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= 0001.3876.p (298 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310675|ref|YP_003774767.1| LysR family transcription regul... 166 3e-42 gi|300314079|ref|YP_003778171.1| LysR family transcription regul... 159 2e-40 gi|300312554|ref|YP_003776646.1| transcription regulator protein... 142 4e-35 gi|300310448|ref|YP_003774540.1| transcription regulator protein... 136 2e-33 gi|300313281|ref|YP_003777373.1| LysR family transcription regul... 136 2e-33 >gi|300310675|ref|YP_003774767.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 309 Score = 166 bits (419), Expect = 3e-42, Method: Compositional matrix adjust. Identities = 102/295 (34%), Positives = 153/295 (51%), Gaps = 9/295 (3%) Query: 5 LRRLDLNLLVTLDALLIEHNVTRAAERLHLAQPTVSLQLARLRDFFGDPLLLPGPRGMRT 64 +DLNLL A+ E ++T A RLHL+QP VS L RLR F DPL + GM+ Sbjct: 4 FNNMDLNLLRVFQAIADERSLTLAGNRLHLSQPAVSYALGRLRQIFDDPLFIRTKEGMQP 63 Query: 65 TARAEELREPLQQALAALAQAVTPSTAFDPAQSQQTWRAAAFDYSEYTILMPALDTLRKA 124 T A EL +P+ +AL A+ A+ + FDPAQS + +RA+ D +E L + L Sbjct: 64 TPAALELAKPINRALQAVQDALRYTERFDPAQSTRVFRASMTDVAEMMFLPDLCEILTAQ 123 Query: 125 APATRLAVIQTTPSLVARKAEQGEIDLAFLTATEAPPELRRLPLFTERYV--LAGRAGHP 182 AP RL V Q P+ + G++D AF P LF E YV + R G P Sbjct: 124 APDVRLQVEQVPPAHLEEALRTGQLDFAFGNLPALKPVTCHELLFRETYVCLMRQRDGLP 183 Query: 183 QLKRRPTLAQFCKLEHVIVSTDGGGFHGVTDTVLAEMGMTRKVALSVPHFLFLTAVLANT 242 Q + + L +F + HV+V + H V ++ ++G+ R+++LS+PHF L +L + Sbjct: 184 Q-RAQLELDEFLAMSHVLVESAESSHHQVENS-FQKLGVQRRISLSIPHFTVLPRILGKS 241 Query: 243 DLVAMLPSRLVR-----GNAVLKVVEAPIEVPGFEMFMLWHERVHRDPAHQWLRE 292 DLVA +P+R+ R V + P+ +P E+ + WH+ D + WLR+ Sbjct: 242 DLVATVPARIARLFHSEHPGVFVSYQLPVNIPVVEVTLHWHQSFDHDAGNSWLRQ 296 >gi|300314079|ref|YP_003778171.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 319 Score = 159 bits (403), Expect = 2e-40, Method: Compositional matrix adjust. Identities = 107/303 (35%), Positives = 162/303 (53%), Gaps = 16/303 (5%) Query: 8 LDLNLLVTLDALLIEHNVTRAAERLHLAQPTVSLQLARLRDFFGDPLLLPGPRGMRTTAR 67 LDLNLL DA++ E N+TRAA L + QP VS L RLRD D L++ G++ T R Sbjct: 6 LDLNLLRVFDAVMTEQNLTRAANLLAMTQPAVSNALRRLRDTLNDDLVIRTAHGVKPTPR 65 Query: 68 AEELREPLQQALAALAQAVTPSTAFDPAQSQQTWRAAAFDYSEYTILMPALDTLRKAAPA 127 AEEL +++AL+ L + P + FD +++Q T+R A D + L + T+ + AP Sbjct: 66 AEELWPTVRRALSELEAVIAPES-FDISRAQNTFRMAMVDATAALWLPSLVRTIMRDAPR 124 Query: 128 