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= 0029.0116.p (300 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310906|ref|YP_003774998.1| LysR family transcription regul... 607 e-175 gi|300312460|ref|YP_003776552.1| LysR family transcription regul... 143 2e-35 gi|300312645|ref|YP_003776737.1| LysR family transcription regul... 137 1e-33 gi|300309845|ref|YP_003773937.1| LysR family transcription regul... 133 2e-32 gi|300312894|ref|YP_003776986.1| LysR family transcription regul... 131 7e-32 >gi|300310906|ref|YP_003774998.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 300 Score = 607 bits (1566), Expect = e-175, Method: Compositional matrix adjust. Identities = 300/300 (100%), Positives = 300/300 (100%) Query: 1 MADLTLPLNAIRAFLAAARHQSFTLAAHELNVTHGAISRQIKNLEGYLGMPLFERRTRQV 60 MADLTLPLNAIRAFLAAARHQSFTLAAHELNVTHGAISRQIKNLEGYLGMPLFERRTRQV Sbjct: 1 MADLTLPLNAIRAFLAAARHQSFTLAAHELNVTHGAISRQIKNLEGYLGMPLFERRTRQV 60 Query: 61 LLTERGRQFFEEASPALEILANAARRVMRDAPTRTVVINVRPSFAVRWLIPHLSDFVERY 120 LLTERGRQFFEEASPALEILANAARRVMRDAPTRTVVINVRPSFAVRWLIPHLSDFVERY Sbjct: 61 LLTERGRQFFEEASPALEILANAARRVMRDAPTRTVVINVRPSFAVRWLIPHLSDFVERY 120 Query: 121 PGIAPQVVTSTATVGKAGSSFDIAVRRGETNWPETLKVQRFMEDELVLVASPALLQAMPL 180 PGIAPQVVTSTATVGKAGSSFDIAVRRGETNWPETLKVQRFMEDELVLVASPALLQAMPL Sbjct: 121 PGIAPQVVTSTATVGKAGSSFDIAVRRGETNWPETLKVQRFMEDELVLVASPALLQAMPL 180 Query: 181 EDVSGLARHTVLLSRSRRNDWEDWRKLAGLKRSRSQAMLHFDHVHFVLQAVVDGLGVALS 240 EDVSGLARHTVLLSRSRRNDWEDWRKLAGLKRSRSQAMLHFDHVHFVLQAVVDGLGVALS Sbjct: 181 EDVSGLARHTVLLSRSRRNDWEDWRKLAGLKRSRSQAMLHFDHVHFVLQAVVDGLGVALS 240 Query: 241 PVSLADNDLRSGRLVCPFPDLRLTLAPYYLGINAQAGSEAQLFARWLAEYRGASLMFAGG 300 PVSLADNDLRSGRLVCPFPDLRLTLAPYYLGINAQAGSEAQLFARWLAEYRGASLMFAGG Sbjct: 241 PVSLADNDLRSGRLVCPFPDLRLTLAPYYLGINAQAGSEAQLFARWLAEYRGASLMFAGG 300 >gi|300312460|ref|YP_003776552.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 312 Score = 143 bits (360), Expect = 2e-35, Method: Compositional matrix adjust. Identities = 100/291 (34%), Positives = 147/291 (50%), Gaps = 4/291 (1%) Query: 7 PLNAIRAFLAAARHQSFTLAAHELNVTHGAISRQIKNLEGYLGMPLFERRTRQVLLTERG 66 PL A++ F AA R +S TLAAHEL +TH A+S+QIK+LE Y PLF R++R V TE Sbjct: 7 PLKALKVFEAAVRTRSLTLAAHELFITHSAVSQQIKSLEEYFEQPLFLRQSRGVEPTEAA 66 Query: 67 RQFFEEASPALEILANAARRVMRDAPTRTVVINVRPSFAVRWLIPHLSDFVERYPGIAPQ 126 F+ E +L+ +A AA ++ +R V + PS A+RWLIP LS F P I + Sbjct: 67 