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= 0056.0015.p (240 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309639|ref|YP_003773731.1| LysR family transcription regul... 202 2e-53 gi|300309921|ref|YP_003774013.1| LysR family transcription regul... 103 1e-23 gi|300309660|ref|YP_003773752.1| LysR family transcription regul... 91 1e-19 gi|300312196|ref|YP_003776288.1| LysR family transcription regul... 91 1e-19 gi|300311868|ref|YP_003775960.1| LysR family transcription regul... 88 8e-19 >gi|300309639|ref|YP_003773731.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 296 Score = 202 bits (514), Expect = 2e-53, Method: Compositional matrix adjust. Identities = 101/226 (44%), Positives = 139/226 (61%) Query: 4 SRLSINALDDLFLDNNHRNDDALSGTVRITAPSTLAHTYLVPVLNQIALRHPDITLDLRL 63 +R S+ LD LF + D +SG VR+ APS+L + L+P++ ++A HP + DLRL Sbjct: 70 ARASLRDLDGLFETDTASPADEMSGLVRLAAPSSLGRSRLLPIVERLAQAHPGLRFDLRL 129 Query: 64 SEIITDAVDDKIDIGIRIGFLRDSRYVARSVAKVAFFVCASPELIARHGAPTTLDELVQR 123 ++ D V +KIDIGIR+G + D+R+V R + KV F+V A+P + RHG P + L Sbjct: 130 TDQRADVVGEKIDIGIRVGTVPDNRFVVRRLGKVRFYVVATPRFLRRHGTPEDTEALRAL 189 Query: 124 PMSAMVDRNTGRLWPWYFAQGQQLGPRLPAFVTDDPQVERRAVLDGIAFGQLGAFMAMPH 183 P +AM+DR TGR WPW FAQ Q F+ DD + E V G+A GQ+ F+ Sbjct: 190 PCTAMLDRGTGRPWPWLFAQENQWMADHARFLCDDSEGEYLLVRSGVAIGQIAGFLCEDD 249 Query: 184 LRDGSLVTVLQDLAPAPWDLYVYRPQRGPVPARVRLVFDALVETLS 229 + G LV V+ D P PWD+Y+YRPQRGPVP R+RLVFD LV + Sbjct: 250 IAAGRLVPVMTDHEPDPWDMYLYRPQRGPVPPRLRLVFDTLVREFA 295 >gi|300309921|ref|YP_003774013.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 299 Score = 103 bits (257), Expect = 1e-23, Method: Compositional matrix adjust. Identities = 75/242 (30%), Positives = 109/242 (45%), Gaps = 20/242 (8%) Query: 5 RLSINALDDLFLDNNHR-------NDDALS-------GTVRITAPSTLAHTYLVPVLNQI 50 RLS+ L+L+ + DD LS G +RI AP T +L P+ Sbjct: 55 RLSLTEAGALYLERCKQIVAALEEADDLLSSGSAKPTGLLRINAPLTFGVLHLAPLWPMF 114 Query: 51 ALRHPDITLDLRLSEIITDAVDDKIDIGIRIGFLRDSRYVARSVAKVAFFVCASPELIAR 110 RHP+I+LD+ LS+ I D +D+ D+ IRI L DS V R + + VCASP + Sbjct: 115 LERHPEISLDITLSDRIVDIIDEGYDMAIRIARLSDSTLVHRKLTSTSLHVCASPAYLDA 174 Query: 111 HGAPTTLDELVQRPMSAMVDRNTGRLWPWYFAQG---QQLGPRLPAFVTDDPQVERRAVL 167 HG P EL Q + + W + +G ++ RL D +A L Sbjct: 175 HGTPAHPHELAQHQTISYSYNQSKDEWQFNGPEGPVSVRVSSRLHVNNGDSCV---QAAL 231 Query: 168 DGIAFGQLGAFMAMPHLRDGSLVTVLQDLAPAPWDLYVYRPQRGPVPARVRLVFDALVET 227 GI + FM +LR G LV++L D +Y P R +PA++R + D L E Sbjct: 232 GGIGITRQPTFMIDQYLRSGQLVSILGDYGAPELGIYAVYPSRAHLPAKMRAMLDFLTEA 291 Query: 228 LS 229 + Sbjct: 292 FA 293 >gi|300309660|ref|YP_003773752.