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= 0301.0021.p (316 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3K9R2.1 B3K9R2_9BACI Helix-turn-helix-domain containing protein... 327 1e-87 B1DD66.1 B1DD66_9BACL Transcriptional regulator, AraC family 236 2e-60 Q5WL10.1 Q5WL10_BACSK AraC/XylS family transcriptional regulator 194 7e-48 B0A659.1 B0A659_9CLOT Putative uncharacterized protein 89 4e-16 A4ITD0.1 A4ITD0_GEOTN Sugar ABC transporter (Permease) 88 1e-15 >B3K9R2.1 B3K9R2_9BACI Helix-turn-helix-domain containing protein AraC type Length = 305 Score = 327 bits (837), Expect = 1e-87, Method: Compositional matrix adjust. Identities = 162/313 (51%), Positives = 207/313 (66%), Gaps = 9/313 (2%) Query: 4 LNGSLFQQALLDGEYGPHFFAYYYKQWNPYTMAFHQHNSTEIMYLISGSCVVEVRQEPDE 63 +NGSLFQQ L +G+Y P F+AYYYKQW Y M +HQH+STEIMY+ISG C ++V+ D Sbjct: 1 MNGSLFQQMLEEGDYVPRFYAYYYKQWMNYEMPYHQHDSTEIMYMISGVCRIDVKA-GDT 59 Query: 64 EERFRLKRGELIMLDANVPHRLIVEEGTSCRMLNVEFGFTAASGAVPSIXXXXXXXXXXX 123 E+ LK+GE ++LDA VPHRLIV++ SCRMLNVEFGF + G PS+ Sbjct: 60 EKSVILKKGEFMVLDAGVPHRLIVDQAASCRMLNVEFGFMESEGMAPSLRHIVGEEEEVS 119 Query: 124 XXXXXPFRSLVLPDPEEVFHVLKSLVLELDQHXXXXXXXXXXXXSIMTGXXXXXXXXXXX 183 PFR LVL D EEV+ VLKSLVLELDQ +MT Sbjct: 120 FLLKRPFRYLVLADQEEVYPVLKSLVLELDQR--------GTDGRMMTHALFIQLLVCIA 171 Query: 184 XXXXXXXXXXXXPAQLYVRRAVEFLHQNYDRSIQVKEVAAEVSLHPGYLHRIFRAHTGRT 243 + Y++R+V++LHQNYDR IQVK+VAAEV+LHPGYLHR+FR TGRT Sbjct: 172 RLYEERERSDMQQSDFYIKRSVDYLHQNYDRQIQVKDVAAEVNLHPGYLHRVFRRGTGRT 231 Query: 244 LTGYLNMLRIEKARMLLGQSEIPVAEIADYVGISSRQYFHLLFKKYTRCTPVEYRNSLER 303 +T YL +R+EKA+MLL Q++IP+ EI+DYVG+ SRQYFH+LFKKYT TPVEYR +R Sbjct: 232 ITEYLTTIRMEKAKMLLEQTDIPIHEISDYVGVGSRQYFHMLFKKYTGSTPVEYRLRKDR 291 Query: 304 FSWSDAQPDIQDR 316 +W+ + D+ D+ Sbjct: 292 NAWNYGEDDVDDK 304 >B1DD66.1 B1DD66_9BACL Transcriptional regulator, AraC family Length = 309 Score = 236 bits (603), Expect = 2e-60, Method: Compositional matrix adjust. Identities = 121/301 (40%), Positives = 174/301 (57%), Gaps = 9/301 (2%) Query: 16 GEYGPHFFAYYYKQWNPYTMAFHQHNSTEIMYLISGSCVVEVRQEPDEEERFRLKRGELI 75 G++ P AYYYKQW + M FHQH+ TE MY+ISG+C VE ++ +++G+LI Sbjct: 15 GDFRPKIMAYYYKQWEDFHMGFHQHDWTEFMYVISGNCTVETNKDV-----IAMRKGDLI 69 Query: 76 MLDANVPHRLIVEEGTSCRMLNVEFGFTAASGAVPSIXXXXXXXXXXXXXXXXPFRSLVL 135 MLDA VPHRLIVE G+ CRMLNVEFGF G PS+ ++VL Sbjct: 70 MLDAGVPHRLIVESGSPCRMLNVEFGFQPCDGIYPSMNQLANHNPMFSKLLEQRLDTIVL 129 Query: 136 PDPEEVFHVLKSLVLELDQHXXXXXXXXXXXXSIMTGXXXXXXXXXXXXXXXXXXXXXXX 195 D E++ L++LV ELD +++ Sbjct: 130 RDYEDIQVNLRNLVFELDLGGEGKEQGREMMTNLLMSQLLVRVGRLVAVEAKNSTERQ-- 187 Query: 196 PAQLYVRRAVEFLHQNYDRSIQVKEVAAEVSLHPGYLHRIFRAHTGRTLTGYLNMLRIEK 255 YVR+A E++HQ YD +IQ K++AA V+LHP YL RIF+++ +T+ YL LR++K Sbjct: 188 -IHHYVRQATEYIHQYYDTAIQAKDIAAAVNLHPVYLQRIFKSNMNKTINEYLVDLRMDK 246 Query: 256 ARMLLGQSEIPVAEIADYVGISSRQYFHLLFKKYTRCTPVEYRNSLERF-SWSDAQPDIQ 314 A+MLL ++++P+ E+AD++G++SRQYF +LFKK T +P EYR S SW+D + +I Sbjct: 247 AKMLLARTDVPIIEVADHIGLNSRQYFSMLFKKMTGISPAEYRKSKNTISSWTDYEVEIV 306 Query: 315 D 315 