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= 0001.0260.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|300309618|ref|YP_003773710.1| LacI family transcription regul... 613 e-177 gi|300311611|ref|YP_003775703.1| transcription regulator DNA-bin... 179 4e-46 gi|300309932|ref|YP_003774024.1| transcription regulator protein... 144 1e-35 gi|300310488|ref|YP_003774580.1| LacI family transcription regul... 112 5e-26 gi|300310825|ref|YP_003774917.1| LacI family transcription regul... 110 2e-25 >gi|300309618|ref|YP_003773710.1| LacI family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 338 Score = 613 bits (1582), Expect = e-177, Method: Compositional matrix adjust. Identities = 302/338 (89%), Positives = 317/338 (93%) Query: 1 MTTLSEVARLAGVTSATVSNVLRQRGKVGEQTRQRVLEAVAQLGYRPHLTARALAEGRAP 60 MTTLSEVARLAGVTSATVSNVLRQRGKVGEQTRQRVL+AVAQLGYRPHLTARALAEGRAP Sbjct: 1 MTTLSEVARLAGVTSATVSNVLRQRGKVGEQTRQRVLDAVAQLGYRPHLTARALAEGRAP 60 Query: 61 TLALVVSSIANPFYPEFALAAERAARAHGRFLIVCNTNDDPDTGRAYLDQIAGTLSDGVL 120 TLALVVSSIANPFYPEFALAAERAAR HGRFLIVCNTNDDPD GRAYLDQIAGTLSDGVL Sbjct: 61 TLALVVSSIANPFYPEFALAAERAARDHGRFLIVCNTNDDPDIGRAYLDQIAGTLSDGVL 120 Query: 121 IMNANLPMDELKKTEQRGAPVVLCMWEKPDAPPELPCIAVDFFAAGAIAARHLLALGHRH 180 IMNANLPMDEL+KTEQRGAPVVLCMWEKPDAPPELPCIAVDFF AGAIAARHLL LGH+ Sbjct: 121 IMNANLPMDELRKTEQRGAPVVLCMWEKPDAPPELPCIAVDFFEAGAIAARHLLGLGHQC 180 Query: 181 IAALVGSKRSGIHAERYRGFAQACTEAGVAHPAERTRYIADTVEAGYQASMALLREDPQL 240 AALVGSK+SGIHAERYRGFA AC EAG HP +RTRYI DTVE+GY+A+M LLRE PQ+ Sbjct: 181 FAALVGSKKSGIHAERYRGFASACKEAGHPHPTQRTRYINDTVESGYRATMELLREHPQV 240 Query: 241 TAIFASNDLPALGAMNAIADLGLSVPRDISVIGITDIQWARVSRPALTTVAVPTEEAARM 300 TAIFASNDLPALGAMNAIAD+G++VPRD+SV GITDIQWARVSRPALTTVAVPTE AARM Sbjct: 241 TAIFASNDLPALGAMNAIADMGMNVPRDVSVTGITDIQWARVSRPALTTVAVPTEAAARM 300 Query: 301 SIDLLLALIEHRSPSPVMRVTATPQLVQRASTAVARPR 338 SI+LLLALIE RSPSPVM VTA PQLV+RASTAV R R Sbjct: 301 SIELLLALIERRSPSPVMHVTAAPQLVERASTAVPRKR 338 >gi|300311611|ref|YP_003775703.1| transcription regulator DNA-binding repressor protein [Herbaspirillum seropedicae SmR1] Length = 337 Score = 179 bits (453), Expect = 4e-46, Method: Compositional matrix adjust. Identities = 124/339 (36%), Positives = 174/339 (51%), Gaps = 14/339 (4%) Query: 1 MTTLSEVARLAGVTSATVSNVLRQRGKVGEQTRQRVLEAVAQLGYRPHLTARALAEGRAP 60 M T+ +VARLAGV+ TVS+VL Q V R+RVL AV +L Y P AR+L Sbjct: 1 MATIKDVARLAGVSYTTVSHVLNQTRPVSSDARERVLAAVKELDYVPSALARSLRSKVTG 60 Query: 61 TLALVVSSIANPFYPEFALAAERAARAHGRFLIVCNTNDDPDTGRAYLDQIAGTLSDGVL 120 ++ L++ + NP++ E A E G +I+CN++DDPD R YL + DG++ Sbjct: 