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= 0001.1334.p (396 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310825|ref|YP_003774917.1| LacI family transcription regul... 682 0.0 gi|300311611|ref|YP_003775703.1| transcription regulator DNA-bin... 123 3e-29 gi|300310423|ref|YP_003774515.1| GntR family transcription regul... 115 6e-27 gi|300309618|ref|YP_003773710.1| LacI family transcription regul... 105 5e-24 gi|300309932|ref|YP_003774024.1| transcription regulator protein... 89 4e-19 >gi|300310825|ref|YP_003774917.1| LacI family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 382 Score = 682 bits (1761), Expect = 0.0, Method: Compositional matrix adjust. Identities = 339/378 (89%), Positives = 354/378 (93%), Gaps = 2/378 (0%) Query: 8 AQINPRSSTIWRATVRQSIKTGTDRVTIAQVAREAGVSKTSVSRYLGGEFDALSVRLREQ 67 AQIN RSSTIWRA VRQSIKTGTDRVTIAQVAREAGVSKTSVSRYLGGEFDALSVRLREQ Sbjct: 3 AQINRRSSTIWRARVRQSIKTGTDRVTIAQVAREAGVSKTSVSRYLGGEFDALSVRLREQ 62 Query: 68 IGQTIARLGYQPSQMARGLKGGRTRLIGMLVADILNPYSVAVLHGAEAACQKHGYTLMLC 127 IG+TIARLGYQPSQMARGLKGGRTRLIGMLVADILNPYSVAVLHGAEAACQKHGYTLMLC Sbjct: 63 IGKTIARLGYQPSQMARGLKGGRTRLIGMLVADILNPYSVAVLHGAEAACQKHGYTLMLC 122 Query: 128 NTGNDEAREKQSLAALHSYSVEGLLFNTQGRNVTPLRELGQAAFPVVLLDRHVEGCDFDL 187 NTGNDEAREKQSLAALHSYSVEGLLFNTQGRNVTPL ELGQAAFPVVLLDRHVEGCDFDL Sbjct: 123 NTGNDEAREKQSLAALHSYSVEGLLFNTQGRNVTPLHELGQAAFPVVLLDRHVEGCDFDL 182 Query: 188 VGLDNVRAAQLGTRHLLAQGYTDIALVVQPLYGVSSRQGRQAGFLQAMSERPDCHGETLE 247 VGLDNV+AAQL TRHLLAQGYTDIALVVQ LYGVSSRQGRQAGFLQAMSER DCHG+TLE Sbjct: 183 VGLDNVKAAQLATRHLLAQGYTDIALVVQSLYGVSSRQGRQAGFLQAMSERRDCHGQTLE 242 Query: 248 VDVEQPGHVATVLREFFLRRVAAGSQGRLALLAGNGMVSLQIALALQSMGLRFPEDVGLL 307 VDVEQPGHVATVLREFFLRR +G GR+ALLAGNGMVSLQIALALQSM L FP+DVGLL Sbjct: 243 VDVEQPGHVATVLREFFLRRARSG--GRVALLAGNGMVSLQIALALQSMKLSFPDDVGLL 300 Query: 308 CFDELSWSPLVGSGISTIEQPTYDIGFTAIERLLVRVRGERSVRMEILLEPRLICRGSTV 367 CFDEL+WSPLVGSGISTIEQPTY+IGFTAIERLLVR++GERSVRME+LL+ RLI RGST Sbjct: 301 CFDELAWSPLVGSGISTIEQPTYEIGFTAIERLLVRIQGERSVRMEMLLDGRLISRGSTA 360 Query: 368 SVASHPQRAIVAGIGEKL 385 +V + RA A + KL Sbjct: 361 AVTAQEGRACSARLAAKL 378 >gi|300311611|ref|YP_003775703.1| transcription regulator DNA-binding repressor protein [Herbaspirillum seropedicae SmR1] Length = 337 Score = 123 bits (308), Expect = 3e-29, Method: Compositional matrix adjust. Identities = 97/335 (28%), Positives = 153/335 (45%), Gaps = 9/335 (2%) Query: 34 TIAQVAREAGVSKTSVSRYLGGEFDALSVRLREQIGQTIARLGYQPSQMARGLKGGRTRL 93 TI VAR AGVS T+VS L + +S RE++ + L Y PS +AR L+ T Sbjct: 3 TIKDVARLAGVSYTTVSHVLN-QTRPVSSDARERVLAAVKELDYVPSALARSLRSKVTGS 61 Query: 94 IGMLVADILNPYSVAVLHGAEAACQKHGYTLMLCNTGNDEAREKQSLAALHSYSVEGLLF 153 IG+++ + NPY + G E