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= 0012.0059.p (208 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309921|ref|YP_003774013.1| LysR family transcription regul... 115 2e-27 gi|300311929|ref|YP_003776021.1| LysR family transcription regul... 99 3e-22 gi|300309660|ref|YP_003773752.1| LysR family transcription regul... 92 4e-20 gi|300313187|ref|YP_003777279.1| transcription regulator protein... 87 1e-18 gi|300311868|ref|YP_003775960.1| LysR family transcription regul... 84 1e-17 >gi|300309921|ref|YP_003774013.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 299 Score = 115 bits (289), Expect = 2e-27, Method: Compositional matrix adjust. Identities = 68/193 (35%), Positives = 109/193 (56%), Gaps = 8/193 (4%) Query: 1 LLPLLPGLSQRYPALSVEVDFDDRISELVQDGYDLAIRGGRIADSSLVSRSICKLNLALV 60 L PL P +R+P +S+++ DRI +++ +GYD+AIR R++DS+LV R + +L + Sbjct: 107 LAPLWPMFLERHPEISLDITLSDRIVDIIDEGYDMAIRIARLSDSTLVHRKLTSTSLHVC 166 Query: 61 ASPAYLEARSTPRRPQDLHKHSLITRKFLGGKVSPWNFQGSDGSIMTWNTEHALLTLSSP 120 ASPAYL+A TP P +L +H I+ + K W F G +G + + L +++ Sbjct: 167 ASPAYLDAHGTPAHPHELAQHQTISYSYNQSK-DEWQFNGPEGPVSVRVSSR--LHVNNG 223 Query: 121 EALVQAALAGMGIAEVGVHHAWRYLQRGRLKVLLLRSHHP--GNYEMCLQYPHRALIAPR 178 ++ VQAAL G+GI +YL+ G+L +L P G Y + YP RA + + Sbjct: 224 DSCVQAALGGIGITRQPTFMIDQYLRSGQLVSILGDYGAPELGIYAV---YPSRAHLPAK 280 Query: 179 VRVAVDYLLEGFA 191 +R +D+L E FA Sbjct: 281 MRAMLDFLTEAFA 293 >gi|300311929|ref|YP_003776021.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 304 Score = 98.6 bits (244), Expect = 3e-22, Method: Compositional matrix adjust. Identities = 64/195 (32%), Positives = 102/195 (52%), Gaps = 6/195 (3%) Query: 1 LLPLLPGLSQRYPALSVEVDFDDRISELVQDGYDLAIRGGRIADSSLVSRSICKLNLALV 60 LLPLLP Q YP + VE+ +R+ + V++GYDLAIR G DS L++ ++ + L L Sbjct: 112 LLPLLPRFQQAYPQIEVELSIANRVVDFVEEGYDLAIRLGVPPDSRLIAHTLEEATLGLF 171 Query: 61 ASPAYLEARSTPRRPQDLHKHSLITRKFL---GGKVSPWNFQGSDGSIMTWNTEHALLTL 117 A+PAYL R PR +L +H I +F+ G+ PW F+ + G M ++ + Sbjct: 172 AAPAYLARRGQPRSIAELEQHDCI--QFILPSSGRAMPWIFKDAQGRDMDFHFKSRQRIH 229 Query: 118 SSPEALVQAALAGMGIAEVGVHHAWRYLQRGRLKVLLLRSHHPGNYEMCLQYPHRALIAP 177 V A+AG G+ ++ A ++RG L V +L+ + YPH ++ Sbjct: 230 DDVLGCVNWAIAGGGLFQIYHFIADAAVRRGEL-VEVLQQAGYRTRRFSILYPHNRHLSA 288 Query: 178 RVRVAVDYLLEGFAA 192 RVR V++L + A+ Sbjct: 289 RVRAFVEFLRQAVAS 303 >gi|300309660|ref|YP_003773752.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 337 Score = 91.7 bits (226), Expect = 4e-20, Method: Compositional matrix adjust. Identities = 61/199 (30%), Positives = 97/199 (48%), Gaps = 14/199 (7%) Query: 1 LLPLLPGLSQRYPALSVEVDFDDRISELVQDGYDLAIRGGRIADSSLVSRSICKLNLALV 60 LLP L RYP + + + DR +LVQ+ D IR G + DSS+V+R I Sbjct: 107 LLPNLCDFYTRYPDIELMMGMGDRPVDLVQEAVDCVIRIGELQDSSMVARRIGTFQTVTC 166 Query: 61 ASPAYLEARSTPRRPQDLHKHSLI----TRKFLGGKVSPWNF--QGSDGSIMTWNTEHAL 