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= 0028.0087.p (340 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311238|ref|YP_003775330.1| LacI family transcription regul... 580 e-167 gi|300310488|ref|YP_003774580.1| LacI family transcription regul... 298 3e-82 gi|300310423|ref|YP_003774515.1| GntR family transcription regul... 216 2e-57 gi|300309932|ref|YP_003774024.1| transcription regulator protein... 128 8e-31 gi|300311611|ref|YP_003775703.1| transcription regulator DNA-bin... 122 5e-29 >gi|300311238|ref|YP_003775330.1| LacI family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 340 Score = 580 bits (1496), Expect = e-167, Method: Compositional matrix adjust. Identities = 284/339 (83%), Positives = 310/339 (91%) Query: 1 MTRKADPAAAPARAITKEDVARAAGVSHITVSRVINTPEKVSPATRERVESFISSMGYIP 60 M+ K +P A P RA+TKEDVARAAGVSHITVSRVIN+PEKVSPATRERVE+FI+SMGYIP Sbjct: 1 MSHKPEPPAMPTRAVTKEDVARAAGVSHITVSRVINSPEKVSPATRERVEAFIASMGYIP 60 Query: 61 NMLAGGLASRRTRIVAAIVPTISHSIFAETVRGLSEQLSLQGYQLLLGQTNYSEDAETGL 120 N+LAGGLASRRTRIVAAIVPTISHSIFAET+RGLSEQL +QGYQLLLGQTNYSE+AETGL Sbjct: 61 NLLAGGLASRRTRIVAAIVPTISHSIFAETLRGLSEQLCMQGYQLLLGQTNYSEEAETGL 120 Query: 121 VEAFIGRRVDGLVLTGVQHSARTRQRLKAAGIPVVETWDMSPQPIDMLVGFDNHAAGRAM 180 VE FIGRRVDGLVLTGVQHS TRQRLKAAGIPVVETWD++ PIDML GFDNHAAGRAM Sbjct: 121 VEVFIGRRVDGLVLTGVQHSPMTRQRLKAAGIPVVETWDLTDTPIDMLAGFDNHAAGRAM 180 Query: 181 GDYLVRKGYRRMAFVGGDDPRGLARFAGMRDALVAQGAPEPVHQVVAMGSFLQAGRETIC 240 GDYL +KGYRRMAFVGGDDPRG+AR AG+R++L GA EPVH V+ MG+FLQAGRE I Sbjct: 181 GDYLYQKGYRRMAFVGGDDPRGMARVAGLRESLRHHGAAEPVHLVMPMGAFLQAGREAIG 240 Query: 241 RLLALQPDIEAAFFSNDVMAAGAALECARRGIAVPKRIALAGFANLEIATEVLPALTTVQ 300 RLL P+++AAFFSNDV+AAGAALECARRGIAVP RIALAGFANLEIATEVLPALTTVQ Sbjct: 241 RLLTQHPEVDAAFFSNDVIAAGAALECARRGIAVPGRIALAGFANLEIATEVLPALTTVQ 300 Query: 301 ISAHQIGVTAAEMLLTRFDGQPVAQAVCDLGYSVLERDS 339 ISAHQIG+TAAEMLLTRFDG P+ QAV DLGYS+LERDS Sbjct: 301 ISAHQIGLTAAEMLLTRFDGDPLDQAVHDLGYSILERDS 339 >gi|300310488|ref|YP_003774580.1| LacI family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 365 Score = 298 bits (764), Expect = 3e-82, Method: Compositional matrix adjust. Identities = 156/334 (46%), Positives = 217/334 (64%), Gaps = 6/334 (1%) Query: 12 ARAITKEDVARAAGVSHITVSRVINTPEKVSPATRERVESFISSMGYIPNMLAGGLASRR 71 A +T DVA+ AGV+ IT SR +NTP VSP ++V + GY+PN+LAGGLAS + Sbjct: 33 AGGVTLRDVAQLAGVAPITASRALNTPSAVSPKVLQKVREAVEKTGYVPNLLAGGLASNK 92 Query: 72 TRIVAAIVPTISHSIFAETVRGLSEQLSLQGYQLLLGQTNYSEDAETGLVEAFIGRRVDG 131 +R+VA +VPT+ +F E V L+E L+ GYQ++LGQ+ Y E L+EA IGRR DG Sbjct: 93 SRLVAVVVPTVIGPVFQEIVHTLTETLAAAGYQVMLGQSGYENSREDALLEAIIGRRPDG 152 Query: 132 