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= 0001.1077.p (308 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310484|ref|YP_003774576.1| LysR family transcription regul... 208 4e-55 gi|300313740|ref|YP_003777832.1| LysR family transcription regul... 105 4e-24 gi|300310375|ref|YP_003774467.1| LysR family transcription regul... 104 8e-24 gi|300313689|ref|YP_003777781.1| LysR family transcription regul... 92 5e-20 gi|300313396|ref|YP_003777488.1| LysR family transcription regul... 91 1e-19 >gi|300310484|ref|YP_003774576.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 322 Score = 208 bits (530), Expect = 4e-55, Method: Compositional matrix adjust. Identities = 120/299 (40%), Positives = 174/299 (58%), Gaps = 1/299 (0%) Query: 10 DLSQLRAFIAIARIGSLGRAAESLHLTQSGLTRILQRLEEQVSAPLFERRASGMVLTAYG 69 +L QL F AI GSLGRAA L+LTQ L+R ++RLEE V LFER GM LT G Sbjct: 4 NLQQLEMFNAIVSAGSLGRAAALLNLTQPALSRAIKRLEESVGGALFERHTKGMHLTVLG 63 Query: 70 QAFEPYASLIVGEADNAIKELAALRGLEKGLIKVGAVGSALAGIVPEAVSCLLSQWPGLQ 129 QA P+A + EA A +EL A+RGL KG+IKVGAVGS + ++P AV +L +WP L+ Sbjct: 64 QALLPHAMSLQREAQQAREELDAIRGLAKGVIKVGAVGSIASLVLPLAVRGVLDKWPNLR 123 Query: 130 VRVEEGLAQELAVWLAKGEIDLAVTFSMPTTEDISLVVESRPQEGCKVVASLDHPLRAKG 189 V + EG+ L L EIDLA++ S TE ++ + + + VVA+ DHPLR +G Sbjct: 124 VEIIEGVWDRLVEGLLTHEIDLALSTSGGQTEGVAAIADCCWTDLSYVVAAPDHPLRQQG 183 Query: 190 NLKKEDLLTAKWVMPPRKLGPREDWQQWFLDSNLEAPPVTVETRAVDAMRSMVVQCGFLS 249 + E L +W + P+ GP Q+ F L P + VE+R+V ++S+V +CGF+ Sbjct: 184 RIALEQTLGQRWALTPKGTGPYLHVQETFARHGLPMPEIAVESRSVTVLKSLVARCGFIG 243 Query: 250 WLPQLLIQSPAITSSLISPLVVESETYMRRFAVYRRRHGVLSSSTAKLLEELKKIVGAM 308 W+ + + + +I L V R +RRR G+L + A+LL+EL+ + G++ Sbjct: 244 WMSGPMFDTER-QAGVIVALEVAGLDAPRTLTAFRRRQGILPAPAARLLDELRHLTGSL 301 >gi|300313740|ref|YP_003777832.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 307 Score = 105 bits (262), Expect = 4e-24, Method: Compositional matrix adjust. Identities = 82/295 (27%), Positives = 139/295 (47%), Gaps = 8/295 (2%) Query: 10 DLSQLRAFIAIARIGSLGRAAESLHLTQSGLTRILQRLEEQVSAPLFERRASGMVLTAYG 69 D L+ F IA G +GRAAE L+ TQ LT+ + RLEEQ+ APLFER G+ LTA G Sbjct: 2 DFRDLKYFTVIAEEGHVGRAAERLYKTQPALTKCIDRLEEQLGAPLFERLGRGIRLTAVG 61 Query: 70 QAFEPYASLIVGEADNAIKELAALRGLEKGLIKVGAVGSALAGIVPEAVSCLLSQWPGLQ 129 +A A I D +E+ +G I++G V + ++P LL + + Sbjct: 62 EALLNRARQISLMMDETAREIGDYAHGREGNIRLGCVPTLAEHVLPGVCQQLLGEAQKVT 121 Query: 130 VRVEEGLAQELAVWLAKGEIDLAVTFSMPTTEDISLV-VESRPQEGCKVVASLDHPLRAK 188 + ++ + L L GE+D+ + P +D L E Q+ V+AS HP+ K Sbjct: 122 IDLKVSMNDALLAGLKAGELDIVLG---PMIQDDELFHTEEIMQDQMVVMASPQHPIFDK 178 Query: 189 GNLKKEDLLTAKWVMPPRKLGPREDWQQWFLDSNLEAPPVTVETRAVDAMRSMVVQCGFL 248 ++ LL +WV+P + + R+ F +L P V + ++ + ++ + L Sbjct: 179 -KIRLRHLLDYQWVLPAQSVLSRQWLDNVFDRHHLPRPKVQITPTVLNMILPLIERSNLL 237 Query: 249 SWLPQLLIQSPAITSSLISPLVVESETYMRRFAVYRRRHGVLSSSTAKLLEELKK 303 + +L + + +V++ T +RR + RR LS + +L+ L + Sbjct: 238 GFASKLNLSE---GRGHLREVVLKETTMLRRMGLTYRRDMYLSPAAQRLIRILHE 289 >gi|300310375|ref|YP_003774467.