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= 0337.0008.p (168 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value Q65IP1.1 Q65IP1_BACLD YvmB 160 3e-38 Q62U48.1 Q62U48_BACLD Possible transcriptional regulator YvmB 159 1e-37 B3KES6.1 B3KES6_9BACI Regulatory protein MarR 156 6e-37 P40762.1 YVMB_BACSU Uncharacterized HTH-type transcriptional reg... 152 8e-36 Q3F0K4.1 Q3F0K4_BACTI Transcriptional regulator, MarR family 133 7e-30 >Q65IP1.1 Q65IP1_BACLD YvmB Length = 163 Score = 160 bits (405), Expect = 3e-38, Method: Compositional matrix adjust. Identities = 73/151 (48%), Positives = 103/151 (68%) Query: 1 MESADAVKQQVYEQFIRFLHVYESFSDTEIDHFLSIAERERIGNFPHNITAVHVIDCIGR 60 M ++ KQ +Y+ +++ LH+ E +DT++ FL A + P N+T +HVI CIG Sbjct: 1 MTMSELTKQLIYDMYVKLLHLNEQKADTDLKAFLKQAAESDVKRLPGNMTTIHVISCIGH 60 Query: 61 HEPINSTAIAGKMELSKASITKIGGKLLADGLVERMQLNDNKKESYFRLTPQGKKIFDLH 120 EPIN+T IA KM LSKA+ITKI KLL +GL++R QL DNKKE YFRLTP GK++F+LH Sbjct: 61 DEPINNTGIAKKMNLSKANITKISSKLLKEGLIKRFQLTDNKKEIYFRLTPSGKQVFELH 120 Query: 121 ERIHANEAERLNRFLSKYSAGELKIIGSFLK 151 E++H +A++ +RFL +S E I FL+ Sbjct: 121 EKLHQQKADQFSRFLDSFSTAEQGAILKFLQ 151 >Q62U48.1 Q62U48_BACLD Possible transcriptional regulator YvmB Length = 161 Score = 159 bits (401), Expect = 1e-37, Method: Compositional matrix adjust. Identities = 72/148 (48%), Positives = 102/148 (68%) Query: 4 ADAVKQQVYEQFIRFLHVYESFSDTEIDHFLSIAERERIGNFPHNITAVHVIDCIGRHEP 63 ++ KQ +Y+ +++ LH+ E +DT++ FL A + P N+T +HVI CIG EP Sbjct: 2 SELTKQLIYDMYVKLLHLNEQKADTDLKAFLKQAAESDVKRLPGNMTTIHVISCIGHDEP 61 Query: 64 INSTAIAGKMELSKASITKIGGKLLADGLVERMQLNDNKKESYFRLTPQGKKIFDLHERI 123 IN+T IA KM LSKA+ITKI KLL +GL++R QL DNKKE YFRLTP GK++F+LHE++ Sbjct: 62 INNTGIAKKMNLSKANITKISSKLLKEGLIKRFQLTDNKKEIYFRLTPSGKQVFELHEKL 121 Query: 124 HANEAERLNRFLSKYSAGELKIIGSFLK 151 H +A++ +RFL +S E I FL+ Sbjct: 122 HQQKADQFSRFLDSFSTAEQGAILKFLQ 149 >B3KES6.1 B3KES6_9BACI Regulatory protein MarR Length = 160 Score = 156 bits (395), Expect = 6e-37, Method: Compositional matrix adjust. Identities = 72/151 (47%), Positives = 102/151 (67%) Query: 1 MESADAVKQQVYEQFIRFLHVYESFSDTEIDHFLSIAERERIGNFPHNITAVHVIDCIGR 60 M+ D +K +YEQ + F H++E + E+ + + ++ P N++ +HV+DCIG+ Sbjct: 1 MDYPDRIKSIIYEQLLHFSHLHEQRMELELKEIQEMVQLHQLKGVPGNLSTIHVLDCIGQ 60 Query: 61 HEPINSTAIAGKMELSKASITKIGGKLLADGLVERMQLNDNKKESYFRLTPQGKKIFDLH 120 HEPIN +AIA K++LSKASITKI KLLA L+ R QLNDN+KE