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= 0542.0007.p (324 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B1D7X7.1 B1D7X7_9BACL Transcriptional regulator, AraC family 168 7e-40 B3KDR1.1 B3KDR1_9BACI Helix-turn-helix-domain containing protein... 157 9e-37 Q9KBM0.1 Q9KBM0_BACHD Transcriptional regulator (AraC/XylS family) 157 1e-36 C1PUY1.1 C1PUY1_ALIAC DNA-binding domain-containing protein, Ara... 155 4e-36 B5YFJ6.1 B5YFJ6_DICT6 Transcriptional regulator, putative 154 1e-35 >B1D7X7.1 B1D7X7_9BACL Transcriptional regulator, AraC family Length = 294 Score = 168 bits (425), Expect = 7e-40, Method: Compositional matrix adjust. Identities = 90/286 (31%), Positives = 155/286 (54%), Gaps = 3/286 (1%) Query: 34 REHKLHGQPEFPLHIYKVEHPAGVHTILPVHWHNEMEIITLASGQAMFYIEGREYALHAG 93 +E + HG P +P+ +Y++ P+ +L +HWH+E+E++ + G A+F ++ ++Y L AG Sbjct: 7 KEARKHGNPIYPVSLYEITCPSDA-PLLDLHWHDELELLLVTEGTAVFRVDLQDYELQAG 65 Query: 94 DALIVHPGELHSGMDTGSGGTCYYSIVFRISWLSSPHPDRVQVQYLDPLLQETARLPVLL 153 +A+ V+ GELHSG G + ++VF S SS D + +Y+ P+L++ +P L Sbjct: 66 EAIFVNSGELHSGYVVGGKPCSFDAVVFHSSLFSSGSIDYLFDRYISPVLEKRYEVPAHL 125 Query: 154 SAADSAHXXXXXXXXXXXXXYDQKAAAYEMSLKALLLLFIADSYPLAQTGMEPDPGARRA 213 + + AA E+++K LL +A L + + P Sbjct: 126 RREPGPGMELLAMLDQIFEVHRNEQAASELTIKGLLFSILAKLVSLGKPSVRVKPEQEGY 185 Query: 214 REDNRQIRQVLSYMEEHSREKLELDQLAAVVSLSRSHFCKFFKDRTGMRPMEYLNYIRIS 273 R + +++ V+ Y+E++ E + L +LA + +S S+FC+FFK T P+EY+N R+ Sbjct: 186 RIE--RLKTVIEYIEQNYAEPIPLQKLAELARMSESYFCRFFKRITTKSPIEYMNSYRVQ 243 Query: 274 QAASLLRSGAYNVLEAALESGFQHVSYFTKWFKHYMDMTPSEYKAR 319 QAAS LR ++E AL+ GF +SYF F+ TP EY++R Sbjct: 244 QAASRLRQTDAKIMEVALDVGFNSLSYFNTVFRQRFGCTPREYRSR 289 >B3KDR1.1 B3KDR1_9BACI Helix-turn-helix-domain containing protein AraC type Length = 292 Score = 157 bits (398), Expect = 9e-37, Method: Compositional matrix adjust. Identities = 87/293 (29%), Positives = 148/293 (50%), Gaps = 8/293 (2%) Query: 29 YEHRYREHKLHGQPEFPLHIYKVEHPAGVHTILPVHWHNEMEIITLASGQAMFYIEGREY 88 + +E +HG FP Y + G H ++ HWH E EI + G+ +F I+ Sbjct: 5 FRQSLKESTVHGNERFPFGAYWYQFAPGAH-VVDSHWHKEAEIFYVMEGEVLFQIDSEYI 63 Query: 89 ALHAGDALIVHPGELHSGMDTGSGGTCYYSIVFRISWLSSPHPDRVQVQYLDPLLQETAR 148 + AG+A+ + G+LH+G G+ G + ++VF + L+S D VQ + P + A Sbjct: 64 PVRAGEAIFIDGGDLHTGHAQGNEGCSFCAMVFDVGMLASSSYDLVQEGMIVPFQERRAA 123 Query: 149 