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= 0352.0001.p (604 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|NP_241349.1| transcriptional regulator (AraC/XylS family) [B... 94 1e-17 ref|NP_244310.1| transcriptional regulator (AraC/XylS family) [B... 86 2e-15 ref|NP_390893.1| similar to transcriptional regulator (AraC/XylS... 81 8e-14 ref|NP_241659.1| two-component sensor response regulator [Bacill... 79 4e-13 ref|NP_782430.1| transcriptional regulatory protein [Clostridium... 75 6e-12 >ref|NP_241349.1| transcriptional regulator (AraC/XylS family) [Bacillus halodurans] pir||C83710 transcription regulator (AraC/XylS family) BH0483 [imported] - Bacillus halodurans (strain C-125) dbj|BAB04202.1| transcriptional regulator (AraC/XylS family) [Bacillus halodurans] Length = 769 Score = 93.6 bits (231), Expect = 1e-17, Method: Compositional matrix adjust. Identities = 81/295 (27%), Positives = 150/295 (50%), Gaps = 25/295 (8%) Query: 318 RGKWEDIAARL-QHSDVSCALGISGLTDDLHLLRAKYNEAADSLQY-IKFHVQQNIIFAD 375 R K E I + Q D+S ++G+S DD+ + Y+E ++L+Y IK Q I F++ Sbjct: 484 REKAEAIMNEVRQQLDISVSIGVSLPYDDITKTQEAYDEGIEALKYRIKLGCQSVIFFSN 543 Query: 376 ----DTIHLNSSPMPDSALEPVLQAVRQTELSGHIPQAVERLLAVACSYRAESATIALAR 431 + H ++ L L+ ++ + H+ ++ + I+L R Sbjct: 544 LAHTHSFHTYYPKQQENELFDALKLGDKSNVKDHLDALIDGIFQKDL--HPSQYQISLLR 601 Query: 432 L---AFELSRTAELNA-DVQQSGFLDNYQRIWQLQSYDKLLHW-----IVDSCYTALKRI 482 L +L +T +++ DV L + +++ LQ+ D++ W I S +T +R+ Sbjct: 602 LLNNTIQLLQTLGIDSVDVYDKKTL--FDQLFSLQTIDEVKQWFFTKLIAPSVHTVAERM 659 Query: 483 ASMSAVQTKSIAVEAICYIRDHYDDSRLSLNALADKLSLSPAYLSRLIADEVNCSFPDFV 542 S Q ++I+ + I I++ +D L+L ++A++L +P YLS + E N SF +++ Sbjct: 660 DS----QYRTISDQIIHIIQNEFD-MELTLESIAERLHYNPNYLSSIFRKETNISFSEYL 714 Query: 543 NLLRLEQAQMLLVTELDLDIREIAEKVGYNSSTYFTTQFKKRFGITPSKWRMNHI 597 + RL A+ L+ E + IREIAE++ Y +S F FKK+ G+TP K+R + + Sbjct: 715 SSYRLAMAKKWLL-ETSMPIREIAERLCYGNSQNFIRSFKKKEGMTPGKYRQSKV 768 >ref|NP_244310.1| transcriptional regulator (AraC/XylS family) [Bacillus halodurans] pir||C84080 transcription regulator (AraC/XylS family) BH3443 [imported] - Bacillus halodurans (strain C-125) dbj|BAB07162.1| transcriptional regulator (AraC/XylS family) [Bacillus halodurans] Length = 207 Score = 85.9 bits (211), Expect = 2e-15, Method: Compositional matrix adjust. Identities = 50/145 (34%), Positives = 86/145 (59%), Gaps = 6/145 (4%) Query: 461 LQSYDKLLHWIVD---SCYTALKRIASMSAVQTKSIAVEAICYIRDHYDDSRLSLNALAD 517 +QSY++L + D S +++ ++ V+ I A Y+ H+ S LSL +AD Sbjct: 66 VQSYERLTGELCDLPQSFQRCKEKVYNL--VEVSQIVKRAEQYMNAHFYQSSLSLETVAD 123 Query: 518 KLSLSPAYLSRLIADEVNCSFPDFVNLLRLEQAQMLLVTELDLDIREIAEKVGYNSSTYF 577 L +S AYLSRL +++ +F + LR+++A LL + +L I EI+EKVGY + YF Sbjct: 124 SLQVSSAYLSRLFKEQLGITFTHALTKLRIKRAIQLLHS-TNLTINEISEKVGYETQHYF 182 Query: 578 TTQFKKRFGITPSKWRMNHILQKQE 602 +T FKK G++P+++R ++ +Q+ Sbjct: 183 STAFKKVMGVSPNRYRKGKVVSQQK 207 >ref|NP_390893.1| similar to transcriptional regulator (AraC/XylS family) [Bacillus subtilis] pir||C69990 transcription regulator AraC/XylS family homolog ytdP - Bacillus subtilis emb|CAB14993.1| ytdP [Bacillus subtilis subsp. subtilis str. 168] Length = 772 Score = 80.9 bits (198), Expect = 8e-14, Method: Compositional matrix adjust. Identities = 128/577 (22%), Positives = 246/577 (42%), Gaps = 67/577 (11%) Query: 55 NNLFTQKEGEITRYAVLDGNASVLMHSALS--GTPLEED-MLKQVVASSPERGSFVYRGS 111 NNLF ++D +++H+ +S G L D +++V+A + G F Sbjct: 219 NNLF-----------IIDEKGLIILHNNMSDVGESLHNDGFVQKVLAQTANSGQFETVID 267 Query: 112 GEPQLITYVYSAADKLWFVSETSYKDSIRDISNARTLMTGXXXXXXXXXXXXXXXXSRRM 171 +TY S + + S S + ++ + + SR Sbjct: 268 RIHYKVTYQKSDYNAWTYFSLVSLPELKKEAKSIGWITFAVCLILLTLSLLFSWLGSRHF 327 Query: 172 YKPIGRLFGNIV-HLSGNEEALKTGGDFDTVSQELEQIGVKLEQLKKESDDSA------L 224 YKPI L+ + H + E+ +F+ + Q +Q+ + + L++ A Sbjct: 328 YKPIRVLYESFARHGAIQEKQQPPQNEFELIEQSFKQLKDRNDDLEETMKQQATHLQQYF 387 Query: 225 MRWLLSPRGTPENSSTPMMSIAASGGAYCVCVLTLLESGQSEGSGQTFGEGIEQIELAFS 284 M L+ + T E S+ + +L L Q + T E + L F+ Sbjct: 388 MVRLMLGKLTDEEVDNRFESLGLKQNWRHLALLVL----QIDTLNHTPYEKKDMDLLLFA 443 Query: 285 ELAAVQSFRP---HQGTAVLILSEL-----RSGSFDDYA-----LFRGKWEDIAARLQHS 331 + ++ P H AV+ + +SG+ +++ R E A LQ Sbjct: 444 VNSLIERNIPTDKHLAPAVVDKQQATILINQSGTKEEFMAELNETARMIQEKAEAELQ-- 501 Query: 332 DVSCALGISGLTDDLHLLRAKYNEAADSLQYIKFHVQQNIIFADDTIHLNS--SPMPDSA 389 +S ++GIS D L + Y E +++L+Y ++IIF +D + + P Sbjct: 502 -LSVSIGISQPFDVLTKAKTAYAEGSEALKYRLKAENKSIIFYEDLDQKKTFKTHFPKQL 560 Query: 390 LEPVLQAVRQTELSGHIPQAVERLLAVACSYRAESAT-----IALARLAFELSRTAELNA 444 + AV+ +G +A + L A+ + ++ IA+AR L+ EL Sbjct: 561 QHELFDAVK----AGDKEKADKCLHAILQAIFTQNTNPYQFQIAIARF---LNHVIELMH 613 Query: 445 -------DVQQSGFLDNYQRIWQLQSYDKLLHWIVDSCYTAL-KRIASMSAVQTKSIAVE 496 +++++ L Y +I++L++++ +W+ + + ++ + + Q K+I+ + Sbjct: 614 VLGIELFELEENKML--YDQIFELKTFEDTENWLKNEFIDPMTDKVNARADAQYKNIS-D 670 Query: 497 AICYIRDHYDDSRLSLNALADKLSLSPAYLSRLIADEVNCSFPDFVNLLRLEQAQMLLVT 556 I +I H +S L+L+ +A +L +P YLS + E+ SF ++V+ R A+ L Sbjct: 671 