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= 0340.0045.p (333 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B1DK34.1 B1DK34_9BACL Transcriptional regulator, AraC family 134 9e-30 B3K6G1.1 B3K6G1_9BACI Helix-turn-helix-domain containing protein... 127 2e-27 B3KHW9.1 B3KHW9_9BACI Helix-turn-helix-domain containing protein... 124 1e-26 B1DGS4.1 B1DGS4_9BACL Transcriptional regulator, AraC family 100 3e-19 Q1VSL0.1 Q1VSL0_9FLAO Putative AraC-family transcriptional regul... 91 2e-16 >B1DK34.1 B1DK34_9BACL Transcriptional regulator, AraC family Length = 291 Score = 134 bits (338), Expect = 9e-30, Method: Compositional matrix adjust. Identities = 90/296 (30%), Positives = 138/296 (46%), Gaps = 34/296 (11%) Query: 33 VFTGEYLFDSCSPVQMLLTHETVTSVRHQHDFLELAYVVQGEGIHLAAEDKMQVVQGDLL 92 V + F+ P+ + +E+ H H+F+E+ YV +G GIH A + + V G L Sbjct: 9 VMSASSFFEPGVPLYVNRAYESFDMGEHSHEFVEITYVSEGAGIHYIAGEAVPVEHGTLF 68 Query: 93 VIPPGVSHVFQPLDLTGSEPLIILNCMLRPELCRIPGELPGQYSEE--DMVPLLKLL--- 147 IP G SHVF+P PLI+ NC+L P Y E D P + Sbjct: 69 FIPVGQSHVFRPKTPKKDRPLIVYNCLL-----------PASYLSELRDGFPYATEILDC 117 Query: 148 ---ELKQWFGYRENNVELSFLLRRMQGIHNNGSAEDQQQLYPLLFELA--------KLIL 196 E WF +++ E + R + L L+ + ++I Sbjct: 118 FADEGLSWFSVKDSTGEYHAMFRELYQEFAAKPPAYMAVLASLVMRILTGLYRHKLQIIA 177 Query: 197 PAASVPFTQQPQINEDPLHDVILYMISNFSEKITLKEISRQIAMSSRQFQRLFKIKTGRS 256 PA P Q ++E I ++ N++ ++ L E++ Q +S RQF RLF+ TG S Sbjct: 178 PAGDRP--QWLSVDE-----AIAFIDRNYASELKLGELAAQAKLSERQFSRLFRRHTGMS 230 Query: 257 YIQMLQEIRMKYSCMLLMFTKLGIQAIALEVGIYDMKYFYRLFREYSGMTPACYRN 312 I+ +Q IRM +C LL ++ IA VG DMK+FYRLF++ +G+TP YR+ Sbjct: 231 LIEYVQSIRMDAACRLLTTRHSSVEDIAGAVGYADMKFFYRLFKKKTGVTPRQYRD 286 >B3K6G1.1 B3K6G1_9BACI Helix-turn-helix-domain containing protein AraC type Length = 290 Score = 127 bits (318), Expect = 2e-27, Method: Compositional matrix adjust. Identities = 94/292 (32%), Positives = 144/292 (49%), Gaps = 16/292 (5%) Query: 33 VFTGEYLFDSCSPVQMLLTHETVTSVRHQHDFLELAYVVQGEGIHLAAEDKMQVVQGDLL 92 + G+Y F + + + E T H HDFLE+AY+ +GEG H +V +G + Sbjct: 7 TYYGDYFFRDDTLMYVNRNAENFTGSYHNHDFLEIAYIAEGEGFHHMENSVQRVRKGHMF 66 Query: 93 VIPPGVSHVFQPLDLTGSEPLIILNCMLRPELCRIPGELPGQYSEEDMVPLLKLLELKQW 152 IP G+ HVF+P G +PLI+ NC+ +L +P +L S+ LLK +E Sbjct: 67 YIPLGMPHVFRPTSSNG-KPLIVNNCIFSVKL--LP-KLIAFASDSRTASLLKQME-DGT 