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= 0502.0019.p (298 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KCS7.1 B3KCS7_9BACI Helix-turn-helix-domain containing protein... 333 9e-90 B1DJS1.1 B1DJS1_9BACL Transcriptional regulator, AraC family 333 2e-89 B3KHU9.1 B3KHU9_9BACI AraC protein arabinose-binding/dimerisation 174 1e-41 B1D506.1 B1D506_9BACL Transcriptional regulator, AraC family 171 5e-41 B1D7X7.1 B1D7X7_9BACL Transcriptional regulator, AraC family 139 3e-31 >B3KCS7.1 B3KCS7_9BACI Helix-turn-helix-domain containing protein AraC type Length = 295 Score = 333 bits (855), Expect = 9e-90, Method: Compositional matrix adjust. Identities = 152/296 (51%), Positives = 213/296 (71%), Gaps = 1/296 (0%) Query: 3 VTYPKELKEYPQLEEKTYPFRLFFNQCRDAKAEQNILFLHWHEHFEIIVMQKGRAIFHVD 62 ++YP+EL E +L +K YP ++F N C AK + IL+LHWHEHFEI+ M++GRA+FH+D Sbjct: 1 MSYPRELHENTRLGDKAYPVQVFHNLCPGAKTKDCILYLHWHEHFEILCMRQGRAVFHID 60 Query: 63 SRPYEAGPGDVIIVPSGGLHVGYSLINGDIAFVSIVFHASLFKDRYQDSQHEQFVAPYLN 122 + PY+ G+ II+P G LHVGY+L +GD+ F +V +ASLF D D H ++VAPY+ Sbjct: 61 TTPYDVKAGEFIIIPGGSLHVGYALEDGDVRFDCVVVNASLFNDSLHDPVHSRYVAPYME 120 Query: 123 NLYRFPVKPVEQNPVCSTYYPLLESLIQEVRDKSPAFQLVVKNQLHLFFTLLSRTFPPQR 182 RFPVKP E +P + YPLL+ +I+E+ + PA++L+ K++L+ F LL+RTF P + Sbjct: 121 GRLRFPVKPAESDPAGADCYPLLDEVIEELAVRRPAYELIAKSKLYTLFVLLARTFMPVQ 180 Query: 183 MSDRHHRERYSVNRERFKPLLEYLEQHLDEKITIESAARFVNLNPYHFCKTFKKLTGRTF 242 ++++ H E Y NRER+K L++++E ++ EK+ +E+AA V LNP+HFCK FK+LTGRTF Sbjct: 181 LAEKTH-EPYFANRERYKKLIQHIENNIGEKLPVEAAAAEVGLNPFHFCKMFKRLTGRTF 239 Query: 243 IDYVNLYRVNEAERXXXXXXXXXXXXAGKVGCDNPNYFTKLYKQYKGLTPSVARKM 298 +DYVNL R+NEAER AG VGC NPNYFTKLYKQYKG+TPS AR + Sbjct: 240 VDYVNLTRMNEAERLLRERTLTITEIAGIVGCSNPNYFTKLYKQYKGMTPSQARMI 295 >B1DJS1.1 B1DJS1_9BACL Transcriptional regulator, AraC family Length = 309 Score = 333 bits (853), Expect = 2e-89, Method: Compositional matrix adjust. Identities = 158/295 (53%), Positives = 212/295 (71%), Gaps = 1/295 (0%) Query: 3 VTYPKELKEYPQLEEKTYPFRLFFNQCRDAKAEQNILFLHWHEHFEIIVMQKGRAIFHVD 62 ++YPKEL+E +++EK +P ++F N+ K + IL+LHWHEHFEIIVMQ+G A+FH+D Sbjct: 1 MSYPKELRENTRIDEKMHPVQIFQNRALQKKPGELILYLHWHEHFEIIVMQQGSAVFHID 60 Query: 63 SRPYEAGPGDVIIVPSGGLHVGYSLINGDIAFVSIVFHASLFKDRYQDSQHEQFVAPYLN 122 S YEA PGDV+ VP+G LHVGYSL GD+++++IV+++SLF++ QDS H ++V PYL Sbjct: 61 SESYEAHPGDVLFVPAGALHVGYSLCEGDLSYLAIVYNSSLFQNWMQDSLHTKYVLPYLE 120 Query: 123 