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= 0504.0023.p (305 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B1DAM7.1 B1DAM7_9BACL Transcriptional regulator, AraC family 223 1e-56 B3KF46.1 B3KF46_9BACI Helix-turn-helix-domain containing protein... 166 3e-39 Q5WKL2.1 Q5WKL2_BACSK AraC/XylS family transcriptional regulator 164 1e-38 Q02Z06.1 Q02Z06_LACLS Transcriptional regulator, AraC family 132 3e-29 A0NKY8.1 A0NKY8_OENOE Transcriptional regulator, AraC family 132 3e-29 >B1DAM7.1 B1DAM7_9BACL Transcriptional regulator, AraC family Length = 293 Score = 223 bits (569), Expect = 1e-56, Method: Compositional matrix adjust. Identities = 121/287 (42%), Positives = 171/287 (59%), Gaps = 14/287 (4%) Query: 16 MSPDLQAAFHIYAAHWRKVNAQWQYPEHTHPMFEINLVLQGRQHMTVGGQAYLQECGDIL 75 M PD+ + F ++ AH R V+ W YP H HP+FEINLVL G Q +V +Y Q+ GD+L Sbjct: 12 MLPDMDSTFRVFGAHSRTVDPGWSYPLHKHPLFEINLVLTGTQQFSVERTSYKQKAGDLL 71 Query: 76 FIRPGVRHASLGADAAGDMTYYCLHFDIDDLSLRRTLLTMDAVSLSGESPVLLAIRSALD 135 RPG +H S DMTYYCLHFD+D+ S R L +S + +AIR ALD Sbjct: 72 LFRPGDQHES-RVSGEEDMTYYCLHFDVDEPSFRELLCRSPRCFYPSDSELAMAIRPALD 130 Query: 136 VMIRTAILTEAEDAQRNRLVRLNASLQLFAALSAWV--LSETPAATRSAQPGVTENTVAL 193 +I + EA R+ L+A +LFA LS + L++ PA R+++ L Sbjct: 131 KLIGLTVSHEAVLRTEARMHILSALFELFAVLSGTLSKLNQDPAGLRNSE---------L 181 Query: 194 ANAVEGLLQESVFTAAATG--SRGGGIEDIAARLGYSPNHCNRAFRHIYGMSPRQYLSGL 251 A+ V +L+E+V AA G + I IAA +GYS + NR F +G+SPRQYLS + Sbjct: 182 ASRVAIMLEEAVEDAADAGIMNDKDTITSIAAAVGYSTSSVNRLFSRAFGVSPRQYLSTI 241 Query: 252 IIRHAKLMLLDNSLSVEAIAHRLGYRDVSHFSKQFKRWTGLPPMAYR 298 +++ AKL+L+D L++E I+ RLGY +++HFS+QFKRWTG P +R Sbjct: 242 MLKKAKLLLMDLELTIEEISSRLGYNNIAHFSRQFKRWTGESPSRFR 288 >B3KF46.1 B3KF46_9BACI Helix-turn-helix-domain containing protein AraC type Length = 304 Score = 166 bits (420), Expect = 3e-39, Method: Compositional matrix adjust. Identities = 97/287 (33%), Positives = 151/287 (52%), Gaps = 9/287 (3%) Query: 14 GRMSPDLQAAFHIYAAHWRKVNAQWQYPEHTHPMFEINLVLQGRQHMTVGGQAYLQECGD 73 GR+ PD++ +F + H RKV ++W YP H H M+EI+ ++ G +M V GQ Y Q GD Sbjct: 11 GRL-PDVRMSFQLLGLHARKVGSRWTYPSHEHSMYEIHWMMDGEMNMVVNGQLYKQSVGD 69 Query: 74 ILFIRPGVRHASLGADAAGDMTYYCLHFDIDDLSLRRTLLTMDAVSLSGESPVLLAIRSA 133 +LFIRPG+ H+ GA G TY+ +HF + D S R L + +S +LA + Sbjct: 70 LLFIRPGMTHSCTGAGPKG-FTYFSVHFSVHDTSFCRELNRCKDIYYPADS--VLAQGLS 126 Query: 134 