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= 0167.0023.p (288 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KJH8.1 B3KJH8_9BACI Helix-turn-helix-domain containing protein... 183 1e-44 B1DGY9.1 B1DGY9_9BACL Transcriptional regulator, AraC family 182 4e-44 Q7UYE3.1 Q7UYE3_RHOBA L-rhamnose operon transcriptional activator 174 7e-42 B5JHR7.1 B5JHR7_9BACT Transcriptional regulator, AraC family pro... 174 9e-42 A6AMR4.1 A6AMR4_VIBHA AraC-type DNA-binding domain-containing pr... 157 1e-36 >B3KJH8.1 B3KJH8_9BACI Helix-turn-helix-domain containing protein AraC type Length = 287 Score = 183 bits (465), Expect = 1e-44, Method: Compositional matrix adjust. Identities = 102/273 (37%), Positives = 158/273 (57%), Gaps = 3/273 (1%) Query: 16 FTFRIQKCPLTHDYYVHSH-DFSELVVILEGSAIHIIEGREYPVSAGQVFFIHSDISHGY 74 F F IQ D YVH H DFSELV++L G A HI+ E + G VF I+ SHGY Sbjct: 15 FKFFIQYGGHEEDMYVHHHVDFSELVIVLHGHATHIVNTEESFIKKGDVFVINGTTSHGY 74 Query: 75 KNVQNIQYVNVMFHPDXXXXX-XXXXXXXGFQALFYLEPFFRKEMFFKGMLSLEPRQLDE 133 K+ + N+M+ P+ G+QALF LEP++R +SL LD Sbjct: 75 KDPHEFRICNIMYKPEMLELTGPEFKRSNGYQALFVLEPYYRNINHSLSKMSLPISSLDY 134 Query: 134 VNLLLDRILEEHDRQSDGYRLMIRTYFTALVGTLSRYY-RQNGGGTENKALRIGEAITYI 192 V+ ++D ++EE+ + GY+ ++R+ F LV LSR Y +Q G + + + +AI+++ Sbjct: 135 VSSVVDFMIEEYANKLQGYQTILRSRFMELVVQLSRQYEKQERYGAQIHLMHLAKAISFM 194 Query: 193 EEHFLQPVSLQDLADLAFMSKRQFLRVFTRNYHTTPMDYIIRKRLDYSCTLLRNPELSIS 252 E+++LQP+S ++A + +S R R+F Y TTP Y+++ RL+++C LL+ L IS Sbjct: 195 EDNYLQPISRDEIAAKSNISVRHLNRIFQSYYQTTPFAYLLQLRLEHACRLLKTTPLPIS 254 Query: 253 QVAMDSGFRDHNYYSRQFKKVFLCTPSEYRTHK 285 +++ SGF D NY++RQF KVF +P YR + Sbjct: 255 EISYRSGFNDSNYFTRQFSKVFGLSPKVYRKRR 287 >B1DGY9.1 B1DGY9_9BACL Transcriptional regulator, AraC family Length = 289 Score = 182 bits (461), Expect = 4e-44, Method: Compositional matrix adjust. Identities = 98/258 (37%), Positives = 151/258 (58%), Gaps = 3/258 (1%) Query: 28 DYYVHSH-DFSELVVILEGSAIHIIEGREYPVSAGQVFFIHSDISHGYKNVQNIQYVNVM 86 D Y+H H DFSELV++L G+A HI+ + G VF I SH YK+ + + N+M Sbjct: 27 DMYLHDHVDFSELVIVLNGNATHIVNTEVSFIKKGDVFVIDGATSHAYKDPHDFRICNIM 86 Query: 87 FHPDXXXXX-XXXXXXXGFQALFYLEPFFRKEMFFKGMLSLEPRQLDEVNLLLDRILEEH 145 + PD G+QALF LEPF+R F LSL L+ V+ L ++EE+ Sbjct: 87 YRPDILTSAGPDLRTSIGYQALFVLEPFYRNIQPFNSKLSLPIPSLEYVSSLAAFMIEEY 