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= 0001.2484.p (337 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311611|ref|YP_003775703.1| transcription regulator DNA-bin... 622 e-179 gi|300309618|ref|YP_003773710.1| LacI family transcription regul... 165 4e-42 gi|300309932|ref|YP_003774024.1| transcription regulator protein... 141 7e-35 gi|300310488|ref|YP_003774580.1| LacI family transcription regul... 130 2e-31 gi|300310423|ref|YP_003774515.1| GntR family transcription regul... 129 2e-31 >gi|300311611|ref|YP_003775703.1| transcription regulator DNA-binding repressor protein [Herbaspirillum seropedicae SmR1] Length = 337 Score = 622 bits (1604), Expect = e-179, Method: Compositional matrix adjust. Identities = 309/337 (91%), Positives = 320/337 (94%) Query: 1 MSTIKDVARLAGVSYTTVSHVLNQTRPVSADARERVLAAVKELDYVPSALARSLRSKVTG 60 M+TIKDVARLAGVSYTTVSHVLNQTRPVS+DARERVLAAVKELDYVPSALARSLRSKVTG Sbjct: 1 MATIKDVARLAGVSYTTVSHVLNQTRPVSSDARERVLAAVKELDYVPSALARSLRSKVTG 60 Query: 61 SIGLIIPNNTNPYFSELARGIEDHCYGAGYSVILCNSDDDPAKQRDYLQVLQTKRCDGLI 120 SIGLIIPNNTNPYFSELARGIEDHCYGAGYSVILCNSDDDP KQRDYLQVLQTK CDGLI Sbjct: 61 SIGLIIPNNTNPYFSELARGIEDHCYGAGYSVILCNSDDDPDKQRDYLQVLQTKHCDGLI 120 Query: 121 LATLNQADLKPNGKLDIPTVLLDRAPKELDIDLVSTDNALGGSLAARHLLQLQRRHVACI 180 +ATLNQADL P GKLDIPTVLLDRAPKELDIDLVSTDNA+GGSLAARHLL L+R VACI Sbjct: 121 IATLNQADLNPAGKLDIPTVLLDRAPKELDIDLVSTDNAVGGSLAARHLLDLRRCRVACI 180 Query: 181 AGPNGLELSDERVHGFRQTLQEGGLTLADSDLLHADFSGIGGYQAAMHLLRDRALELRPD 240 AGP+GLELSDERV GFRQTL++GGL LADSDLLHADFSGIGGYQAAM LL+ R + RPD Sbjct: 181 AGPDGLELSDERVRGFRQTLEQGGLALADSDLLHADFSGIGGYQAAMRLLQGRPADQRPD 240 Query: 241 AIFCCNDMMAIGVLRAAGELQIEVPGQLSVVGFDDIELAQFVHPPLTTVAQNTRKLGNLT 300 AIFCCNDMMAIGVLRAAGELQIEVPG+LSVVGFDDIELAQFVHPPLTTVAQNTRKLGNLT Sbjct: 241 AIFCCNDMMAIGVLRAAGELQIEVPGELSVVGFDDIELAQFVHPPLTTVAQNTRKLGNLT 300 Query: 301 AQFLLERIADPSLPARRETVAPQLQLRGSTAPLKKPT 337 AQFLLERIADPSLPARRETVAPQLQLRGSTAP PT Sbjct: 301 AQFLLERIADPSLPARRETVAPQLQLRGSTAPRVNPT 337 >gi|300309618|ref|YP_003773710.1| LacI family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 338 Score = 165 bits (418), Expect = 4e-42, Method: Compositional matrix adjust. Identities = 119/343 (34%), Positives = 172/343 (50%), Gaps = 14/343 (4%) Query: 1 MSTIKDVARLAGVSYTTVSHVLNQTRPVSADARERVLAAVKELDYVPSALARSLRSKVTG 60 M+T+ +VARLAGV+ TVS+VL Q V R+RVL AV +L Y P AR+L Sbjct: 1 MTTLSEVARLAGVTSATVSNVLRQRGKVGEQTRQRVLDAVAQLGYRPHLTARALAEGRAP 60 Query: 61 SIGLIIPNNTNPYFSELARGIEDHCYGAGYSVILCNSDDDPAKQRDYLQVLQTKRCDGLI 120 ++ L++ + NP++ E A E G +I+CN++DDP R YL + DG++ Sbjct: 61 TLALVVSSIANPFYPEFALAAERAARDHGRFLIVCNTNDDPDIGRAYLDQIAGTLSDGVL 120 