbjct: 248 MHHVTAPTTLGQGRQGLAELLQAQPDLDAIFCSSDLLALGVMIEAQSRGIAIPEQLAVVG 307 Query: 314 FGDLEFSRDLQPRLTTVRIDGTGIGQRAARFIIDRAAGIEVAERIIDVGFSIIERESA 371 FGDLEFSRDLQPRLTTVRIDGTGIGQRAARFIIDRAAGIEVAER++DVGFSII R+SA Sbjct: 308 FGDLEFSRDLQPRLTTVRIDGTGIGQRAARFIIDRAAGIEVAERVVDVGFSIIARDSA 365 >gi|300311238|ref|YP_003775330.1| LacI family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 340 Score = 278 bits (711), Expect = 5e-76, Method: Compositional matrix adjust. Identities = 147/331 (44%), Positives = 210/331 (63%), Gaps = 8/331 (2%) Query: 42 VTLRDVAQLAGVAPITASRALNTPAAVSPKVLQKVRAAVEKTGYVPNLLAGGLASNKSRL 101 VT DVA+ AGV+ IT SR +N+P VSP ++V A + GY+PNLLAGGLAS ++R+ Sbjct: 15 VTKEDVARAAGVSHITVSRVINSPEKVSPATRERVEAFIASMGYIPNLLAGGLASRRTRI 74 Query: 102 VAVVVPTVIGPVFQEIVHTLTETLAAAGYQVMLGQSGYENSREDALLEAIIGRRPDGVVL 161 VA +VPT+ +F E + L+E L GYQ++LGQ+ Y E L+E IGRR DG+VL Sbjct: 75 VAAIVPTISHSIFAETLRGLSEQLCMQGYQLLLGQTNYSEEAETGLVEVFIGRRVDGLVL 134 Query: 162 TGIMRSPQARKRLLASGIPVVETWDLTASPIDMLVGFSHEAIGREVARYLHGRARQRVAV 221 TG+ SP R+RL A+GIPVVETWDLT +PIDML GF + A GR + YL+ + +R+A Sbjct: 135 TGVQHSPMTRQRLKAAGIPVVETWDLTDTPIDMLAGFDNHAAGRAMGDYLYQKGYRRMAF 194 Query: 222 VGGRDERSQRRMNAFAQQAMALGMHQGPAPLAMHHVSAP--TTLGQGRQGLAELLQRQPD 279 VGG D R R+ + +L H P+ H+ P L GR+ + LL + P+ Sbjct: 195 VGGDDPRGMARVAGLRE---SLRHHGAAEPV---HLVMPMGAFLQAGREAIGRLLTQHPE 248 Query: 280 IDAIFCSSDLLALGVMIEAQSRGIAIPRQLAVVGFGDLEFSRDLQPRLTTVRIDGTGIGQ 339 +DA F S+D++A G +E RGIA+P ++A+ GF +LE + ++ P LTTV+I IG Sbjct: 249 VDAAFFSNDVIAAGAALECARRGIAVPGRIALAGFANLEIATEVLPALTTVQISAHQIGL 308 Query: 340 RAARFIIDRAAGIEVAERIIDVGFSIIERES 370 AA ++ R G + + + D+G+SI+ER+S Sbjct: 309 TAAEMLLTRFDGDPLDQAVHDLGYSILERDS 339 >gi|300310423|ref|YP_003774515.1| GntR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 352 Score = 217 bits (553), Expect = 1e-57, Method: Compositional matrix adjust. Identities = 129/342 (37%), Positives = 195/342 (57%), Gaps = 6/342 (1%) Query: 30 PRRRGPRKSAGGVTLRDVAQLAGVAPITASRALNTPAAVSPKVLQKVRAAVEKTGYVPNL 89 P RG R + G VT+ DVA AGV+P+T SRAL TPA V + Q++ A++K GYVPN Sbjct: 15 PAVRGSRAT-GRVTIIDVAAEAGVSPMTVSRALKTPALVQEQSRQRILEAIDKLGYVPNQ 73 Query: 90 LAGGLASNKSRLVAVVVPTVIGPVFQEIVHTLTETLAAAGYQVMLGQSGYENSREDALLE 149 A LAS +S++VAV+VP++ VF E + + + LA+ GYQ ++G++GY+ +E+ L+ Sbjct: 74 AAATLASARSQVVAVLVPSLTNAVFIETLSGIRDYLASVGYQFLIGETGYDRHKEEELIA 133 Query: 150 AIIGRRPDGVVLTGIMRSPQARKRLLASGIPVVETWDLTASPIDMLVGFSHEAIGREVAR 209 + P G +L+ + + R + IP V +DL S D VGFS G VAR Sbjct: 134 TYLAHAPAGFLLSSSQQHDILQSRPASRAIPAVRMFDLGRSQQDYSVGFSQTRAGHAVAR 193 Query: 210 YLHGRARQRVAVVGGR-DERSQRRMNAFAQQAMALGMHQGPAPLAMHHVSAPTTLGQGRQ 268 +L R +R A + + D R +R F + G+ L + PTT+ G Q Sbjct: 194 HLAERGYRRPAFLAAQLDPRMMKRREGFRKGLQEAGLAADIEVL----LPQPTTVDMGAQ 249 Query: 269 GLAELLQRQPDIDAIFCSSDLLALGVMIEAQSRGIAIPRQLAVVGFGDLEFSRDLQPRLT 328 L +LQ PD D++FC +D LALG + E Q +GI++PRQ+A+ GF DL ++ P +T Sbjct: 250 LLRRVLQDHPDCDSVFCCNDDLALGALFECQRQGISVPRQMAIAGFNDLSWAACATPSIT 309 Query: 329 TVRIDGTGIGQRAARFIIDRAAGIEVAERIIDVGFSIIERES 370 TV IG ++A ++ + G E+A+ +D+GF + RES Sbjct: 310 TVVTPRYDIGYQSAEMLVRQLKGEEIAKGRLDLGFELAVRES 351 >gi|300311611|ref|YP_003775703.1| transcription regulator DNA-binding