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: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B1D5W3.1 B1D5W3_9BACL Transcriptional regulator, AraC family 421 e-116 Q840D9.1 Q840D9_CLOBU Putative transcriptional regulator 333 2e-89 C4IC74.1 C4IC74_CLOBU Transcriptional regulator, AraC family 332 3e-89 B1QUV2.1 B1QUV2_CLOBU Transcriptional regulator, AraC family 332 3e-89 A7FSM4.1 A7FSM4_CLOB1 Transcriptional regulator, AraC family 330 1e-88 >B1D5W3.1 B1D5W3_9BACL Transcriptional regulator, AraC family Length = 341 Score = 421 bits (1082), Expect = e-116, Method: Compositional matrix adjust. Identities = 211/350 (60%), Positives = 262/350 (74%), Gaps = 12/350 (3%) Query: 2 MLSKYDLKSIIDLEKWQALQDSLSLVTQMAIITVDYKGVPVTRHSRCQAFCQAVRQDAEL 61 M ++YDLK I+D++KW LQDS+SLVT+MAIITVDYKG PV++HS CQAFC+ VR+D+ L Sbjct: 1 MNARYDLKQIMDIDKWHKLQDSMSLVTKMAIITVDYKGNPVSKHSECQAFCREVRKDSTL 60 Query: 62 SSYCQKCDARGGLEAVRLNEPYVYLCHFSILDIAIPITVDNQYVGAVMAGQVRLADNDGS 121 SSYCQKCDARGGLEAVR N+PY+Y CHF ILDIAIPI VDNQY+GAVMAGQV+L+D + Sbjct: 61 SSYCQKCDARGGLEAVRSNKPYIYQCHFQILDIAIPIVVDNQYIGAVMAGQVKLSDPEVP 120 Query: 122 RLEQIVTRPATPESAGTFAALRQEYEQLPVMPYAQVVTIAEMLSHLCNYIVEEASRKNEI 181 +EQIVTRP E+ F AL++ Y LPV+ + +V IA+ML HLCNYIVEEA RK+++ Sbjct: 121 -IEQIVTRPPNVETDKKFNALQEHYRSLPVLSFEEVEKIADMLFHLCNYIVEEAIRKSDM 179 Query: 182 MDLYRQALA-ASPVDILPHKTLADSSCPAPQAVQQELSDSASLIESG-NNAAVIPDLSVV 239 + +YR +L+ +P L H DSS QA+Q ELS+ +LIE N+A SV Sbjct: 180 LQMYRDSLSRENPAAALVHTI--DSSYEHIQALQSELSN--TLIEKKLKNSA-----SVY 230 Query: 240 TCTNPTLQPAFDFIYSNKHENFSLEAMARLCHISPSYFSRLFVRESGENFSAYVSRLKIG 299 N LQPAFD+IY +KH N L+ MA LCH+SPSYFSR+F +E+GENFS +V LKIG Sbjct: 231 QAGNSILQPAFDYIYRHKHVNADLKEMAALCHVSPSYFSRIFTKETGENFSVFVPHLKIG 290 Query: 300 QAKQLLETTGLSVNEISDHLSFCDAGYFIKIFKKYEQRTPAAYRSFIKGE 349 AK+LLETT LSVN+ISD L F DAGYFIK FKK+E TPAAYR + + Sbjct: 291 WAKELLETTDLSVNQISDELGFADAGYFIKTFKKFESLTPAAYRKIYRDK 340 >Q840D9.1 Q840D9_CLOBU Putative transcriptional regulator Length = 344 Score = 333 bits (853), Expect = 2e-89, 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 >C4IC74.1 C4IC74_CLOBU Transcriptional regulator, AraC family Length = 344 Score = 332 bits (852), Expect = 3e-89, Method: Compositional matrix adjust. Identities = 168/347 (48%), Positives = 240/347 (69%), Gaps = 6/347 (1%) Query: 2 MLSKYDLKSIIDLEKWQALQDSLSLVTQMAIITVDYKGVPVTRHSRCQAFCQAVRQDAEL 61 M + ++L +IDLEKW+ LQ++++ VT +AII VDYKG PVT+HS C FC+ +R + EL Sbjct: 1 MNNNFNLDKLIDLEKWEDLQEAIASVTNVAIIIVDYKGNPVTKHSGCHRFCKEIRANPEL 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 ++ IA+ML LCNY++EEA KN Sbjct: 121 SSLEKILVLSKDSSARKALDDFKEYYYELPVLSYEKIKKIADMLFSLCNYLIEEALEKNL 180 Query: 181 IMDLYRQALAASPVDILPHKTLADSSCPAPQAVQQELSDSASLIESGNNAAVIPDLSVVT 240 I D+Y + + + L + + V++E+S++ I + + ++ + + + Sbjct: 181 ISDIYLKIVNDQQE--IDSNILGNYTLKNIDHVKKEMSNAK--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 >B1QUV2.1 B1QUV2_CLOBU Transcriptional regulator, AraC family Length = 344 Score = 332 bits (852), Expect = 3e-89, Method: Compositional matrix adjust. Identities = 168/347 (48%), Positives = 240/347 (69%), Gaps = 6/347 (1%) Query: 2 MLSKYDLKSIIDLEKWQALQDSLSLVTQMAIITVDYKGVPVTRHSRCQAFCQAVRQDAEL 61 M + ++L +IDLEKW+ LQ++++ VT +AII VDYKG PVT+HS C FC+ +R + EL Sbjct: 1 MNNNFNLDKLIDLEKWEDLQEAIASVTNVAIIIVDYKGNPVTKHSGCHRFCKEIRANPEL 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 ++ IA+ML LCNY++EEA KN Sbjct: 121 SSLEKILVLSKDSSARKALDDFKEYYYELPVLSYEKIKKIADMLFSLCNYLIEEALEKNL 180 Query: 181 IMDLYRQALAASPVDILPHKTLADSSCPAPQAVQQELSDSASLIESGNNAAVIPDLSVVT 240 I D+Y + + + L + + V++E+S++ I + + ++ + + + Sbjct: 181 ISDIYLKIVNDQQE--IDSNILGNYTLKNIDHVKKEMSNAK--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 >A7FSM4.1 A7FSM4_CLOB1 Transcriptional regulator, AraC family Length = 345 Score = 330 bits (847), Expect = 1e-88, Method: Compositional matrix adjust. Identities = 168/348 (48%), Positives = 238/348 (68%), Gaps = 6/348 (1%) Query: 1 MMLSKYDLKSIIDLEKWQALQDSLSLVTQMAIITVDYKGVPVTRHSRCQAFCQAVRQDAE 60 M+ +L +ID +KW LQ+SL+LVT+ AII VDYKG PVT HSRC FC+AVR + + Sbjct: 1 MIKENLNLDKVIDFKKWIKLQESLALVTKAAIIVVDYKGNPVTEHSRCNRFCKAVRSNPD 60 Query: 61 LSSYCQKCDARGGLEAVRLNEPYVYLCHFSILDIAIPITVDNQYVGAVMAGQVRLADN-D 119 L YC KCD+RGGLEAVRLN+PY+YLCH++I+DIAIPI +D +Y+GA+MAGQ++L+DN D Sbjct: 61 LVKYCHKCDSRGGLEAVRLNKPYIYLCHYNIVDIAIPIIIDGKYIGAIMAGQIKLSDNKD 120 Query: 120 GSRLEQIVTRPATPESAGTFAALRQEYEQLPVMPYAQVVTIAEMLSHLCNYIVEEASRKN 179 LEQIV P + ++ Y+++PV+ +V IA ML LCNY+VEEA KN Sbjct: 121 SDFLEQIVITPKNSTARHALKEFKEYYDEIPVLSLKEVQEIANMLFSLCNYLVEEALDKN 180 Query: 180 EIMDLYRQALAASPVDILPHKTLADSSCPAPQAVQQELSDSASLIESGNNAAVIPDLSVV 239 I ++Y++ + +P + TL + + ++E+S+ L+ S + D V Sbjct: 181 LISEIYKKTV--TPKSEIDSNTLTGYTMKNIENAKKEMSN--VLLNSYVKENLSSDNLDV 236 Query: 240 TCTNPTLQPAFDFIYSNKHENFSLEAMARLCHISPSYFSRLFVRESGENFSAYVSRLKIG 299 + +N TL+PA ++IY++K EN + + +A +CHISPSYFSRLF +E+G++FS+++S LK+ Sbjct: 237 SVSN-TLKPAIEYIYNHKSENITAKKLAEVCHISPSYFSRLFAKETGKSFSSFISNLKVD 295 Query: 300 QAKQLLETTGLSVNEISDHLSFCDAGYFIKIFKKYEQRTPAAYRSFIK 347 AK LLE T + +NEISD L F + GYFIKIFKKYE TP YR + K Sbjct: 296 WAKSLLEETDMPINEISDELGFNETGYFIKIFKKYESVTPFVYRKYCK 343 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 0.320 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: 9421015 Number of Hits to DB: 1,932,434,987 Number of extensions: 74553436 Number of successful extensions: 200271 Number of sequences better than 1.0e-05: 2073 Number of HSP's gapped: 201054 Number of HSP's successfully gapped: 2137 Length of query: 351 Length of database: 3,060,696,203 Length adjustment: 136 Effective length of query: 215 Effective length of database: 1,779,438,163 Effective search space: 382579205045 Effective search space used: 382579205045 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: 132 (55.5 bits)