LVLTGVQHSARTRQRLKAAGIPVVETWDMSPQPIDMLVGFDNHAAGRAMGDYLVRKGYRR 191 +VLTG+ SA R+RL A+GIPVVETWD++P PIDMLVGF + A GR + YL ++G ++ Sbjct: 153 VVLTGIMRSAEARKRLLASGIPVVETWDLTPTPIDMLVGFSHEAIGREVARYLHQRGRKK 212 Query: 192 MAFVGGDDPRGLARFAGMRDALVAQG-----APEPVHQVVAMGSFLQAGRETICRLLALQ 246 +A VGG D R R VA G AP P+H V A + Q GR+ + LL Q Sbjct: 213 VAVVGGRDERSQRRMNAFAQECVALGMHEGRAPLPMHHVTAPTTLGQ-GRQGLAELLQAQ 271 Query: 247 PDIEAAFFSNDVMAAGAALECARRGIAVPKRIALAGFANLEIATEVLPALTTVQISAHQI 306 PD++A F S+D++A G +E RGIA+P+++A+ GF +LE + ++ P LTTV+I I Sbjct: 272 PDLDAIFCSSDLLALGVMIEAQSRGIAIPEQLAVVGFGDLEFSRDLQPRLTTVRIDGTGI 331 Query: 307 GVTAAEMLLTRFDGQPVAQAVCDLGYSVLERDSA 340 G AA ++ R G VA+ V D+G+S++ RDSA Sbjct: 332 GQRAARFIIDRAAGIEVAERVVDVGFSIIARDSA 365 >gi|300310423|ref|YP_003774515.1| GntR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 352 Score = 216 bits (550), Expect = 2e-57, Method: Compositional matrix adjust. Identities = 121/340 (35%), Positives = 191/340 (56%), Gaps = 4/340 (1%) Query: 4 KADPAAAPARA---ITKEDVARAAGVSHITVSRVINTPEKVSPATRERVESFISSMGYIP 60 K+ PA +RA +T DVA AGVS +TVSR + TP V +R+R+ I +GY+P Sbjct: 12 KSPPAVRGSRATGRVTIIDVAAEAGVSPMTVSRALKTPALVQEQSRQRILEAIDKLGYVP 71 Query: 61 NMLAGGLASRRTRIVAAIVPTISHSIFAETVRGLSEQLSLQGYQLLLGQTNYSEDAETGL 120 N A LAS R+++VA +VP++++++F ET+ G+ + L+ GYQ L+G+T Y E L Sbjct: 72 NQAAATLASARSQVVAVLVPSLTNAVFIETLSGIRDYLASVGYQFLIGETGYDRHKEEEL 131 Query: 121 VEAFIGRRVDGLVLTGVQHSARTRQRLKAAGIPVVETWDMSPQPIDMLVGFDNHAAGRAM 180 + ++ G +L+ Q + R + IP V +D+ D VGF AG A+ Sbjct: 132 IATYLAHAPAGFLLSSSQQHDILQSRPASRAIPAVRMFDLGRSQQDYSVGFSQTRAGHAV 191 Query: 181 GDYLVRKGYRRMAFVGGD-DPRGLARFAGMRDALVAQGAPEPVHQVVAMGSFLQAGRETI 239 +L +GYRR AF+ DPR + R G R L G + ++ + + G + + Sbjct: 192 ARHLAERGYRRPAFLAAQLDPRMMKRREGFRKGLQEAGLAADIEVLLPQPTTVDMGAQLL 251 Query: 240 CRLLALQPDIEAAFFSNDVMAAGAALECARRGIAVPKRIALAGFANLEIATEVLPALTTV 299 R+L PD ++ F ND +A GA EC R+GI+VP+++A+AGF +L A P++TTV Sbjct: 252 RRVLQDHPDCDSVFCCNDDLALGALFECQRQGISVPRQMAIAGFNDLSWAACATPSITTV 311 Query: 300 QISAHQIGVTAAEMLLTRFDGQPVAQAVCDLGYSVLERDS 339 + IG +AEML+ + G+ +A+ DLG+ + R+S Sbjct: 312 VTPRYDIGYQSAEMLVRQLKGEEIAKGRLDLGFELAVRES 351 >gi|300309932|ref|YP_003774024.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 358 Score = 128 bits (321), Expect = 8e-31, Method: Compositional matrix adjust. Identities = 99/313 (31%), Positives = 151/313 (48%), Gaps = 22/313 (7%) Query: 18 EDVARAAGVSHITVSRVINTPEKVSPATRERVESFISSMGYIPNMLAGGLASRRTRIVAA 77 + VA AGVS TVSR++N P VS T E++ I+ +G+ PN L + +R V Sbjct: 6 KQVAHLAGVSIATVSRLLNKPGSVSAETAEKIHRSIAELGFRPNFTGRNLRAGNSRTVGV 65 Query: 78 IVPTISHSIFAETVRGLSEQLSLQGYQLLLGQTNYSEDAETGLVEAFIGRRVDGLVLTGV 137 +VPT+S+++FA+ ++G+ Y ++ T Y + ET