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= 0001.0886.p (360 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310423|ref|YP_003774515.1| GntR family transcription regul... 637 0.0 gi|300311238|ref|YP_003775330.1| LacI family transcription regul... 224 9e-60 gi|300310488|ref|YP_003774580.1| LacI family transcription regul... 205 6e-54 gi|300311611|ref|YP_003775703.1| transcription regulator DNA-bin... 121 7e-29 gi|300309932|ref|YP_003774024.1| transcription regulator protein... 118 6e-28 >gi|300310423|ref|YP_003774515.1| GntR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 352 Score = 637 bits (1644), Expect = 0.0, Method: Compositional matrix adjust. Identities = 318/360 (88%), Positives = 332/360 (92%), Gaps = 8/360 (2%) Query: 1 MTQRAAPKSKPKATTPAAKSAKSAVRGSRATGRVTIMDVAAEAGVSSMTVSRALKTPALV 60 MTQRAA KSKPK+ AVRGSRATGRVTI+DVAAEAGVS MTVSRALKTPALV Sbjct: 1 MTQRAASKSKPKS--------PPAVRGSRATGRVTIIDVAAEAGVSPMTVSRALKTPALV 52 Query: 61 QEQSRLRIQQAIQKLGYVPNQAASTLASARSQVVAVLVPSLTNAVFIETLSGIRDYLAQA 120 QEQSR RI +AI KLGYVPNQAA+TLASARSQVVAVLVPSLTNAVFIETLSGIRDYLA Sbjct: 53 QEQSRQRILEAIDKLGYVPNQAAATLASARSQVVAVLVPSLTNAVFIETLSGIRDYLASV 112 Query: 121 GYQFLIGETGYVRAKEEQLIATYLAHAPAGFLLSSSEQYEILQSQAASRHIPAVRMFDLG 180 GYQFLIGETGY R KEE+LIATYLAHAPAGFLLSSS+Q++ILQS+ ASR IPAVRMFDLG Sbjct: 113 GYQFLIGETGYDRHKEEELIATYLAHAPAGFLLSSSQQHDILQSRPASRAIPAVRMFDLG 172 Query: 181 RSQQDYSVGFSQTRAGHAVARHLVERGYRRPAFLAAQLDPRMMKRREGFRKGLLEAGIAP 240 RSQQDYSVGFSQTRAGHAVARHL ERGYRRPAFLAAQLDPRMMKRREGFRKGL EAG+A Sbjct: 173 RSQQDYSVGFSQTRAGHAVARHLAERGYRRPAFLAAQLDPRMMKRREGFRKGLQEAGLAA 232 Query: 241 DIEVLLPQPTTVDMGAQLLRCVLEQHPDCDSVFCCNDDLALGALFECQRQGISVPREMAI 300 DIEVLLPQPTTVDMGAQLLR VL+ HPDCDSVFCCNDDLALGALFECQRQGISVPR+MAI Sbjct: 233 DIEVLLPQPTTVDMGAQLLRRVLQDHPDCDSVFCCNDDLALGALFECQRQGISVPRQMAI 292 Query: 301 AGFNDLSWAACATPSITTVVTPRYEIGYQSAEMLVRQLKGEAIPKGRLDLGFELALREST 360 AGFNDLSWAACATPSITTVVTPRY+IGYQSAEMLVRQLKGE I KGRLDLGFELA+REST Sbjct: 293 AGFNDLSWAACATPSITTVVTPRYDIGYQSAEMLVRQLKGEEIAKGRLDLGFELAVREST 352 >gi|300311238|ref|YP_003775330.1| LacI family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 340 Score = 224 bits (571), Expect = 9e-60, Method: Compositional matrix adjust. Identities = 119/327 (36%), Positives = 188/327 (57%), Gaps = 1/327 (0%) Query: 34 VTIMDVAAEAGVSSMTVSRALKTPALVQEQSRLRIQQAIQKLGYVPNQAASTLASARSQV 93 VT DVA AGVS +TVSR + +P V +R R++ I +GY+PN A LAS R+++ Sbjct: 15 VTKEDVARAAGVSHITVSRVINSPEKVSPATRERVEAFIASMGYIPNLLAGGLASRRTRI 74 Query: 94 VAVLVPSLTNAVFIETLSGIRDYLAQAGYQFLIGETGYVRAKEEQLIATYLAHAPAGFLL 153 VA +VP++++++F ETL G+ + L GYQ L+G+T Y E L+ ++ G +L Sbjct: 75 VAAIVPTISHSIFAETLRGLSEQLCMQGYQLLLGQTNYSEEAETGLVEVFIGRRVDGLVL 134 Query: 154 