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= 0389.0008.p (309 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KEG7.1 B3KEG7_9BACI Helix-turn-helix-domain containing protein... 437 e-121 B1D7A3.1 B1D7A3_9BACL Transcriptional regulator, AraC family 426 e-117 C1WEX4.1 C1WEX4_9ACTO DNA-binding domain-containing protein, Ara... 126 3e-27 C4DTW1.1 C4DTW1_9ACTO Transcriptional regulator containing an am... 114 1e-23 B5JG79.1 B5JG79_9BACT Transcriptional regulator, AraC family pro... 96 6e-18 >B3KEG7.1 B3KEG7_9BACI Helix-turn-helix-domain containing protein AraC type Length = 261 Score = 437 bits (1125), Expect = e-121, Method: Compositional matrix adjust. Identities = 205/261 (78%), Positives = 230/261 (88%) Query: 49 MLHASPSSFVILPALAKIVCEPGWKWQKREKPLQNYDLFYVWSGEGTVVRRGVPYQVGQG 108 ML+ASPSSF+I+PALAKIVCEPGWKWQKRE+P+QNYDLFYVWSGEGTV P+ VG+G Sbjct: 1 MLNASPSSFIIMPALAKIVCEPGWKWQKRERPMQNYDLFYVWSGEGTVELNDEPFTVGKG 60 Query: 109 SCFLFRPGDHTSATHNPQKPLVLTYIHFDVAEDVTDIPEPYRVLSETVEFEHLLARYVRL 168 SCFLFRPGDHTSATHNPQKPLVLTYIHFDV + V +IP YR L+ET++FE+LLARYVRL Sbjct: 61 SCFLFRPGDHTSATHNPQKPLVLTYIHFDVTDPVEEIPASYRKLTETMDFEYLLARYVRL 120 Query: 169 FLVKTFAAQEEGQLILKQLMIHLLREDQVMPVERHVSNQLAEVIHEVANYVSQHPGAMHR 228 +L K + + EEGQLILKQLMIHLLR D PV + SNQL+E IHE+ANYV QHPG HR Sbjct: 121 YLDKPYGSLEEGQLILKQLMIHLLRSDLDAPVVKKASNQLSEAIHEIANYVRQHPGVPHR 180 Query: 229 VEDLAARAGLSPRYFSIKFKEITGSSVQSYVIRTRIERAQHLLLYAGMNVTEVADALGYR 288 VEDLAARAGLSPRYFSIKFKE+ G+ VQSY+I+ RIERAQHLLL+ GMNVTEVADALGYR Sbjct: 181 VEDLAARAGLSPRYFSIKFKELIGTPVQSYIIQMRIERAQHLLLHQGMNVTEVADALGYR 240 Query: 289 DIFFFSRQFKQHTGKSPSEIR 309 DIFFFSRQFKQ+TGKSPSEIR Sbjct: 241 DIFFFSRQFKQYTGKSPSEIR 261 >B1D7A3.1 B1D7A3_9BACL Transcriptional regulator, AraC family Length = 261 Score = 426 bits (1096), Expect = e-117, Method: Compositional matrix adjust. Identities = 200/261 (76%), Positives = 224/261 (85%) Query: 49 MLHASPSSFVILPALAKIVCEPGWKWQKREKPLQNYDLFYVWSGEGTVVRRGVPYQVGQG 108 MLH S S++ LP +AKIVCEP W+WQ+REKP+ NYDLFYVWSGEG V G Y VG+G Sbjct: 1 MLHLSTDSYIKLPPIAKIVCEPNWRWQRREKPMANYDLFYVWSGEGEVEVNGTAYPVGKG 60 Query: 109 SCFLFRPGDHTSATHNPQKPLVLTYIHFDVAEDVTDIPEPYRVLSETVEFEHLLARYVRL 168 SCFLFRPGDHTSATHNPQKPLVLTYIHFDV E V +PE YR L++TV+FE+LL+RYVRL