61 SIGLIIPNNTNPYFSELARGIEDHCYGAGYSVILCNSDDDPDKQRDYLQVLQTKHCDGLI 120 Query: 121 IMNANLPMDELKKTEQRGAPVVLCMWEKPDAPPELPC--IAVDFFAAGAIAARHLLALGH 178 I A L +L + P VL AP EL ++ D G++AARHLL L Sbjct: 121 I--ATLNQADLNPAGKLDIPTVLLDR----APKELDIDLVSTDNAVGGSLAARHLLDLRR 174 Query: 179 RHIAALVGSKRSGIHAERYRGFAQACTEAGVAHPAERTRYIADTVEAGYQASMALLR--- 235 +A + G + ER RGF Q + G+A + + GYQA+M LL+ Sbjct: 175 CRVACIAGPDGLELSDERVRGFRQTLEQGGLALADSDLLHADFSGIGGYQAAMRLLQGRP 234 Query: 236 EDPQLTAIFASNDLPALGAMNAIADLGLSVPRDISVIGITDIQWARVSRPALTTVAVPTE 295 D + AIF ND+ A+G + A +L + VP ++SV+G DI+ A+ P LTTVA T Sbjct: 235 ADQRPDAIFCCNDMMAIGVLRAAGELQIEVPGELSVVGFDDIELAQFVHPPLTTVAQNTR 294 Query: 296 EAARMSIDLLLALIEHRSPS-PVMRVTATPQLVQRASTA 333 + ++ LL I PS P R T PQL R STA Sbjct: 295 KLGNLTAQFLLERIA--DPSLPARRETVAPQLQLRGSTA 331 >gi|300309932|ref|YP_003774024.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 358 Score = 144 bits (363), Expect = 1e-35, Method: Compositional matrix adjust. Identities = 109/318 (34%), Positives = 168/318 (52%), Gaps = 16/318 (5%) Query: 3 TLSEVARLAGVTSATVSNVLRQRGKVGEQTRQRVLEAVAQLGYRPHLTARALAEGRAPTL 62 ++ +VA LAGV+ ATVS +L + G V +T +++ ++A+LG+RP+ T R L G + T+ Sbjct: 4 SIKQVAHLAGVSIATVSRLLNKPGSVSAETAEKIHRSIAELGFRPNFTGRNLRAGNSRTV 63 Query: 63 ALVVSSIANPFYPEFALAAERAARAHGRFLIVCNTNDDPDTGRAYLDQIAGTLSDGVLIM 122 +VV +++N + + E AARA ++ T P+ A ++ + G DG+++ Sbjct: 64 GVVVPTLSNTVFAQCLQGIELAARALDYSVMFTTTEYLPEEETAAVELLLGHRVDGMILT 123 Query: 123 ----NANLPMDELKKTEQRGAPVVLC---MWEKPDAPPELPCIAVDFFAAGAIAARHLLA 175 +AN +D L E+ P VL + A P ++VD AA A HL+ Sbjct: 124 VADASANATLDLL---ERERIPFVLAYNQLGTDQTAAPARASVSVDNRAAACDAVAHLIG 180 Query: 176 LGHRHIAALVGSKRSGIHA-ERYRGFAQACTEAGVAHPA--ERTRYIADTVEAGYQASMA 232 LGHR I L G + A +RY G+ A AG+A A E R+ T A YQ MA Sbjct: 181 LGHRRIQMLSGRFNASDRAMQRYYGYLDAMRAAGLAPMAVIEVERHTL-TAAADYQQMMA 239 Query: 233 LLREDPQLTAIFASNDLPALGAMNAIADLGLSVPRDISVIGITDIQWARVSRPALTTVAV 292 R+ P TA+F SNDL A+ AM + LG+ VP DISV+G I + P L +V Sbjct: 240 DPRQRP--TALFCSNDLLAMSAMRDLRALGMKVPNDISVMGFDGIPVGALMEPVLASVVQ 297 Query: 293 PTEEAARMSIDLLLALIE 310 P+E+ +++ +L+ IE Sbjct: 298 PSEQIGEVALRVLVEAIE 315 >gi|300310488|ref|YP_003774580.1| LacI family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 365 Score = 112 bits (280), Expect = 5e-26, Method: Compositional matrix adjust. Identities = 95/309 (30%), Positives = 143/309 (46%), Gaps = 12/309 (3%) Query: 3 TLSEVARLAGVTSATVSNVLRQRGKVGEQTRQRVLEAVAQLGYRPHLTARALAEGRAPTL 62 TL +VA+LAGV T S L V + Q+V EAV + GY P+L A LA ++ + Sbjct: 37 TLRDVAQLAGVAPITASRALNTPSAVSPKVLQKVREAVEKTGYVPNLLAGGLASNKSRLV 