146 Query: 146 DRQSDGYRLMIRTYFTALVGTLSRYYR-QNGGGTENKALRIGEAITYIEEHFLQPVSLQD 204 + GY+ M+R+ F LV LSR Y+ Q+ G + + + AI+++E+H+L+P++ + Sbjct: 147 TNKLQGYQTMLRSRFMELVVYLSRQYQNQDQQGIQGNLMHLANAISFMEDHYLEPLTREQ 206 Query: 205 LADLAFMSKRQFLRVFTRNYHTTPMDYIIRKRLDYSCTLLRNPELSISQVAMDSGFRDHN 264 +AD + +S R R+F Y TTP Y++R RL+++C LL+ + I++V+ SGF D N Sbjct: 207 IADKSGISVRHLNRIFQSYYPTTPFAYLLRLRLEHACHLLKTTPVPITEVSYKSGFNDSN 266 Query: 265 YYSRQFKKVFLCTPSEYR 282 Y++RQF KV+ P YR Sbjct: 267 YFTRQFTKVYGLAPKVYR 284 >Q7UYE3.1 Q7UYE3_RHOBA L-rhamnose operon transcriptional activator Length = 290 Score = 174 bits (441), Expect = 7e-42, Method: Compositional matrix adjust. Identities = 94/269 (34%), Positives = 145/269 (53%), Gaps = 1/269 (0%) Query: 15 GFTFRIQKCPLTHDYYVHSHDFSELVVILEGSAIHIIEGREYPVSAGQVFFIHSDISHGY 74 GF +++ + +H H+F+E+V+I G +HI Y + G F I D H Y Sbjct: 18 GFPIVVERRDPQEPFGLHCHEFAEIVIITGGKGVHITGEDSYELVTGDTFVIGGDRPHDY 77 Query: 75 KNVQNIQYVNVMFHP-DXXXXXXXXXXXXGFQALFYLEPFFRKEMFFKGMLSLEPRQLDE 133 N+ + +N++F P + G+ ALF LEP +RK F L L P +L E Sbjct: 78 LNMDQLSLINILFDPLELPLSIGDLQSLSGYHALFTLEPAWRKRHQFTSRLQLNPAELIE 137 Query: 134 VNLLLDRILEEHDRQSDGYRLMIRTYFTALVGTLSRYYRQNGGGTENKALRIGEAITYIE 193 ++ + +E ++S G+R M LV LSR Y + K LRI EAI++I+ Sbjct: 138 TLRYVESLDQELKQRSAGFRTMATLTMLQLVTFLSRCYIRTRNPESKKLLRIAEAISHIQ 197 Query: 194 EHFLQPVSLQDLADLAFMSKRQFLRVFTRNYHTTPMDYIIRKRLDYSCTLLRNPELSISQ 253 HF +P+SL DL +++ MS+R F+R F T+P+ Y+I+ R+ + LLR+ + SI+ Sbjct: 198 RHFDRPISLDDLVEISGMSRRNFIRTFEGTMETSPIKYLIQVRIQEASRLLRSTDRSITD 257 Query: 254 VAMDSGFRDHNYYSRQFKKVFLCTPSEYR 282 +A D GF D NY+SRQF+ +P EYR Sbjct: 258 IAFDVGFSDSNYFSRQFRTHLGLSPREYR 286 >B5JHR7.1 B5JHR7_9BACT Transcriptional regulator, AraC family protein Length = 316 Score = 174 bits (441), Expect = 9e-42, Method: Compositional matrix adjust. Identities = 94/257 (36%), Positives = 141/257 (54%), Gaps = 1/257 (0%) Query: 32 HSHDFSELVVILEGSAIHIIEGREYPVSAGQVFFIHSDISHGYKNVQNIQYVNVMFHPDX 91 H+HDF EL +I GSA+H +EG E+P++AG VF + SH Y ++Q ++ +N+MF P+ Sbjct: 55 HTHDFCELALITRGSAMHWLEGAEFPITAGDVFVLQGQQSHYYYDLQKLEMINIMFDPEQ 114 Query: 92 XXXXXXXXXXX-GFQALFYLEPFFRKEMFFKGMLSLEPRQLDEVNLLLDRILEEHDRQSD 150 G++ALF LEP FRK+ F L L L + + E + + Sbjct: 115 LNLPETRLRKIPGYRALFLLEPLFRKQHRFTSHLHLSRSTLAHSERIAVELDNEVRGKME 