NLYRFPVKPVEQNPVCSTYYPLLESLIQEVRDKSPAFQLVVKNQLHLFFTLLSRTFPPQR 182 + PVKP +P C+ YY LLE E + K PA+QL+VK+QLH+ TLLSR F P + Sbjct: 121 GRVQLPVKPTRLDPSCADYYYLLEQANSEFKAKQPAYQLMVKSQLHMLLTLLSRKFLPHQ 180 Query: 183 MSDRHHRERYSVNRERFKPLLEYLEQHLDEKITIESAARFVNLNPYHFCKTFKKLTGRTF 242 + ++ +Y NRE+FK L+EY+E + +K T+ AAR +NLN +HFCK FKKLTGRTF Sbjct: 181 LPEQ-ATNQYVHNREQFKALIEYIEANFADKQTVADAARRMNLNVHHFCKMFKKLTGRTF 239 Query: 243 IDYVNLYRVNEAERXXXXXXXXXXXXAGKVGCDNPNYFTKLYKQYKGLTPSVARK 297 IDYVN+ RVNEAER AG VGCDN NYFTK+YK+YKG+ PS RK Sbjct: 240 IDYVNVCRVNEAERLLLAGDLSITEIAGCVGCDNSNYFTKMYKKYKGVAPSQLRK 294 >B3KHU9.1 B3KHU9_9BACI AraC protein arabinose-binding/dimerisation Length = 297 Score = 174 bits (440), Expect = 1e-41, Method: Compositional matrix adjust. Identities = 97/298 (32%), Positives = 162/298 (54%), Gaps = 11/298 (3%) Query: 3 VTYPKELKEYPQLEEKTYPFRLFFNQCRDAKAEQNILFLHWHEHFEIIVMQKGRAIFHVD 62 +T P ++K+ ++ +PF +F + +L LHWH+ E+I +G A F++ Sbjct: 1 MTNPYQIKQDVPHRDQDFPFDVF----HIIPPGKEVLHLHWHDDLELIYFIRGNATFYIG 56 Query: 63 SRPYEAGPGDVIIVPSGGLHVGYSLINGDIAFVSIVFHASLFKDRYQDSQHEQFVAPYLN 122 S + PGD++ V G +H G++ + + ++VFH+ L + R S H Q PY + Sbjct: 57 SETVKPEPGDLMFVNKGMIHTGFADDEHQVEYYALVFHSVLAESRVAGSSHVQITNPYAS 116 Query: 123 NLYRFPVKPVEQNPVCSTYYPLLESLIQEVRDKSPAFQLVVKNQLHLFFTLLSR---TFP 179 FP+ + S +++ +I E ++ +Q+ +++ LHL LSR Sbjct: 117 GKRFFPILLPVTDAYNSLIAGIVKQMIAEYEQQAIGYQVAIQSMLHLLLVHLSRHHHLHG 176 Query: 180 PQRMSDRHHRERYSVNRERFKPLLEYLEQHLDEKITIESAARFVNLNPYHFCKTFKKLTG 239 P +D E +RFK L+ ++E+H EK+T++ AA VNL+ YHFC+TFKK+TG Sbjct: 177 PTGSADTVGAEL----TDRFKELIAFVERHYPEKLTVQQAAGIVNLSEYHFCRTFKKVTG 232 Query: 240 RTFIDYVNLYRVNEAERXXXXXXXXXXXXAGKVGCDNPNYFTKLYKQYKGLTPSVARK 297 +TF++YVNL R+N AE+ A KVG + NYF+++++QYK +PS RK Sbjct: 233 KTFVEYVNLLRINAAEQLLIHSSDPITEIAFKVGFGSVNYFSQMFRQYKRHSPSQCRK 290 >B1D506.1 B1D506_9BACL Transcriptional regulator, AraC family Length = 291 Score = 171 bits (434), Expect = 5e-41, Method: Compositional matrix adjust. Identities = 95/262 (36%), Positives = 144/262 (54%), Gaps = 12/262 (4%) Query: 41 LHWHEHFEIIVMQKGRAIFHVDSRPYEAGPGDVIIVPSGGLHVGYSLI-NGDIAFVSIVF 99 LHWHEHFE+I ++ G ++ + +P+ PGD++ V SG LH SL N ++VF Sbjct: 33 LHWHEHFELIYVESGEVLYTIGGQPFPTKPGDMLFVNSGELHSAASLNPNEPFTVYALVF 92 Query: 100 HASLFKDRYQDSQHEQFVAPYLNNLYRFPVKPVEQNPVCSTYYPLLES----LIQEVRDK 155 + S+ ++ VAPY N + + +EQ + YPLL+ L E K Sbjct: 93 NPSILG--LKEPHIVDLVAPYTNGMSMIASR-IEQT---DSLYPLLKQTTLRLAGEFEQK 146 Query: 156 