LDVMIRTAILTEAEDAQRNRLVRLNASLQLFAALSAWV--LSETPAATRSAQPGVTENTV 191 + ++ TE + ++ +F L + V LS+TP+ S + + Sbjct: 127 SSLSTLYSLATEHLSSPLPAFKQMRVHAAVFELLGSLVGQLSQTPSVILSKKEAIARQ-- 184 Query: 192 ALANAVEGLLQESVFTAAATGSRGGGIEDIAARLGYSPNHCNRAFRHIYGMSPRQYLSGL 251 +A +E ++ + I DIA L SP+ NR FR +YG +PR++LS Sbjct: 185 -IAEQIEDSVRYIHLHGEIQETERTWIHDIAKSLNLSPSQVNRIFREVYGKAPRKFLSET 243 Query: 252 IIRHAKLMLLDNSLSVEAIAHRLGYRDVSHFSKQFKRWTGLPPMAYR 298 ++ A+ +L LS++ IA LGY+ +HFS+QFKRWT + P YR Sbjct: 244 LLGEAQRLLKQTDLSMDHIAMMLGYKTNAHFSRQFKRWTRMAPSEYR 290 >Q5WKL2.1 Q5WKL2_BACSK AraC/XylS family transcriptional regulator Length = 307 Score = 164 bits (414), Expect = 1e-38, Method: Compositional matrix adjust. Identities = 95/293 (32%), Positives = 148/293 (50%), Gaps = 36/293 (12%) Query: 18 PDLQAAFHIYAAHWRKVNAQWQYPEHTHPMFEINLVLQGRQHMTVGGQAYLQECGDILFI 77 P+ + ++ H R V W YPEH H ++EIN V++G+Q T G+ + Q GD++ + Sbjct: 32 PNTKTELELFGVHVRTVKGSWFYPEHQHAIYEINWVIEGQQIFTTNGKRHEQNAGDLVLV 91 Query: 78 RPGVRHASLGADAAGDMTYYCLHFDIDDLSLRRTLLTMDAVSLSGESPVLLAIRSALDVM 137 RPG HAS G + TY C+HF+IDD L +D + + + L+ + Sbjct: 92 RPGEFHASKGGNTE-PFTYLCIHFNIDDKLFLPYLTNIDPLFFKASGSLAKKMAPFLERI 150 Query: 138 IR-----TAILTEAEDAQRNRLVRLNASLQLFAALSAWVLS-ETPAATRSAQPGVTENTV 191 + T L E ++N +F L L E R ++E +V Sbjct: 151 AKLLGHHTFGLVE----------KMNMQAVMFEMLGMLALGLEELEGKR-----LSERSV 195 Query: 192 ALANAVEGLLQESVFTAAATGSRGGG------IEDIAARLGYSPNHCNRAFRHIYGMSPR 245 ALA + ++ ++ GGG IE IA +L S ++CN+ F+ +Y MSPR Sbjct: 196 ALAYQIAEQIERNL--------EGGGQLEKSNIEQIAKKLNISVSYCNQLFKKVYQMSPR 247 Query: 246 QYLSGLIIRHAKLMLLDNSLSVEAIAHRLGYRDVSHFSKQFKRWTGLPPMAYR 298 +Y S + AK +L+ +++E +A +LGY D+SHFS+QFKRWTGL P +R Sbjct: 248 KYWSFKQLNKAKALLVQKDVTIEMVADQLGYYDISHFSRQFKRWTGLAPSQFR 300 >Q02Z06.1 Q02Z06_LACLS Transcriptional regulator, AraC family Length = 299 Score = 132 bits (333), Expect = 3e-29, Method: Compositional matrix adjust. Identities = 79/285 (27%), Positives = 137/285 (48%), Gaps = 12/285 (4%) Query: 18 PDLQAAFHIYAAHWRKVNAQWQYPEHTHPMFEINLVLQGRQHMTVGGQAYLQECGDILFI 77 P++ + H + V W+ H FEI ++L G Q G ++ DI+ I Sbjct: 15 PEINMNMKFFGGHQQSVPLGWKIEREAHFAFEIMIILDGVQQTKFDGCSFNCYQDDIILI 74 Query: 78 RPGVRHASLGADAAGDMTYYCLHFDIDDLSLRRTLLTMDAVSLSGESPVLLAIRSALDVM 137 PG+ H + G M Y+C+HFDIDD ++ +L + +V L+ + I+S L Sbjct: 75 PPGMPHENSCISPTG-MHYFCVHFDIDDPEIQLNILMLCSVKLNKNNDAFTKIKSVLQKY 133 Query: 138 