LPVLLSAADSAHXXXXXXXXXXXXXYDQKAAAYEMSLKALLLLFIADSYPLAQTGMEPDP 208 P +++ + K A YE ++K L L + + A +G + Sbjct: 124 FPRRMTSGTDERLLEHIKEMMLLSKH--KPAGYEAAIKGHLFLML---FQAASSGRLANR 178 Query: 209 GARRAREDNR--QIRQVLSYMEEHSREKLELDQLAAVVSLSRSHFCKFFKDRTGMRPMEY 266 A + R ++++V+ Y++ H + L +LA ++ +S FC+FFK TG P++Y Sbjct: 179 SRSEAADMTRTERLKKVILYIQSHYHRPIRLSELADLIPMSEGQFCRFFKSMTGQTPVDY 238 Query: 267 LNYIRISQAASLLRSGAYNVLEAALESGFQHVSYFTKWFKHYMDMTPSEYKAR 319 +N R+ QAA LLRS + + AL+ GF H+SYF + F+ M+ TPSEY+ + Sbjct: 239 MNSYRVRQAAELLRSPDNKISDIALDVGFGHISYFVRVFRKIMNCTPSEYRKK 291 >Q9KBM0.1 Q9KBM0_BACHD Transcriptional regulator (AraC/XylS family) Length = 299 Score = 157 bits (397), Expect = 1e-36, Method: Compositional matrix adjust. Identities = 92/293 (31%), Positives = 147/293 (50%), Gaps = 10/293 (3%) Query: 28 MYEHRYREHKLHGQPEFPLHIYKVEHPAGVHTILPVHWHNEMEIITLASGQAMFYIEGRE 87 M + ++ E + HG P FP ++Y+V+ G I+ HWH+EME I + +G+A F I + Sbjct: 1 MKDDQWLEARAHGDPMFPCNVYRVKEVNG-QVIIHCHWHHEMEWIYMEAGEAEFQIGTKM 59 Query: 88 YALHAGDALIVHPGELHSGMDTGSGGTCYYSIVFRISWLSSPHPDRVQVQYLDPLLQETA 147 + AG+ L + G LH Y+ V ++SS D +Q +Y+DP Sbjct: 60 TTVRAGEGLFIPSGHLHGAYPVSDKPFSLYATVVHPDFISSFGYDLIQSRYIDPFKDSER 119 Query: 148 RLPVLLSAADSAHXXXXXXXXXXXXXYDQKAAAYEMSLKALLLLFIAD---SYPLAQTGM 204 P+ L + QK YE+ +KA LL +A+ +P + Sbjct: 120 TGPIKLCPTHYWMSDMLTMLQATISQFQQKEEGYELVIKANLLQMMAELVKHFPRTEEQK 179 Query: 205 EPDPGARRAREDNRQIRQVLSYMEEHSREKLELDQLAAVVSLSRSHFCKFFKDRTGMRPM 264 P + RQI++VL +++EH EKL + QLA +V +S HF +FFK M + Sbjct: 180 TGTP------QQIRQIKKVLQFIDEHYDEKLTIKQLANLVQMSEGHFSRFFKSIVRMTAV 233 Query: 265 EYLNYIRISQAASLLRSGAYNVLEAALESGFQHVSYFTKWFKHYMDMTPSEYK 317 EY++ R+++AA LLR +++ ++ GF H SYF K FK + TPSE++ Sbjct: 234 EYIHTQRLNKAARLLRETDRTIMDISMSVGFDHPSYFIKLFKRHKRCTPSEFR 286 >C1PUY1.1 C1PUY1_ALIAC DNA-binding domain-containing protein, AraC-type Length = 300 Score = 155 bits (393), Expect = 4e-36, Method: Compositional matrix adjust. Identities = 93/286 (32%), Positives = 143/286 (50%), Gaps = 6/286 (2%) Query: 35 EHKLHGQPEFPLHIYKVEHPAGVHT-ILPVHWHNEMEIITLASGQAMFYIEGREYALHAG 93 EH+ HG F + Y V G H + +HWH+E E I + G + + + L G Sbjct: 8 EHRQHGDATFHIQAYHVVLTPGPHQQTVNLHWHSEAEFIVVTRGSVCLQVGSQRHVLADG 67 Query: 94 DALIVHPGELHSGMDTGSGGTCYYSIVFRISWLSSPHPDRVQVQYLDPLLQETARLPVLL 153 ++ GELHS G G + +IVF + L P DRVQ YL PL RLP + Sbjct: 68 GVALLSGGELHSMASPGKGPSECKAIVFGLDLLEGPSGDRVQQSYLSPLASGKLRLPGAI 