96 Query: 63 ALVVSSIANPFYPEFALAAERAARAHGRFLIVCNTNDDPDTGRAYLDQIAGTLSDGVLIM 122 A+VV ++ P + E A G +++ + + A L+ I G DGV++ Sbjct: 97 AVVVPTVIGPVFQEIVHTLTETLAAAGYQVMLGQSGYENSREDALLEAIIGRRPDGVVLT 156 Query: 123 NANLPMDELKKTEQRGAPVVLCMWEKPDAPPELPCIAVDFFAAGAIAARHLLALGHRHIA 182 + K+ G PVV W+ P ++ + A G AR+L G + +A Sbjct: 157 GIMRSAEARKRLLASGIPVVET-WDLTPTPIDM-LVGFSHEAIGREVARYLHQRGRKKVA 214 Query: 183 ALVGSKRSGIHAERYRGFAQACTEAGVAH---PAERTRYIA-DTVEAGYQASMALLREDP 238 + G R R FAQ C G+ P A T+ G Q LL+ P Sbjct: 215 VVGG--RDERSQRRMNAFAQECVALGMHEGRAPLPMHHVTAPTTLGQGRQGLAELLQAQP 272 Query: 239 QLTAIFASNDLPALGAMNAIADLGLSVPRDISVIGITDIQWARVSRPALTTVAVP----T 294 L AIF S+DL ALG M G+++P ++V+G D++++R +P LTTV + Sbjct: 273 DLDAIFCSSDLLALGVMIEAQSRGIAIPEQLAVVGFGDLEFSRDLQPRLTTVRIDGTGIG 332 Query: 295 EEAARMSID 303 + AAR ID Sbjct: 333 QRAARFIID 341 >gi|300310825|ref|YP_003774917.1| LacI family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 382 Score = 110 bits (275), Expect = 2e-25, Method: Compositional matrix adjust. Identities = 96/341 (28%), Positives = 163/341 (47%), Gaps = 19/341 (5%) Query: 3 TLSEVARLAGVTSATVSNVLR-QRGKVGEQTRQRVLEAVAQLGYRPHLTARALAEGRAPT 61 T+++VAR AGV+ +VS L + + + R+++ + +A+LGY+P AR L GR Sbjct: 29 TIAQVAREAGVSKTSVSRYLGGEFDALSVRLREQIGKTIARLGYQPSQMARGLKGGRTRL 88 Query: 62 LALVVSSIANPFYPEFALAAERAARAHGRFLIVCNTNDDPDTGRAYLDQIAGTLSDGVLI 121 + ++V+ I NP+ AE A + HG L++CNT +D + L + +G+L Sbjct: 89 IGMLVADILNPYSVAVLHGAEAACQKHGYTLMLCNTGNDEAREKQSLAALHSYSVEGLLF 148 Query: 122 MNANLPMDELKKTEQRGAPVVLCMWEKPDAPPELPCIAVDFFAAGAIAARHLLALGHRHI 181 + L + Q PVVL ++ + + +D A +A RHLLA G+ I Sbjct: 149 NTQGRNVTPLHELGQAAFPVVL--LDRHVEGCDFDLVGLDNVKAAQLATRHLLAQGYTDI 206 Query: 182 AALVGSKRSGIHAERYR--GFAQACTEAGVAHPAERTRYIADTVEAGYQASMALLRE--- 236 A +V S G+ + + R GF QA +E H D + G+ A+ +LRE Sbjct: 207 ALVVQSL-YGVSSRQGRQAGFLQAMSERRDCHGQTLE---VDVEQPGHVAT--VLREFFL 260 Query: 237 ----DPQLTAIFASNDLPALGAMNAIADLGLSVPRDISVIGITDIQWARVSRPALTTVAV 292 A+ A N + +L A+ + LS P D+ ++ ++ W+ + ++T+ Sbjct: 261 RRARSGGRVALLAGNGMVSLQIALALQSMKLSFPDDVGLLCFDELAWSPLVGSGISTIEQ 320 Query: 293 PTEEAARMSIDLLLALIEHRSPSPVMRVTATPQLVQRASTA 333 PT E +I+ LL I+ S M + +L+ R STA Sbjct: 321 PTYEIGFTAIERLLVRIQG-ERSVRMEMLLDGRLISRGSTA 360 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 0.320 0.132 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: 972,921 Number of extensions: 37802 Number of successful extensions: 182 Number of sequences better than 1.0e-08: 8 Number of HSP's gapped: 172 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 (21.8 bits) S2: 131 (55.1 bits)