IRTAILTEAEDAQRNRLVRLNASLQLFAALSAWVLSETPAATRSAQPGVTENTVALANAV 197 I ++ + R +L+ ++L +L + L E AT S +++ LA ++ Sbjct: 134 I--TLIETNTFSLREKLMTEKLLIELMLSLYDYTLLEQNIATLS-----DNSSLILAKSI 186 Query: 198 EGLLQESVFTAAATGSRGG----GIEDIAARLGYSPNHCNRAFRHIYGMSPRQYLSGLII 253 +Q++ T + + +IA L S + + FR +Y +SP+ YL L Sbjct: 187 ADTIQQNFRTFTKQPIKENQQLLSMHEIAYSLNISESTMLKVFRKVYSISPKNYLDQLRY 246 Query: 254 RHAKLMLLDNSLSVEAIAHRLGYRDVSHFSKQFKRWTGLPPMAYR 298 +K +L +L + IA +GY+++SHFS+QFK+W+ L P YR Sbjct: 247 NESKFLLHQPNLPISEIAETIGYQNLSHFSRQFKQWSNLSPKEYR 291 >A0NKY8.1 A0NKY8_OENOE Transcriptional regulator, AraC family Length = 293 Score = 132 bits (333), Expect = 3e-29, Method: Compositional matrix adjust. Identities = 85/295 (28%), Positives = 138/295 (46%), Gaps = 26/295 (8%) Query: 18 PDLQAAFHIYAAHWRKVNAQWQYPEHTHPMFEINLVLQGRQHMTVGGQAYLQECGDILFI 77 P L + + H +KV+ W P + H FE+ V+ G++ + +YL GD + I Sbjct: 11 PVLDWNLNFFGGHSQKVDDTWIVPLNKHQAFELIFVVNGQEIVNFEHDSYLLNSGDFVLI 70 Query: 78 RPGVRHASLGADAAGDMTYYCLHFDIDDLSLRRTLLTMDAVSLSGESPV---LLAIRSAL 134 PG H A ++TY+C HFDIDD S L+ + +S V + I + Sbjct: 71 PPGFIHT---VSAVKNLTYFCFHFDIDDPSFVVGLIQNSPIYFPKDSSVNQEITPIIEDM 127 Query: 135 DVMIRTAILTEAEDAQRNRLVRLNASLQLFAALSAWVLSETPAATRSAQPGVTENTVALA 194 + MI + + + + + N + L+ L F +L +++ P S+Q + ++ Sbjct: 128 NKMISSKVYSFKD--KMNLQIYLSKMLLKFNSL----INKQPTVIGSSQSKYAK---TIS 178 Query: 195 NAVEGLLQESVFTAAATGSRGGG-----------IEDIAARLGYSPNHCNRAFRHIYGMS 243 ++ + V A G I+ I G S + NR FR +YG+S Sbjct: 179 EMIKNEFNDHVLYFATRFLNGPDNQKIQVPEMPTIKHIMEATGISVGYGNRVFRSVYGLS 238 Query: 244 PRQYLSGLIIRHAKLMLLDNSLSVEAIAHRLGYRDVSHFSKQFKRWTGLPPMAYR 298 P YLS L ++ A+ ML +++ IA LGY + +HFS+QFKRWTG+ P YR Sbjct: 239 PCDYLSKLKLKWAQQMLAKPQYNIDEIALVLGYSNSTHFSRQFKRWTGVSPKKYR 293 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 0.322 0.134 0.400 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: 1,714,272,556 Number of extensions: 64817968 Number of successful extensions: 192469 Number of sequences better than 1.0e-05: 1332 Number of HSP's gapped: 193326 Number of HSP's successfully gapped: 1341 Length of query: 305 Length of database: 3,060,696,203 Length adjustment: 135 Effective length of query: 170 Effective length of database: 1,788,859,178 Effective search space: 304106060260 Effective search space used: 304106060260 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 (21.9 bits) S2: 131 (55.1 bits)