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= 0249.0028.p (272 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value A6TKQ3.1 A6TKQ3_ALKMQ Helix-turn-helix-domain containing protein... 192 4e-47 B1DB31.1 B1DB31_9BACL Transcriptional regulator, AraC family 177 1e-42 B1DBR2.1 B1DBR2_9BACL Transcriptional regulator, AraC family 174 1e-41 B3KIJ0.1 B3KIJ0_9BACI Helix-turn-helix-domain containing protein... 167 1e-39 B3K424.1 B3K424_9BACI Helix-turn-helix-domain containing protein... 161 6e-38 >A6TKQ3.1 A6TKQ3_ALKMQ Helix-turn-helix-domain containing protein, AraC type Length = 282 Score = 192 bits (487), Expect = 4e-47, Method: Compositional matrix adjust. Identities = 97/257 (37%), Positives = 152/257 (59%) Query: 14 GNFNMDTDHFHDSYEIYYLLSGERHYYIHNRIYALQAGDLVFINKNQLHRTTSRNRSRHE 73 G++ M ++HFHD YEIYYLLSGERHY+I +RI+ +++G LV IN+ +HRTT + H Sbjct: 24 GHYTMLSNHFHDQYEIYYLLSGERHYFIKDRIFHVKSGTLVLINRQDVHRTTDADTQDHV 83 Query: 74 RILVNFDDLFLEPAAGLVPDLAEMFQGESFLLRPNAHEQGEIADLFQAMLQEQREEALWS 133 R+L+NF +L + ++ L +F ++++ + EQ + L M+ E ++ Sbjct: 84 RVLLNFSKDYLLSSPYVIALLDGLFMNNNYVIPFLSAEQQYVEVLLDKMIHEIEHQSTGF 143 Query: 134 RPYXXXXXXXXXXXXXXXXKAKPAVVIPEQSEAQRRVYGIIEYLDAHYGDKLTLGGIAEH 193 + ++ V+ S+ ++ I++Y++ +Y LTL +A++ Sbjct: 144 QVALQALLMDLLVYTSRYIESNRHDVLAPPSQVHEKISQIVQYINTNYQTPLTLSSVAQN 203 Query: 194 FFISSTYLCRTFKQTTGFTVIEYLNYVRIRETKTLLRTTDWPMTRIARETGFDSIAHFGR 253 FF+S YL RTFKQ TGFT +EY+N +RIRE + LLR T+ + I+ GF SI+HFGR Sbjct: 204 FFVSQYYLSRTFKQATGFTFVEYINNIRIREAQRLLRETNHKVIDISEAVGFGSISHFGR 263 Query: 254 VFKGLTGRSPLQYRKQN 270 VFK +T SPL YR+ N Sbjct: 264 VFKEVTRFSPLNYRRLN 280 >B1DB31.1 B1DB31_9BACL Transcriptional regulator, AraC family Length = 289 Score = 177 bits (448), Expect = 1e-42, Method: Compositional matrix adjust. Identities = 95/271 (35%), Positives = 159/271 (58%), Gaps = 8/271 (2%) Query: 2 EPFFQVEQLRRSGNFNMDTDHFHDSYEIYYLLSGERHYYIHNRIYALQAGDLVFINKNQL 61 EP + +E RR G +MDT H+H SYE +YL SGER ++I + +Y +Q+GDL+ +N N + Sbjct: 17 EPLW-IEFDRRIGYHSMDTTHYHRSYEFFYLYSGERKFFIRDSVYQIQSGDLILVNTNDV 75 Query: 62 HRTTSRNRSRHERILVNFDDLFLEPAAGLVPDLAEM----FQGESFLLRPNAHEQGEIAD 117 HRT+ ++ HERI++++D F + GL + E+ F +++ N E+ + Sbjct: 76 HRTSELSQPNHERIVLHYDLPFFD---GLSREETELLLSPFASAHPIIKLNLQERMHLEA 132 Query: 