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= 0001.2806.p (313 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312111|ref|YP_003776203.1| LysR family transcription regul... 569 e-163 gi|300312305|ref|YP_003776397.1| LysR family transcription regul... 244 4e-66 gi|300311542|ref|YP_003775634.1| LysR family transcription regul... 92 4e-20 gi|300309393|ref|YP_003773485.1| LysR family transcription regul... 89 4e-19 gi|300314076|ref|YP_003778168.1| LysR family transcription regul... 86 4e-18 >gi|300312111|ref|YP_003776203.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 321 Score = 569 bits (1466), Expect = e-163, Method: Compositional matrix adjust. Identities = 280/317 (88%), Positives = 296/317 (93%), Gaps = 4/317 (1%) Query: 1 MLFDLTDLRLFILIAELNSLTRSAERMNLSLAATSNRIKELEARLGTRLLYRESKGVQLT 60 MLFDLTDLRLFILIAE NSLTRSAERMNLSL ATSNRIKELE R GTRLLYRESKGVQLT Sbjct: 1 MLFDLTDLRLFILIAEHNSLTRSAERMNLSLGATSNRIKELETRFGTRLLYRESKGVQLT 60 Query: 61 PAGHTLLHHAQLFMQQVEHLKSDMQQYNNGIKGYIRIFANTTAVTEFMPEILGKFLARHP 120 PAGHTLLHHAQ FMQQVEHLKSDMQQYNNGIKGYIRIFANTTAVTEFMPEILGKFLARHP Sbjct: 61 PAGHTLLHHAQQFMQQVEHLKSDMQQYNNGIKGYIRIFANTTAVTEFMPEILGKFLARHP 120 Query: 121 QVNVALEERLNHDILRGIQEGTADIGIVAGPVQGDGLQILNFSTDRLVLATALEHPLAGT 180 QVNVALEERLNHDILRGIQEGTADIGIVAGPVQG+GLQILNFSTDRLVLATALEHPLA Sbjct: 121 QVNVALEERLNHDILRGIQEGTADIGIVAGPVQGEGLQILNFSTDRLVLATALEHPLADA 180 Query: 181 GSIAFLDTLEYEHIGLHEGSTLHHFLNRIVSEHGQRLKLRIQVRSFEAMCRMIETNVGIG 240 S+ F+ TLEYEHIGLHEGSTLHHFL++IV+E+GQRLKLRIQVRSFEAMCRMIETNVGIG Sbjct: 181 PSLPFIQTLEYEHIGLHEGSTLHHFLSKIVAENGQRLKLRIQVRSFEAMCRMIETNVGIG 240 Query: 241 IVPRSAALRHQQTMQLAVVELSDPWSVRERSMVVQNMETLSPHARNLVEFIREQTAQPSD 300 I+PRSAA RHQQTMQL+VVELSDPWSVRERSMVVQ+++TLSPHARNLVEFIREQTAQ ++ Sbjct: 241 ILPRSAAQRHQQTMQLSVVELSDPWSVRERSMVVQDIDTLSPHARNLVEFIREQTAQGAE 300 Query: 301 DDK----ALLLNAKTGT 313 DD A+ AK G+ Sbjct: 301 DDALVPGAMARPAKAGS 317 >gi|300312305|ref|YP_003776397.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 297 Score = 244 bits (624), Expect = 4e-66, Method: Compositional matrix adjust. Identities = 119/290 (41%), Positives = 187/290 (64%) Query: 3 FDLTDLRLFILIAELNSLTRSAERMNLSLAATSNRIKELEARLGTRLLYRESKGVQLTPA 62 F+L+DLRLF+ I E S+T A+R +++LA+ S RI+ +E LGT LL R +GVQ T A Sbjct: 5 FELSDLRLFLHIVESGSITGGAQRAHMALASASARIRNMEDALGTPLLERGRRGVQTTDA 64 Query: 63 GHTLLHHAQLFMQQVEHLKSDMQQYNNGIKGYIRIFANTTAVTEFMPEILGKFLARHPQV 122 G L HHA++ QQ+E