SSSEQYEILQSQAASRHIPAVRMFDLGRSQQDYSVGFSQTRAGHAVARHLVERGYRRPAF 213 + + + + + + IP V +DL + D GF AG A+ +L ++GYRR AF Sbjct: 135 TGVQHSPMTRQRLKAAGIPVVETWDLTDTPIDMLAGFDNHAAGRAMGDYLYQKGYRRMAF 194 Query: 214 LAAQLDPRMMKRREGFRKGLLEAGIAPDIEVLLPQPTTVDMGAQLLRCVLEQHPDCDSVF 273 + DPR M R G R+ L G A + +++P + G + + +L QHP+ D+ F Sbjct: 195 VGGD-DPRGMARVAGLRESLRHHGAAEPVHLVMPMGAFLQAGREAIGRLLTQHPEVDAAF 253 Query: 274 CCNDDLALGALFECQRQGISVPREMAIAGFNDLSWAACATPSITTVVTPRYEIGYQSAEM 333 ND +A GA EC R+GI+VP +A+AGF +L A P++TTV ++IG +AEM Sbjct: 254 FSNDVIAAGAALECARRGIAVPGRIALAGFANLEIATEVLPALTTVQISAHQIGLTAAEM 313 Query: 334 LVRQLKGEAIPKGRLDLGFELALREST 360 L+ + G+ + + DLG+ + R+ST Sbjct: 314 LLTRFDGDPLDQAVHDLGYSILERDST 340 >gi|300310488|ref|YP_003774580.1| LacI family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 365 Score = 205 bits (521), Expect = 6e-54, Method: Compositional matrix adjust. Identities = 123/354 (34%), Positives = 201/354 (56%), Gaps = 6/354 (1%) Query: 11 PKATTPAAKSAKSAVRGSRAT-GRVTIMDVAAEAGVSSMTVSRALKTPALVQEQSRLRIQ 69 P A+ +A RGSR + G VT+ DVA AGV+ +T SRAL TP+ V + +++ Sbjct: 12 PAASHQDGDAASPRRRGSRKSAGGVTLRDVAQLAGVAPITASRALNTPSAVSPKVLQKVR 71 Query: 70 QAIQKLGYVPNQAASTLASARSQVVAVLVPSLTNAVFIETLSGIRDYLAQAGYQFLIGET 129 +A++K GYVPN A LAS +S++VAV+VP++ VF E + + + LA AGYQ ++G++ Sbjct: 72 EAVEKTGYVPNLLAGGLASNKSRLVAVVVPTVIGPVFQEIVHTLTETLAAAGYQVMLGQS 131 Query: 130 GYVRAKEEQLIATYLAHAPAGFLLSSSEQYEILQSQAASRHIPAVRMFDLGRSQQDYSVG 189 GY ++E+ L+ + P G +L+ + + + + IP V +DL + D VG Sbjct: 132 GYENSREDALLEAIIGRRPDGVVLTGIMRSAEARKRLLASGIPVVETWDLTPTPIDMLVG 191 Query: 190 FSQTRAGHAVARHLVERGYRRPAFLAAQLDPRMMKRREGFRKGLLEAGI----APDIEVL 245 FS G VAR+L +RG ++ A + + D R +R F + + G+ AP Sbjct: 192 FSHEAIGREVARYLHQRGRKKVAVVGGR-DERSQRRMNAFAQECVALGMHEGRAPLPMHH 250 Query: 246 LPQPTTVDMGAQLLRCVLEQHPDCDSVFCCNDDLALGALFECQRQGISVPREMAIAGFND 305 + PTT+ G Q L +L+ PD D++FC +D LALG + E Q +GI++P ++A+ GF D Sbjct: 251 VTAPTTLGQGRQGLAELLQAQPDLDAIFCSSDLLALGVMIEAQSRGIAIPEQLAVVGFGD 310 Query: 306 LSWAACATPSITTVVTPRYEIGYQSAEMLVRQLKGEAIPKGRLDLGFELALRES 359 L ++ P +TTV IG ++A ++ + G + + +D+GF + R+S Sbjct: 311 LEFSRDLQPRLTTVRIDGTGIGQRAARFIIDRAAGIEVAERVVDVGFSIIARDS 364 >gi|300311611|ref|YP_003775703.1| transcription regulator DNA-binding repressor protein [Herbaspirillum seropedicae SmR1] Length = 337 Score = 121 bits (304), Expect = 7e-29, Method: Compositional matrix adjust. Identities = 98/336 (29%), Positives = 158/336 (47%), Gaps = 18/336 (5%) Query: 35 TIMDVAAEAGVSSMTVSRALKTPALVQEQSRLRIQQAIQKLGYVPNQAASTLASARSQVV 94 TI DVA AGVS TVS L V +R R+ A+++L YVP+ A +L S + + Sbjct: 3 TIKDVARLAGVSYTTVSHVLNQTRPVSSDARERVLAAVKELDYVPSALARSLRSKVTGSI 62 Query: 95 AVLVPSLTNAVFIETLSGIRDYLAQAGYQFLIGETGYVRAKEEQLIATYLAHAPAGFLLS 