118 LFQAMLQEQREEALWSRPYXXXXXXXXXXXXXXXXKAKPAVVIPEQSEAQRRVYGIIEYL 177 LF+++L+E +E + + + ++ E + Q++V II ++ Sbjct: 133 LFESLLRELQECPPGYQLHVRNMATEILLFTARHALKRKSLPSIELTPVQQKVTDIIRHI 192 Query: 178 DAHYGDKLTLGGIAEHFFISSTYLCRTFKQTTGFTVIEYLNYVRIRETKTLLRTTDWPMT 237 + H+ + L L +A+ FFIS +L R FK+ TGF +Y+N RI+E + LL+ TDW +T Sbjct: 193 NQHFREPLPLDELAKQFFISKGHLSRVFKEVTGFGFSQYINVTRIKEAELLLKETDWSIT 252 Query: 238 RIARETGFDSIAHFGRVFKGLTGRSPLQYRK 268 +I+ GF++ +HFG+VFK L+G SP YRK Sbjct: 253 QISERCGFENFSHFGKVFKELSGLSPRDYRK 283 >B1DBR2.1 B1DBR2_9BACL Transcriptional regulator, AraC family Length = 276 Score = 174 bits (440), Expect = 1e-41, Method: Compositional matrix adjust. Identities = 91/258 (35%), Positives = 141/258 (54%), Gaps = 1/258 (0%) Query: 11 RRSGNFNMDTDHFHDSYEIYYLLSGERHYYIHNRIYALQAGDLVFINKNQLHRTTSRNRS 70 R++ + NM HFH +YEI+ L+SG+R ++I +R + GD+V I+ N LHRTT+ Sbjct: 18 RKARSHNMPVSHFHSTYEIFCLMSGKREFFIKDRTLVIHEGDIVIISPNILHRTTNTETP 77 Query: 71 RHERILVNFDDLFLEPAAGLVPDLAEMFQGESFLLRPNAHEQGEIADLFQAMLQEQREEA 130 HER++VN + + A V L + + E +++ ++ I + Q M+ E E+ Sbjct: 78 EHERLIVNIHEKHM-AAGSYVDVLHPLSEREYLIVKCTLQDRLAIETMLQTMIAEMSEKK 136 Query: 131 LWSRPYXXXXXXXXXXXXXXXXKAKPAVVIPEQSEAQRRVYGIIEYLDAHYGDKLTLGGI 190 Y K+ + S R+ ++ Y+++HY ++L+L + Sbjct: 137 PGFELYALTLALQLLLICCRHAKSSSMETLESPSPMHERISEVVRYMNSHYMNELSLHLL 196 Query: 191 AEHFFISSTYLCRTFKQTTGFTVIEYLNYVRIRETKTLLRTTDWPMTRIARETGFDSIAH 250 AE F++S YL R FK+ TGFT +EYLN VRI+E K LL + + IA+ GF S+ H Sbjct: 197 AEKFYVSPYYLSRFFKEATGFTFVEYLNSVRIKEAKKLLEQSSMKVNLIAKRVGFGSVTH 256 Query: 251 FGRVFKGLTGRSPLQYRK 268 FGRVFK +TG PL YRK Sbjct: 257 FGRVFKSVTGYVPLHYRK 274 >B3KIJ0.1 B3KIJ0_9BACI Helix-turn-helix-domain containing protein AraC type Length = 243 Score = 167 bits (422), Expect = 1e-39, Method: Compositional matrix adjust. Identities = 90/243 (37%), Positives = 131/243 (53%), Gaps = 7/243 (2%) Query: 32 LLSGERHYYIHNRIYALQAGDLVFINKNQLHRTTSRNRSRHERILVNFDDLFLEPAAGLV 91 ++SGERHY+I ++Y+++AGDL+ INK +H+T+ HERI++NF D FL L+ Sbjct: 1 MVSGERHYFIKEKLYSIRAGDLILINKFDVHKTSGHGDPEHERIVINFSDSFLGKGHPLL 60 Query: 92 PD-LAEMFQGESFLLRPNAHEQGEIADLFQAMLQEQREEALWSRPYXXXXXXXXXXXXXX 150 L MF + LLR EQ I + M E RE S Y Sbjct: 61 ASGLLGMFNQDRPLLRLTVPEQAIIMQILNKMADEIRER---SASYEHMLQVLLTELLIK 117 Query: 151 