Sbjct: 61 SCFLFRPGDHTSATHNPQKPLVLTYIHFDVREPVQFVPERYRKLTDTVDFEYLLSRYVRL 120 Query: 169 FLVKTFAAQEEGQLILKQLMIHLLREDQVMPVERHVSNQLAEVIHEVANYVSQHPGAMHR 228 FLV+T+AA+EE L+LKQLMIHLLRED+ MPVER SNQL E I EVANYV QHP HR Sbjct: 121 FLVETYAAEEEALLVLKQLMIHLLREDREMPVERKGSNQLTEAIQEVANYVKQHPSVAHR 180 Query: 229 VEDLAARAGLSPRYFSIKFKEITGSSVQSYVIRTRIERAQHLLLYAGMNVTEVADALGYR 288 VEDLA RA LSPRYFS+KFKE+ G SVQSY+IRTRIERAQHLL+Y GMNVTEVADALGYR Sbjct: 181 VEDLAMRAQLSPRYFSVKFKEMIGMSVQSYMIRTRIERAQHLLMYEGMNVTEVADALGYR 240 Query: 289 DIFFFSRQFKQHTGKSPSEIR 309 DIFFFSRQFKQ+TG+SPSEIR Sbjct: 241 DIFFFSRQFKQYTGRSPSEIR 261 >C1WEX4.1 C1WEX4_9ACTO DNA-binding domain-containing protein, AraC-type Length = 271 Score = 126 bits (316), Expect = 3e-27, Method: Compositional matrix adjust. Identities = 92/252 (36%), Positives = 129/252 (51%), Gaps = 18/252 (7%) Query: 68 CEPGWKWQKREKPLQNYDLFYVWSGEGTVVRRGVPYQVGQGSCFLFRPGDHTSATHNPQK 127 CEPGW W R PL ++ L+ V G G + G + G+C +F PGD A H+P++ Sbjct: 26 CEPGWSWVSR--PLPDHLLWCVLDGIGRIELDGRTRDLAPGTCAVFAPGDAPRAQHDPRR 83 Query: 128 PLVLTYIHFDVAED--VTDIPE------PYRVLSETVEFEHLLARYVRLFLVKTFAAQEE 179 L++ +HF+ D + +PE P RVL LA+ + AA + Sbjct: 84 RLLVFGMHFEPDGDGPASVVPEVRWGDVPDRVLLGA------LAKACDAAYRRQDAAGGQ 137 Query: 180 GQLILKQLMIHLLREDQVMPVERHVSNQLAE--VIHEVANYVSQHPGAMHRVEDLAARAG 237 +L L+Q + L + + H S Q A I EVA + Q PG V ++AA A Sbjct: 138 DRLGLRQAELCLEQILCSIWEAAHRSGQSASDAAIDEVAQLIRQDPGRDWSVAEMAAAAA 197 Query: 238 LSPRYFSIKFKEITGSSVQSYVIRTRIERAQHLLLYAGMNVTEVADALGYRDIFFFSRQF 297 LS F+ +F G S Y+I+ RI+RA LL +GM VT A ALGY D+ +FSRQ+ Sbjct: 198 LSRAQFTRRFVAQHGRSPAQYLIQARIDRAHQLLTESGMTVTRTAAALGYTDVPYFSRQY 257 Query: 298 KQHTGKSPSEIR 309 KQ TG+ PSE R Sbjct: 258 KQRTGRLPSEDR 269 >C4DTW1.1 C4DTW1_9ACTO Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain Length = 431 Score = 114 bits (284), Expect = 1e-23, Method: Compositional matrix adjust. Identities = 83/238 (34%), Positives = 115/238 (48%), Gaps = 9/238 (3%) Query: 74 WQKREKPLQNYDLFYVWSGEGTVVRRGVPYQVGQGSCFLFRPGDHTSATHNPQKPLVLTY 133 WQ R PL ++ L++V G G + ++ G C +F PGD ATH+P+ PL++ Sbjct: 2 WQAR--PLTDHLLWHVHDGAGELRLDDRHVRLRPGFCAVFAPGDAPVATHDPRHPLLVFG 59 Query: 134 IHFDVAE-DVTDIPEPYRVLSETVEFEHLLARYVRLFLVK-TFAAQEEGQLILKQLMIHL 191 +HF D +PE EF LAR+ + Q + L L+Q + L Sbjct: 60 MHFTATGFDGDLVPEQRWCRLWDQEFAVRLARHCDYAHRRGDDLGQRQAVLGLEQFLCLL 119 Query: 192 LREDQVMPVERHVSNQLAEVIHEVANYVSQHPGAMHRVEDLAARAGLSPRYFSIKFKEIT 251 V R + ++A V Q P V LA RA LS F+ +F T Sbjct: 120 WDN-----VTRPAPGPGDAAVEDIARAVRQEPSRDWTVATLAKRANLSRAQFTRRFTAHT 174 Query: 252 GSSVQSYVIRTRIERAQHLLLYAGMNVTEVADALGYRDIFFFSRQFKQHTGKSPSEIR 309 G S YVIR R++RA+ LL M+V +VA LGY D+ +FSRQ+K HTG SPS R Sbjct: 175 GYSPARYVIRARLDRARQLLTETNMSVGQVAATLGYPDVGYFSRQYKVHTGSSPSRDR 232 >B5JG79.1 B5JG79_9BACT Transcriptional regulator, AraC family protein Length = 271 Score = 95.5 bits (236), Expect = 6e-18, Method: Compositional matrix adjust. Identities = 71/252 (28%), Positives = 111/252 (44%), Gaps = 21/252 (8%) Query: 68 CEPGWKWQKREKPLQNYDLFYVWSGEGTVVRRGVPYQVGQGSCFLFRPGDHTSATHNPQK 127 CEP W W R L +Y L + G G + + + QG CF +PG A NP Sbjct: 26 CEPIWSW--RMDALPDYALILILDGRGHLRINDEDFALRQGLCFFLKPGSRIEAQQNPSY 83 Query: 128 PLVLTYIHFDVAEDVTD--IPE-----PYRVLSETVEFEHLLARYVRLFLVKTFAAQEEG 180 PL L FD+ + D +P+ P RV +V L+ + V + + G Sbjct: 84 PLFLFLARFDILDTDGDTILPDTLSDAPRRVFIRSVRNLEALSELI----VSRSSTLKYG 139 Query: 181 QLILK---QLMIHLLREDQVMPVERHVSNQLAEVIHEVANYVSQHPGAMHRVEDLAARAG 237 +L +++ LL E+ SN E +H + N +++ V+DLA A Sbjct: 140 DPLLTDALNMLVRLLVEEATHHAGDFNSNAY-EALHAIENDLARK----WTVQDLAKEAE 194 Query: 238 LSPRYFSIKFKEITGSSVQSYVIRTRIERAQHLLLYAGMNVTEVADALGYRDIFFFSRQF 297 +S F+ F+ + YVIR R+E A+ + + + + E+A LGY DI FF F Sbjct: 195 MSASSFARAFRRMMNEPPIHYVIRRRMEEAKRQIQQSSLPIEEIAINLGYNDIAFFHELF 254 Query: 298 KQHTGKSPSEIR 309 ++ G P +R Sbjct: 255 QKRIGYLPESLR 266 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 0.321 0.136 0.402 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: 1,803,830,733 Number of extensions: 72483338 Number of successful extensions: 181611 Number of sequences better than 1.0e-05: 2990 Number of HSP's gapped: 182610 Number of HSP's successfully gapped: 2990 Length of query: 309 Length of database: 3,060,696,203 Length adjustment: 135 Effective length of query: 174 Effective length of database: 1,788,859,178 Effective search space: 311261496972 Effective search space used: 311261496972 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: 131 (55.1 bits)