LSFYAEVKASLDRIALAAEQLALAGKSRVVRLIAAPSVAMRWLIPRLSQFQIDNPRIEVR 126 Query: 127 VVTSTATVGK-AGSSFDIAVRRGETNWPETLKVQRFMEDELVLVASPALLQAMPLEDVSG 185 V T+ + + FD+ + R + RF++D V +ASP L+ P+ Sbjct: 127 VTTTMSEYFEDVKDPFDVIIWRSPLE-RSGYECMRFLDDVSVPLASPHFLETHPIRVPRD 185 Query: 186 LARHTVLLSRSRRNDWEDWRKLAGLKRSRSQAMLHFDHVHFVLQAVVDGLGVALSPVSLA 245 ++ SR W W AG+ R ++H LQA GV + ++L Sbjct: 186 FVEVPLIHLSSRSAAWSQWLSKAGVAVRRKMPGTVYEHSFLSLQAAATDQGVGMGTLALV 245 Query: 246 DNDLRSGRLVCPFPDLRLTLAPYYLGINAQAGSEAQL--FARWLAEYRGAS 294 D+DL +GRLV FP++ L Y++ + A + L F WL + AS Sbjct: 246 DDDLAAGRLVRLFPEIVLHGEGYHMLCRSGAETNPALKTFITWLKQMGQAS 296 >gi|300312645|ref|YP_003776737.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 287 Score = 137 bits (345), Expect = 1e-33, Method: Compositional matrix adjust. Identities = 100/292 (34%), Positives = 150/292 (51%), Gaps = 8/292 (2%) Query: 4 LTLPLNAIRAFLAAARHQSFTLAAHELNVTHGAISRQIKNLEGYLGMPLFERRTRQVLLT 63 + LPLNA+RAF +ARH SFT AA EL+VT A+S Q+KNLE LG+ LF R R + LT Sbjct: 1 MYLPLNALRAFEVSARHLSFTRAAEELSVTQTAVSMQVKNLEQRLGVALFRRLPRGLALT 60 Query: 64 ERGRQFFEEASPALEILANAARRVMRDAPTRTVVINVRPSFAVRWLIPHLSDFVERYPGI 123 + G + + +A+ + + + V +FAV WL+P L F +++P + Sbjct: 61 DEGLALLPVVAQSFGRIADVLAQFEDGRRREVLTVGVVGTFAVGWLMPRLRQFQQQHPFV 120 Query: 124 APQVVTSTATVGKAGSSFDIAVRRGETNWPETLKVQRFMEDELVLVASPALLQAMPLEDV 183 +++T+ V AG D A+R G+ W T + +R E L + +PA+ A L Sbjct: 121 DLRLLTNNNRVDLAGEGLDYAIRFGDGAWHGT-QAERLFEAPLAPMCAPAI--AARLRSP 177 Query: 184 SGLARHTVLLSRSRRNDWEDWRKLAGLKRSRSQAMLHFDHVHFVLQAVVDGLGVALSPVS 243 + L T+L S R ++W W AG + + FD + +A GVAL PV Sbjct: 178 ADLGAETLLRS-YRSDEWGRWFAAAGAACPPLRGFV-FDSSLALAEAAAQEAGVALLPVL 235 Query: 244 LADNDLRSGRLVCPFPDLRLTLAPYYLGINAQAGSEAQL--FARWLAEYRGA 293 + + +L+ GRLVCPF R+ L Y+L A + F +WL + GA Sbjct: 236 MFERELQQGRLVCPFGQ-RIVLGAYWLTSLKSRPQTAAMAAFRQWLQSHAGA 286 >gi|300309845|ref|YP_003773937.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 294 Score = 133 bits (335), Expect = 2e-32, Method: Compositional matrix adjust. Identities = 99/294 (33%), Positives = 147/294 (50%), Gaps = 9/294 (3%) Query: 7 PLNAIRAFLAAARHQSFTLAAHELNVTHGAISRQIKNLEGYLGMPLFERRTRQVLLTERG 66 PL ++ AF A AR +SF LAA EL++T AIS Q+ LE LG+ LFER T+ V LT G Sbjct: 4 PLTSLMAFEAIARRKSFNLAAAELHLTPSAISHQVARLEKLLGLRLFERSTKGVELTPAG 63 Query: 67 RQFFEEASPALEILANAARRVMRDAPTRTVVINVRPSFAVRWLIPHLSDFVERYPGIAPQ 126 + + + AL + N+A +R ++ I+ PSFA WL+P + F +R+P IA Sbjct: 64 