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= 0437.0012.p (375 letters) Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF 2,715,099 sequences; 757,237,578 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value ref|ZP_00121712.1| COG1940: Transcriptional regulator/sugar kina... 231 2e-59 ref|NP_696729.1| probable repressor in the Rok (NagC/XylR) famil... 228 2e-58 ref|NP_350254.1| XylR transcriptional regulator [Clostridium ace... 155 1e-36 sp|P16557|XYLR_BACSU XYLOSE REPRESSOR >gi|98448|pir||A32885 xylo... 132 2e-29 emb|CAB02313.1| Xyl repressor [Bacillus licheniformis] 126 7e-28 >ref|ZP_00121712.1| COG1940: Transcriptional regulator/sugar kinase [Bifidobacterium longum DJO10A] Length = 380 Score = 231 bits (589), Expect = 2e-59, Method: Compositional matrix adjust. Identities = 122/371 (32%), Positives = 204/371 (54%), Gaps = 2/371 (0%) Query: 6 LNSMEVKKMNRNAIYRYLYHREATSIQEIAQALNLSLPTVTQNIKELQERELIVETGLFQ 65 + S VK NR+A+ +YLY + QE+ + L LSLPT+TQN++ L++ LI + L Sbjct: 4 MPSTAVKAHNRSAMTQYLYGHSHVTKQELERELGLSLPTITQNLRALEDDGLIRKGELQD 63 Query: 66 STGGRKAKSMACNSVAGYAIGLDVTRNHVGIVIIDLRGTIIKHVRNHFPFANTEVYFKSV 125 STGGRKA++ N AIG+ + N + + I+L G +I+ + P+ NT VY++ + Sbjct: 64 STGGRKAQNYEFNPDHRTAIGVVMRSNELRLCAINLYGNVIEKRNDALPYRNTNVYYQRI 123 Query: 126 GKLVDDCVEESRIDSSKILGVGIALPAILSDDRQTVNYATVIDFKGGSIRRFAEFIRYPC 185 G ++++ + K+LGV A+ ILS D T+ + T++ G ++ ++ + YPC Sbjct: 124 GGIINNFAADVEKKHGKVLGVSFAIQGILSPDATTITFGTIMGNTGLTLETISQSVHYPC 183 Query: 186 ILSNDANAAGFTELWGEKDIHNVVYLSLNNSVGGSIIVNNQIYTGQNHRGGEFGHMTIMP 245 ++ +D++A+ ELW + + + V + L GG++I ++Y G N G HMT++P Sbjct: 184 MMIHDSDASAMAELWFDSTLTDAVCVYLERRPGGAVIAGGKLYQGPNQCNGAIEHMTLVP 243 Query: 246 EGRTCYCGQKGCVDAYCSARILSDSTQGSISEFFRRLREGHEPQKAIWQEYIGYLVITVN 305 GR CYCGQ+GC+D YCS L + + SI FF L +G + E++ Y+ + Sbjct: 244 GGRECYCGQRGCMDTYCSPETLPEDYE-SIPGFFSVLEQGERHHRERMDEWLDYVAQAIV 302 Query: 306 NLRMLYDCDVILGGYAGAYMEEY-IDTLQGLAAQKNTFERDGTYLRVCKYKLEATAVGAA 364 N R + DVI+GG A ++E+ I+ L+ ++ F D LR + +GAA Sbjct: 303 NARSIIAGDVIVGGEAAQHLEDSDIEDLKARVIARSPFGTDHFNLRKSYCAEDQNIIGAA 362 Query: 365 LELVTEFIDSI 375 L ++D I Sbjct: 363 LRFAENYLDDI 373 >ref|NP_696729.1| probable repressor in the Rok (NagC/XylR) family [Bifidobacterium longum NCC2705] gb|AAN25365.1| probable repressor in the Rok (NagC/XylR) family [Bifidobacterium longum NCC2705] Length = 397 Score = 228 bits (580), Expect = 2e-58, Method: Compositional matrix adjust. Identities = 122/371 (32%), Positives = 203/371 (54%), Gaps = 2/371 (0%) Query: 6 LNSMEVKKMNRNAIYRYLYHREATSIQEIAQALNLSLPTVTQNIKELQERELIVETGLFQ 65 + S VK NR+A+ +YLY + QE+ + L LSLPT+TQN+ L++ LI + L Sbjct: 4 MPSTAVKAHNRSAMAQYLYGHSHVTKQELERELGLSLPTITQNLHALEDDGLIRKGELQD 63 Query: 66 STGGRKAKSMACNSVAGYAIGLDVTRNHVGIVIIDLRGTIIKHVRNHFPFANTEVYFKSV 125 STGGRKA++ N AIG+ + N + + I+L G +I+ + P+ NT VY++ + Sbjct: 64 STGGRKAQNYEFNPDHRTAIGVVMRSNELRLCAINLYGNVIEKRNDALPYRNTNVYYQRI 123 Query: 126 GKLVDDCVEESRIDSSKILGVGIALPAILSDDRQTVNYATVIDFKGGSIRRFAEFIRYPC 185 G ++++ + K+LGV A+ ILS D T+ + T++ G ++ ++ + YPC Sbjct: 124 GGIINNFAADVEKKHGKVLGVSFAIQGILSPDATTIIFGTIMGNTGLTLETISQSVHYPC 183 Query: 186 ILSNDANAAGFTELWGEKDIHNVVYLSLNNSVGGSIIVNNQIYTGQNHRGGEFGHMTIMP 245 ++ +D++A+ ELW + + + V + L GG++I ++Y G N G HMT++P Sbjct: 184 MMIHDSDASAMAELWFDSTLTDAVCVYLERRPGGAVIAGGKLYQGPNQCNGAIEHMTLVP 243 Query: 246 EGRTCYCGQKGCVDAYCSARILSDSTQGSISEFFRRLREGHEPQKAIWQEYIGYLVITVN 305 GR CYCGQ+GC+D YCS L + + SI FF L +G + E++ Y+ + Sbjct: 244 GGRECYCGQRGCMDTYCSPETLPEDYE-SIPGFFSVLEQGERHHRERMDEWLDYVAQAIV 302 Query: 306 NLRMLYDCDVILGGYAGAYMEEY-IDTLQGLAAQKNTFERDGTYLRVCKYKLEATAVGAA 364 N R + DVI+GG A ++E+ I+ L+ ++ F D LR + +GAA Sbjct: 303 NARSIIAGDVIVGGEAAQHLEDSDIEDLKTRVIARSPFGTDHFNLRKSYCAEDQNIIGAA 362 Query: 365 LELVTEFIDSI 375 L ++D I Sbjct: 363 LRFAENYLDGI 373 >ref|NP_350254.1| XylR transcriptional regulator [Clostridium acetobutylicum] pir||G97350 xylR transcription regulator [imported] - Clostridium acetobutylicum gb|AAK81594.1| XylR transcriptional regulator [Clostridium acetobutylicum] Length = 385 Score = 155 bits (393), Expect = 1e-36, Method: Compositional matrix adjust. Identities = 101/363 (27%), Positives = 184/363 (50%), Gaps = 12/363 (3%) Query: 15 NRNAIYRYLYHREATSIQEIAQALNLSLPTVTQNIKELQERELIVETGLFQSTGGRKAKS 74 N+ I LY + + +I+ + +S+PTV N+ EL + E+G+ STGGRK Sbjct: 9 NKGKILNLLYRKRELTKLDISNEIGVSVPTVISNVNELIREGFVEESGVASSTGGRKPII 68 Query: 75 MACNSVAGYAIGLDVTRNHVGIVIIDLRGTIIKHVRNHFP-FANTEVYFKSVGKLVDDCV 