127 Query: 154 SAADSAHXXXXXXXXXXXXXYDQKAAAYEMSLKALLLLFIADSYPLAQTGMEPDPGARRA 213 + +++ YE+++K L +A + A+ +E P RR Sbjct: 128 AHDHPVRPHLAARLCEIAEALEEQPVGYELAVKGCLYDVLAQLF-RAKLLVEDSP--RRE 184 Query: 214 REDNR--QIRQVLSYMEEHSREKLELDQLAAVVSLSRSHFCKFFKDRTGMRPMEYLNYIR 271 +D R ++ VL+Y++EH +KL L LA V ++S HFC+FFK+ T +PM+Y+N R Sbjct: 185 MDDRRADTLKAVLTYIDEHLSDKLRLADLARVANMSEGHFCRFFKEMTHRKPMQYVNERR 244 Query: 272 ISQAASLLRSGAYNVLEAALESGFQHVSYFTKWFKHYMDMTPSEYK 317 +++AA LL+ ++ ++ GF VSYF K F+ Y TP Y+ Sbjct: 245 VARAADLLKDPNRSITAIGMDLGFHDVSYFIKVFRSYKHCTPLAYR 290 >B5YFJ6.1 B5YFJ6_DICT6 Transcriptional regulator, putative Length = 287 Score = 154 bits (389), Expect = 1e-35, Method: Compositional matrix adjust. Identities = 90/287 (31%), Positives = 148/287 (51%), Gaps = 22/287 (7%) Query: 39 HGQPEFPLHIYKVEHPAGVHTILPVHWHNEMEIITLASGQAMFYIEGREYALHAGDALIV 98 HG P+FPL +++ + P HWHNE EI+ + G FY++G EY L+ G+ L V Sbjct: 15 HGTPDFPLFVHEDIFVYRNGVVNP-HWHNEFEILYMERGIGKFYVDGYEYKLNEGEYLFV 73 Query: 99 HPGELHSGMDTGSGGTCYYSIVFRISWLSSPHPDRVQVQYLDPLLQETARLPVLLSAADS 158 + G +HSG++ Y +IVF + L S PD + +Y PL+ + +P S + Sbjct: 74 NSGSIHSGLEMIKRSIGY-AIVFDLRLLYSEEPDYCKHEYFLPLINKRYHIP---SNLND 129 Query: 159 AHXXXXXXXXXXXXXYDQKAAAYEMSLKALLLLFIADSYPLAQTGMEPDPGARRAREDNR 218 H + +K+ YE+ +K+LL + A R +D R Sbjct: 130 EHIRNDICRIIEV--FKEKSYGYELYIKSLLFDIFWRVFKYY---------AERRNQDGR 178 Query: 219 ------QIRQVLSYMEEHSREKLELDQLAAVVSLSRSHFCKFFKDRTGMRPMEYLNYIRI 272 +I+ VL+Y+ ++ + L LD+L+ V +S+ + C+ FK+ M P+EY+N +R+ Sbjct: 179 LGYKIERIKDVLNYINQNYNKNLSLDELSRQVDMSKFYLCRLFKESLRMSPVEYINKVRV 238 Query: 273 SQAASLLRSGAYNVLEAALESGFQHVSYFTKWFKHYMDMTPSEYKAR 319 +A LL + +V E A E GF ++SYF K FK YM TP +++ + Sbjct: 239 DKAMELLINTDMSVSEIAFECGFDNISYFIKVFKKYMHTTPLKFRKQ 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 0.321 0.134 0.406 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: 1,813,829,953 Number of extensions: 71685154 Number of successful extensions: 181066 Number of sequences better than 1.0e-05: 4479 Number of HSP's gapped: 181291 Number of HSP's successfully gapped: 4493 Length of query: 324 Length of database: 3,060,696,203 Length adjustment: 136 Effective length of query: 188 Effective length of database: 1,779,438,163 Effective search space: 334534374644 Effective search space used: 334534374644 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)