121 Query: 153 FGYR-----ENNVELSFL-LRRMQGIHNNGSAEDQQQLY-PLLFELAKLILPAASVPFTQ 205 GYR + E F+ L + +GSA L L+ E ++ I S P T Sbjct: 122 LGYRAITDRHDRFEKLFVSLYEQYAMQISGSAVYLHTLLLQLIIEFSRAI--EHSQPITS 179 Query: 206 QPQINEDPLHDVILYMISNFSEKITLKEISRQIAMSSRQFQRLFKIKTGRSYIQMLQEIR 265 +P + HDV+ Y+ + ++TL +++ S R QRLF+ TG+S+ LQ +R Sbjct: 180 EP--SHPSFHDVLQYVEGQYMHELTLTRLAQISGFSERHLQRLFRRYTGQSWHHYLQTVR 237 Query: 266 MKYSCMLLMFTKLGIQAIALEVGIYDMKYFYRLFREYSGMTPACYRNRFHSH 317 ++ S LL T I IA +VG DM F +F+ +G+TP YR+ H Sbjct: 238 IRMSRELLRTTTDKISMIAEKVGYKDMHSFNSVFKRSTGLTPGQYRSETQHH 289 >B3KHW9.1 B3KHW9_9BACI Helix-turn-helix-domain containing protein AraC type Length = 293 Score = 124 bits (310), Expect = 1e-26, Method: Compositional matrix adjust. Identities = 87/261 (33%), Positives = 132/261 (50%), Gaps = 21/261 (8%) Query: 59 RHQHDFLELAYVVQGEGIHLAAEDKMQVVQGDLLVIPPGVSHVFQPLDLTGSEPLIILNC 118 +H HDF+E++YV +G G H + + + +GDL VIP G SHVF+P + L+I NC Sbjct: 33 QHTHDFIEISYVEEGSGYHYVEDQLIPIKRGDLFVIPIGTSHVFRPS--SQDNQLVIYNC 90 Query: 119 MLRPELCRIPGELPGQYSEEDMVPLLKLL----ELKQWFGYRENNVELSFLLRRMQGIH- 173 + R L +L E L LL +W Y++ + L M G+ Sbjct: 91 IFRTCLLE---QLKSVICES--TKLHSLLYGSSPSAKWLQYQD---KFDKFLSIMHGMFR 142 Query: 174 ---NNGSAEDQQQLYPLLFELAKLILPAASVPFTQQPQINEDPLHDVILYMISNFSEKIT 230 G + + L+ LA L P N D D I Y+ +F+ +T Sbjct: 143 EYLKKGPRYEFLMMGQLIQVLAMLQRYECDGSMVSTPTNNMD---DAIQYINDHFATNLT 199 Query: 231 LKEISRQIAMSSRQFQRLFKIKTGRSYIQMLQEIRMKYSCMLLMFTKLGIQAIALEVGIY 290 +++++ + MS FQRLFK TG +++Q LQ IR++ C LL T++ IQ A +VG Sbjct: 200 VQQVAERSFMSPSHFQRLFKKTTGVTFMQFLQNIRVQRCCELLKSTEISIQEAANQVGYQ 259 Query: 291 DMKYFYRLFREYSGMTPACYR 311 DMK+F+ LFR+ +G+TP YR Sbjct: 260 DMKFFHSLFRKKTGVTPREYR 280 >B1DGS4.1 B1DGS4_9BACL Transcriptional regulator, AraC family Length = 305 Score = 99.8 bits (247), Expect = 3e-19, Method: Compositional matrix adjust. Identities = 66/256 (25%), Positives = 121/256 (47%), Gaps = 6/256 (2%) Query: 60 HQHDFLELAYVVQGEGIHLAAEDKMQVVQGDLLVIPPGVSHVFQPLDLTGSEPLIILNCM 119 H H +LE+ YV+ GEG H A++ + +G L +IP G SH+F+P + L++ N Sbjct: 43 HDHAYLEIVYVMSGEGYHYVADEVNKTSKGSLYIIPIGTSHIFRPNGT--ANRLLVYNLC 100 Query: 120 LRPELCRIPGELPGQYSEEDMVPLLKLLELKQWFGYRENNVELSFLLRRMQGIHNNGSAE 179 +RP+ G QY + V + + R+ +EL+ ++ S Sbjct: 101 