133 ++ + YA G+D+ +V+ +L I V + + K + +V + + Sbjct: 69 VSFIPNSRYAFGVDINPYMARVVLTNLDLEIKYDVEFLIEELKDIKSIMKRISLIVKEAL 128 Query: 134 EESRIDSSKILGVGIALPAILSDDRQTVNYATVIDFKGGSIRRFAEFIRYPCILSNDANA 193 E ++ID K+LG+G +L + ++ + A I K + F ++P + N+ANA Sbjct: 129 EFTKIDEKKVLGIGFSLQGTVDEENLVLKRAINIGVKDWDFKLFENLFQFPLFIENEANA 188 Query: 194 AGFT--ELWGEKDIHNVVYLSLNNSVGGSIIVNNQIYTGQNHRGGEFGHMTIMPEGRTCY 251 A ++ K+ N+VY+S+++ +G I++ Q+Y G+N R GE GHMT++P G+ C Sbjct: 189 AALAELKIGIAKEERNLVYISVSSGLGTGIVIEGQLYKGKNKRAGEMGHMTLVPHGKLCR 248 Query: 252 CGQKGCVDAYCSARI-------LSDSTQGSISEFFRRLREGHEPQKAIWQEYIGYLVITV 304 CG+KGC + Y S + LSD + +FF + ++ + Y+ L + Sbjct: 249 CGRKGCWEMYASQKALLDEFNELSDVKVTKLEQFFNLIMIKNKVAEKCLNNYLNNLASGI 308 Query: 305 NNLRMLYDCD-VILGGYAGAYMEEYIDTLQGLAAQKNTFERDGTY-LRVCKYKLEATAVG 362 N+ +++D ++LGG Y + Y+D+L+ +N F G + L + K ++ +G Sbjct: 309 QNIVLIFDPHYIVLGGEISGYSDVYLDSLKDKIFDENEFYNRGDFKLFPSRLKRNSSILG 368 Query: 363 AAL 365 AAL Sbjct: 369 AAL 371 >sp|P16557|XYLR_BACSU XYLOSE REPRESSOR pir||A32885 xylose operon repressor protein xylR - Bacillus subtilis gb|AAA22896.1| xylose repressor Length = 384 Score = 132 bits (331), Expect = 2e-29, Method: Compositional matrix adjust. Identities = 75/265 (28%), Positives = 136/265 (51%), Gaps = 4/265 (1%) Query: 11 VKKMNRNAIYRYLYHREATSIQEIAQALNLSLPTVTQNIKELQERELIVETGLFQSTGGR 70 VKK+N+ + + + S ++++ L+ TV+ + L + L+ E G QS+GGR Sbjct: 9 VKKVNQKLLLKEILKNSPISRAKLSEMTGLNKSTVSSQVNTLMKENLVFEIGQGQSSGGR 68 Query: 71 KAKSMACNSVAGYAIGLDVTRNHVGIVIIDLRGTIIKHVRNHFPFANTEVYFKSVGKLVD 130 + + N AGY+IG+DV +++ ++ DL GTII +H + E+ + ++ Sbjct: 69 RPVMLVFNKKAGYSIGIDVGVDYISGILTDLEGTIILDQHHHLESNSPEITKDILIDMIH 128 Query: 131 DCVEESRIDSSKILGVGIALPAILSDDRQTVNYATVIDFKGGSIRRF-AEFIRYPCILSN 189 + ++G+GI +P ++ D Q + + +++ ++ F E P + N Sbjct: 129 HFITRMPQSPYGLIGIGICVPGLI-DKNQKIVFTPNSNWRDIDLKSFIQEKFNVPVFIEN 187 Query: 190 DANAAGFTE--LWGEKDIHNVVYLSLNNSVGGSIIVNNQIYTGQNHRGGEFGHMTIMPEG 247 +ANA + E K+ +N++Y S++ +G +I+NN +Y G + GE GHMTI G Sbjct: 188 EANAGAYGEKVFGAAKNHNNIIYASISTGIGIGVIINNHLYRGVSGFSGEMGHMTIDFNG 247 Query: 248 RTCYCGQKGCVDAYCSARILSDSTQ 272 C CG +GC + Y S + L S Q Sbjct: 248 PKCSCGNRGCWELYASEKALLKSLQ 272 >emb|CAB02313.1| Xyl repressor [Bacillus