L+ ++ QY G+KG+IR+ NT+A+TEF+PE+L +FLARHP Sbjct: 65 GRALAHHARMMAQQMEQLRDELGQYARGLKGHIRLLCNTSAMTEFLPEVLARFLARHPHT 124 Query: 123 NVALEERLNHDILRGIQEGTADIGIVAGPVQGDGLQILNFSTDRLVLATALEHPLAGTGS 182 ++ LEE+L++++++ + +G AD+GI+A LQ F D LV + HPLA S Sbjct: 125 DIELEEKLSYEVVQAVIDGVADVGIIADSTDSGPLQTYPFRQDHLVAVLSKRHPLARRKS 184 Query: 183 IAFLDTLEYEHIGLHEGSTLHHFLNRIVSEHGQRLKLRIQVRSFEAMCRMIETNVGIGIV 242 +AF + L + +GL S L L+ + G+RL+ R+++RSF+ +CRM+E VG+ ++ Sbjct: 185 LAFAELLGEDFVGLSGDSALQQHLSGHATRAGKRLQYRVRLRSFDGICRMVEHQVGVAVL 244 Query: 243 PRSAALRHQQTMQLAVVELSDPWSVRERSMVVQNMETLSPHARNLVEFIR 292 P +AAL M + + LSD WS R+ + V+ +E L R L++ ++ Sbjct: 245 PETAALASTPHMDIRAIPLSDGWSRRQLLICVRGLEGLPGPTRELIQALQ 294 >gi|300311542|ref|YP_003775634.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 335 Score = 92.4 bits (228), Expect = 4e-20, Method: Compositional matrix adjust. Identities = 75/303 (24%), Positives = 136/303 (44%), Gaps = 12/303 (3%) Query: 8 LRLFILIAELNSLTRSAERMNLSLAATSNRIKELEARLGTRLLYRESKGVQLTPAGHTLL 67 L+ F+ +A+ +A+R ++S +A S I+++EA G RL R+++ V LTP G + Sbjct: 10 LQAFLALADCRHFGHAAQRCHVSQSAFSAMIQKIEAAAGARLFERDTRNVTLTPEGELFV 69 Query: 68 HHAQLFMQQVEHLKSDMQQYNNGIKGYIRIFANTTAVTEFMPEILGKFLARHPQVNVALE 127 A+ + +E SDM Y KG + I A + ++P +L + R+P V V L Sbjct: 70 QVARQLVSDIEAAFSDMSDYVARRKGRVAIAALPSLAAGWLPPVLADYRQRYPGVTVELF 129 Query: 128 ERLNHDILRGIQEGTADIGIVAGPVQGDGLQILNFST-----DRLVLATALEHPLAGTGS 182 + ++ L ++ G DI + A G +L F T D L +H LA Sbjct: 130 DAISDQCLDLLRHGKVDIALTA-----PGPNLLEFDTRPLCSDPFYLVCRKDHKLASKRR 184 Query: 183 IAFLDTLEYEHIGLHEGSTLHHFLNRIVSEHGQRLKLRIQVRSFEAMCRMIETNVGIGIV 242 I E I L +++ L+ ++ G + ++V + +IE+ +G+ +V Sbjct: 185 IKVPQLAGCEMIHLARSTSVRQHLDAVLRPGGV-IHTGLEVEHLATVAALIESGLGVSVV 243 Query: 243 PRSAALRHQQTMQLAVVELSDPWSVRERSMVVQNMETLSPHARNLVEFIREQTAQPSDDD 302 P L + L + L P R +V +LS A+ L+E + + ++ + Sbjct: 244 P-ELTLFQFRLPNLVAIPLDAPELKRPLLIVTPKERSLSVAAQGLLELVEGKAKAETETE 302 Query: 303 KAL 305 A+ Sbjct: 303 AAV 305 >gi|300309393|ref|YP_003773485.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 296 Score = 89.0 bits (219), Expect = 4e-19, Method: Compositional matrix adjust. Identities = 81/272 (29%), Positives = 130/272 (47%), Gaps = 20/272 (7%) Query: 4 DLTDLRLFILIAELNSLTRSAERMNLSLAATSNRIKELEARLGTRLLYRESKGVQLTPAG 63 +L LR F+ +AE S TR+AE++ + S +IK LE +G L R S+GV+L+ G Sbjct: 2 ELRHLRYFLAVAEQRSFTRAAEKVGIGQPPLSMQIKALEEEVGGALFLRSSQGVELSEVG 61 Query: 64 