C GY+++LCN+ +D +++ L L + +GL+ Sbjct: 62 IGLIIPNNTNPYFSELARGIEDHCYGAGYSVILCNSDDDPDKQRDYLQVLQTKHCDGLII 121 Query: 154 NTQGRNVTPLRELGQAAFPVVLLDRHVEGCDFDLVGLDNVRAAQLGTRHLLAQGYTDIAL 213 T N L G+ P VLLDR + D DLV DN L RHLL +A Sbjct: 122 ATL--NQADLNPAGKLDIPTVLLDRAPKELDIDLVSTDNAVGGSLAARHLLDLRRCRVAC 179 Query: 214 VVQPLYGVSSRQGRQAGFLQAMSE--RPDCHGETLEVDVEQPGHVATVLREFFLRRVAAG 271 + P G+ R GF Q + + + L D G +R L + Sbjct: 180 IAGP-DGLELSDERVRGFRQTLEQGGLALADSDLLHADFSGIGGYQAAMR---LLQGRPA 235 Query: 272 SQGRLALLAGNGMVSLQIALALQSMGLRFPEDVGLLCFDELSWSPLVGSGISTIEQPTYD 331 Q A+ N M+++ + A + + P ++ ++ FD++ + V ++T+ Q T Sbjct: 236 DQRPDAIFCCNDMMAIGVLRAAGELQIEVPGELSVVGFDDIELAQFVHPPLTTVAQNTRK 295 Query: 332 IGFTAIERLLVRVRGERSVRMEILLEPRLICRGST 366 +G + LL R+ + P+L RGST Sbjct: 296 LGNLTAQFLLERIADPSLPARRETVAPQLQLRGST 330 >gi|300310423|ref|YP_003774515.1| GntR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 352 Score = 115 bits (288), Expect = 6e-27, Method: Compositional matrix adjust. Identities = 99/346 (28%), Positives = 159/346 (45%), Gaps = 11/346 (3%) Query: 22 VRQSIKTGTDRVTIAQVAREAGVSKTSVSRYLGGEFDALSVRLREQIGQTIARLGYQPSQ 81 VR S TG RVTI VA EAGVS +VSR L + + R++I + I +LGY P+Q Sbjct: 17 VRGSRATG--RVTIIDVAAEAGVSPMTVSRALKTP-ALVQEQSRQRILEAIDKLGYVPNQ 73 Query: 82 MARGLKGGRTRLIGMLVADILNPYSVAVLHGAEAACQKHGYTLMLCNTGNDEAREKQSLA 141 A L R++++ +LV + N + L G GY ++ TG D +E++ +A Sbjct: 74 AAATLASARSQVVAVLVPSLTNAVFIETLSGIRDYLASVGYQFLIGETGYDRHKEEELIA 133 Query: 142 ALHSYSVEG-LLFNTQGRNVTPLRELGQAAFPVVLLDRHVEGCDFDLVGLDNVRAAQLGT 200 +++ G LL ++Q ++ R +A V + D D+ VG RA Sbjct: 134 TYLAHAPAGFLLSSSQQHDILQSRPASRAIPAVRMFDLGRSQQDYS-VGFSQTRAGHAVA 192 Query: 201 RHLLAQGYTDIALVVQPLYGVSSRQGRQAGFLQAMSERPDCHGETLEVDVEQPGHVATVL 260 RHL +GY A + L R+ GF + + E G +++V P + Sbjct: 193 RHLAERGYRRPAFLAAQLD--PRMMKRREGFRKGLQE----AGLAADIEVLLPQPTTVDM 246 Query: 261 REFFLRRVAAGSQGRLALLAGNGMVSLQIALALQSMGLRFPEDVGLLCFDELSWSPLVGS 320 LRRV ++ N ++L Q G+ P + + F++LSW+ Sbjct: 247 GAQLLRRVLQDHPDCDSVFCCNDDLALGALFECQRQGISVPRQMAIAGFNDLSWAACATP 306 Query: 321 GISTIEQPTYDIGFTAIERLLVRVRGERSVRMEILLEPRLICRGST 366 I+T+ P YDIG+ + E L+ +++GE + + L L R ST Sbjct: 307 SITTVVTPRYDIGYQSAEMLVRQLKGEEIAKGRLDLGFELAVREST 352 >gi|300309618|ref|YP_003773710.1| LacI family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 338 Score = 105 bits (263), Expect = 5e-24, Method: Compositional matrix adjust. Identities = 96/342 (28%), Positives = 157/342 (45%), Gaps = 21/342 (6%) Query: 34 TIAQVAREAGVSKTSVSRYLGGEFDALSVRLREQIGQTIARLGYQPSQMARGLKGGRTRL 93 T+++VAR AGV+ +VS L + + + R+++ +A+LGY+P AR L GR Sbjct: 3 TLSEVARLAGVTSATVSNVLR-QRGKVGEQTRQRVLDAVAQLGYRPHLTARALAEGRAPT 61 Query: 94 IGMLVADILNPYSVAVLHGAEAACQKHGYTLMLCNTGNDEAREKQSLAALHSYSVEGLLF 