Query: 121 L--ATLNQADLKPNGKLDIPTVLL----DRAPKELDIDLVSTDNALGGSLAARHLLQLQR 174 + A L +L+ + P VL AP EL ++ D G++AARHLL L Sbjct: 121 IMNANLPMDELRKTEQRGAPVVLCMWEKPDAPPELPC--IAVDFFEAGAIAARHLLGLGH 178 Query: 175 RHVACIAGPNGLELSDERVHGFRQTLQEGGLTLADSDLLHADFSGIGGYQAAMHLLRDRA 234 + A + G + ER GF +E G + + + GY+A M LLR+ Sbjct: 179 QCFAALVGSKKSGIHAERYRGFASACKEAGHPHPTQRTRYINDTVESGYRATMELLREHP 238 Query: 235 LELRPDAIFCCNDMMAIGVLRAAGELQIEVPGQLSVVGFDDIELAQFVHPPLTTVAQNTR 294 + AIF ND+ A+G + A ++ + VP +SV G DI+ A+ P LTTVA T Sbjct: 239 ---QVTAIFASNDLPALGAMNAIADMGMNVPRDVSVTGITDIQWARVSRPALTTVAVPTE 295 Query: 295 KLGNLTAQFLLERIA--DPSLPARRETVAPQLQLRGSTAPLKK 335 ++ + LL I PS P T APQL R STA +K Sbjct: 296 AAARMSIELLLALIERRSPS-PVMHVTAAPQLVERASTAVPRK 337 >gi|300309932|ref|YP_003774024.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 358 Score = 141 bits (356), Expect = 7e-35, Method: Compositional matrix adjust. Identities = 99/322 (30%), Positives = 164/322 (50%), Gaps = 27/322 (8%) Query: 3 TIKDVARLAGVSYTTVSHVLNQTRPVSADARERVLAAVKELDYVPSALARSLRSKVTGSI 62 +IK VA LAGVS TVS +LN+ VSA+ E++ ++ EL + P+ R+LR+ + ++ Sbjct: 4 SIKQVAHLAGVSIATVSRLLNKPGSVSAETAEKIHRSIAELGFRPNFTGRNLRAGNSRTV 63 Query: 63 GLIIPNNTNPYFSELARGIEDHCYGAGYSVILCNSDDDPAKQRDYLQVLQTKRCDGLILA 122 G+++P +N F++ +GIE YSV+ ++ P ++ +++L R DG+IL Sbjct: 64 GVVVPTLSNTVFAQCLQGIELAARALDYSVMFTTTEYLPEEETAAVELLLGHRVDGMILT 123 Query: 123 TLNQADLKPNGKLD------IPTVLLDRAPKELDIDL--------VSTDNALGGSLAARH 168 AD N LD IP VL A +L D VS DN A H Sbjct: 124 V---ADASANATLDLLERERIPFVL---AYNQLGTDQTAAPARASVSVDNRAAACDAVAH 177 Query: 169 LLQLQRRHVACIAGP-NGLELSDERVHGFRQTLQEGGLT-LADSDLLHADFSGIGGYQAA 226 L+ L R + ++G N + + +R +G+ ++ GL +A ++ + YQ Sbjct: 178 LIGLGHRRIQMLSGRFNASDRAMQRYYGYLDAMRAAGLAPMAVIEVERHTLTAAADYQQM 237 Query: 227 MHLLRDRALELRPDAIFCCNDMMAIGVLRAAGELQIEVPGQLSVVGFDDIELAQFVHPPL 286 M R RP A+FC ND++A+ +R L ++VP +SV+GFD I + + P L Sbjct: 238 MADPRQ-----RPTALFCSNDLLAMSAMRDLRALGMKVPNDISVMGFDGIPVGALMEPVL 292 Query: 287 TTVAQNTRKLGNLTAQFLLERI 308 +V Q + ++G + + L+E I Sbjct: 293 ASVVQPSEQIGEVALRVLVEAI 314 >gi|300310488|ref|YP_003774580.1| LacI family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 365 Score = 130 bits (327), Expect = 2e-31, Method: Compositional matrix adjust. Identities = 100/317 (31%), Positives = 163/317 (51%), Gaps = 19/317 (5%) Query: 3 TIKDVARLAGVSYTTVSHVLNQTRPVSADARERVLAAVKELDYVPSALARSLRSKVTGSI 62 T++DVA+LAGV+ T S LN VS ++V AV++ YVP+ LA L S + + Sbjct: 37 TLRDVAQLAGVAPITASRALNTPSAVSPKVLQKVREAVEKTGYVPNLLAGGLASNKSRLV 96 Query: 63 GLIIPNNTNPYFSELARGIEDHCYGAGYSVILCNSDDDPAKQRDYLQVLQTKRCDGLILA 122 +++P P F E+ + + AGY V+L S + +++ L+ + +R DG++L Sbjct: 97 