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= 0001.4171.p (301 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313602|ref|YP_003777694.1| LysR family transcription regul... 528 e-151 gi|300311935|ref|YP_003776027.1| LysR family transcription regul... 89 6e-19 gi|300311724|ref|YP_003775816.1| LysR family transcription regul... 87 2e-18 gi|300313085|ref|YP_003777177.1| LysR family transcription regul... 84 1e-17 gi|300313396|ref|YP_003777488.1| LysR family transcription regul... 79 4e-16 >gi|300313602|ref|YP_003777694.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 300 Score = 528 bits (1361), Expect = e-151, Method: Compositional matrix adjust. Identities = 268/297 (90%), Positives = 282/297 (94%) Query: 1 MRITLRQLQIFLAVAQSGSTTAAAGMVALSQSAASASLNELESLLGVQLFDRVGKRLVLN 60 M+ITLRQLQIFLAVAQSGSTTAAA +VALSQSAASA+LNELE LLGVQLFDRVGKRLVLN Sbjct: 1 MKITLRQLQIFLAVAQSGSTTAAADLVALSQSAASAALNELEHLLGVQLFDRVGKRLVLN 60 Query: 61 DSGRQLLPQARHMLDAAQTIERQFSDPAAGSELHLGASTTIGSYLLPAMIAAYRRIHAGA 120 DSGRQLLPQARHMLDAAQTIERQFSDP AGSELH+GASTTIGSY+LPAMIAAYR+ HAGA Sbjct: 61 DSGRQLLPQARHMLDAAQTIERQFSDPEAGSELHIGASTTIGSYMLPAMIAAYRKDHAGA 120 Query: 121 RVRALVANTADIVEAVVNFEVDAGLIEGPCHADDVRVEPWMTDELIVVAAPTHPIVAQAR 180 RVRALVANTADIV+AVVNFEVDAGLIEGPCHADDV VEPWM DELIVVAAP HP+V R Sbjct: 121 RVRALVANTADIVDAVVNFEVDAGLIEGPCHADDVEVEPWMMDELIVVAAPRHPLVKSGR 180 Query: 181 KITLKMLRQADWLLREAGSGTREAVEHALIPYLHHLPSSFEFGNSEAIKRATAEGLGISC 240 KITLK LR+A+WLLREAGSGTREAVEHALIPYLHHLPSSFEFGNSEAIKRATAEGLGISC Sbjct: 181 KITLKRLREAEWLLREAGSGTREAVEHALIPYLHHLPSSFEFGNSEAIKRATAEGLGISC 240 Query: 241 LSRSVVEDLIESGKLVELETPLPTLRRHFYMVVSRHRAPSPSLAALLSFCRQWAQQQ 297 LSR+VVED+IES KLVEL+TPLPTLRRHFYMVVSRHRAPSPSL ALL FCR WAQ+Q Sbjct: 241 LSRAVVEDMIESRKLVELDTPLPTLRRHFYMVVSRHRAPSPSLGALLGFCRAWAQRQ 297 >gi|300311935|ref|YP_003776027.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 286 Score = 88.6 bits (218), Expect = 6e-19, Method: Compositional matrix adjust. Identities = 82/280 (29%), Positives = 137/280 (48%), Gaps = 17/280 (6%) Query: 3 ITLRQLQIFLAVAQSGSTTAAAGMVALSQSAASASLNELESLLGVQLFDRVGKRLVLNDS 62 +T QL+ FLAVA+ +AAA + +SQ + + LE V+LF R G+R+ L+++ Sbjct: 1 MTPSQLRAFLAVARHRGFSAAARALGVSQPTLTTQVQSLEREHNVELFFRRGRRVDLSET 60 Query: 63 GRQLLPQARHM----LDAAQTIERQFSDPAAGSELHLGASTTIGSYLLPAMIAAYRRIHA 