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= 0001.3037.p (305 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312373|ref|YP_003776465.1| LysR family transcription regul... 613 e-177 gi|300310059|ref|YP_003774151.1| LysR family transcription regul... 116 2e-27 gi|300312300|ref|YP_003776392.1| LysR family transcription regul... 115 6e-27 gi|300310322|ref|YP_003774414.1| LysR family transcription regul... 107 1e-24 gi|300312785|ref|YP_003776877.1| transcription regulator protein... 102 3e-23 >gi|300312373|ref|YP_003776465.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 305 Score = 613 bits (1580), Expect = e-177, Method: Compositional matrix adjust. Identities = 293/305 (96%), Positives = 300/305 (98%) Query: 1 MLDWDNLRIFLELTRSQGLVDAAKKLGIDHSTVSRRMKRFEEQVGSQLFDRNNHGYKLTA 60 MLDWDNLRIFLELTRSQGLVDAAKKLGIDHSTVSRRMKRFEEQVGSQLFDRNNHGYKLTA Sbjct: 1 MLDWDNLRIFLELTRSQGLVDAAKKLGIDHSTVSRRMKRFEEQVGSQLFDRNNHGYKLTA 60 Query: 61 DGYRLVDYAEQVESTLYAATEELGGHNSKLSGQVRLGATEGFGTFVLAPHLAHFCARNPH 120 DGYRLV+YAEQVESTLYAATEELGGHNSKLSGQVRLGATEGFGTFVLAPH+AHFCARNPH Sbjct: 61 DGYRLVEYAEQVESTLYAATEELGGHNSKLSGQVRLGATEGFGTFVLAPHIAHFCARNPH 120 Query: 121 ITVDMLPMPRFVNLSKHEADISVSIERPLSGNYVVTKLSDYVLKLYASRDYLARHAPIHS 180 ITVDMLPMPRFVNLSKHEADISVSIERPLSGNYVVTKLSDYVLKLYASRDYLA+H PIH+ Sbjct: 121 ITVDMLPMPRFVNLSKHEADISVSIERPLSGNYVVTKLSDYVLKLYASRDYLAQHPPIHT 180 Query: 181 TADLAQHHFIGYIDDLVFSEELRYKDTVAPDAFRAFRSTSVVAQYTAACAGRALAILPCF 240 DLAQHHFIGYIDDLVFSEELRYKDTVAPDAFRAFRSTSVVAQYTAACAGRALAILPCF Sbjct: 181 MDDLAQHHFIGYIDDLVFSEELRYKDTVAPDAFRAFRSTSVVAQYTAACAGRALAILPCF 240 Query: 241 LAQQSEQLVPVLAQEIAITRSFWLVASSEQRHVARVSALWSYLRECVELNRDFLMGQSRQ 300 LAQQSE+L PVL Q+IAITRSFWLVASSEQRHVARVSALWSYLRECVELNRDFLMGQSR+ Sbjct: 241 LAQQSEELAPVLPQQIAITRSFWLVASSEQRHVARVSALWSYLRECVELNRDFLMGQSRR 300 Query: 301 MRWLE 305 MRWLE Sbjct: 301 MRWLE 305 >gi|300310059|ref|YP_003774151.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 283 Score = 116 bits (291), Expect = 2e-27, Method: Compositional matrix adjust. Identities = 81/290 (27%), Positives = 136/290 (46%), Gaps = 20/290 (6%) Query: 3 DWDNLRIFLELTRSQGLVDAAKKLGIDHSTVSRRMKRFEEQVGSQLFDRNNHGYKLTADG 62 DW++LR F + AA+ LG+ H+T+ RR+++ E+ + + LF R +LT G Sbjct: 4 DWESLRSFAAFVDAGSFSGAARVLGVTHATIGRRLQQLEQTLAAPLFIRRADDIELTRLG 63 Query: 63 YRLVDYAEQVESTLYAATEELGGHNSKLSGQVRLGATEGFGTFVLAPHLAHFCARNPHIT 122 ++ A ++ L G + ++ G++RL T+ GT LAP L + P + Sbjct: 64 ESVLAAARAMQDQTRQLARTLAGEDLRMEGKLRLACTDAMGTLFLAPRLPSLLQQWPALD 123 Query: 123 VDMLPMPRFVNLSKHEADISVSIERPLSGNYVVTKLSDYVLKLYASRDYLA--RH----A 176 +++ + ++L++ EAD+++ RP G + +L L + D +A RH A Sbjct: 124 IELAMGHQTLSLARREADLALRFARPQDGELIARRLGVVRFYLCGTADQVAAWRHQRGSA 183 Query: 177 PIHSTADLAQHHFIGYIDDLVFSEELRYKDTVAPDAFRAFRSTSVVAQYTAACAGRALAI 236 P+ IGY D + E R+ A RS S+VAQ AA AG LA+ Sbjct: 184 PV-----------IGYDDSVPDIPETRWLAAHADGNPVRLRSASLVAQCMAARAGVGLAL 232 Query: 237 LPCFLAQQSEQLVPVLAQEIAITRSFWLVASSEQRHVARVSALWSYLREC 286 LP +L Q V Q + R W V + + + R+ A+ +L+ C Sbjct: 233 LPSYLLAPELQTVESTPQ---LVRELWAVFHRDLKALPRLRAVLEWLQAC 279 >gi|300312300|ref|YP_003776392.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 305 Score = 115 bits (287), Expect = 6e-27, Method: Compositional matrix adjust. Identities = 82/287 (28%), Positives = 141/287 (49%), Gaps = 10/287 (3%) Query: 2 LDWDNLRIFLELTRSQGLVDAAKKLGIDHSTVSRRMKRFEEQVGSQLFDRNNHGYKLTAD 61 L WD++R FL L+R L +A+ L ++HSTV+R + E+ + +LFDR G+ LT + Sbjct: 23 LQWDDVRYFLTLSREGSLSASARVLKVEHSTVARHVGNLEKTLRVKLFDRLARGWVLTTE 82 Query: 62 GYRLVDYAEQVESTLYAATEELGGHNSKLSGQVRLGATEGFGTFVLAPHLAHFCARNPHI 121 G L AEQ+E +++ N+ LSG+VR+ A + L P L F + P I Sbjct: 83 GAELSKQAEQLEVEMHSLWRA-ALANTTLSGKVRVSAPPILMSDFLVPRLPAFQEKYPDI 141 Query: 122 TVDMLPMPRFVNLSKHEADISVSIERPLSGNYVVTKLSDYVLKLYASRDYLARHAPIHST 181 ++++ R V+L++ EADI++ + P+S V L + +Y +L R Sbjct: 142 ELEVIGEARGVDLTRGEADIALRMGEPVSPLLVARMLCNVSYSVYGIPAWLERPE----- 196 Query: 182 ADLAQHHFIGYIDDLVFSEELRYKDTVAPDAFRAFRSTSVVAQYTAACAGRALAILPCFL 241 ++ FIG +D + + ++ A R+ + A AA +G LA+LP F+ Sbjct: 197 ---SERSFIG-LDQESPCRQKAWLESQVDQRRYALRTNDIRAMCHAAMSGIGLALLPRFM 252 Query: 242 AQQSEQLVPVLAQEIAITRSFWLVASSEQRHVARVSALWSYLRECVE 288 + +LV + E +LV S+ R R+ A +L + ++ Sbjct: 253 VAEDTRLVAIPMPETPPPCPLYLVMHSDVRRAPRIRATADFLIDLIQ 299 >gi|300310322|ref|YP_003774414.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 288 Score = 107 bits (267), Expect = 1e-24, Method: Compositional matrix adjust. Identities = 84/278 (30%), Positives = 126/278 (45%), Gaps = 1/278 (0%) Query: 2 LDWDNLRIFLELTRSQGLVDAAKKLGIDHSTVSRRMKRFEEQVGSQLFDRNNHGYKLTAD 61 +DWDN RIFL + R L AA+ L +D +TV RR+ E +G++LF R +GY T Sbjct: 1 MDWDNARIFLAIYRVGTLRGAAETLELDQATVGRRLAALERSLGARLFLRTPNGYVPTPA 60 Query: 62 GYRLVDYAEQVESTLYAATEELGGHNSKLSGQVRLGATEGFGTFVLAPHLAHFCARNPHI 121 G A+Q+E ++ G + +L G VRL