licheniformis] Length = 390 Score = 126 bits (317), Expect = 7e-28, Method: Compositional matrix adjust. Identities = 94/375 (25%), Positives = 183/375 (48%), Gaps = 22/375 (5%) Query: 11 VKKMNRNAIYRYLYHREATSIQEIAQALNLSLPTVTQNIKELQERELIVETGLFQSTGGR 70 VKKMN+ I+ + S ++++ L+ TV+ + L ++++I ETG +S+GGR Sbjct: 12 VKKMNKALIFEQIIENGPVSRAKLSEITGLNKATVSSQVSSLLQKDIIYETGPGESSGGR 71 Query: 71 KAKSMACNSVAGYAIGLDVTRNHVGIVIIDLRGTIIKHVRNHFPFANTEVYFKSVGKLVD 130 + + N AGYA+G+DV N++ + + DL G +I+ + + +++ +L Sbjct: 72 RPVMLKFNRKAGYAVGVDVGTNYIIVALTDLEGHLIEQFERTLDEEDIQATEEALIELTG 131 Query: 131 DCVEESRIDSSKILGVGIALPAILSDDRQTVNYAT----VIDFKGGSIRRFAEFIRYPCI 186 V++ + G+G+ +P ++ ++R V +I K RF P + Sbjct: 132 LPVDKIPPSPFGLTGIGVCVPGLVDNERHVVFTPNKPIHLIPIKEKLEERFG----VPIL 187 Query: 187 LSNDANAAGFTEL-WGE-KDIHNVVYLSLNNSVGGSIIVNNQIYTGQNHRGGEFGHMTIM 244 + N+ANA E +GE + + V++S+N +G I++N +++ G GE GHM+I Sbjct: 188 IENEANAGAVAEKEYGEGGQLEHAVFVSINTGIGLGILMNGKLFRGVQGFSGEAGHMSIH 247 Query: 245 PEGRTCYCGQKGCVDAYCSAR-ILSDSTQGSISEFFRRLRE----GHEPQKAIWQEYIGY 299 +G C CG +GC + Y S + + S S ++ + ++E G ++ + + Sbjct: 248 FDGPLCRCGNRGCWELYASEKAVFSHYAANSGAQLYETVKELADRGDPGMMETFERFGFH 307 Query: 300 LVITVNNLRMLYDCDVILGGYAGAYMEEY---IDTLQGLAAQKNTFERDGTY-LRVCKYK 355 + I + N+ + D I+ +E Y +D ++ A ++ E Y L++ Sbjct: 308 IGIGLLNILKTLNPDTII--LRNTIVESYPSIVDAIKKTIASRSAAEALSNYHLKISTLG 365 Query: 356 LEATAVGAALELVTE 370 A+A+G + LVTE Sbjct: 366 RTASALGMS-SLVTE 379 Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF Posted date: Mar 24, 2004 1:53 AM Number of letters in database: 757,237,578 Number of sequences in database: 2,715,099 Lambda K H 0.321 0.137 0.402 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 2715099 Number of Hits to DB: 541,198,350 Number of extensions: 22336272 Number of successful extensions: 51091 Number of sequences better than 1.0e-05: 490 Number of HSP's gapped: 50684 Number of HSP's successfully gapped: 490 Length of query: 375 Length of database: 757,237,578 Length adjustment: 127 Effective length of query: 248 Effective length of database: 412,420,005 Effective search space: 102280161240 Effective search space used: 102280161240 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: 127 (53.5 bits)