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= 0541.0004.p (351 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 gb|AAN17728.1| putative transcriptional regulator [Clostridium b... 333 4e-90 ref|NP_815078.1| transcriptional regulator, AraC family [Enteroc... 266 4e-70 ref|NP_561843.1| two-component sensor histidine kinase [Clostrid... 183 6e-45 gb|AAM54726.1| two-component sensor histidine kinase [Clostridiu... 157 5e-37 ref|NP_464675.1| Regulatory protein similar to Salmonella typhim... 135 2e-30 >gb|AAN17728.1| putative transcriptional regulator [Clostridium butyricum] Length = 344 Score = 333 bits (853), Expect = 4e-90, Method: Compositional matrix adjust. Identities = 167/347 (48%), Positives = 241/347 (69%), Gaps = 6/347 (1%) Query: 2 MLSKYDLKSIIDLEKWQALQDSLSLVTQMAIITVDYKGVPVTRHSRCQAFCQAVRQDAEL 61 M + ++L +IDLEKW+ LQ++++ VT +AII VDYKG PVT+HS C FC+ +R + EL Sbjct: 1 MNNNFNLDKLIDLEKWEDLQETIASVTNVAIIIVDYKGNPVTKHSGCHRFCKEIRANPEL 60 Query: 62 SSYCQKCDARGGLEAVRLNEPYVYLCHFSILDIAIPITVDNQYVGAVMAGQVRLAD-NDG 120 YCQKCD+RGGLEAVRLNEPY+YLCH++I+DIAIPI +D +Y+GA+MAGQV+L D Sbjct: 61 VKYCQKCDSRGGLEAVRLNEPYIYLCHYNIIDIAIPIMIDGKYIGAIMAGQVKLLDVKVE 120 Query: 121 SRLEQIVTRPATPESAGTFAALRQEYEQLPVMPYAQVVTIAEMLSHLCNYIVEEASRKNE 180 S LE+I+ + ++ Y +LPV+ Y ++ I++ML LCNY++EEA KN Sbjct: 121 SSLEKILVLSKDSSARKALDDFKEYYYELPVLSYEKIKKISDMLFSLCNYLIEEALEKNL 180 Query: 181 IMDLYRQALAASPVDILPHKTLADSSCPAPQAVQQELSDSASLIESGNNAAVIPDLSVVT 240 I D+Y + + + L + + + V++E+S++ I + + ++ + + + Sbjct: 181 ISDIYLKIVNDQQE--IDSNVLGNYTLKNIEHVKKEMSNAK--INTYIDEKILNNENHIK 236 Query: 241 CTNPTLQPAFDFIYSNKHENFSLEAMARLCHISPSYFSRLFVRESGENFSAYVSRLKIGQ 300 + TL+PA ++IY +K E F++E MA+LCHISPSYFSRLF +E GENFS+YVS+LKI Sbjct: 237 IID-TLKPAIEYIYKHKSETFNIETMAKLCHISPSYFSRLFTKEMGENFSSYVSKLKIEW 295 Query: 301 AKQLLETTGLSVNEISDHLSFCDAGYFIKIFKKYEQRTPAAYRSFIK 347 +K LLE T +S+NEISD L F + GYFIKIFKKYE+ TP+ YR + K Sbjct: 296 SKNLLEETSMSINEISDELGFSEVGYFIKIFKKYERVTPSLYRKYCK 342 >ref|NP_815078.1| transcriptional regulator, AraC family [Enterococcus faecalis V583] gb|AAO81148.1| transcriptional regulator, AraC family [Enterococcus faecalis V583] Length = 328 Score = 266 bits (681), Expect = 4e-70, Method: Compositional matrix adjust. Identities = 145/339 (42%), Positives = 204/339 (60%), Gaps = 20/339 (5%) Query: 7 DLKSIIDLEKWQALQDSLSLVTQMAIITVDYKGVPVTRHSRCQAFCQAVRQDAELSSYCQ 66 +LK+I+DLEKW+ LQ+SL+L T++AII VDYKG PVT+HS+ Q FCQ VR ELS C+ Sbjct: 4 ELKNILDLEKWEKLQESLALSTRLAIILVDYKGRPVTKHSQVQPFCQLVRHSPELSKLCE 