AT+ L P L +PHI Sbjct: 61 GEMAAAAAQQMEQGAEQLQRQMQGIDERLCGVVRLAATDVTARHFLIPALHRLRQEHPHI 120 Query: 122 TVDMLPMPRFVNLSKHEADISVSIERPLSGNYVVTKLSDYVLKLYASRDYLARHAPIHST 181 V + + NL+K EADI+V RP + + + L +YASR Y+ + Sbjct: 121 RVVLSTSTQITNLTKREADIAVRTLRPDAPDLIARHLKRLHTAIYASRSYVKKRGLPEPG 180 Query: 182 ADLAQHHFIGYIDDLVFSEELRYKDTVAPDAFRAFRSTSVVAQYTAACAGRALAILPCFL 241 L H + Y + ++ + +A A ++ + Y AG L LP + Sbjct: 181 TGLKGHDVVIYQRSVSPAKSEQICGESIINAQVAMEVSTGLVMYDCLQAGFGLGELPTHV 240 Query: 242 AQQSEQLVPVLAQEIAITRSFWLVASSEQRHVARVSAL 279 ++ LV V Q WLV S+ ARV A+ Sbjct: 241 GDKASGLVRVWPQR-ETPYDMWLVLHSDLNRTARVRAV 277 >gi|300312785|ref|YP_003776877.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 297 Score = 102 bits (255), Expect = 3e-23, Method: Compositional matrix adjust. Identities = 80/290 (27%), Positives = 131/290 (45%), Gaps = 8/290 (2%) Query: 3 DWDNLRIFLELTRSQGLVDAAKKLGIDHSTVSRRMKRFEEQVGSQLFDRNNHGYKLTADG 62 +W+ R FL++ + L A +++G+ TV R ++ E +G +LF R+ G+ T Sbjct: 7 NWEWYRSFLKVLETGSLSAAGREMGLTQPTVGRHIENLESTLGLKLFVRSFDGFSPTDAA 66 Query: 63 YRLVDYAEQVESTLYAATEELGGHNSKLSGQVRLGATEGFGTFVLAPHLAHFCARNPHIT 122 L YA + + A ++ G VRL A+E VL P LA R+P + Sbjct: 67 LELKPYAAAIAANSAALRRAASSQGKEVRGTVRLTASEVISVEVLPPILAALRHRHPELR 126 Query: 123 VDMLPMPRFVNLSKHEADISVSIERPLSGNYVVTKLSDYVLKLYASRDYLARHAPIHSTA 182 V+++ + +L + EADI+V + RP V +L L L+A + YL H S Sbjct: 127 VELVLSNKADDLLQREADIAVRMFRPAQDALVAKRLGSIELGLHAHQSYLTVHGAPKSVD 186 Query: 183 DLAQHHFIGYIDDLVFSEELRYKDTVAPDAFRAFRSTSVVAQYTAACAGRALAILPCFLA 242 LA H IG+ + + + + A A R+ S +AQ A AG + I LA Sbjct: 187 ALADHTLIGFDQESAYVRNVLKQIPWLSRAALALRTDSDLAQLAAIRAGFGIGICQVALA 246 Query: 243 QQSEQLVPVLAQEIAITRSFWLVASSEQRHVAR--------VSALWSYLR 284 + LV +L ++ A+ W+ + R R V+ L +Y+R Sbjct: 247 ARDVALVRLLPRQFALKMETWVAMHEDLRASPRCAVTFAALVAGLGAYIR 296 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 0.135 0.399 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: 919,012 Number of extensions: 35664 Number of successful extensions: 191 Number of sequences better than 1.0e-08: 44 Number of HSP's gapped: 191 Number of HSP's successfully gapped: 44 Length of query: 305 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 220 Effective length of database: 1,217,395 Effective search space: 267826900 Effective search space used: 267826900 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 (22.0 bits) S2: 130 (54.7 bits)