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 337 Score = 90.5 bits (223), Expect = 1e-19, Method: Compositional matrix adjust. Identities = 63/210 (30%), Positives = 93/210 (44%), Gaps = 8/210 (3%) Query: 27 SGTVRITAPSTLAHTYLVPVLNQIALRHPDITLDLRLSEIITDAVDDKIDIGIRIGFLRD 86 G +RI P+++ L+P L R+PDI L + + + D V + +D IRIG L+D Sbjct: 91 QGRLRIDVPASVGRLMLLPNLCDFYTRYPDIELMMGMGDRPVDLVQEAVDCVIRIGELQD 150 Query: 87 SRYVARSVAKVAFFVCASPELIARHGAPTTLDELVQRPMSAMVDRNTGRLWPWYF----- 141 S VAR + CA+P + RHG P T+++L Q TGR W F Sbjct: 151 SSMVARRIGTFQTVTCAAPAYLERHGVPHTIEDLQQHKAVHYFSSRTGRTIDWDFVVEGV 210 Query: 142 AQGQQLGPRLPAFVTDDPQVERRAVLDGIAFGQLGAFMAMPHLRDGSLVTVLQDLAPAPW 201 + ++ +L A D VE L G Q +M H+ +G LV VL PAP Sbjct: 211 TREVKMNGKL-AVNEADAYVE--CALQGFGMVQAPLYMVTRHIDEGRLVEVLSQWKPAPM 267 Query: 202 DLYVYRPQRGPVPARVRLVFDALVETLSAS 231 + V + +VR D + E + Sbjct: 268 PISVVYLHNRHLSPKVRAFVDWVAELFATC 297 >gi|300312196|ref|YP_003776288.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 308 Score = 90.5 bits (223), Expect = 1e-19, Method: Compositional matrix adjust. Identities = 62/207 (29%), Positives = 96/207 (46%), Gaps = 2/207 (0%) Query: 22 NDDALSGTVRITAPSTLAHTYLVPVLNQIALRHPDITLDLRLSEIITDAVDDKIDIGIRI 81 N D G +RI AP L P+ + +HP ITL++ LS+ D +++ D+ IRI Sbjct: 86 NSDQACGRLRIGAPQDFGVEQLAPLWGKFTEQHPLITLNITLSDRTIDLLEEGFDMAIRI 145 Query: 82 GFLRDSRYVARSVAKVAFFVCASPELIARHGAPTTLDELVQRPMSAMVDRNTGRLWPWYF 141 L DSR VAR +A V CA+PE +ARHG P T EL P + R G W + Sbjct: 146 SALGDSRMVARPLAPVRMIACAAPEFLARHGTPGTPAELRDYPFISYSYRAGGDDWSFRH 205 Query: 142 AQGQQLGPRLPAFV-TDDPQVERRAVLDGIAFGQLGAFMAMPHLRDGSLVTVLQDLAPAP 200 G R+ + V ++ R + G F+ ++ G LV + + + Sbjct: 206 VHGDTCQVRVRSTVYVNNGATCRAMAIAGQGIAIQPDFIVNAAIQAGQLVELFEGWSTGE 265 Query: 201 W-DLYVYRPQRGPVPARVRLVFDALVE 226 ++ P R +P +V+ + D L+E Sbjct: 266 QLVVHTLYPTRTHLPPKVQRMRDFLIE 292 >gi|300311868|ref|YP_003775960.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 307 Score = 87.8 bits (216), Expect = 8e-19, Method: Compositional matrix adjust. Identities = 69/228 (30%), Positives = 99/228 (43%), Gaps = 6/228 (2%) Query: 3 FSRLSINALDDL--FLDNNHRNDDALSGTVRITAPSTLAHTYLVPVLNQIALRHPDITLD 60 F R S LD+ H ALSG +R+ S +A ++P L +HP + ++ Sbjct: 65 FYRRSRELLDEFESLRGMFHDGAQALSGRLRVDMSSAMAREVVLPALPSFLDKHPQLEIE 124 Query: 61 LRLSEIITDAVDDKIDIGIRIGFLRDSRYVARSVAKVAFFVCASPELIARHGAPTTLDEL 120 L S+ D V + D +R G L DS VAR + + CASPE + R+G P TL++L Sbjct: 125 LSASDRRVDLVAEGFDCVLRTGTLDDSSLVARPIGHLVQINCASPEYLRRYGTPQTLEDL 184 Query: 121 VQRPMSAMVDRNTGRL--WPWYFAQGQQLGPRLPAFVTDDPQVERRAVLDGIAFGQLGAF 178 Q + GR W W+ Q + P + + + A L G+ QL Sbjct: 185 AQHRLVHYRQVLGGRSPGWEWFDGQQTRSLPMAGSITVNSTETYYAACLAGLGLIQLPLV 244 Query: 179 MAMPH--LRDGSLVTVLQDLAPAPWDLYVYRPQRGPVPARVRLVFDAL 224 A L G +V VL PAP + + R VPAR+ D L Sbjct: 245 GAQKRQMLDGGHVVEVLPQYRPAPMPVSLLYASRRHVPARLAGFMDWL 292 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 0.325 0.140 0.427 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: 790,915 Number of extensions: 34542 Number of successful extensions: 199 Number of sequences better than 1.0e-08: 28 Number of HSP's gapped: 180 Number of HSP's successfully gapped: 28 Length of query: 240 Length of database: 1,619,870 Length adjustment: 83 Effective length of query: 157 Effective length of database: 1,226,865 Effective search space: 192617805 Effective search space used: 192617805 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 129 (54.3 bits)