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 313 Score = 104 bits (260), Expect = 8e-24, Method: Compositional matrix adjust. Identities = 78/292 (26%), Positives = 138/292 (47%), Gaps = 1/292 (0%) Query: 13 QLRAFIAIARIGSLGRAAESLHLTQSGLTRILQRLEEQVSAPLFERRASGMVLTAYGQAF 72 QL IA+ ++ RAA L++TQ ++ L+ LE+ + LFER GM T YG+A Sbjct: 18 QLLLLIALDDTRNIHRAASELNMTQPAASKQLKDLEDMLGVALFERLPRGMRPTIYGEAM 77 Query: 73 EPYASLIVGEADNAIKELAALRGLEKGLIKVGAVGSALAGIVPEAVSCLLSQWPGLQVRV 132 +A + + A +++ AL+ G + VG + S ++P A++ + Q P L++ V Sbjct: 78 IRHARMALTSLSKAHEDIVALKSGLSGQVDVGGILSPAMALLPPAIARVKEQAPMLRIGV 137 Query: 133 EEGLAQELAVWLAKGEIDLAVTFSMPTTEDISLVVESRPQEGCKVVASLDHPLRAKGNLK 192 E + L L GE+D + + L+ E E VA + HP A+ +L Sbjct: 138 EVESSNILLSRLLHGELDFIIGRILDDEARGGLLYEELADEPICAVARVGHPFHARTDLS 197 Query: 193 KEDLLTAKWVMPPRKLGPREDWQQWFLDSNLEAPPVTVETRAVDAMRSMVVQCGFLSWLP 252 DL + W+M P+ R Q F + L P V+T A+ + S++ Q F+ +P Sbjct: 198 LADLASEAWIMAPKGSILRARCDQMFREQGLAPPSNVVDTTAILFITSLLQQTDFIYAMP 257 Query: 253 QLLIQSPAITSSLISPLVVESETYMRRFAVYRRRHGVLSSSTAKLLEELKKI 304 + + + L+ L +E M F + R+ +LS +L+ ++++ Sbjct: 258 TEVARY-YTQARLMDILPIELPCRMAGFGIITRQDNLLSPGANLVLQAIREV 308 >gi|300313689|ref|YP_003777781.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 307 Score = 92.0 bits (227), Expect = 5e-20, Method: Compositional matrix adjust. Identities = 60/193 (31%), Positives = 94/193 (48%), Gaps = 2/193 (1%) Query: 12 SQLRAFIAIARIGSLGRAAESLHLTQSGLTRILQRLEEQVSAPLFERRASGMVLTAYGQA 71 + LR F + R GSL AAE L + S ++R + ++EE+ PLFERRA GMVLT G+ Sbjct: 4 TSLRYFYQVGRTGSLTAAAERLDVAVSAVSRQIAKMEEETGVPLFERRARGMVLTPAGEV 63 Query: 72 FEPYASLIVGEADNAIKELAALRGLEKGLIKVGAVGSALAGIVPEAVSCLLSQWPGLQVR 131 YA + E + + E+ L + +G+I + ++P + Q+PGLQ + Sbjct: 64 LMAYARRNLLEMEQVLAEVRGLHAVGQGVITLACSEGFAWDLLPNVTAQFREQYPGLQFK 123 Query: 132 VEEGLAQELAVWLAKGEIDLAVTFSMPTTEDISLVVESRPQEGCKVVASLDHPLRAKGNL 191 + A + + GE D++VT+S+ E L V R + DHPL ++ L Sbjct: 124 LHVVGAARASQMVIDGEADISVTYSLAPAE--GLAVAYRESGPVFALMKRDHPLASRTLL 181 Query: 192 KKEDLLTAKWVMP 204 DL +P Sbjct: 182 ALSDLSPYPLALP 194 >gi|300313396|ref|YP_003777488.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 305 Score = 90.5 bits (223), Expect = 1e-19, Method: Compositional matrix adjust. Identities = 65/247 (26%), Positives = 119/247 (48%), Gaps = 4/247 (1%) Query: 11 LSQLRAFIAIARIGSLGRAAESLHLTQSGLTRILQRLEEQVSAPLFERRASGMVLTAYGQ 70 L Q+R F+A A +G + +AA LH++QS +T +Q LE + APLF R GM+LT G+ Sbjct: 5 LRQIRYFVATAEVGQISQAAIHLHISQSSVTSAIQELEALLGAPLFIRSPQGMILTDSGR 64 Query: 71 AFEPYASLIVGEADNAIKELAALRGLEKGLIKVGAVGSALAGIVPEAVSCLLSQWPGLQV 130 F +A I+ D+A+K G ++V A + L +P + L +PG+++ Sbjct: 65 HFLNHAYSILRSVDDAMKS-PLPDNTASGSLRVAASYTVLGYFLPHHLQRLSQSYPGIKI 123 Query: 131 RVEEGLAQELAVWLAKGEIDLAVTFSMPTTEDISLVVESRPQEGCKVVASLDHPLRAKGN 190 V E E+ L +GEID+AV + + E+ ++ HPL + Sbjct: 124 HVHEKERAEIEQSLVEGEIDMAVVLT-SNLRHREIAYETLFGSVRRLWLPARHPLGERTA 182 Query: 191 LKKEDLLTAKWVMPPRKLGPREDWQQWFLDSNLEAPPVTVETRAVDAMRSMVVQCGFLSW 250 + ++ +++ + + W + + P + + T +++A+RSMV ++ Sbjct: 183 VNLAEVANEPFILLTVDEADKTALRYW--NQSGRKPNIIMRTSSIEAVRSMVANGSGVAI 240 Query: 251 LPQLLIQ 257 L L+ + Sbjct: 241 LSDLVYR 247 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 0.319 0.134 0.387 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: 944,340 Number of extensions: 37923 Number of successful extensions: 245 Number of sequences better than 1.0e-08: 50 Number of HSP's gapped: 236 Number of HSP's successfully gapped: 50 Length of query: 308 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 223 Effective length of database: 1,217,395 Effective search space: 271479085 Effective search space used: 271479085 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 (21.8 bits) S2: 130 (54.7 bits)