IRPDWIGELGVWLSQYCRDTDVLHVLDGNPGTYLFLRDTPLELAPSFEQLHREFTEESWG 160 Query: 180 DQQQLYPLLFELAKLILPAASVPFTQQPQINEDPLHD----VILYMISNFSEKITLKEIS 235 + + L +L I + Q H ++ ++ + +E + +++++ Sbjct: 161 FETTVLAGLLQLLTRISRKLKTQDSTGDQTTGSTRHSEFVSIVEHINRHIAEPLKMEQLA 220 Query: 236 RQIAMSSRQFQRLFKIKTGRSYIQMLQEIRMKYSCMLLMFTKLGIQAIALEVGIYDMKYF 295 Q +S R F RLF+ +TG + + +Q R++ +C LL T + IA +VG D +F Sbjct: 221 DQAGISQRHFIRLFRQQTGMGFSEYVQNKRVELACQLLTGTSQSVADIAKKVGYQDPAHF 280 Query: 296 YRLFREYSGMTPACYR 311 +FR+ G+TP+ YR Sbjct: 281 REVFRKVMGITPSQYR 296 >Q1VSL0.1 Q1VSL0_9FLAO Putative AraC-family transcriptional regulator Length = 287 Score = 90.5 bits (223), Expect = 2e-16, Method: Compositional matrix adjust. Identities = 72/272 (26%), Positives = 132/272 (48%), Gaps = 33/272 (12%) Query: 60 HQHDFLELAYVVQGEGIHLAAEDKMQVVQGDLLVIPPGVSHVFQP-LDLTGSEPLIILNC 118 HQH+ ++++ +++GEG + + +GD+ VI + HVF+ L +T + + L Sbjct: 33 HQHEEIQISLIIKGEGTLIVGDTVNSYKKGDIFVIGSNIPHVFKSDLKVTKTSHMFTLFF 92 Query: 119 MLRPELCRIPGELPGQYSEEDMVPLLKLLELKQWF-----GYR---ENNV--ELSFLLRR 168 R D L +L E+K +F G+R E N+ EL F L Sbjct: 93 TDRSFGV-------------DFFNLEELNEIKPFFKRSKHGFRITSEKNILTELFFKLET 139 Query: 169 MQGIHNNGSAEDQQQLYPLLFELAKLILPA-ASVPFTQQPQINE-DPLHDVILYMISNFS 226 + +++ AK + +S + ++ NE + + +V Y ++NF+ Sbjct: 140 ASKLSQLIILLQLLKIF------AKTNYKSLSSFVYNKKYSDNEGNRMRNVFEYTMNNFT 193 Query: 227 EKITLKEISRQIAMSSRQFQRLFKIKTGRSYIQMLQEIRMKYSCMLLMFTK-LGIQAIAL 285 ++ITL IS+ M+ F + FK +T ++Y Q L E+R++++C LL+ K I +IA Sbjct: 194 QEITLDAISKVANMTKNAFCKYFKKRTNKTYFQFLTELRIEHACKLLIKQKETPIVSIAE 253 Query: 286 EVGIYDMKYFYRLFREYSGMTPACYRNRFHSH 317 + G ++ F R F+ Y +P ++N FHS+ Sbjct: 254 QCGYNNISNFNRQFQIYKQQSPTAFKNSFHSN 285 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 0.324 0.139 0.416 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: 1,921,164,201 Number of extensions: 77438602 Number of successful extensions: 184067 Number of sequences better than 1.0e-05: 1831 Number of HSP's gapped: 185150 Number of HSP's successfully gapped: 1832 Length of query: 333 Length of database: 3,060,696,203 Length adjustment: 136 Effective length of query: 197 Effective length of database: 1,779,438,163 Effective search space: 350549318111 Effective search space used: 350549318111 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 131 (55.1 bits)