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= 0012.0011.p (303 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313810|ref|YP_003777902.1| LysR family transcription regul... 556 e-160 gi|300311849|ref|YP_003775941.1| LysR family transcription regul... 77 1e-15 gi|300309487|ref|YP_003773579.1| LysR family transcription regul... 65 6e-12 gi|300313131|ref|YP_003777223.1| LysR family transcription regul... 59 6e-10 gi|300312785|ref|YP_003776877.1| transcription regulator protein... 57 2e-09 >gi|300313810|ref|YP_003777902.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 301 Score = 556 bits (1432), Expect = e-160, Method: Compositional matrix adjust. Identities = 276/300 (92%), Positives = 288/300 (96%) Query: 1 MAFSSDNVRVFLAVLDSGSFSAAARQLGRVPSSVSMTISQLEAELDLVLFDRTARDARPT 60 MAFSSDNVRVFLAVLDSGSFSAAAR+LGRVPSSVSMTISQLEAELDL LFDRTARDARPT Sbjct: 1 MAFSSDNVRVFLAVLDSGSFSAAARELGRVPSSVSMTISQLEAELDLQLFDRTARDARPT 60 Query: 61 ELARALEPDARLLASTLRQLDAHALAMHQGLERKLTLAVAPELLSVPWAKPLAVLAEEFP 120 ++ARALEPDARLLASTLRQLDAHALAMHQGLERKLTLAVAPELLS PWAKPLAVLA+EFP Sbjct: 61 DMARALEPDARLLASTLRQLDAHALAMHQGLERKLTLAVAPELLSAPWAKPLAVLAQEFP 120 Query: 121 SLEVEVLSSPQADAMRMLYDNTAQLALVFERHAGNDREAFQEFSSEMMVAVIAPEHPARL 180 SLEVEVLSSPQADAMRMLYD+TAQLALVFER AGNDREAFQEFSSEM+VAVIAP+HPA Sbjct: 121 SLEVEVLSSPQADAMRMLYDDTAQLALVFERPAGNDREAFQEFSSEMLVAVIAPDHPALR 180 Query: 181 RKKRKLRYEDLYDIRQIAVASRDASISDPRFFLARHLWRTDNHLATLSLVREGLGWAYLP 240 RKKRKLRYEDLYDIRQIAVASRDA +SDPRFFLAR +WRTDNHLATLSLVREGLGWAYLP Sbjct: 181 RKKRKLRYEDLYDIRQIAVASRDARVSDPRFFLARQIWRTDNHLATLSLVREGLGWAYLP 240 Query: 241 HSLVQAQIEAGTLVVIDFDNISNQQRMWVDVVWNKDQPLGLGAQRFIALMREMAPSRRKR 300 SLVQAQIEAG L VIDFDNISNQQR WVDVVW KD+PLGLGAQRF+ALMREMAP+RRKR Sbjct: 241 QSLVQAQIEAGALTVIDFDNISNQQRQWVDVVWCKDRPLGLGAQRFVALMREMAPARRKR 300 >gi|300311849|ref|YP_003775941.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 309 Score = 77.4 bits (189), Expect = 1e-15, Method: Compositional matrix adjust. Identities = 86/266 (32%), Positives = 127/266 (47%), Gaps = 24/266 (9%) Query: 3 FSSDNVRVFLAVLDSGSFSAAARQLGRVPSSVSMTISQLEAELDLVLFDRTARDARPTEL 62 S D +RVF+ V DSGSF AAAR+L R S+VS I+ LE +L L+LFDR+ + T Sbjct: 6 LSLDQLRVFVQVADSGSFLAAARKLARAQSAVSYAIASLEEQLGLLLFDRSGYRPQLTAP 65 Query: 63 ARALEPDARLLASTLRQLDAHALAMHQGLERKLTLAVAPELLSVPWAKPLAVLAE----- 117 AL DAR + + L A + +G E ++ LAV PL L + Sbjct: 66 GEALLADARQVLDHVDSLQVRASSYARGQELEMALAVDVFF-------PLDCLVDLLQRF 118 Query: 118 --EFPS----LEVEVLSSPQADAMRMLYDNTAQLALVFERHAGNDREAFQEFSSEMMVAV 171 FP+ LEVE L A A R++ D A L ++ S +VAV Sbjct: 119 RAAFPAVTVRLEVEALG---AVAERVI-DGRAMLGILGTLPTTPPNLMRITLPSVRLVAV 174 Query: 172 IAPEHPARLRKKRKLRYEDLYDIRQIAVASRDASISDPRFFL-ARHLWRTDNHLATLSLV 230 +AP HP + K ++ + L Q+ ++ R + F + +R WR + +L+ Sbjct: 175 VAPHHPLA-KVKGRIAEKMLLQQTQLVLSDRSELTARQDFSVHSRLTWRMSDLGTKHALL 233 Query: 231 REGLGWAYLPHSLVQAQIEAGTLVVI 256 R G+GW +P +V+ + AG LV I Sbjct: 234 RAGMGWGNMPLHVVKEDLAAGRLVSI 259 >gi|300309487|ref|YP_003773579.