AVVVPTVIGPVFQEIVHTLTETLAAAGYQVMLGQSGYENSREDALLEAIIGRRPDGVVLT 156 Query: 123 TLNQADLKPNGKL--DIPTV-LLDRAPKELDIDLVSTDNALGGSLAARHLLQLQRRHVAC 179 + ++ L IP V D P +D+ + + A+G + AR+L Q R+ VA Sbjct: 157 GIMRSAEARKRLLASGIPVVETWDLTPTPIDMLVGFSHEAIGREV-ARYLHQRGRKKVAV 215 Query: 180 IAGPNGLELSDERVHGFRQT-----LQEGGLTLADSDLLHADFSGIGGYQAAMHLLRDRA 234 + G + E S R++ F Q + EG L + G G Q L Sbjct: 216 VGGRD--ERSQRRMNAFAQECVALGMHEGRAPLPMHHVTAPTTLG-QGRQGLAEL----- 267 Query: 235 LELRP--DAIFCCNDMMAIGVLRAAGELQIEVPGQLSVVGFDDIELAQFVHPPLTTVAQN 292 L+ +P DAIFC +D++A+GV+ A I +P QL+VVGF D+E ++ + P LTTV + Sbjct: 268 LQAQPDLDAIFCSSDLLALGVMIEAQSRGIAIPEQLAVVGFGDLEFSRDLQPRLTTVRID 327 Query: 293 TRKLGNLTAQFLLERIA 309 +G A+F+++R A Sbjct: 328 GTGIGQRAARFIIDRAA 344 >gi|300310423|ref|YP_003774515.1| GntR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 352 Score = 129 bits (325), Expect = 2e-31, Method: Compositional matrix adjust. Identities = 103/334 (30%), Positives = 160/334 (47%), Gaps = 14/334 (4%) Query: 3 TIKDVARLAGVSYTTVSHVLNQTRPVSADARERVLAAVKELDYVPSALARSLRSKVTGSI 62 TI DVA AGVS TVS L V +R+R+L A+ +L YVP+ A +L S + + Sbjct: 27 TIIDVAAEAGVSPMTVSRALKTPALVQEQSRQRILEAIDKLGYVPNQAAATLASARSQVV 86 Query: 63 GLIIPNNTNPYFSELARGIEDHCYGAGYSVILCNSDDDPAKQRDYLQVLQTKRCDGLILA 122 +++P+ TN F E GI D+ GY ++ + D K+ + + G +L+ Sbjct: 87 AVLVPSLTNAVFIETLSGIRDYLASVGYQFLIGETGYDRHKEEELIATYLAHAPAGFLLS 146 Query: 123 TLNQADL---KPNGKLDIPTV-LLDRAPKELDIDLVSTDNALGGSLAARHLLQLQRRHVA 178 + Q D+ +P + IP V + D + D V G ARHL + R A Sbjct: 147 SSQQHDILQSRPASRA-IPAVRMFDLGRSQQDYS-VGFSQTRAGHAVARHLAERGYRRPA 204 Query: 179 CIAGPNGLELSDERVHGFRQTLQEGGLTLADSDLLHADFSGIGGYQAAMHLLRDRALELR 238 +A + R GFR+ LQE GL AD ++L + + LLR R L+ Sbjct: 205 FLAAQLDPRMMKRR-EGFRKGLQEAGLA-ADIEVLLPQPTTV---DMGAQLLR-RVLQDH 258 Query: 239 P--DAIFCCNDMMAIGVLRAAGELQIEVPGQLSVVGFDDIELAQFVHPPLTTVAQNTRKL 296 P D++FCCND +A+G L I VP Q+++ GF+D+ A P +TTV + Sbjct: 259 PDCDSVFCCNDDLALGALFECQRQGISVPRQMAIAGFNDLSWAACATPSITTVVTPRYDI 318 Query: 297 GNLTAQFLLERIADPSLPARRETVAPQLQLRGST 330 G +A+ L+ ++ + R + +L +R ST Sbjct: 319 GYQSAEMLVRQLKGEEIAKGRLDLGFELAVREST 352 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 0.391 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: 1,027,658 Number of extensions: 41386 Number of successful extensions: 156 Number of sequences better than 1.0e-08: 8 Number of HSP's gapped: 144 Number of HSP's successfully gapped: 8 Length of query: 337 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 251 Effective length of database: 1,212,660 Effective search space: 304377660 Effective search space used: 304377660 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)