118 ++LLP A+++ LDA + S L +GA +G + + M+ AYR + Sbjct: 61 AQRLLPIAQNIAELELDALNLLVN--SGALHVGHLRIGA---VGPFHVIEMVDAYRARYP 115 Query: 119 GARVRALVANTADIVEAVVNFEVDAGLIEGPCHADDVRVE--PWMTDELIVVAAPTHPIV 176 + + N+A + + N+ D ++ DD R P+ +++ A +HP Sbjct: 116 RVELSIRLGNSAQTLADLENYVTDVAVL--ASFTDDARFHALPYADHAVVLFAHRSHPFY 173 Query: 177 AQARKITLKMLRQADWLLREAGSGTREAVEHALIPYLHHLPSSFEFGNSEAIKRATAEGL 236 Q +TL L Q L+RE GS TR A+E AL + E G+ EA++ A A GL Sbjct: 174 -QRDSVTLAELDQQPMLMREQGSTTRLALEKALQQAGVKVQVVMEIGSREALREAVARGL 232 Query: 237 GISCLSRS-VVEDLIESGKLVELETPLPTLRRHFYMVVSR 275 G+ +S + V D E ++V +E + + Y + R Sbjct: 233 GLGAVSEAEFVPD--ERFRMVRIEGDPVSTHTYVYCLAER 270 >gi|300311724|ref|YP_003775816.1| LysR family transcription regulator [Herbaspirillum seropedicae SmR1] Length = 297 Score = 87.0 bits (214), Expect = 2e-18, Method: Compositional matrix adjust. Identities = 83/301 (27%), Positives = 145/301 (48%), Gaps = 18/301 (5%) Query: 1 MRITLRQLQIFLAVAQSGSTTAAAGMVALSQSAASASLNELESLLGVQLFDRVGKRLVLN 60 M+I + +Q F+A+A GS AAG + ++Q+A + L +LE LGV L +R + + L Sbjct: 1 MKIDILGVQAFVAIADHGSFQGAAGALHVTQTAVTLRLRKLEDFLGVTLIERTTRSIALT 60 Query: 61 DSGRQLLPQARHMLD--AAQTIERQFSDPAAGSELHLGASTTIGSYLLPAMIAAYRRIHA 118 + GR LPQAR +L A +E + + A ++ + T+G LP ++ AY + Sbjct: 61 EIGRDFLPQARRLLAELAGALVEIRETGIARRGDVSIACVPTVGVQYLPRILQAYSARYP 120 Query: 119 GARVRALVANTADIVEAVVNFEVDAGL-IEGPCHADDVRVEPWMTDELIVVAAPTHPIVA 177 R++ L ++ + EAV+ EV+ G+ I G H + + V D +++ HP+ A Sbjct: 121 HNRIKILDHASSAVAEAVLRREVEFGIHIAGEHHPELISVA-LTEDRYVLICPKDHPL-A 178 Query: 178 QARKITLKMLRQADWLLREAGSGTREAVEHALIPYLHHLPSSFEFGNSEAIKRATAEGLG 237 + R+I + L+ + S R ++ L L S +E S +TA GL Sbjct: 179 RRRRIAWRQLQSYPLIFAGEVSSNRALLDPTLKANGFALRSFYEVQRS-----STAVGLV 233 Query: 238 ISCLSRSVVEDL-IESG-----KLVELETPLPTLRRHFYMVVSRHRAPSPSLAALLSFCR 291 + +VV L I+ G +++EL P+ + R ++ + SP+ AL R Sbjct: 234 AQGVGVAVVPKLAIQEGAYPTVRVIELVDPV--VSRSLVLITRKAAHLSPAAQALYDMIR 291 Query: 292 Q 292 + Sbjct: 292 E 292 >gi|300313085|ref|YP_003777177.