repressor protein [Herbaspirillum seropedicae SmR1] Length = 337 Score = 129 bits (324), Expect = 4e-31, Method: Compositional matrix adjust. Identities = 100/317 (31%), Positives = 160/317 (50%), Gaps = 19/317 (5%) Query: 43 TLRDVAQLAGVAPITASRALNTPAAVSPKVLQKVRAAVEKTGYVPNLLAGGLASNKSRLV 102 T++DVA+LAGV+ T S LN VS ++V AAV++ YVP+ LA L S + + Sbjct: 3 TIKDVARLAGVSYTTVSHVLNQTRPVSSDARERVLAAVKELDYVPSALARSLRSKVTGSI 62 Query: 103 AVVVPTVIGPVFQEIVHTLTETLAAAGYQVMLGQSGYENSREDALLEAIIGRRPDGVVLT 162 +++P P F E+ + + AGY V+L S + ++ L+ + + DG+++ Sbjct: 63 GLIIPNNTNPYFSELARGIEDHCYGAGYSVILCNSDDDPDKQRDYLQVLQTKHCDGLIIA 122 Query: 163 GIMRSPQARKRLLASGIPVVETWDLTASPIDM---LVGFSHEAIGREVARYLHGRARQRV 219 + ++ L +G + T L +P ++ LV + G AR+L R RV Sbjct: 123 TLNQAD-----LNPAGKLDIPTVLLDRAPKELDIDLVSTDNAVGGSLAARHLLDLRRCRV 177 Query: 220 AVVGGRD--ERSQRRMNAFAQQAMALGMHQGPAPLAMHHVSAPTTLG-QGRQGLAELLQR 276 A + G D E S R+ F Q + QG LA + G G Q LLQ Sbjct: 178 ACIAGPDGLELSDERVRGFRQT-----LEQGGLALADSDLLHADFSGIGGYQAAMRLLQG 232 Query: 277 QPDI---DAIFCSSDLLALGVMIEAQSRGIAIPRQLAVVGFGDLEFSRDLQPRLTTVRID 333 +P DAIFC +D++A+GV+ A I +P +L+VVGF D+E ++ + P LTTV + Sbjct: 233 RPADQRPDAIFCCNDMMAIGVLRAAGELQIEVPGELSVVGFDDIELAQFVHPPLTTVAQN 292 Query: 334 GTGIGQRAARFIIDRAA 350 +G A+F+++R A Sbjct: 293 TRKLGNLTAQFLLERIA 309 >gi|300309932|ref|YP_003774024.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 358 Score = 124 bits (311), Expect = 1e-29, Method: Compositional matrix adjust. Identities = 96/313 (30%), Positives = 154/313 (49%), Gaps = 12/313 (3%) Query: 43 TLRDVAQLAGVAPITASRALNTPAAVSPKVLQKVRAAVEKTGYVPNLLAGGLASNKSRLV 102 +++ VA LAGV+ T SR LN P +VS + +K+ ++ + G+ PN L + SR V Sbjct: 4 SIKQVAHLAGVSIATVSRLLNKPGSVSAETAEKIHRSIAELGFRPNFTGRNLRAGNSRTV 63 Query: 103 AVVVPTVIGPVFQEIVHTLTETLAAAGYQVMLGQSGYENSREDALLEAIIGRRPDGVVLT 162 VVVPT+ VF + + + A Y VM + Y E A +E ++G R DG++LT Sbjct: 64 GVVVPTLSNTVFAQCLQGIELAARALDYSVMFTTTEYLPEEETAAVELLLGHRVDGMILT 123 Query: 163 GIMRSPQARKRLLA-SGIPVVETW-----DLTASPIDMLVGFSHEAIGREVARYLHGRAR 216 S A LL IP V + D TA+P V + A + +L G Sbjct: 124 VADASANATLDLLERERIPFVLAYNQLGTDQTAAPARASVSVDNRAAACDAVAHLIGLGH 183 Query: 217 QRVAVVGGRDERSQRRMNAFAQQAMALGMHQGPAPLAMHHVS--APTTLGQGRQGLAELL 274 +R+ ++ GR S R M + A+ G AP+A+ V T +Q +A+ Sbjct: 184 RRIQMLSGRFNASDRAMQRYYGYLDAM-RAAGLAPMAVIEVERHTLTAAADYQQMMADPR 242 Query: 275 QRQPDIDAIFCSSDLLALGVMIEAQSRGIAIPRQLAVVGFGDLEFSRDLQPRLTTVRIDG 334 QR A+FCS+DLLA+ M + ++ G+ +P ++V+GF + ++P L +V Sbjct: 243 QRP---TALFCSNDLLAMSAMRDLRALGMKVPNDISVMGFDGIPVGALMEPVLASVVQPS 299 Query: 335 TGIGQRAARFIID 347 IG+ A R +++ Sbjct: 300 EQIGEVALRVLVE 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 0.319 0.136 0.384 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: 1,131,779 Number of extensions: 47586 Number of successful extensions: 206 Number of sequences better than 1.0e-08: 8 Number of HSP's gapped: 199 Number of HSP's successfully gapped: 8 Length of query: 371 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 284 Effective length of database: 1,207,925 Effective search space: 343050700 Effective search space used: 343050700 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: 131 (55.1 bits)