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= 0001.1782.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... 583 e-168 gi|300310488|ref|YP_003774580.1| LacI family transcription regul... 281 4e-77 gi|300310423|ref|YP_003774515.1| GntR family transcription regul... 223 1e-59 gi|300311611|ref|YP_003775703.1| transcription regulator DNA-bin... 117 2e-27 gi|300309932|ref|YP_003774024.1| transcription regulator protein... 116 2e-27 >gi|300311238|ref|YP_003775330.1| LacI family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 340 Score = 583 bits (1502), Expect = e-168, Method: Compositional matrix adjust. Identities = 286/340 (84%), Positives = 311/340 (91%) Query: 1 MTRKSDTPTPPARAITKEDVARAAGVSHITVSRVINTPEKVAPATRERVEAFISSMGYIP 60 M+ K + P P RA+TKEDVARAAGVSHITVSRVIN+PEKV+PATRERVEAFI+SMGYIP Sbjct: 1 MSHKPEPPAMPTRAVTKEDVARAAGVSHITVSRVINSPEKVSPATRERVEAFIASMGYIP 60 Query: 61 NMLAGGLASRRTRIVAAIVPTISHSIFAESVRGLSEQLSLQGYQLLLGQTNYSEQAETAL 120 N+LAGGLASRRTRIVAAIVPTISHSIFAE++RGLSEQL +QGYQLLLGQTNYSE+AET L Sbjct: 61 NLLAGGLASRRTRIVAAIVPTISHSIFAETLRGLSEQLCMQGYQLLLGQTNYSEEAETGL 120 Query: 121 VEAFIGRRVDGLVLTGVQHSARTRQRLKVAGIPVVETWDLSEHPIDMLVGFDNHAAGRAM 180 VE FIGRRVDGLVLTGVQHS TRQRLK AGIPVVETWDL++ PIDML GFDNHAAGRAM Sbjct: 121 VEVFIGRRVDGLVLTGVQHSPMTRQRLKAAGIPVVETWDLTDTPIDMLAGFDNHAAGRAM 180 Query: 181 GHYLYRKGYRHMAFVGGDDPRGLARFAGMREALLAQGAAQPLHLVMPMGAFLQAGREAIC 240 G YLY+KGYR MAFVGGDDPRG+AR AG+RE+L GAA+P+HLVMPMGAFLQAGREAI Sbjct: 181 GDYLYQKGYRRMAFVGGDDPRGMARVAGLRESLRHHGAAEPVHLVMPMGAFLQAGREAIG 240 Query: 241 RLLAHHPPIDAAFFSNDVIAAGAALECARRGIAVPQRMALAGFANLEIAQEVLPALTTVQ 300 RLL HP +DAAFFSNDVIAAGAALECARRGIAVP R+ALAGFANLEIA EVLPALTTVQ Sbjct: 241 RLLTQHPEVDAAFFSNDVIAAGAALECARRGIAVPGRIALAGFANLEIATEVLPALTTVQ 300 Query: 301 ISAHQIGLTAADMLLTRFDGDPVPQTVCDLGYTILEREST 340 ISAHQIGLTAA+MLLTRFDGDP+ Q V DLGY+ILER+ST Sbjct: 301 ISAHQIGLTAAEMLLTRFDGDPLDQAVHDLGYSILERDST 340 >gi|300310488|ref|YP_003774580.1| LacI family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 365 Score = 281 bits (720), Expect = 4e-77, Method: Compositional matrix adjust. Identities = 148/333 (44%), Positives = 211/333 (63%), Gaps = 6/333 (1%) Query: 12 ARAITKEDVARAAGVSHITVSRVINTPEKVAPATRERVEAFISSMGYIPNMLAGGLASRR 71 A +T DVA+ AGV+ IT SR +NTP V+P ++V + GY+PN+LAGGLAS + Sbjct: 33 AGGVTLRDVAQLAGVAPITASRALNTPSAVSPKVLQKVREAVEKTGYVPNLLAGGLASNK 92 Query: 72 TRIVAAIVPTISHSIFAESVRGLSEQLSLQGYQLLLGQTNYSEQAETALVEAFIGRRVDG 131 +R+VA +VPT+ +F E V L+E L+ GYQ++LGQ+ Y E AL+EA IGRR DG Sbjct: 93 SRLVAVVVPTVIGPVFQEIVHTLTETLAAAGYQVMLGQSGYENSREDALLEAIIGRRPDG 