QSYLNRVAGALGAI-NSATDDLRHGVENSLQIHSSPSFASLWLMPRIGRFTQRHPDIALG 122 Query: 127 VVTSTATVGKAGSSFDIAVRRGETNWPETLKVQRFMEDELVLVASPALLQAMPLEDVSGL 186 + S D+ +R G +WP+ L+++ + + ++ +ASP L ++ L Sbjct: 123 LSASPEISDFEIGQVDLDIRCGVPHWPD-LEIEAVLSERVIPMASPDFLARHRIDTPDDL 181 Query: 187 ARHTVLLSRSRRNDWEDW--RKLAGLKRSRSQAMLHFDHVHFVLQAVVDGLGVALSPVSL 244 ++ SR W +W R L+ R L FD ++A V GLGV + Sbjct: 182 VLAPLIQSRGSLLQWPEWFARYAPDLRPER--IALRFDRAMMSIEAAVQGLGVVFESDAF 239 Query: 245 ADNDLRSGRLVCPFPD-LRLTLAPYYLGINAQAGS--EAQLFARWLAEYRGASL 295 L SGRL F D L L + +Y A+ S E LF +WL E GA+L Sbjct: 240 GAVALASGRLQPVFADGLALEITQHYAVCPARNKSRPEVMLFLQWLREESGAAL 293 >gi|300312894|ref|YP_003776986.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 299 Score = 131 bits (329), Expect = 7e-32, Method: Compositional matrix adjust. Identities = 100/288 (34%), Positives = 145/288 (50%), Gaps = 13/288 (4%) Query: 9 NAIRAFLAAARHQSFTLAAHELNVTHGAISRQIKNLEGYLGMPLFERRTRQVLLTERGRQ 68 +++ AF AAARH SF AA EL +T GAISRQI LEG+LG+ LFER +V L G++ Sbjct: 9 SSLMAFEAAARHGSFARAAEELALTEGAISRQISRLEGFLGVTLFERIGNRVRLLPHGQR 68 Query: 69 FFEEASPALEILANAARRVMRDAPT-RTVVINVRPSFAVRWLIPHLSDFVERYPGIAPQV 127 + LE L ++ +M P ++ I V P+FA+RWLIP L F +P I + Sbjct: 69 YASHVRETLERLDRDSQHLMSQPPNGASLDIAVSPTFAMRWLIPRLPRFAALHPHITVHL 128 Query: 128 VTSTATVGKAGSSFDIAVRRGETNWPETLKVQRFMEDELVLVASPALLQAMPLEDVSGLA 187 GS D A+ W ++ +++ LV V PAL+ SG+ Sbjct: 129 SERMEPFLLPGSGLDAAIHFLHPAW-TGMQTYSLLDEVLVPVCHPALVAG-----TSGVP 182 Query: 188 RHTVLLSRSRRNDWEDWRKLA---GLKRSRSQAMLHFDHVHFVLQAVVDGLGVALSPVSL 244 L RR + + W++ A G+ S S +D +++A + GLGVAL P Sbjct: 183 ALDALPRLHRRQNHDAWQRYAAQTGISLSHSAQGPRYDLHGMLIEAALAGLGVALVPRLY 242 Query: 245 ADNDLRSGRLVCPFP-DLRLTLA-PYYLGINAQAGSEA-QLFARWLAE 289 + +L GRLV P+P D R++ L Q GSE + FA+W+ E Sbjct: 243 VETELAQGRLVAPWPQDSRISKTFCLVLPEPLQLGSEPLKAFAQWILE 290 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 0.323 0.136 0.402 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: 956,123 Number of extensions: 39429 Number of successful extensions: 314 Number of sequences better than 1.0e-08: 52 Number of HSP's gapped: 265 Number of HSP's successfully gapped: 52 Length of query: 300 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 215 Effective length of database: 1,217,395 Effective search space: 261739925 Effective search space used: 261739925 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 130 (54.7 bits)