HTLLHHAQLFMQQVEHLKSDMQQYNNGIKGYIRIFANTTAVTEFMPEI---LGKFLARHP 120 LL HAQ + Q E +Q +G G +R+ ++AV F P + L +F RH Sbjct: 62 RVLLPHAQRAVDQAEQALRAARQAASGETGLLRMGFTSSAV--FHPLVSHALQQFRERHR 119 Query: 121 QVNVALEERLNHDILRGI---QEGTADIGIVAGPVQGDGLQILNFSTDRLVLATALEHPL 177 ++ ++L E + +L I Q A + IV P L ++ ++L +A HPL Sbjct: 120 KLEISLSEGITEQLLADIAASQLDAAFVRIVTTP--SAALGVVELPAEKLKVALPRSHPL 177 Query: 178 AGTGSIAFLDTLEYEHIGLH--EGSTLHHFLNRIVSEHG---QRLKLRIQVRSFEAMCRM 232 A S+ D I + +GS L+ + G Q ++L Q+ S + Sbjct: 178 ARRKSLRLQDLASENFIMVPRGKGSALYDSIFSACQAAGFDPQVIQLAPQLTS---AINL 234 Query: 233 IETNVGIGIVPRSAALRHQQTMQLAVVELSDP 264 + + +GI IVP A+ Q Q+ VE+ +P Sbjct: 235 VASGLGISIVPE--AIEQVQLAQVRYVEIVEP 264 >gi|300314076|ref|YP_003778168.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 294 Score = 85.9 bits (211), Expect = 4e-18, Method: Compositional matrix adjust. Identities = 77/271 (28%), Positives = 130/271 (47%), Gaps = 20/271 (7%) Query: 4 DLTDLRLFILIAELNSLTRSAERMNLSLAATSNRIKELEARLGTRLLYRESKGVQLTPAG 63 DLT LR FI +A +LTR+A++++L+ A S +IK L+ LG +L R + G+ LT G Sbjct: 2 DLTQLRAFISVAHEGNLTRAADKLHLTQPAVSLQIKGLQESLGLQLFNRSAAGMVLTAEG 61 Query: 64 HTLLHHAQLFMQQVEHLK---SDMQQYNNGIKGYIRIFANTTAVTEFMPEILGKFLA--- 117 + LL A+ + V+ L+ +D + + G + I T EF+ LG FL Sbjct: 62 NKLLPLAERVLADVQELRRHAADFRSSTGELSGSLAI--GTILDPEFIR--LGGFLKLLV 117 Query: 118 -RHPQVNVALEERLNHDILRGIQEGTADIGIVAGPVQGDGLQILNFS--TDRLVLATALE 174 RHPQ++ L ++ +L I+ G D+G G G G Q + + T +++ + Sbjct: 118 ERHPQLSTQLAHHMSGSVLNEIRAGKLDVGFFLG-APGQGFQSMELTSFTYKVIAPAGWK 176 Query: 175 HPLAGTGSIAFLDTLEYEHIGLHEGSTLHHFLNRIVSEHGQRLKLRIQVRSFEAMCRMIE 234 + ++G G + + I S H L+RI ++H + V +M +++ Sbjct: 177 NRVSGKG---WKELSRLPWIWTPPESAHHRLLSRIFAQHQVKPHTVALVDQESSMLDLVK 233 Query: 235 TNVGIGIVPRSAALRHQQTMQLAV---VELS 262 + VG+ + S AL L + VELS Sbjct: 234 SGVGLSLARASIALNQAHAHGLVIADAVELS 264 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 0.321 0.135 0.379 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: 879,357 Number of extensions: 35638 Number of successful extensions: 241 Number of sequences better than 1.0e-08: 69 Number of HSP's gapped: 224 Number of HSP's successfully gapped: 69 Length of query: 313 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 228 Effective length of database: 1,217,395 Effective search space: 277566060 Effective search space used: 277566060 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: 130 (54.7 bits)