TRLAVIQTTPSLVARKAEQGEIDLAF-----LTAT------EAPPELRRLPLFTERYVLA 176 ++ ++ T +G+IDLA +TA A ++ L+T +YV Sbjct: 125 IKIRMMPLTTRDPRAMLLRGDIDLAVGFFPGVTAQLADGQGMAKSQISHARLYTGQYVCV 184 Query: 177 GRAGHPQLKRRPTLAQFCKLEHVIVSTDGGGFHGVTDTVLAEMGMTRKVALSVPHFLFLT 236 HP + TL +C +H++VS G H V D VLA M RK+ L+V F Sbjct: 185 MHKSHPLAGQPLTLDSYCNADHLLVSLSGKP-HAVIDDVLAGMNRERKILLTVNQFFTAG 243 Query: 237 AVLANTDLVAMLPSRLVRGNAV---LKVVEAPIEVPGFEMFMLWHERVHRDPAHQWLREH 293 ++A+++L+ +LP LV + L V E P + P + MLWHER R+PAH+WLR H Sbjct: 244 RIVASSELITVLPRHLVAATGMAEALVVKELPFQTPEEHVDMLWHERDARNPAHKWLRAH 303 Query: 294 IAS 296 +++ Sbjct: 304 LSA 306 >gi|300312554|ref|YP_003776646.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 314 Score = 142 bits (357), Expect = 4e-35, Method: Compositional matrix adjust. Identities = 93/298 (31%), Positives = 138/298 (46%), Gaps = 8/298 (2%) Query: 8 LDLNLLVTLDALLIEHNVTRAAERLHLAQPTVSLQLARLRDFFGDPLLLPGPRGMRTTAR 67 LDL+L+ L LL E NV+R A +L+ QP++S L +LR+ GDPLL+ G RGM T Sbjct: 8 LDLHLIRILYLLLCEKNVSRVALKLNQPQPSISASLRKLRELTGDPLLVRGARGMVPTQH 67 Query: 68 AEELREPLQQALAALAQAVTPSTAFDPAQSQQTWRAAAFDYSEYTILMPALDTLRKAAPA 127 E L +P ++ L + P T F P + ++ + AA DY + LR+ +P Sbjct: 68 GESLLKPAKRILDETERLFIPKTEFVPQEEERIFHIAAPDYMNTPFFTEVIARLRRESPR 127 Query: 128 TRLAVIQTTPSL-VARKAEQGEIDLAFLTATEAPPELRRLPLFTERYVLAGRAGHPQLKR 186 +R+ + P R+ GE+DL P L LF + V RA +R Sbjct: 128 SRIVIHALGPDTDYVRRLSDGELDLVIANWDAPPAHLHLSKLFDDPIVCLMRADCAYARR 187 Query: 187 RP----TLAQFCKLEHVIVSTDGGGFHGVTDTVLAEMGMTRKVALSVPHFLFLTAVLANT 242 ++ + L H S G+HG D+ L + + R V + HF L ++A T Sbjct: 188 TAREAMSVEDYLSLPHAAPSQILPGYHGSIDSFLEKQNLRRNVVVESAHFRMLPYMVAQT 247 Query: 243 DLVAMLPSRLVRGNA---VLKVVEAPIEVPGFEMFMLWHERVHRDPAHQWLREHIASA 297 DLV + LK PI+ P + LWHER H+ H+WLR + +A Sbjct: 248 DLVLTAGQQFASFYEKLLSLKSYAVPIKFPPLRFYQLWHERSHQATEHKWLRAQVGAA 305 >gi|300310448|ref|YP_003774540.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 306 Score = 136 bits (343), Expect = 2e-33, Method: Compositional matrix adjust. Identities = 93/297 (31%), Positives = 145/297 (48%), Gaps = 9/297 (3%) Query: 6 RRLDLNLLVTLDALLIEHNVTRAAERLHLAQPTVSLQLARLRDFFGDPLLLPGPRGMRTT 65 R +DLNLLV + E ++ A RL L+QP VS LARLR F D L + +GM+ T Sbjct: 7 RDIDLNLLVVFQEVFQERQISSVARRLGLSQPAVSNALARLRRSFEDELFVRTAQGMQPT 66 Query: 66 ARAEELREPLQQALAALAQAVTPSTAFDPAQSQQTWRAAAFDYSEYTILMPAL-DTLRKA 124 AE+L EP+ AL +A+A+ F P S + + A D E MPAL + + Sbjct: 67 PFAEQLAEPVAAALQQVARALNLQEGFAPQTSARRFTIAMTDVGE-VYFMPALIEACARC 