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 315 Score = 84.0 bits (206), Expect = 1e-17, Method: Compositional matrix adjust. Identities = 88/315 (27%), Positives = 146/315 (46%), Gaps = 36/315 (11%) Query: 3 ITLRQLQIFLAVAQSGSTTAAAGMVALSQSAASASLNELESLLGVQLFDRVGKRLVLNDS 62 +TL +L+ +AVA+ AA ++Q S ++ +LE LGV +F+R G + + Sbjct: 1 MTLTELKYIVAVAREKHFGHAAEACFVAQPTLSVAIKKLEDELGVVIFERGGTEVSVTPL 60 Query: 63 GRQLLPQARHMLD---AAQTIERQFSDPAAGSELHLGASTTIGSYLLPAMIAAY-RRIHA 118 G Q++ QA +L+ A + I Q DP +G L LG TIG YLLP+++ R+ Sbjct: 61 GAQIVAQAERVLEQTAAIKEIANQNKDPLSGP-LRLGIIYTIGPYLLPSLVKTMIERVPQ 119 Query: 119 GARVRALVAN-TADIVEAVVNFEVDAGLIEGPCHADDVRVEPWMTDELIVVAAPTHPIVA 177 + L N T ++E + E+DA ++ P + V P + DE +VA P A Sbjct: 120 MPLI--LQENFTTRLIELLRQGELDAAIMALPFPEHGLNVLP-LYDEEFMVALPRQHKWA 176 Query: 178 QARKITLKMLRQADWLLREAGSGTREAVEHALIPYLHHLPS-------SFEFGNSEAIKR 230 + ++I + L+ LL G R+ V + P + + +FE + E I+ Sbjct: 177 ERKEIDARELKSETMLLLGNGHCFRDQVLE-VCPEMSRFSTNGDGIARTFEGSSLETIRH 235 Query: 231 ATAEGLGISCLSRSVVEDLIESGKLVELETPLPTLRRHFYMVVSRHRAPSPSLAALL--- 287 + G+G++ L R+ + D+ +V R+ V AP+PS ++ Sbjct: 236 MVSSGIGVTVLPRASIPDVDTRDGMV----------RYVPFV-----APAPSRRVVIAWR 280 Query: 288 -SFCRQWAQQQAHQA 301 SF RQ A HQA Sbjct: 281 KSFTRQAAIDAVHQA 295 >gi|300313396|ref|YP_003777488.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 305 Score = 79.0 bits (193), Expect = 4e-16, Method: Compositional matrix adjust. Identities = 47/147 (31%), Positives = 81/147 (55%), Gaps = 1/147 (0%) Query: 1 MRITLRQLQIFLAVAQSGSTTAAAGMVALSQSAASASLNELESLLGVQLFDRVGKRLVLN 60 M ITLRQ++ F+A A+ G + AA + +SQS+ ++++ ELE+LLG LF R + ++L Sbjct: 1 MAITLRQIRYFVATAEVGQISQAAIHLHISQSSVTSAIQELEALLGAPLFIRSPQGMILT 60 Query: 61 DSGRQLLPQARHMLDAA-QTIERQFSDPAAGSELHLGASTTIGSYLLPAMIAAYRRIHAG 119 DSGR L A +L + ++ D A L + AS T+ Y LP + + + G Sbjct: 61 DSGRHFLNHAYSILRSVDDAMKSPLPDNTASGSLRVAASYTVLGYFLPHHLQRLSQSYPG 120 Query: 120 ARVRALVANTADIVEAVVNFEVDAGLI 146 ++ A+I +++V E+D ++ Sbjct: 121 IKIHVHEKERAEIEQSLVEGEIDMAVV 147 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 0.132 0.375 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: 887,395 Number of extensions: 36070 Number of successful extensions: 253 Number of sequences better than 1.0e-08: 46 Number of HSP's gapped: 222 Number of HSP's successfully gapped: 46 Length of query: 301 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 216 Effective length of database: 1,217,395 Effective search space: 262957320 Effective search space used: 262957320 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)