SPAFQLVVKNQLHLFFTLLSRTFPPQRMSDRHHRERYSVNRERFKPLLEYLEQHLDEKIT 215 ++L V++ L FT LSR F + SD + RFK LL LE + E++T Sbjct: 147 PRGYELAVRSYCQLLFTWLSREFTVMQRSDTEMNA-FRARTNRFKELLTRLESDVAERVT 205 Query: 216 IESAARFVNLNPYHFCKTFKKLTGRTFIDYVNLYRVNEAERXXXXXXXXXXXXAGKVGCD 275 +E AA FV+++PYHFC+ FKK+TG+TF+ Y+NL R+N AE A ++GC Sbjct: 206 VEQAASFVHMSPYHFCRMFKKITGQTFVQYMNLNRINRAEYLLKNTAMSVTDIAAEIGCS 265 Query: 276 NPNYFTKLYKQYKGLTPSVARK 297 + N F+KL++Q +G++P RK Sbjct: 266 SINSFSKLFRQLRGVSPRDLRK 287 >B1D7X7.1 B1D7X7_9BACL Transcriptional regulator, AraC family Length = 294 Score = 139 bits (351), Expect = 3e-31, Method: Compositional matrix adjust. Identities = 83/284 (29%), Positives = 145/284 (51%), Gaps = 6/284 (2%) Query: 9 LKEYPQLEEKTYPFRLFFNQCRDAKAEQNILFLHWHEHFEIIVMQKGRAIFHVDSRPYEA 68 LKE + YP L+ C ++ +L LHWH+ E++++ +G A+F VD + YE Sbjct: 6 LKEARKHGNPIYPVSLYEITC---PSDAPLLDLHWHDELELLLVTEGTAVFRVDLQDYEL 62 Query: 69 GPGDVIIVPSGGLHVGYSLINGDIAFVSIVFHASLFKDRYQDSQHEQFVAPYLNNLYRFP 128 G+ I V SG LH GY + +F ++VFH+SLF D +++++P L Y P Sbjct: 63 QAGEAIFVNSGELHSGYVVGGKPCSFDAVVFHSSLFSSGSIDYLFDRYISPVLEKRYEVP 122 Query: 129 VKPVEQNPVCSTYYPLLESLIQEVRDKSPAFQLVVKNQLHLFFTLLSRTFPPQRMSDRHH 188 + +L+ + + R++ A +L +K L F++L++ + S R Sbjct: 123 AHLRREPGPGMELLAMLDQIFEVHRNEQAASELTIKG---LLFSILAKLVSLGKPSVRVK 179 Query: 189 RERYSVNRERFKPLLEYLEQHLDEKITIESAARFVNLNPYHFCKTFKKLTGRTFIDYVNL 248 E+ ER K ++EY+EQ+ E I ++ A ++ +FC+ FK++T ++ I+Y+N Sbjct: 180 PEQEGYRIERLKTVIEYIEQNYAEPIPLQKLAELARMSESYFCRFFKRITTKSPIEYMNS 239 Query: 249 YRVNEAERXXXXXXXXXXXXAGKVGCDNPNYFTKLYKQYKGLTP 292 YRV +A A VG ++ +YF +++Q G TP Sbjct: 240 YRVQQAASRLRQTDAKIMEVALDVGFNSLSYFNTVFRQRFGCTP 283 Database: pfamseq Posted date: Aug 5, 2010 3:22 PM Number of letters in database: 3,060,696,203 Number of sequences in database: 9,421,015 Lambda K H 0.324 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: 9421015 Number of Hits to DB: 1,751,739,929 Number of extensions: 70139004 Number of successful extensions: 162193 Number of sequences better than 1.0e-05: 1266 Number of HSP's gapped: 163108 Number of HSP's successfully gapped: 1266 Length of query: 298 Length of database: 3,060,696,203 Length adjustment: 135 Effective length of query: 163 Effective length of database: 1,788,859,178 Effective search space: 291584046014 Effective search space used: 291584046014 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: 41 (22.0 bits) S2: 131 (55.1 bits)