152 Query: 132 LVLTGVQHSARTRQRLKVAGIPVVETWDLSEHPIDMLVGFDNHAAGRAMGHYLYRKGYRH 191 +VLTG+ SA R+RL +GIPVVETWDL+ PIDMLVGF + A GR + YL+++G + Sbjct: 153 VVLTGIMRSAEARKRLLASGIPVVETWDLTPTPIDMLVGFSHEAIGREVARYLHQRGRKK 212 Query: 192 MAFVGGDDPRGLARFAGMREALLAQG-----AAQPLHLVMPMGAFLQAGREAICRLLAHH 246 +A VGG D R R + +A G A P+H V Q GR+ + LL Sbjct: 213 VAVVGGRDERSQRRMNAFAQECVALGMHEGRAPLPMHHVTAPTTLGQ-GRQGLAELLQAQ 271 Query: 247 PPIDAAFFSNDVIAAGAALECARRGIAVPQRMALAGFANLEIAQEVLPALTTVQISAHQI 306 P +DA F S+D++A G +E RGIA+P+++A+ GF +LE ++++ P LTTV+I I Sbjct: 272 PDLDAIFCSSDLLALGVMIEAQSRGIAIPEQLAVVGFGDLEFSRDLQPRLTTVRIDGTGI 331 Query: 307 GLTAADMLLTRFDGDPVPQTVCDLGYTILERES 339 G AA ++ R G V + V D+G++I+ R+S Sbjct: 332 GQRAARFIIDRAAGIEVAERVVDVGFSIIARDS 364 >gi|300310423|ref|YP_003774515.1| GntR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 352 Score = 223 bits (569), Expect = 1e-59, Method: Compositional matrix adjust. Identities = 126/345 (36%), Positives = 193/345 (55%), Gaps = 8/345 (2%) Query: 4 KSDTPTPPA----RA---ITKEDVARAAGVSHITVSRVINTPEKVAPATRERVEAFISSM 56 KS +PPA RA +T DVA AGVS +TVSR + TP V +R+R+ I + Sbjct: 8 KSKPKSPPAVRGSRATGRVTIIDVAAEAGVSPMTVSRALKTPALVQEQSRQRILEAIDKL 67 Query: 57 GYIPNMLAGGLASRRTRIVAAIVPTISHSIFAESVRGLSEQLSLQGYQLLLGQTNYSEQA 116 GY+PN A LAS R+++VA +VP++++++F E++ G+ + L+ GYQ L+G+T Y Sbjct: 68 GYVPNQAAATLASARSQVVAVLVPSLTNAVFIETLSGIRDYLASVGYQFLIGETGYDRHK 127 Query: 117 ETALVEAFIGRRVDGLVLTGVQHSARTRQRLKVAGIPVVETWDLSEHPIDMLVGFDNHAA 176 E L+ ++ G +L+ Q + R IP V +DL D VGF A Sbjct: 128 EEELIATYLAHAPAGFLLSSSQQHDILQSRPASRAIPAVRMFDLGRSQQDYSVGFSQTRA 187 Query: 177 GRAMGHYLYRKGYRHMAFVGGD-DPRGLARFAGMREALLAQGAAQPLHLVMPMGAFLQAG 235 G A+ +L +GYR AF+ DPR + R G R+ L G A + +++P + G Sbjct: 188 GHAVARHLAERGYRRPAFLAAQLDPRMMKRREGFRKGLQEAGLAADIEVLLPQPTTVDMG 247 Query: 236 REAICRLLAHHPPIDAAFFSNDVIAAGAALECARRGIAVPQRMALAGFANLEIAQEVLPA 295 + + R+L HP D+ F ND +A GA EC R+GI+VP++MA+AGF +L A P+ Sbjct: 248 AQLLRRVLQDHPDCDSVFCCNDDLALGALFECQRQGISVPRQMAIAGFNDLSWAACATPS 307 Query: 296 LTTVQISAHQIGLTAADMLLTRFDGDPVPQTVCDLGYTILEREST 340 +TTV + IG +A+ML+ + G+ + + DLG+ + REST Sbjct: 308 ITTVVTPRYDIGYQSAEMLVRQLKGEEIAKGRLDLGFELAVREST 352 >gi|300311611|ref|YP_003775703.1| transcription regulator DNA-binding repressor protein [Herbaspirillum seropedicae SmR1] Length = 337 Score = 117 bits (292), Expect = 2e-27, Method: Compositional matrix adjust. Identities = 95/315 (30%), Positives = 145/315 (46%), Gaps = 14/315 (4%) Query: 16 TKEDVARAAGVSHITVSRVINTPEKVAPATRERVEAFISSMGYIPNMLAGGLASRRTRIV 75 T +DVAR AGVS+ TVS V+N