VE +G RVDG++LT Sbjct: 66 VVPTLSNTVFAQCLQGIELAARALDYSVMFTTTEYLPEEETAAVELLLGHRVDGMILTVA 125 Query: 138 QHSAR-TRQRLKAAGIPVVETW-----DMSPQPIDMLVGFDNHAAGRAMGDYLVRKGYRR 191 SA T L+ IP V + D + P V DN AA +L+ G+RR Sbjct: 126 DASANATLDLLERERIPFVLAYNQLGTDQTAAPARASVSVDNRAAACDAVAHLIGLGHRR 185 Query: 192 MAFVGGD---DPRGLARFAGMRDALVAQG-APEPV-----HQVVAMGSFLQAGRETICRL 242 + + G R + R+ G DA+ A G AP V H + A + Q + R Sbjct: 186 IQMLSGRFNASDRAMQRYYGYLDAMRAAGLAPMAVIEVERHTLTAAADYQQMMADPRQRP 245 Query: 243 LALQPDIEAAFFSNDVMAAGAALECARRGIAVPKRIALAGFANLEIATEVLPALTTVQIS 302 AL F SND++A A + G+ VP I++ GF + + + P L +V Sbjct: 246 TAL-------FCSNDLLAMSAMRDLRALGMKVPNDISVMGFDGIPVGALMEPVLASVVQP 298 Query: 303 AHQIGVTAAEMLL 315 + QIG A +L+ Sbjct: 299 SEQIGEVALRVLV 311 >gi|300311611|ref|YP_003775703.1| transcription regulator DNA-binding repressor protein [Herbaspirillum seropedicae SmR1] Length = 337 Score = 122 bits (305), Expect = 5e-29, Method: Compositional matrix adjust. Identities = 97/314 (30%), Positives = 151/314 (48%), Gaps = 19/314 (6%) Query: 16 TKEDVARAAGVSHITVSRVINTPEKVSPATRERVESFISSMGYIPNMLAGGLASRRTRIV 75 T +DVAR AGVS+ TVS V+N VS RERV + + + Y+P+ LA L S+ T + Sbjct: 3 TIKDVARLAGVSYTTVSHVLNQTRPVSSDARERVLAAVKELDYVPSALARSLRSKVTGSI 62 Query: 76 AAIVPTISHSIFAETVRGLSEQLSLQGYQLLLGQTNYSEDAETGLVEAFIGRRVDGLVLT 135 I+P ++ F+E RG+ + GY ++L ++ D + ++ + DGL++ Sbjct: 63 GLIIPNNTNPYFSELARGIEDHCYGAGYSVILCNSDDDPDKQRDYLQVLQTKHCDGLIIA 122 Query: 136 GVQHSARTRQRLKAAG---IPVVETWDMSPQPIDM-LVGFDNHAAGRAMGDYLVRKGYRR 191 + + L AG IP V D +P+ +D+ LV DN G +L+ R Sbjct: 123 TLNQA-----DLNPAGKLDIPTV-LLDRAPKELDIDLVSTDNAVGGSLAARHLLDLRRCR 176 Query: 192 MAFVGGDDPRGLA--RFAGMRDAL----VAQGAPEPVH-QVVAMGSFLQAGRETICRLLA 244 +A + G D L+ R G R L +A + +H +G + A R R Sbjct: 177 VACIAGPDGLELSDERVRGFRQTLEQGGLALADSDLLHADFSGIGGYQAAMRLLQGRPAD 236 Query: 245 LQPDIEAAFFSNDVMAAGAALECARRGIAVPKRIALAGFANLEIATEVLPALTTVQISAH 304 +PD A F ND+MA G I VP +++ GF ++E+A V P LTTV + Sbjct: 237 QRPD--AIFCCNDMMAIGVLRAAGELQIEVPGELSVVGFDDIELAQFVHPPLTTVAQNTR 294 Query: 305 QIGVTAAEMLLTRF 318 ++G A+ LL R Sbjct: 295 KLGNLTAQFLLERI 308 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 0.134 0.380 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: 959,437 Number of extensions: 39898 Number of successful extensions: 180 Number of sequences better than 1.0e-08: 8 Number of HSP's gapped: 170 Number of HSP's successfully gapped: 8 Length of query: 340 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 254 Effective length of database: 1,212,660 Effective search space: 308015640 Effective search space used: 308015640 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: 131 (55.1 bits)