D Sbjct: 307 D 307 >Q5WL10.1 Q5WL10_BACSK AraC/XylS family transcriptional regulator Length = 298 Score = 194 bits (494), Expect = 7e-48, Method: Compositional matrix adjust. Identities = 106/302 (35%), Positives = 155/302 (51%), Gaps = 20/302 (6%) Query: 7 SLFQQALLDGEYGPHFFAYYYKQWNPYTMAFHQHNSTEIMYLISGSCVVEVRQEPDEEER 66 S+F L Y P YYYK+W + M FH H + E M+++SGSC VE +E Sbjct: 2 SVFDPKLQKEPYYPVVKFYYYKEWRQFEMKFHSHEAAECMHVLSGSCKVET-----DEGS 56 Query: 67 FRLKRGELIMLDANVPHRLIVEEGTSCRMLNVEFGFTAASGAVPSIXXXXXXXXXXXXXX 126 ++LK+G++I LDA HRLIV E CRM NVEF F A P Sbjct: 57 YQLKKGQIIFLDAGTRHRLIVSE--RCRMFNVEFSFEQGCTAFPPFFKLCKENRALGNMV 114 Query: 127 XXPFRSLVLPDPEEVFHVLKSLVLELDQHXXXXXXXXXXXXSIMTGXXXXXXXXXXXXXX 186 L+L D ++ + L+ L+LE+D+ S Sbjct: 115 NKQASQLLLHDTDDTYQCLRRLILEVDKKSEQTDFMVQLLLS----------EYLIRIAE 164 Query: 187 XXXXXXXXXPAQLYVRRAVEFLHQNYDRSIQVKEVAAEVSLHPGYLHRIFRAHTGRTLTG 246 Q YV+RA+ ++HQNYDR + V ++A V LHPGYL R+F+A TG+++ Sbjct: 165 LAEAKVAEPDQQAYVKRALAYIHQNYDREVSVADIANSVHLHPGYLQRVFKAFTGKSIHE 224 Query: 247 YLNMLRIEKARMLLGQSEIPVAEIADYVGISSRQYFHLLFKKYTRCTPVEYRNSLERFSW 306 +L RI KA+ +L Q++I + +I Y+G++S+QYF FKK+ +CTP EYR +R + Sbjct: 225 FLISYRINKAKAMLKQTDISITDIPHYIGMNSQQYFSTTFKKHVKCTPSEYR---KRHQY 281 Query: 307 SD 308 +D Sbjct: 282 ND 283 >B0A659.1 B0A659_9CLOT Putative uncharacterized protein Length = 406 Score = 89.4 bits (220), Expect = 4e-16, Method: Compositional matrix adjust. Identities = 39/101 (38%), Positives = 66/101 (65%) Query: 201 VRRAVEFLHQNYDRSIQVKEVAAEVSLHPGYLHRIFRAHTGRTLTGYLNMLRIEKARMLL 260 V+ AV F++ N ++ VK+V++++ L P YL R+F+ G + Y+N RIE + LL Sbjct: 304 VKEAVTFINLNLSSNLTVKKVSSKIGLSPDYLTRLFKKEMGMNIITYINKKRIETSLELL 363 Query: 261 GQSEIPVAEIADYVGISSRQYFHLLFKKYTRCTPVEYRNSL 301 +++ +AEI D +G+++ YF+ LFKK T +P +YRNS+ Sbjct: 364 KVTDLSIAEIGDLIGLNNTSYFYTLFKKETGTSPKQYRNSI 404 >A4ITD0.1 A4ITD0_GEOTN Sugar ABC transporter (Permease) Length = 366 Score = 87.8 bits (216), Expect = 1e-15, Method: Compositional matrix adjust. Identities = 43/103 (41%), Positives = 62/103 (60%) Query: 201 VRRAVEFLHQNYDRSIQVKEVAAEVSLHPGYLHRIFRAHTGRTLTGYLNMLRIEKARMLL 260 + RA+E++ Q Y I+ EVA V++ Y IFR TG+T Y+N+LR+ +AR LL Sbjct: 260 IERALEYIRQFYREPIKASEVANVVNISANYFSTIFRQKTGKTFNEYVNLLRVNEARKLL 319 Query: 261 GQSEIPVAEIADYVGISSRQYFHLLFKKYTRCTPVEYRNSLER 303 ++ + V IA+ VG +YF +FKK+T TP EYRN R Sbjct: 320 SETSLRVGVIANNVGFHEYKYFVEVFKKFTGMTPTEYRNLYNR 362 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 0.323 0.138 0.414 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: 1,546,829,801 Number of extensions: 52987256 Number of successful extensions: 124510 Number of sequences better than 1.0e-05: 2812 Number of HSP's gapped: 125109 Number of HSP's successfully gapped: 2816 Length of query: 316 Length of database: 3,060,696,203 Length adjustment: 135 Effective length of query: 181 Effective length of database: 1,788,859,178 Effective search space: 323783511218 Effective search space used: 323783511218 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 131 (55.1 bits)