NIIHIIHHEFESELTLDEIARRLHYNPNYLSSIFKKEMGISFSEYVSSYRHHMAKSWLA- 729 Query: 557 ELDLDIREIAEKVGYNSSTYFTTQFKKRFGITPSKWR 593 E D+ +++IAEK+ Y +S F FKK GITP +R Sbjct: 730 ETDMAVKDIAEKLKYKNSQNFIRSFKKLEGITPGNYR 766 >ref|NP_241659.1| two-component sensor response regulator [Bacillus halodurans] pir||A83749 two-component sensor response regulator BH0793 [imported] - Bacillus halodurans (strain C-125) dbj|BAB04512.1| two-component sensor response regulator [Bacillus halodurans] Length = 508 Score = 78.6 bits (192), Expect = 4e-13, Method: Compositional matrix adjust. Identities = 43/127 (33%), Positives = 68/127 (53%), Gaps = 3/127 (2%) Query: 471 IVDSCYTALKRIASMSAVQTKSIAVEAIC-YIRDHYDDSRLSLNALADKLSLSPAYLSRL 529 ++D C L+ + S ++ + +I H+ LSL L ++P YL +L Sbjct: 381 MIDRCIDLLEDDHLQENEKNYSPIIQTVLQHIHQHFSQD-LSLKTLGHSFHINPIYLGQL 439 Query: 530 IADEVNCSFPDFVNLLRLEQAQMLLVTELDLDIREIAEKVGYNSSTYFTTQFKKRFGITP 589 EV CSF ++N LR+++A+ LL+ D +I +KVGY +TYF QFKK +TP Sbjct: 440 FQREVGCSFTKYLNQLRIDRAKKLLLNSYD-RAGQIGKKVGYGDATYFYKQFKKYEAMTP 498 Query: 590 SKWRMNH 596 ++WR H Sbjct: 499 TEWRKVH 505 >ref|NP_782430.1| transcriptional regulatory protein [Clostridium tetani E88] gb|AAO36367.1| transcriptional regulatory protein [Clostridium tetani E88] Length = 259 Score = 74.7 bits (182), Expect = 6e-12, Method: Compositional matrix adjust. Identities = 44/137 (32%), Positives = 73/137 (53%), Gaps = 7/137 (5%) Query: 458 IWQLQSYDKLLHWIVDSCYTALKRIASMSAVQTKSIAVEAICYIRDHYDDSRLSLNALAD 517 I + SY K + W + ++I S K + AI YI+ ++ ++ +SLN +A Sbjct: 117 IKAMDSYSKRM-WEISKIKEGKEKIES-----CKDVGNLAISYIKKNFSNNEISLNLVAQ 170 Query: 518 KLSLSPAYLSRLIADEVNCSFPDFVNLLRLEQAQMLLV-TELDLDIREIAEKVGYNSSTY 576 + +S +YL+R+I + SF D++N LR+ A+ LL D I +I+ VGY+S Y Sbjct: 171 QFYISQSYLTRVIKQKTGVSFTDYLNKLRINMAKKLLTDNNNDYTINDISNMVGYSSQHY 230 Query: 577 FTTQFKKRFGITPSKWR 593 F+ FK I+P +R Sbjct: 231 FSRAFKNYMEISPKNYR 247 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 0.318 0.132 0.376 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: 817,684,275 Number of extensions: 32031170 Number of successful extensions: 83884 Number of sequences better than 1.0e-05: 187 Number of HSP's gapped: 84449 Number of HSP's successfully gapped: 187 Length of query: 604 Length of database: 757,237,578 Length adjustment: 132 Effective length of query: 472 Effective length of database: 398,844,510 Effective search space: 188254608720 Effective search space used: 188254608720 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 129 (54.3 bits)