174 Query: 151 GYRLMIRTYFTALVGTLSRYYRQNGGGTENKALRIGEAITYIEEHFLQPVSLQDLADLAF 210 GY + F LV LSR Y++ LR+ + I IE+ F +P ++D A +A Sbjct: 175 GYEAAMFAKFVELVVYLSRLYQETESTNAEALLRVAKVIGSIEDEFTKPWKVEDFAAMAH 234 Query: 211 MSKRQFLRVFTRNYHTTPMDYIIRKRLDYSCTLLRNPELSISQVAMDSGFRDHNYYSRQF 270 MS+ F+RVF TP++Y+++ R+ S TLL + +LSIS++A + GF D NYY+RQF Sbjct: 235 MSRANFMRVFRTATGETPINYLLQLRIQKSMTLLTSTKLSISEIAFEVGFNDSNYYTRQF 294 Query: 271 KKVFLCTPSEYRTHKAG 287 K +P YR G Sbjct: 295 KASQGISPLAYRRTHTG 311 >A6AMR4.1 A6AMR4_VIBHA AraC-type DNA-binding domain-containing protein Length = 292 Score = 157 bits (397), Expect = 1e-36, Method: Compositional matrix adjust. Identities = 88/258 (34%), Positives = 140/258 (54%), Gaps = 3/258 (1%) Query: 28 DYYVHSHDFSELVVILEGSAIHIIEGREYPVSAGQVFFIHSDISHGYKNVQNIQYVNVMF 87 D+ H HDFSEL +++ GS H + EYP+ G VF I+ DI HG+++V ++ +N+MF Sbjct: 28 DFAAHKHDFSELFLVVSGSGKHTVAEYEYPLRKGDVFVINGDIEHGFRDVNKLKIINLMF 87 Query: 88 HPDXX-XXXXXXXXXXGFQALFYLEPFFRKEMFFKGMLSLEPRQLDEVNLLLDRILEEHD 146 + G+QA+F +EP R+ +K L+L+ +QL E+ LL + E++ Sbjct: 88 DSNTPFFEIPSMRQLSGYQAMFKVEPIARQTTEYKAKLTLDRQQLPEIERLLSVLKAEYE 147 Query: 147 RQSDGYRLMIRTYFTALVGTLSRYYRQNGGGTENKALRIGEAITYIEEHFLQ-PVSLQDL 205 G+ +M+ + LV LSR Y+ L + A+ +IE+HF V+ + Sbjct: 148 ASQPGFEVMLTSLMQQLVIALSRMYQDQSQELPQTTLALSRALVFIEQHFSDVGVNSDAI 207 Query: 206 ADLAFMSKRQFLRVFTRNYHTTPMDYIIRKRLDYSCTLL-RNPELSISQVAMDSGFRDHN 264 A AF+SKRQ R+F + T+P Y+ +L+Y+ LL E S+ +A GF D N Sbjct: 208 AKAAFISKRQLERLFRQFLDTSPNQYLRDVQLNYATKLLCEENERSVQHIAELCGFSDSN 267 Query: 265 YYSRQFKKVFLCTPSEYR 282 Y+S+ FK+ F +P YR Sbjct: 268 YFSKCFKQKFQHSPRSYR 285 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 0.326 0.141 0.424 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: 1,645,024,459 Number of extensions: 62874756 Number of successful extensions: 182735 Number of sequences better than 1.0e-05: 3702 Number of HSP's gapped: 183302 Number of HSP's successfully gapped: 3702 Length of query: 288 Length of database: 3,060,696,203 Length adjustment: 134 Effective length of query: 154 Effective length of database: 1,798,280,193 Effective search space: 276935149722 Effective search space used: 276935149722 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 130 (54.7 bits)