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= 0001.4394.p (295 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313740|ref|YP_003777832.1| LysR family transcription regul... 537 e-154 gi|300310484|ref|YP_003774576.1| LysR family transcription regul... 114 1e-26 gi|300310159|ref|YP_003774251.1| LysR family transcription regul... 100 1e-22 gi|300313164|ref|YP_003777256.1| LysR family transcription regul... 100 2e-22 gi|300310375|ref|YP_003774467.1| LysR family transcription regul... 99 6e-22 >gi|300313740|ref|YP_003777832.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 307 Score = 537 bits (1384), Expect = e-154, Method: Compositional matrix adjust. Identities = 258/292 (88%), Positives = 276/292 (94%) Query: 1 MDFRDLKYFAVIAEEGHVGRAAERLFKTQPALTKCIDRLEEQLGAPLFERAGRGIRLTAV 60 MDFRDLKYF VIAEEGHVGRAAERL+KTQPALTKCIDRLEEQLGAPLFER GRGIRLTAV Sbjct: 1 MDFRDLKYFTVIAEEGHVGRAAERLYKTQPALTKCIDRLEEQLGAPLFERLGRGIRLTAV 60 Query: 61 GQALLNRARQISLMMDETAREIGDYAHGREGNIRLGCIPTLAEHILPGLCQELLREAPKV 120 G+ALLNRARQISLMMDETAREIGDYAHGREGNIRLGC+PTLAEH+LPG+CQ+LL EA KV Sbjct: 61 GEALLNRARQISLMMDETAREIGDYAHGREGNIRLGCVPTLAEHVLPGVCQQLLGEAQKV 120 Query: 121 TIELKVSMNDVLLAGLKTGELDIVLGPMIQEDEVFHTEEIMQDQMVVMASPHHPIFERRI 180 TI+LKVSMND LLAGLK GELDIVLGPMIQ+DE+FHTEEIMQDQMVVMASP HPIF+++I Sbjct: 121 TIDLKVSMNDALLAGLKAGELDIVLGPMIQDDELFHTEEIMQDQMVVMASPQHPIFDKKI 180 Query: 181 KLRHLLEYQWVLPAQSVLSRQWLDNVFDRHHLPRPTVQIMPTVLNMIMPLIERSNLLGFA 240 +LRHLL+YQWVLPAQSVLSRQWLDNVFDRHHLPRP VQI PTVLNMI+PLIERSNLLGFA Sbjct: 181 RLRHLLDYQWVLPAQSVLSRQWLDNVFDRHHLPRPKVQITPTVLNMILPLIERSNLLGFA 240 Query: 241 SKLNLQAGRGHLREVVLKETTMLRRMGLTYRRDIYLSPAAQRLLTIIRRRPL 292 SKLNL GRGHLREVVLKETTMLRRMGLTYRRD+YLSPAAQRL+ I+ L Sbjct: 241 SKLNLSEGRGHLREVVLKETTMLRRMGLTYRRDMYLSPAAQRLIRILHEASL 292 >gi|300310484|ref|YP_003774576.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 322 Score = 114 bits (285), Expect = 1e-26, Method: Compositional matrix adjust. Identities = 80/246 (32%), Positives = 128/246 (52%), Gaps = 7/246 (2%) Query: 1 MDFRDLKYFAVIAEEGHVGRAAERLFKTQPALTKCIDRLEEQLGAPLFERAGRGIRLTAV 60 + + L+ F I G +GRAA L TQPAL++ I RLEE +G LFER +G+ LT + Sbjct: 3 FNLQQLEMFNAIVSAGSLGRAAALLNLTQPALSRAIKRLEESVGGALFERHTKGMHLTVL 62 Query: 61 GQALLNRARQISLMMD-ETAREIGDYAHG-REGNIRLGCIPTLAEHILPGLCQELLREAP 118 GQALL A +SL + + ARE D G +G I++G + ++A +LP + +L + P Sbjct: 63 GQALLPHA--MSLQREAQQAREELDAIRGLAKGVIKVGAVGSIASLVLPLAVRGVLDKWP 120 Query: 119 KVTIELKVSMNDVLLAGLKTGELDIVLGPMIQEDEVFH--TEEIMQDQMVVMASPHHPIF 176 + +E+ + D L+ GL T E+D+ L + E + D V+A+P HP+ Sbjct: 121 NLRVEIIEGVWDRLVEGLLTHEIDLALSTSGGQTEGVAAIADCCWTDLSYVVAAPDHPLR 180 Query: 177 ER-RIKLRHLLEYQWVLPAQSVLSRQWLDNVFDRHHLPRPTVQIMPTVLNMIMPLIERSN 235 ++ RI L L +W L + + F RH LP P + + + ++ L+ R Sbjct: 181 QQGRIALEQTLGQRWALTPKGTGPYLHVQETFARHGLPMPEIAVESRSVTVLKSLVARCG 240 Query: 236 LLGFAS 241 +G+ S Sbjct: 241 FIGWMS 246 >gi|300310159|ref|YP_003774251.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 309 Score = 100 bits (249), Expect = 1e-22, Method: Compositional matrix adjust. Identities = 72/204 (35%), Positives = 106/204 (51%), Gaps = 22/204 (10%) Query: 1 MDFRDLKYFAVIAEEGHVGRAAERLFKTQPALTKCIDRLEEQLGAPLFERAGRGIRLTAV 60 M+FR L+YF + E G V AA RL QPAL++ I LEE+LGA LF+R+ RG LTA Sbjct: 1 MEFRHLRYFLGVVEHGSVAEAARRLHIAQPALSRQIKYLEEELGAALFDRSVRGATLTAA 60 Query: 61 GQALLNRARQISLMMDETAREIGDYAHGREGNIRLGCIPTLAEH--ILPGLCQELLREAP 118 GQ L+ AR++ + ET + + A G EGN+R+G P H IL G + + P Sbjct: 61 GQQLVIDARRMLADLQETRQRVARVAEGLEGNLRMGITPNFGWHPRIL-GSLRHFHQAEP 119 Query: 119 KVTIELKVSMNDVLLAGLKTGELDI-VLGPMIQEDEVFHTEEIMQDQMVVMASPHHPIFE 177 ++ + L+ ++ L +++G+LD L ++ F E + Q +FE Sbjct: 120 QIAVSLEPGLSARQLERIRSGDLDAGFLAWRYPPNDQFLAHEFGEIQ----------VFE 169 Query: 178 RRIKLRHLLEYQWVLPAQSVLSRQ 201 R+KL LP S L+RQ Sbjct: 170 CRLKL--------ALPRDSQLARQ 185 >gi|300313164|ref|YP_003777256.