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 314 Score = 65.5 bits (158), Expect = 6e-12, Method: Compositional matrix adjust. Identities = 72/236 (30%), Positives = 110/236 (46%), Gaps = 23/236 (9%) Query: 12 LAVLDSGSFSAAARQLGRVPSSVSMTISQLEAELDLVLFDRTARDARPTELARALEPDAR 71 +A+ D GS AA Q+ S + ++E+ L + LF RT R PTEL + AR Sbjct: 24 IALSDHGSLLKAAEQVALTQPGASKALQEIESTLGVQLFTRTNRGLEPTELGHCVIRYAR 83 Query: 72 LLASTLRQLDAHALAMHQGLERKLTLAVAPELLSVP-WAKPLAVLAEEFPSLEVEVLSSP 130 L+ + L L LA+ QG + LAV + +VP L L E P+L VE++ Sbjct: 84 LIQTDLTHLREEMLAIMQGHGGR--LAVGTIMGAVPLLTDALTRLLEAHPALSVEIVEDT 141 Query: 131 QADAMRMLYDNTAQLALVFERHAGNDR----EAFQEFSSEMMVAVIAPEHPARLRKKRKL 186 A +R+L + +L L R + + R +AF E+ V V + +HP L L Sbjct: 142 SARLLRLL--DQGRLDLAICRTSISQRPDLYDAFNIHEEELAV-VASVQHP--LADAPSL 196 Query: 187 RYEDLYDIRQIAVAS---------RDASISDPRFFLARHLWRTDNHLATLSLVREG 233 + DL D R + ++ R+ +D RF L HL T + TLSL+++ Sbjct: 197 QLADLADSRWVVYSANMPMRLTLEREFHDADLRFPL--HLMETTSAFTTLSLLQKN 250 >gi|300313131|ref|YP_003777223.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 307 Score = 58.5 bits (140), Expect = 6e-10, Method: Compositional matrix adjust. Identities = 67/263 (25%), Positives = 112/263 (42%), Gaps = 18/263 (6%) Query: 3 FSSDNVRVFLAVLDSGSFSAAARQLGRVPSSVSMTISQLEAELDLVLFDRTARDARPTEL 62 S +R F+ ++++ ++ AA +L S++S I +LEA+LD+VL R A+ T+ Sbjct: 2 ISIRQLRYFVEIVEARGYTRAAERLFVAQSALSRQIKELEADLDVVLLRREAKTFELTQA 61 Query: 63 ARALEPDARLLASTLRQLDAHALAMHQGLERKLTLAVAPELLSVPWAKPLAVLAEE---- 118 + +R + L + A A + +G L L + SVP PL + E Sbjct: 62 GQDFYERSRKILLDLDRAVAQARTIGKGEHGALRLLHSS---SVPLTAPLGPMLNEALKA 118 Query: 119 FPSLEVEVLSSPQADAMRMLYDNTAQLALV-FERHAGNDREAFQEFSSEMMVAVIAPEHP 177 FP + +E+ +P R + + +A + L N A E +VA + H Sbjct: 119 FPGISLEISQAPSEYQAREIVEGSADIGLARLPILRANPNLASTVLYRERLVAAVPAGH- 177 Query: 178 ARLRKKRKLRYEDLYDIRQIAVASRD--------ASISDPRFFLARHLWRTDNHLATLSL 229 RL +++++ +L D + V RD A F R T + LSL Sbjct: 178 -RLAQRQEVEIAELRDEFFVTVPHRDRGGLSYLVAERCIAHGFYPRVARATSRKNSLLSL 236 Query: 230 VREGLGWAYLPHSLVQAQIEAGT 252 V G G A +P S+ + AG Sbjct: 237 VNAGFGIAVVPQSMASTSLAAGV 259 >gi|300312785|ref|YP_003776877.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 297 Score = 57.0 bits (136), Expect = 2e-09, Method: Compositional matrix adjust. Identities = 78/238 (32%), Positives = 107/238 (44%), Gaps = 23/238 (9%) Query: 9 RVFLAVLDSGSFSAAARQLGRVPSSVSMTISQLEAELDLVLFDRTARDARPTELARALEP 68 R FL VL++GS SAA R++G +V I LE+ L L LF R+ PT+ A L+P Sbjct: 12 RSFLKVLETGSLSAAGREMGLTQPTVGRHIENLESTLGLKLFVRSFDGFSPTDAALELKP 71 Query: 69 DARLLASTLRQLDAHALAMHQGLERKLTLAV-APELLSVPWAKP-LAVLAEEFPSLEVEV 126 A +A+ L A QG E + T+ + A E++SV P LA L P L VE+ Sbjct: 72 YAAAIAANSAAL--RRAASSQGKEVRGTVRLTASEVISVEVLPPILAALRHRHPELRVEL 129 Query: 127 LSSPQAD---------AMRMLYDNTAQLALVFERHAGNDREAFQEFSSEMMVAVIAPEHP 177 + S +AD A+RM AQ ALV +R G+ S + V H Sbjct: 130 VLSNKADDLLQREADIAVRMF--RPAQDALVAKR-LGSIELGLHAHQSYLTV------HG 180 Query: 178 ARLRKKRKLRYEDLYDIRQIAVASRDASISDPRFFLARHLWRTDNHLATLSLVREGLG 235 A + L L Q + R+ P A RTD+ LA L+ +R G G Sbjct: 181 AP-KSVDALADHTLIGFDQESAYVRNVLKQIPWLSRAALALRTDSDLAQLAAIRAGFG 237 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 0.132 0.380 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: 911,246 Number of extensions: 36838 Number of successful extensions: 248 Number of sequences better than 1.0e-08: 20 Number of HSP's gapped: 251 Number of HSP's successfully gapped: 20 Length of query: 303 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 218 Effective length of database: 1,217,395 Effective search space: 265392110 Effective search space used: 265392110 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)