YFRLTPQGK++F+LH Sbjct: 61 HEPINHSAIAEKLKLSKASITKISKKLLALDLIHRTQLNDNRKEVYFRLTPQGKQLFELH 120 Query: 121 ERIHANEAERLNRFLSKYSAGELKIIGSFLK 151 +H E +R RFL YS EL+ + F + Sbjct: 121 RTLHEAEEQRFMRFLDDYSESELQTMLKFFQ 151 >P40762.1 YVMB_BACSU Uncharacterized HTH-type transcriptional regulator yvmB Length = 169 Score = 152 bits (385), Expect = 8e-36, Method: Compositional matrix adjust. Identities = 69/165 (41%), Positives = 106/165 (64%) Query: 4 ADAVKQQVYEQFIRFLHVYESFSDTEIDHFLSIAERERIGNFPHNITAVHVIDCIGRHEP 63 +D KQ +Y+ ++R LH+ E ++T + F A E + P N+T++HVIDCIG+HEP Sbjct: 2 SDLTKQMIYDIYVRLLHLNEQKANTSLQQFFKEAAEEDVAEIPKNMTSIHVIDCIGQHEP 61 Query: 64 INSTAIAGKMELSKASITKIGGKLLADGLVERMQLNDNKKESYFRLTPQGKKIFDLHERI 123 IN+ IA KM LSKA++TKI KL+ + + QL DNKKE YF+LT +G++IFDLHE++ Sbjct: 62 INNAGIARKMNLSKANVTKISTKLIKEEFINSYQLTDNKKEVYFKLTRKGRRIFDLHEKL 121 Query: 124 HANEAERLNRFLSKYSAGELKIIGSFLKDYSAEMEVRISEGTAKR 168 H + +FL +S E K + FL+ ++ +E ++GT + Sbjct: 122 HKKKELAFYQFLDSFSQEEQKAVLKFLEQLTSTLEAEQTDGTPDK 166 >Q3F0K4.1 Q3F0K4_BACTI Transcriptional regulator, MarR family Length = 158 Score = 133 bits (334), Expect = 7e-30, Method: Compositional matrix adjust. Identities = 62/152 (40%), Positives = 99/152 (65%) Query: 6 AVKQQVYEQFIRFLHVYESFSDTEIDHFLSIAERERIGNFPHNITAVHVIDCIGRHEPIN 65 +KQ++Y+ ++ LH+ E +D +I+ F A+ E I + P N+T++HVI CIG ++PIN Sbjct: 4 GIKQKIYDNYLHLLHLNEQKADKDIETFFKQAKMEEIEHVPTNMTSIHVIACIGENQPIN 63 Query: 66 STAIAGKMELSKASITKIGGKLLADGLVERMQLNDNKKESYFRLTPQGKKIFDLHERIHA 125 + IA KM LSKA+ITKI KL+ + L+ R Q DNKKE Y++LTP G+ + +LH++IH Sbjct: 64 NITIARKMNLSKANITKINTKLIKENLITRFQSVDNKKEVYYQLTPAGQSLCELHQKIHD 123 Query: 126 NEAERLNRFLSKYSAGELKIIGSFLKDYSAEM 157 + +F+ +S E I FL++ + +M Sbjct: 124 QKENEFYQFVDSFSEIEQNAILKFLQNINDKM 155 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 0.319 0.135 0.373 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: 892,108,217 Number of extensions: 33307845 Number of successful extensions: 100214 Number of sequences better than 1.0e-05: 243 Number of HSP's gapped: 100224 Number of HSP's successfully gapped: 243 Length of query: 168 Length of database: 3,060,696,203 Length adjustment: 125 Effective length of query: 43 Effective length of database: 1,883,069,328 Effective search space: 80971981104 Effective search space used: 80971981104 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 (21.7 bits) S2: 126 (53.1 bits)