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 324 Score = 99.8 bits (247), Expect = 2e-22, Method: Compositional matrix adjust. Identities = 75/294 (25%), Positives = 147/294 (50%), Gaps = 8/294 (2%) Query: 3 FRDLKYFAVIAEEGHVGRAAERLFKTQPALTKCIDRLEEQLGAPLFERAGRGIRLTAVGQ 62 FR + + E+G + +AAE + TQPA TK + +E+ LG LF+R+ RGI T +G+ Sbjct: 32 FRQVALLTALDEQGSLHKAAEVMHMTQPAATKALHEMEDALGVTLFDRSPRGIEATELGR 91 Query: 63 ALLNRARQISLMMDETAREIGDYAHGREGNIRLGCIPTLAEHILPGLCQELLRE-APKVT 121 ++ AR I + E+ + GR G + +G I A + L + LRE P+V+ Sbjct: 92 CVIRYARLIQSDVANLRDELQNMISGRGGRLAIGTIMGAAPFVTRALSR--LREIQPEVS 149 Query: 122 IELKVSMNDVLLAGLKTGELDIVLG--PMIQEDEVFHTEEIMQDQMVVMASPHHPI-FER 178 IE+ + L L G +D+++G + + ++H E + + M +++ HP+ + Sbjct: 150 IEISEDTSARQLLLLDQGRIDLMIGRSSVSSQPNLYHYEMLRGEPMCIVSGIDHPLATAQ 209 Query: 179 RIKLRHLLEYQWVLPAQSVLSRQWLDNVFDRHHLPRPTVQIMPTVLNMIMPLIERSNLLG 238 +++L+ L E W+L + ++ R W+++ F + P I + + L+ +SN++ Sbjct: 210 KVRLQELAEASWILYSSNMPMRIWIEHEFKLEGVKVPGNVIETASPFVTITLLAQSNMVA 269 Query: 239 FA--SKLNLQAGRGHLREVVLKETTMLRRMGLTYRRDIYLSPAAQRLLTIIRRR 290 + A + L + + T + G+ R++ LS A+ + I+R++ Sbjct: 270 VMPLDIAHFFAAKQMLGILPVNLKTRIEHYGIVTRKNTTLSSLAKMFIQILRQQ 323 >gi|300310375|ref|YP_003774467.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 313 Score = 98.6 bits (244), Expect = 6e-22, Method: Compositional matrix adjust. Identities = 79/291 (27%), Positives = 139/291 (47%), Gaps = 7/291 (2%) Query: 4 RDLKYFAVIAEEGHVGRAAERLFKTQPALTKCIDRLEEQLGAPLFERAGRGIRLTAVGQA 63 R L + + ++ RAA L TQPA +K + LE+ LG LFER RG+R T G+A Sbjct: 17 RQLLLLIALDDTRNIHRAASELNMTQPAASKQLKDLEDMLGVALFERLPRGMRPTIYGEA 76 Query: 64 LLNRARQISLMMDETAREIGDYAHGREGNIRLGCIPTLAEHILPGLCQELLREAPKVTIE 123 ++ AR + + +I G G + +G I + A +LP + +AP + I Sbjct: 77 MIRHARMALTSLSKAHEDIVALKSGLSGQVDVGGILSPAMALLPPAIARVKEQAPMLRIG 136 Query: 124 LKVSMNDVLLAGLKTGELDIVLGPMIQEDEV---FHTEEIMQDQMVVMASPHHPIFERR- 179 ++V +++LL+ L GELD ++G I +DE EE+ + + +A HP R Sbjct: 137 VEVESSNILLSRLLHGELDFIIG-RILDDEARGGLLYEELADEPICAVARVGHPFHARTD 195 Query: 180 IKLRHLLEYQWVLPAQSVLSRQWLDNVFDRHHLPRPTVQIMPTVLNMIMPLIERSNLL-G 238 + L L W++ + + R D +F L P+ + T + I L+++++ + Sbjct: 196 LSLADLASEAWIMAPKGSILRARCDQMFREQGLAPPSNVVDTTAILFITSLLQQTDFIYA 255 Query: 239 FASKLNLQAGRGHLREVVLKETTM-LRRMGLTYRRDIYLSPAAQRLLTIIR 288 +++ + L +++ E + G+ R+D LSP A +L IR Sbjct: 256 MPTEVARYYTQARLMDILPIELPCRMAGFGIITRQDNLLSPGANLVLQAIR 306 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 0.410 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: 907,195 Number of extensions: 36826 Number of successful extensions: 259 Number of sequences better than 1.0e-08: 59 Number of HSP's gapped: 242 Number of HSP's successfully gapped: 59 Length of query: 295 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 210 Effective length of database: 1,217,395 Effective search space: 255652950 Effective search space used: 255652950 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: 130 (54.7 bits)