154 +++P+ TN F E GI D+ AGY ++ + K+ + G +++ Sbjct: 63 GLIIPNNTNPYFSELARGIEDHCYGAGYSVILCNSDDDPDKQRDYLQVLQTKHCDGLIIA 122 Query: 155 SSEQYEILQSQAASRHIPAV------RMFDLGRSQQDYSVGFSQTRAGHAVARHLVERGY 208 + Q ++ + A IP V + D+ D +VG G ARHL++ Sbjct: 123 TLNQADL--NPAGKLDIPTVLLDRAPKELDIDLVSTDNAVG------GSLAARHLLDLRR 174 Query: 209 RRPAFLAAQLDPRMMKRR-EGFRKGLLEAGIAPDIEVLLPQPTTVDMGAQLLRCVLEQHP 267 R A +A + R GFR+ L + G+A LL + G Q +L+ P Sbjct: 175 CRVACIAGPDGLELSDERVRGFRQTLEQGGLALADSDLLHADFSGIGGYQAAMRLLQGRP 234 Query: 268 ---DCDSVFCCNDDLALGALFECQRQGISVPREMAIAGFNDLSWAACATPSITTVVTPRY 324 D++FCCND +A+G L I VP E+++ GF+D+ A P +TTV Sbjct: 235 ADQRPDAIFCCNDMMAIGVLRAAGELQIEVPGELSVVGFDDIELAQFVHPPLTTVAQNTR 294 Query: 325 EIGYQSAEMLVRQLKGEAIPKGRLDLGFELALREST 360 ++G +A+ L+ ++ ++P R + +L LR ST Sbjct: 295 KLGNLTAQFLLERIADPSLPARRETVAPQLQLRGST 330 >gi|300309932|ref|YP_003774024.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 358 Score = 118 bits (296), Expect = 6e-28, Method: Compositional matrix adjust. Identities = 91/319 (28%), Positives = 154/319 (48%), Gaps = 17/319 (5%) Query: 33 RVTIMDVAAEAGVSSMTVSRALKTPALVQEQSRLRIQQAIQKLGYVPNQAASTLASARSQ 92 R +I VA AGVS TVSR L P V ++ +I ++I +LG+ PN L + S+ Sbjct: 2 RPSIKQVAHLAGVSIATVSRLLNKPGSVSAETAEKIHRSIAELGFRPNFTGRNLRAGNSR 61 Query: 93 VVAVLVPSLTNAVFIETLSGIRDYLAQAGYQFLIGETGYVRAKEEQLIATYLAHAPAGFL 152 V V+VP+L+N VF + L GI Y + T Y+ +E + L H G + Sbjct: 62 TVGVVVPTLSNTVFAQCLQGIELAARALDYSVMFTTTEYLPEEETAAVELLLGHRVDGMI 121 Query: 153 L-----SSSEQYEILQSQAASRHIPAVRMFD-LGRSQQ----DYSVGFSQTRAGHAVARH 202 L S++ ++L+ + IP V ++ LG Q SV A H Sbjct: 122 LTVADASANATLDLLERE----RIPFVLAYNQLGTDQTAAPARASVSVDNRAAACDAVAH 177 Query: 203 LVERGYRRPAFLAAQLD--PRMMKRREGFRKGLLEAGIAPDIEVLLPQPTTVDMGAQLLR 260 L+ G+RR L+ + + R M+R G+ + AG+AP + V+ + T+ A + Sbjct: 178 LIGLGHRRIQMLSGRFNASDRAMQRYYGYLDAMRAAGLAP-MAVIEVERHTLTAAADYQQ 236 Query: 261 CVLEQHPDCDSVFCCNDDLALGALFECQRQGISVPREMAIAGFNDLSWAACATPSITTVV 320 + + ++FC ND LA+ A+ + + G+ VP ++++ GF+ + A P + +VV Sbjct: 237 MMADPRQRPTALFCSNDLLAMSAMRDLRALGMKVPNDISVMGFDGIPVGALMEPVLASVV 296 Query: 321 TPRYEIGYQSAEMLVRQLK 339 P +IG + +LV ++ Sbjct: 297 QPSEQIGEVALRVLVEAIE 315 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 0.131 0.371 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: 1,006,701 Number of extensions: 40774 Number of successful extensions: 156 Number of sequences better than 1.0e-08: 8 Number of HSP's gapped: 148 Number of HSP's successfully gapped: 9 Length of query: 360 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 274 Effective length of database: 1,212,660 Effective search space: 332268840 Effective search space used: 332268840 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)