XXKAKPAVVIP---EQSEAQRRVYGIIEYLDAHYGDKLTLGGIAEHFFISSTYLCRTFKQ 207 + + +P + +++ +++++ HY DK+TL G++E F+IS YL R FK+ Sbjct: 118 TYRLTHSASLPANVSMNPLHQKITDVVKFIHVHYADKITLQGLSETFYISPFYLSRIFKE 177 Query: 208 TTGFTVIEYLNYVRIRETKTLLRTTDWPMTRIARETGFDSIAHFGRVFKGLTGRSPLQYR 267 TGFT+I YLN RIRE + LL TD + IA GF+S+ HF R FK + + QYR Sbjct: 178 ITGFTIINYLNLTRIREAQRLLTDTDLKIVDIAESIGFESLTHFDRTFKKIMNMTASQYR 237 Query: 268 KQN 270 K N Sbjct: 238 KIN 240 >B3K424.1 B3K424_9BACI Helix-turn-helix-domain containing protein AraC type Length = 288 Score = 161 bits (407), Expect = 6e-38, Method: Compositional matrix adjust. Identities = 105/279 (37%), Positives = 152/279 (54%), Gaps = 19/279 (6%) Query: 4 FFQVEQLRRSGNFNMDTDHFHDSYEIYYLLSGERHYYIHNRIYALQAGDLVFINKNQLHR 63 + +E RR G F+M DH HD YE+YYLLSGER Y+I +R Y ++AGDLVF+++N +H+ Sbjct: 15 YLSMEYDRRIGYFSMSADHLHDHYELYYLLSGERIYFIKDRSYRVRAGDLVFVDRNAVHK 74 Query: 64 TTSRNRSRHERILVN-----FDDLFLEPAAGLVPDLAEMFQGESFLLR-PN-AHEQGE-- 114 T R H+R+++ F DL + P L L E F + +LR P+ A E E Sbjct: 75 TLDSGRPDHDRLVLYINPELFADLAVPPE--LAEGLKEPFGWDVPILRLPSPASEAVERM 132 Query: 115 IADLFQAMLQEQREEA--LWSRPYXXXXXXXXXXXXXXXXKAKPAVVIPEQSEAQRRVYG 172 + D+ M+ Q + L R A V+ +++A Sbjct: 133 VGDMVNEMIHPQAGSSWLLRHRTVELLLFAYRSRHLGMVRSADTEPVLHPKTQA------ 186 Query: 173 IIEYLDAHYGDKLTLGGIAEHFFISSTYLCRTFKQTTGFTVIEYLNYVRIRETKTLLRTT 232 ++ YL+ +Y LTL +AE F IS YL R FKQTTGFT +YLN +R++E + LLR + Sbjct: 187 VVRYLNDNYRQALTLPEVAEAFRISPHYLSRLFKQTTGFTFSDYLNLLRVKEAQRLLRES 246 Query: 233 DWPMTRIARETGFDSIAHFGRVFKGLTGRSPLQYRKQNR 271 D +T IA +GF + +HFG++FK SP YR+Q R Sbjct: 247 DDSITDIAWRSGFSNFSHFGKMFKRTVQLSPRAYRQQYR 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 0.323 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: 1,554,750,098 Number of extensions: 59787204 Number of successful extensions: 137059 Number of sequences better than 1.0e-05: 3890 Number of HSP's gapped: 137385 Number of HSP's successfully gapped: 3909 Length of query: 272 Length of database: 3,060,696,203 Length adjustment: 133 Effective length of query: 139 Effective length of database: 1,807,701,208 Effective search space: 251270467912 Effective search space used: 251270467912 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 (22.0 bits) S2: 130 (54.7 bits)