63 Query: 67 KCDARGGLEAVRLNEPYVYLCHFSILDIAIPITVDNQYVGAVMAGQVRLADNDGSRLEQI 126 KCDARGGLEAVR +P++Y CHF+I+D+AIPI VD+QYVGA+MAG+V L D+ LEQ+ Sbjct: 64 KCDARGGLEAVRTGQPFIYRCHFNIVDMAIPIIVDDQYVGAIMAGEVLLEDHQ-EELEQV 122 Query: 127 VTRPATPESAGTFAALRQE-YEQLPVMPYAQVVTIAEMLSHLCNYIVEEASRKNEIMDLY 185 +T F QE Y+Q PV+ A + A +++ L YI+ EA +K+ +++ Y Sbjct: 123 LT--MNDAFIQEFLVTHQELYQQYPVLELADLEKSATLIADLSQYIISEAIKKDYLINTY 180 Query: 186 RQALAASPVDILPHKTLADSSCPAPQAVQQELSDSASLIESGNNAAVIPDLSVVTCTNPT 245 +Q+L S K + + +QQ L A + P S N Sbjct: 181 KQSLQIS-----SRKEELEPLNMIQKDIQQTLL----------TAQLTPS-SAYQTKNKQ 224 Query: 246 LQPAFDFIYSNKHENFSLEAMARLCHISPSYFSRLFVRESGENFSAYVSRLKIGQAKQLL 305 LQP D ++ NK +L+ +A L H++P+Y SRL E G FS + +LKI AKQLL Sbjct: 225 LQPVLDALWENKSLRLNLQELADLVHLTPTYLSRLLKEEFGIPFSQFYRQLKITWAKQLL 284 Query: 306 ETTGLSVNEISDHLSFCDAGYFIKIFKKYEQRTPAAYRS 344 T ++ +IS+ L F + YF++IFK+ TP YR Sbjct: 285 LETDKTIAQISEDLGFVEDSYFVRIFKQETGETPLKYRK 323 >ref|NP_561843.1| two-component sensor histidine kinase [Clostridium perfringens] dbj|BAB80633.1| two-component sensor histidine kinase [Clostridium perfringens str. 13] Length = 410 Score = 183 bits (464), Expect = 6e-45, Method: Compositional matrix adjust. Identities = 81/188 (43%), Positives = 125/188 (66%), Gaps = 1/188 (0%) Query: 2 MLSKYDLKSIIDLEKWQALQDSLSLVTQMAIITVDYKGVPVTRHSRCQAFCQAVRQDAEL 61 M + D++ I+D+ +Q +QD ++ T+ A+ITVDYKG+PVT+HSRC FC+ +R+ E Sbjct: 1 MANLLDIREILDVNSFQKIQDDIAKATEFAMITVDYKGIPVTKHSRCSEFCRLIREQKEF 60 Query: 62 SSYCQKCDARGGLEAVRLNEPYVYLCHFSILDIAIPITVDNQYVGAVMAGQVRLADNDGS 121 S C+KCD+RGGLEA R Y+Y CH ++D+A+PI +D QY+GAVM GQV L D D Sbjct: 61 SKLCEKCDSRGGLEAAREGSFYIYKCHRGLVDVAVPIIIDGQYLGAVMVGQVLLMDADDH 120 Query: 122 RLEQIVTRPATPESAGTFAALRQEYEQLPVMPYAQVVTIAEMLSHLCNYIVEEASRKNEI 181 LE ++T+ +S + YE++PV+ + ++ ++EM+SH+ NYIVEEA K Sbjct: 121 ELEAVLTKELEYDSE-IKDKIIDAYEKIPVLSFDKIKAVSEMMSHVSNYIVEEALLKRTQ 179 Query: 182 MDLYRQAL 189 ++Y + + Sbjct: 180 NEIYTKNI 187 >gb|AAM54726.1| two-component sensor histidine kinase [Clostridium butyricum] Length = 405 Score = 157 bits (396), Expect = 5e-37, Method: Compositional matrix adjust. Identities = 69/172 (40%), Positives = 108/172 (62%), Gaps = 3/172 (1%) Query: 7 DLKSIIDLEKWQALQDSLSLVTQMAIITVDYKGVPVTRHSRCQAFCQAVRQDAELSSYCQ 66 +LK II +E++Q++QD ++ T ++IIT DY G PVT+HS C FC +R+D + S C+ Sbjct: 6 NLKDIISIEEFQSIQDDIAKATGISIITTDYTGKPVTKHSCCTEFCSIIRRDKKQSELCE 65 Query: 67 KCDARGGLEAVRLNEPYVYLCHFSILDIAIPITVDNQYVGAVMAGQVRLADNDGSRLEQI 126 +CD+RGG+E+ R +PY+Y+CH ++D A+PI V QY+G +M GQ+ + D++ LE Sbjct: 66 RCDSRGGIESTRTGKPYIYICHKGLVDFAVPIIVQGQYMGDIMGGQILITDDEQKYLESF 125 Query: 127 VTRPATPESAGTFAALRQEYEQLPVMPYAQVVTIAEMLSHLCNYIVEEASRK 178 T + L Y +LP+M ++ IA+M+ HL Y+VEE K Sbjct: 126 ---KNTNYNLDDNEELICAYNKLPIMSLEKIKNIAQMILHLSKYLVEEGMYK 174 >ref|NP_464675.1| Regulatory protein similar to Salmonella typhimurium PocR protein [Listeria monocytogenes EGD-e] pir||AF1218 Salmonella typhimurium PocR protein homolog lmo1150 [imported] - Listeria monocytogenes (strain EGD-e) emb|CAC99228.1| Regulatory protein similar to Salmonella typhimurium PocR protein [Listeria monocytogenes] Length = 294 Score = 135 bits (339), Expect = 2e-30, Method: Compositional matrix adjust. Identities = 90/333 (27%), Positives = 150/333 (45%), Gaps = 54/333 (16%) Query: 18 QALQDSLSLVTQMAIITVDYKGVPVTRHSRCQAFCQAVRQDAELSSYCQKCDARGGLEAV 77 + + D S T +A + VD G V+R FCQ +R + + S CQKCD GGLEA Sbjct: 13 EKVMDEFSAATSLASVVVDIHGTEVSRLCNFTPFCQLIRSNPKYRSLCQKCDMFGGLEAS 72 Query: 78 RLNEPYVYLCHFSILDIAIPITVDNQYVGAVMAGQVRLADNDGSRLEQIVTRPATPESAG 137 + +P +Y CH + D ++PI V+NQ G +++GQV + S + I T ++ Sbjct: 73 KTGKPLIYRCHAGLTDFSVPIVVENQLSGFLLSGQVICE--ESSEVGNIQTEETDWKND- 129 Query: 138 TFAALRQEYEQLPVMPYAQVVTIAEMLSHLCNYIVE---EASRKNEIMDLYRQALAASPV 194 L + +PV ++ + AEML+ + Y ++ E SR+ + +Q + Sbjct: 130 --KDLISAFRSVPVFSSKKINSSAEMLTIISQYYLKSEMEKSREEQ-----KQKIVFHHT 182 Query: 195 DILPHKTLADSSCPAPQAVQQELSDSASLIESGNNAAVIPDLSVVTCTNPTLQPAFDFIY 254 + H+ N ++ A +I Sbjct: 183 KVAHHE-----------------------------------------ENKEIRKALKYIE 201 Query: 255 SNKHENFSLEAMARLCHISPSYFSRLFVRESGENFSAYVSRLKIGQAKQLLETTGLSVNE 314 N + +L+ +A ++S YFS+LF +E NF YV++ K+ AK++L+ LS++ Sbjct: 202 KNLNRPITLDEVASHVYLSSYYFSKLFKKEMNVNFINYVNQKKMSLAKEMLKNPRLSIDN 261 Query: 315 ISDHLSFCDAGYFIKIFKKYEQRTPAAYRSFIK 347 I+ +L F YF K+F+K TP YR K Sbjct: 262 IARNLGFTQTSYFCKVFRKEFDVTPKGYRETFK 294 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 0.320 0.132 0.382 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: 479,925,326 Number of extensions: 18276778 Number of successful extensions: 44713 Number of sequences better than 1.0e-05: 215 Number of HSP's gapped: 44830 Number of HSP's successfully gapped: 219 Length of query: 351 Length of database: 757,237,578 Length adjustment: 126 Effective length of query: 225 Effective length of database: 415,135,104 Effective search space: 93405398400 Effective search space used: 93405398400 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 (21.8 bits) S2: 126 (53.1 bits)