153 + ++V+ I NP+ AE A + HG L++CNT +D + L + +G+L Sbjct: 62 LALVVSSIANPFYPEFALAAERAARDHGRFLIVCNTNDDPDIGRAYLDQIAGTLSDGVLI 121 Query: 154 NTQGRNVTPLRELGQAAFPVVL--LDRHVEGCDFDLVGLDNVRAAQLGTRHLLAQGYTDI 211 + LR+ Q PVVL ++ + + +D A + RHLL G+ Sbjct: 122 MNANLPMDELRKTEQRGAPVVLCMWEKPDAPPELPCIAVDFFEAGAIAARHLLGLGHQCF 181 Query: 212 -ALVVQPLYGVSSRQGRQAGFLQAMSE--RPDCHGETLEV-DVEQPGHVATV--LREFFL 265 ALV G+ + + R GF A E P T + D + G+ AT+ LRE Sbjct: 182 AALVGSKKSGIHAERYR--GFASACKEAGHPHPTQRTRYINDTVESGYRATMELLREH-- 237 Query: 266 RRVAAGSQGRLALLAGNGMVSLQIALALQSMGLRFPEDVGLLCFDELSWSPLVGSGISTI 325 A+ A N + +L A+ MG+ P DV + ++ W+ + ++T+ Sbjct: 238 -------PQVTAIFASNDLPALGAMNAIADMGMNVPRDVSVTGITDIQWARVSRPALTTV 290 Query: 326 EQPTYDIGFTAIERLLVRV-RGERSVRMEILLEPRLICRGST 366 PT +IE LL + R S M + P+L+ R ST Sbjct: 291 AVPTEAAARMSIELLLALIERRSPSPVMHVTAAPQLVERAST 332 >gi|300309932|ref|YP_003774024.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 358 Score = 89.4 bits (220), Expect = 4e-19, Method: Compositional matrix adjust. Identities = 85/318 (26%), Positives = 148/318 (46%), Gaps = 15/318 (4%) Query: 32 RVTIAQVAREAGVSKTSVSRYLGGEFDALSVRLREQIGQTIARLGYQPSQMARGLKGGRT 91 R +I QVA AGVS +VSR L + ++S E+I ++IA LG++P+ R L+ G + Sbjct: 2 RPSIKQVAHLAGVSIATVSRLLN-KPGSVSAETAEKIHRSIAELGFRPNFTGRNLRAGNS 60 Query: 92 RLIGMLVADILNPYSVAVLHGAEAACQKHGYTLMLCNTGNDEAREKQSLAALHSYSVEGL 151 R +G++V + N L G E A + Y++M T E ++ L + V+G+ Sbjct: 61 RTVGVVVPTLSNTVFAQCLQGIELAARALDYSVMFTTTEYLPEEETAAVELLLGHRVDGM 120 Query: 152 LFNTQGRNVTP-LRELGQAAFPVVLLDRHVEGCDFDL------VGLDNVRAAQLGTRHLL 204 + + L L + P VL + G D V +DN AA HL+ Sbjct: 121 ILTVADASANATLDLLERERIPFVLAYNQL-GTDQTAAPARASVSVDNRAAACDAVAHLI 179 Query: 205 AQGYTDIALVVQPLYGVSSRQGRQAGFLQAMSERPDCHGETLEVDVEQPGHVATVLREFF 264 G+ I ++ R G+L AM R ++VE+ H T ++ Sbjct: 180 GLGHRRIQMLSGRFNASDRAMQRYYGYLDAM--RAAGLAPMAVIEVER--HTLTAAADY- 234 Query: 265 LRRVAAGSQGRLALLAGNGMVSLQIALALQSMGLRFPEDVGLLCFDELSWSPLVGSGIST 324 + +A Q AL N ++++ L+++G++ P D+ ++ FD + L+ +++ Sbjct: 235 QQMMADPRQRPTALFCSNDLLAMSAMRDLRALGMKVPNDISVMGFDGIPVGALMEPVLAS 294 Query: 325 IEQPTYDIGFTAIERLLV 342 + QP+ IG A+ R+LV Sbjct: 295 VVQPSEQIGEVAL-RVLV 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 0.320 0.135 0.388 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: 1,270,021 Number of extensions: 54696 Number of successful extensions: 207 Number of sequences better than 1.0e-08: 8 Number of HSP's gapped: 194 Number of HSP's successfully gapped: 8 Length of query: 396 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 309 Effective length of database: 1,207,925 Effective search space: 373248825 Effective search space used: 373248825 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)