114 A+PAYLE P +DL +H + +R G+ W+F +G + + Sbjct: 167 AAPAYLERHGVPHTIEDLQQHKAVHYFSSRT---GRTIDWDFVVEGVTREVKM----NGK 219 Query: 115 LTLSSPEALVQAALAGMGIAEVGVHHAWRYLQRGRLKVLLLRSHHPGNYEMCLQYPHRAL 174 L ++ +A V+ AL G G+ + ++ R++ GRL V +L P + + Y H Sbjct: 220 LAVNEADAYVECALQGFGMVQAPLYMVTRHIDEGRL-VEVLSQWKPAPMPISVVYLHNRH 278 Query: 175 IAPRVRVAVDYLLEGFAAS 193 ++P+VR VD++ E FA Sbjct: 279 LSPKVRAFVDWVAELFATC 297 >gi|300313187|ref|YP_003777279.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 308 Score = 86.7 bits (213), Expect = 1e-18, Method: Compositional matrix adjust. Identities = 59/191 (30%), Positives = 99/191 (51%), Gaps = 3/191 (1%) Query: 1 LLPLLPGLSQRYPALSVEVDFDDRISELVQDGYDLAIRGGRIADSSLVSRSICKLNLALV 60 ++PLL RYP + + F++R +L+ +G+D AI GG +V+R + + L+ Sbjct: 107 IVPLLGEFLGRYPGIQPDWHFENRPVDLISEGFDAAIAGGTELSPGVVARELAPAHRVLL 166 Query: 61 ASPAYLEARSTPRRPQDLHKHS-LITRKFLGGKVSPWNFQGSDGSIMTWNTEHALLTLSS 119 ASPAYL+A P DL +H+ ++ R G+V P++ + G + +T+S Sbjct: 167 ASPAYLDAHPPLHSPADLAEHAGILIRSPQTGRVRPFSLRDRSGQQAPVTLQQR-MTMSD 225 Query: 120 PEALVQAALAGMGIAEVGVHHAWRYLQRGRLKVLLLRSHHPGNYEMCLQYPHRALIAPRV 179 A + A AG+GI V + HA YL+ G L V +L + + L + L+ + Sbjct: 226 ANAACEVAEAGLGITLVAMPHALPYLEGGTL-VRVLPDWYVDTGMLSLYFTAARLLPAKT 284 Query: 180 RVAVDYLLEGF 190 RV VD+++E F Sbjct: 285 RVFVDFVVEHF 295 >gi|300311868|ref|YP_003775960.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 307 Score = 83.6 bits (205), Expect = 1e-17, Method: Compositional matrix adjust. Identities = 61/188 (32%), Positives = 95/188 (50%), Gaps = 4/188 (2%) Query: 1 LLPLLPGLSQRYPALSVEVDFDDRISELVQDGYDLAIRGGRIADSSLVSRSICKLNLALV 60 +LP LP ++P L +E+ DR +LV +G+D +R G + DSSLV+R I L Sbjct: 107 VLPALPSFLDKHPQLEIELSASDRRVDLVAEGFDCVLRTGTLDDSSLVARPIGHLVQINC 166 Query: 61 ASPAYLEARSTPRRPQDLHKHSLI-TRKFLGGKVSPWNFQGSDGSIMTWNTEHALLTLSS 119 ASP YL TP+ +DL +H L+ R+ LGG+ W + DG +T++S Sbjct: 167 ASPEYLRRYGTPQTLEDLAQHRLVHYRQVLGGRSPGWEW--FDGQQTRSLPMAGSITVNS 224 Query: 120 PEALVQAALAGMGIAEVGVHHAW-RYLQRGRLKVLLLRSHHPGNYEMCLQYPHRALIAPR 178 E A LAG+G+ ++ + A R + G V +L + P + L Y R + R Sbjct: 225 TETYYAACLAGLGLIQLPLVGAQKRQMLDGGHVVEVLPQYRPAPMPVSLLYASRRHVPAR 284 Query: 179 VRVAVDYL 186 + +D+L Sbjct: 285 LAGFMDWL 292 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 0.137 0.410 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: 695,971 Number of extensions: 29010 Number of successful extensions: 172 Number of sequences better than 1.0e-08: 26 Number of HSP's gapped: 149 Number of HSP's successfully gapped: 26 Length of query: 208 Length of database: 1,619,870 Length adjustment: 81 Effective length of query: 127 Effective length of database: 1,236,335 Effective search space: 157014545 Effective search space used: 157014545 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: 128 (53.9 bits)