V+ RERV A + + Y+P+ LA L S+ T + Sbjct: 3 TIKDVARLAGVSYTTVSHVLNQTRPVSSDARERVLAAVKELDYVPSALARSLRSKVTGSI 62 Query: 76 AAIVPTISHSIFAESVRGLSEQLSLQGYQLLLGQTNYSEQAETALVEAFIGRRVDGLVLT 135 I+P ++ F+E RG+ + GY ++L ++ + ++ + DGL++ Sbjct: 63 GLIIPNNTNPYFSELARGIEDHCYGAGYSVILCNSDDDPDKQRDYLQVLQTKHCDGLIIA 122 Query: 136 GVQHSARTRQRLKVAGIPVVETWDLSEHPIDM---LVGFDNHAAGRAMGHYLYRKGYRHM 192 + + L AG + T L P ++ LV DN G +L + Sbjct: 123 TLNQA-----DLNPAGKLDIPTVLLDRAPKELDIDLVSTDNAVGGSLAARHLLDLRRCRV 177 Query: 193 AFVGGDDPRGLA--RFAGMREALLAQGAAQPLHLVMPMGAFLQAGREAICRLLAHHPPI- 249 A + G D L+ R G R+ L G A ++ G +A RLL P Sbjct: 178 ACIAGPDGLELSDERVRGFRQTLEQGGLALADSDLLHADFSGIGGYQAAMRLLQGRPADQ 237 Query: 250 --DAAFFSNDVIAAGAALECARRGIAVPQRMALAGFANLEIAQEVLPALTTVQISAHQIG 307 DA F ND++A G I VP +++ GF ++E+AQ V P LTTV + ++G Sbjct: 238 RPDAIFCCNDMMAIGVLRAAGELQIEVPGELSVVGFDDIELAQFVHPPLTTVAQNTRKLG 297 Query: 308 LTAADMLLTRFDGDP 322 A LL R DP Sbjct: 298 NLTAQFLLERI-ADP 311 >gi|300309932|ref|YP_003774024.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 358 Score = 116 bits (291), Expect = 2e-27, Method: Compositional matrix adjust. Identities = 92/307 (29%), Positives = 148/307 (48%), Gaps = 10/307 (3%) Query: 18 EDVARAAGVSHITVSRVINTPEKVAPATRERVEAFISSMGYIPNMLAGGLASRRTRIVAA 77 + VA AGVS TVSR++N P V+ T E++ I+ +G+ PN L + +R V Sbjct: 6 KQVAHLAGVSIATVSRLLNKPGSVSAETAEKIHRSIAELGFRPNFTGRNLRAGNSRTVGV 65 Query: 78 IVPTISHSIFAESVRGLSEQLSLQGYQLLLGQTNYSEQAETALVEAFIGRRVDGLVLTGV 137 +VPT+S+++FA+ ++G+ Y ++ T Y + ETA VE +G RVDG++LT Sbjct: 66 VVPTLSNTVFAQCLQGIELAARALDYSVMFTTTEYLPEEETAAVELLLGHRVDGMILTVA 125 Query: 138 QHSAR-TRQRLKVAGIPVVETW-----DLSEHPIDMLVGFDNHAAGRAMGHYLYRKGYRH 191 SA T L+ IP V + D + P V DN AA +L G+R Sbjct: 126 DASANATLDLLERERIPFVLAYNQLGTDQTAAPARASVSVDNRAAACDAVAHLIGLGHRR 185 Query: 192 MAFVGGD---DPRGLARFAGMREALLAQGAAQPLHLVMPMGAFLQAGREAICRLLAHHPP 248 + + G R + R+ G +A+ A G A P+ ++ L A + + Sbjct: 186 IQMLSGRFNASDRAMQRYYGYLDAMRAAGLA-PMAVIEVERHTLTAAADYQQMMADPRQR 244 Query: 249 IDAAFFSNDVIAAGAALECARRGIAVPQRMALAGFANLEIAQEVLPALTTVQISAHQIGL 308 A F SND++A A + G+ VP +++ GF + + + P L +V + QIG Sbjct: 245 PTALFCSNDLLAMSAMRDLRALGMKVPNDISVMGFDGIPVGALMEPVLASVVQPSEQIGE 304 Query: 309 TAADMLL 315 A +L+ Sbjct: 305 VALRVLV 311 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 0.135 0.390 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: 1,028,064 Number of extensions: 42699 Number of successful extensions: 186 Number of sequences better than 1.0e-08: 8 Number of HSP's gapped: 177 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)