125 Query: 125 APATRLAVIQTTPSLVARKAEQGEIDLAFLTATEAPPELRRLPLFTERYVLAGRAGHPQL 184 AP ++ ++ + + E G +DLA L + LF + YV R GH Sbjct: 126 APGVSISTVRAGAIDLKSEMESGRVDLAIGAFDNLSEALYQRRLFRQEYVSMFRIGHALD 185 Query: 185 K---RRPTLAQFCKLEHVIVSTDGGGFHGVTDTVLAEMGMTRKVALSVPHFLFLTAVLAN 241 K +L +F EH++VS+ + + L + G+ V VPHF + ++++ Sbjct: 186 KPGRGEVSLKEFLAAEHLMVSSQESPYDRINQN-LEKAGILPSVRFRVPHFTAVPYIVSS 244 Query: 242 TDLVAMLPSRLVRGNAV---LKVVEAPIEVPGFEMFMLWHERVHRDPAHQWLREHIA 295 T LV +P +L A L+ ++ P+ +P + M WH R ++D + WLR I+ Sbjct: 245 TALVVTVPRKLAESAAAPFGLRYIKPPLRLPSLQTNMFWHRRYNQDEGNVWLRGFIS 301 >gi|300313281|ref|YP_003777373.1| LysR family transcription regulator [Herbaspirillum seropedicae SmR1] Length = 323 Score = 136 bits (342), Expect = 2e-33, Method: Compositional matrix adjust. Identities = 95/294 (32%), Positives = 145/294 (49%), Gaps = 17/294 (5%) Query: 8 LDLNLLVTLDALLIEHNVTRAAERLHLAQPTVSLQLARLRDFFGDPLLLPGPRGMRTTAR 67 DLNLL A+ E +V+ AA +L ++QP VS+ L +LR GDPL + RGM+ T R Sbjct: 4 FDLNLLPIALAVFEERSVSAAARKLDMSQPAVSVALNKLRSALGDPLFVKTGRGMQPTPR 63 Query: 68 AEELREPLQQALAALAQAVTPSTAFDPAQSQQTWRAAAFDYSEYTILMPALDTLRKAAPA 127 A L P ++ L + V S F PA + + + A D E +L L+ +R AP Sbjct: 64 AVSLIGPTREILQRVHAEVLSSDQFTPATTTKRFVLALSDIGELMLLPRLLERIRDEAPH 123 Query: 128 TRLAVIQTTPSLVARKAEQGEIDLAFLTATEAPPELRRLPLFTER-----YVLAGRAGHP 182 + + P+ + E GE+DLA P+LR F +R +V RAGHP Sbjct: 124 ASVVTVTMAPAELVAALESGEVDLAIGYF----PDLRNRNFFQQRLFSQDFVCLLRAGHP 179 Query: 183 QLKRRPTLAQFCKLEHVIVSTDGGGFHGVTDTVLAEMGMTRKVALSVPHFLFLTAVLANT 242 ++ +L + H++V +G + + L + R+V LS HF+ + ++A + Sbjct: 180 LPAQKISLEHYQAAGHIVVKAEGRD-QPMCERFLLRRKIRRRVVLSTAHFMAIPLLVATS 238 Query: 243 DLVAMLPSRLVRGNAVLKVVEAPIEVPGFEMFML-----WHERVHRDPAHQWLR 291 DLVA +P G V++ + PGFEM ML WH + H+D + WLR Sbjct: 239 DLVATVPRAF--GEFVVRFAGIRLVEPGFEMPMLDLKQHWHRKYHKDAGNAWLR 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 0.135 0.397 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: 885,860 Number of extensions: 35113 Number of successful extensions: 215 Number of sequences better than 1.0e-08: 14 Number of HSP's gapped: 201 Number of HSP's successfully gapped: 14 Length of query: 298 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 213 Effective length of database: 1,217,395 Effective search space: 259305135 Effective search space used: 259305135 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: 41 (22.0 bits) S2: 130 (54.7 bits)