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= 0599.0002.p (289 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KAL3.1 B3KAL3_9BACI Helix-turn-helix-domain containing protein... 473 e-131 A6LYZ8.1 A6LYZ8_CLOB8 Transcription activator, effector binding 90 3e-16 B3CE13.1 B3CE13_9BACE Putative uncharacterized protein 86 5e-15 C1EU44.1 C1EU44_BACC3 Transcriptional regulator, AraC family 86 5e-15 C2YKY8.1 C2YKY8_BACCE Transcriptional regulator, AraC 84 1e-14 >B3KAL3.1 B3KAL3_9BACI Helix-turn-helix-domain containing protein AraC type Length = 289 Score = 473 bits (1216), Expect = e-131, Method: Compositional matrix adjust. Identities = 221/289 (76%), Positives = 258/289 (89%) Query: 1 MDHNEVIERALIHIEGHLQQSLTVESVANTFNMSKYYFHRLFSAMMSCSLNQYILSRRLN 60 M+H+ +IE+ALIHIE +L+Q L+V SVA TFNMSKYYFHRLFSAMM CSLNQYILSRRLN Sbjct: 1 MNHHRIIEQALIHIEENLEQPLSVSSVALTFNMSKYYFHRLFSAMMGCSLNQYILSRRLN 60 Query: 61 ASLTFIQNNNRSLTDIAYQLNFGTQASFTRAFKRQYGVAPSSLKTGLTTLSPVPIPAVVK 120 A+L+ I NNN SLTDIAYQL FGTQASFTRAFK+ YGVAPSSL+ G +SP PIP VVK Sbjct: 61 AALSLIHNNNLSLTDIAYQLAFGTQASFTRAFKQHYGVAPSSLRAGFNKISPTPIPTVVK 120 Query: 121 RPIKNINGDIVTDFTLTEFKETRISGIAFEVNLANDDYKEKIRAHSEMLLSHIDETIHGP 180 RP KN+NGD+VTDFTLTEFKETRISGIAFEV+LA DDYK+KI +HS+MLL+HID+ I+G Sbjct: 121 RPFKNMNGDVVTDFTLTEFKETRISGIAFEVDLATDDYKKKIHSHSKMLLNHIDDNINGS 180 Query: 181 CYVIYSNCQPGSTRFKVLFGIPSSIEIDKPYFFTVDVPQIFCARFNYCGEILDIGDVLKS 240 C+VIYSNCQP STRFKVLFGIPS I+I KP++FTVDVP IFCARFNY G++LDIG+VLK+ Sbjct: 181 CFVIYSNCQPNSTRFKVLFGIPSDIQIHKPFYFTVDVPTIFCARFNYFGDLLDIGEVLKT 240 Query: 241 DYARFLKISRQETAETDIELIQAFDDVHHLDSTYHIYAPIKKLPTDSDL 289 DYARFLKIS+QE+ ++DIELIQ F+DVH+LDSTYHIYAPIKKLP D ++ Sbjct: 241 DYARFLKISKQESDQSDIELIQVFNDVHNLDSTYHIYAPIKKLPDDLEI 289 >A6LYZ8.1 A6LYZ8_CLOB8 Transcription activator, effector binding Length = 290 Score = 89.7 bits (221), Expect = 3e-16, Method: Compositional matrix adjust. Identities = 51/137 (37%), Positives = 80/137 (58%), Gaps = 5/137 (3%) Query: 1 MDHNEVIERALIHIEGHLQQSLTVESVANTFNMSKYYFHRLFSAMMSCSLNQYILSRRLN 60 M ++I RA+I IE +L + LTVESVA+ + S Y+FHR F +M ++ YI SRRL Sbjct: 1 MKDKQIIGRAIIFIETNLYEPLTVESVASAVSYSYYHFHRYFQVVMGETIGSYIRSRRLT 60 Query: 61 ASLTFIQNNNRSLTDIAYQLNFGTQASFTRAFKRQYGVAPSSLK-TGLTTL----SPVPI 115 + + ++ + + DIA L F + SFTRAFK++YG+ P + G+ L +P+ I Sbjct: 61 QAAYNLVHSKKRILDIAILLYFESAESFTRAFKKRYGITPMEYRENGIDVLIGNHNPMQI 120 Query: 116 PAVVKRPIKNINGDIVT 132 + + N+ +IVT Sbjct: 121 DKITESNYANLQPEIVT 137 >B3CE13.1 B3CE13_9BACE Putative uncharacterized protein Length = 283 Score = 85.5 bits (210), Expect = 5e-15, Method: Compositional matrix adjust. Identities = 39/114 (34%), Positives = 72/114 (63%) Query: 3 HNEVIERALIHIEGHLQQSLTVESVANTFNMSKYYFHRLFSAMMSCSLNQYILSRRLNAS 62 H E+I + + +I HL ++LT+E +A +MS Y+FHRLF + + +L+ YI +R+ + Sbjct: 9 HQELINQVIDYIHTHLHKALTLEMLAAEMHMSVYHFHRLFKSHLQETLSAYITRQRMERA 68 Query: 63 LTFIQNNNRSLTDIAYQLNFGTQASFTRAFKRQYGVAPSSLKTGLTTLSPVPIP 116 + ++Q + SL +++ ++ + T SF++AFKR +GV+P + LT +P P Sbjct: 69 VMYLQTRDLSLQELSEKMGYDTAQSFSKAFKRYFGVSPVAFGNTLTFNTPETTP 122 >C1EU44.1 C1EU44_BACC3 Transcriptional regulator, AraC family Length = 299 Score = 85.5 bits (210), Expect = 5e-15, Method: Compositional matrix adjust. Identities = 40/103 (38%), Positives = 64/103 (62%) Query: 2 DHNEVIERALIHIEGHLQQSLTVESVANTFNMSKYYFHRLFSAMMSCSLNQYILSRRLNA 61 ++NE+I++A+ +IE HL + LT E VA+ +S Y+FHR+F + S+ YI RRL Sbjct: 4 EYNEMIKKAIEYIENHLHEELTTERVASHSAVSMYHFHRIFQRYIGMSVTDYIRKRRLTH 63 Query: 62 SLTFIQNNNRSLTDIAYQLNFGTQASFTRAFKRQYGVAPSSLK 104 + + + R++ DIA Q F +Q +FTRAFKR + + P + Sbjct: 64 AAQALVSTERAVIDIAVQYGFSSQEAFTRAFKRMFQLPPKKYR 106 >C2YKY8.1 C2YKY8_BACCE Transcriptional regulator, AraC Length = 299 Score = 84.3 bits (207), Expect = 1e-14, Method: Compositional matrix adjust. Identities = 39/103 (37%), Positives = 64/103 (62%) Query: 2 DHNEVIERALIHIEGHLQQSLTVESVANTFNMSKYYFHRLFSAMMSCSLNQYILSRRLNA 61 ++ E+I++A+ +IEGHL + LT + VA+ +S Y+FHR+F + S+ YI RRL Sbjct: 4 EYKEMIKQAIEYIEGHLHEELTTDRVASHSAVSMYHFHRIFQRYVGMSVTDYIRKRRLTH 63 Query: 62 SLTFIQNNNRSLTDIAYQLNFGTQASFTRAFKRQYGVAPSSLK 104 + + + R++ DIA Q F +Q +FTRAFKR + + P + Sbjct: 64 AAQVLVSTERAVIDIAVQYGFSSQEAFTRAFKRMFQLPPKKYR 106 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 0.322 0.137 0.399 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: 1,610,211,395 Number of extensions: 63044501 Number of successful extensions: 158027 Number of sequences better than 1.0e-05: 2200 Number of HSP's gapped: 159025 Number of HSP's successfully gapped: 2200 Length of query: 289 Length of database: 3,060,696,203 Length adjustment: 134 Effective length of query: 155 Effective length of database: 1,798,280,193 Effective search space: 278733429915 Effective search space used: 278733429915 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: 130 (54.7 bits)