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= 0040.0008.p (302 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KBZ3.1 B3KBZ3_9BACI Helix-turn-helix-domain containing protein... 417 e-115 B1D8D7.1 B1D8D7_9BACL Transcriptional regulator, AraC family 365 4e-99 B1DLI4.1 B1DLI4_9BACL Transcriptional regulator, AraC family 293 1e-77 B3KBD7.1 B3KBD7_9BACI Helix-turn-helix-domain containing protein... 96 3e-18 B5EUY9.1 B5EUY9_VIBFM Transcriptional regulator, AraC family 87 2e-15 >B3KBZ3.1 B3KBZ3_9BACI Helix-turn-helix-domain containing protein AraC type Length = 294 Score = 417 bits (1073), Expect = e-115, Method: Compositional matrix adjust. Identities = 195/276 (70%), Positives = 233/276 (84%), Gaps = 1/276 (0%) Query: 1 MQNDTKNFVISMERFMPHTFQAEKGEGLFMSHSHEYDELTLILEGEGYYSSAEQNIKVSK 60 M+N K+FVISMERF PHTFQAE+GEGLF SH+HEYDELTL+L+GEGYYSS+EQNIKV+ Sbjct: 18 MENSEKSFVISMERFKPHTFQAEQGEGLFQSHAHEYDELTLVLDGEGYYSSSEQNIKVAA 77 Query: 61 GDLILIPSRLHHGFVCTEPWQGISVHFYHDKLPAYCQYLFHNAEREQDRIRSAYLSEEDM 120 GDLILIP+RLHHGFVCT PWQGISVHF+HD+LP +CQYLFH E + RIRS++L E+DM Sbjct: 78 GDLILIPARLHHGFVCTRPWQGISVHFFHDRLPVHCQYLFHEIESKPHRIRSSHLHEDDM 137 Query: 121 RWAEISLIQLEKEWKLESYNADSYVLMRVALETILLLFQRNRVTMLLPHVLNDQFTIQEV 180 RWAEIS QLEKEW + + D+Y +MR+A ET LL+FQRNR T + D+ ++ + Sbjct: 138 RWAEISFYQLEKEWNSKRQDIDAYNMMRIAFETTLLIFQRNRETSIRA-AGTDEVVLEAI 196 Query: 181 LKEIHAGYHTQITVSELASRYFLSESNLRKKFTELIGVSPKQYIINLRLREAKRLLQQTD 240 LKEIH+ YHTQITV+ELA+R+F+SESNLR+KF+E GVSPKQYIINLRL EAKRLL+QTD Sbjct: 197 LKEIHSSYHTQITVNELAARHFISESNLRRKFSESFGVSPKQYIINLRLMEAKRLLRQTD 256 Query: 241 KAVEIISHEVGFTSSSRFYHFFVKAAGATPLEWRKK 276 KA+E IS EVGFTSSSRFY FF K+ GATPLEWRK+ Sbjct: 257 KAIESISAEVGFTSSSRFYEFFTKSNGATPLEWRKQ 292 >B1D8D7.1 B1D8D7_9BACL Transcriptional regulator, AraC family Length = 279 Score = 365 bits (936), Expect = 4e-99, Method: Compositional matrix adjust. Identities = 176/279 (63%), Positives = 223/279 (79%), Gaps = 6/279 (2%) Query: 1 MQNDTKNFVISMERFMPHTFQAEKGEGLFMSHSHEYDELTLILEGEGYYSSAEQNIKVSK 60 M++ ++F++S++RF PHTF E+G+GLF+SHSH+YDELTL+L+GEGYYSS EQNIKVS Sbjct: 1 MEHCNESFIVSIDRFKPHTFHLEEGDGLFISHSHDYDELTLVLDGEGYYSSPEQNIKVSA 60 Query: 61 GDLILIPSRLHHGFVCTEPWQGISVHFYHDKLPAYCQYLFHNAEREQDRIRSAYLSEEDM 120 G LILIP LHHGFVCT+PW+G+SVHF H+++P +YLFH A E +RI L+EED Sbjct: 61 GSLILIPPGLHHGFVCTKPWRGVSVHFNHERIPLQSRYLFH-AGYECNRIHHIQLAEEDT 119 Query: 121 RWAEISLIQLEKEWKLESYNADSYVLMRVALETILLLFQRNRVTMLLPHVL---NDQFTI 177 WAEIS QLEKEWK + + DS+ +MR+A ET+++LFQR + L NDQ I Sbjct: 120 EWAEISYSQLEKEWKKDRSSMDSFNIMRIAFETVIVLFQRYQA--LFSQTAGGKNDQTVI 177 Query: 178 QEVLKEIHAGYHTQITVSELASRYFLSESNLRKKFTELIGVSPKQYIINLRLREAKRLLQ 237 EVLKEIHA +++Q+TV ELAS++F+SESNLRKKFTE++GVSPKQY+INLR+ EAKRLL+ Sbjct: 178 HEVLKEIHARFYSQLTVHELASKHFVSESNLRKKFTEIVGVSPKQYMINLRMEEAKRLLR 237 Query: 238 QTDKAVEIISHEVGFTSSSRFYHFFVKAAGATPLEWRKK 276 QTDKA+E IS EVGFTSSSRFY FFVK+ G TP EWRK+ Sbjct: 238 QTDKAIESISSEVGFTSSSRFYDFFVKSVGVTPFEWRKQ 276 >B1DLI4.1 B1DLI4_9BACL Transcriptional regulator, AraC family Length = 278 Score = 293 bits (750), Expect = 1e-77, Method: Compositional matrix adjust. Identities = 154/272 (56%), Positives = 190/272 (69%), Gaps = 5/272 (1%) Query: 7 NFVISMERFMPHTFQAEKGEGLFMSHSHEYDELTLILEGEGYYSSAEQNIKVSKGDLILI 66 +F++S+ERF AE + SHSHEY+ELT+I EGEGYYSS ++N KV GDLI I Sbjct: 3 DFIVSLERFAA---SAEMSSYPYKSHSHEYEELTMIDEGEGYYSSPDRNRKVGPGDLIYI 59 Query: 67 PSRLHHGFVCTEPWQGISVHFYHDKLPAYCQYLFHNAEREQDRIRSAYLSEEDMRWAEIS 126 PS L H +VCT+ WQG+SVHF DKLP CQ ER ++ A LS D RWA S Sbjct: 60 PSGLLHSYVCTKRWQGVSVHFRKDKLPVQCQQYLQQ-ERGMAQLEVAALSHIDRRWARAS 118 Query: 127 LIQLEKEWKLESYNADSYVLMRVALETILLLFQRNRVTMLLPHV-LNDQFTIQEVLKEIH 185 L+QLE+ WK D+ VL RVA+ET L LFQ N+ H N Q ++EVL+EIH Sbjct: 119 LVQLERRWKEAEAAVDAEVLQRVAIETALSLFQANKRESSNSHDHTNIQSVMREVLREIH 178 Query: 186 AGYHTQITVSELASRYFLSESNLRKKFTELIGVSPKQYIINLRLREAKRLLQQTDKAVEI 245 A + + ITV ELASR++LSES+LRK+F+ IGVSPKQYII LRL+EA+RLL+QTDKA+E Sbjct: 179 ARFDSPITVHELASRHYLSESHLRKQFSAAIGVSPKQYIIRLRLKEAQRLLKQTDKAIET 238 Query: 246 ISHEVGFTSSSRFYHFFVKAAGATPLEWRKKV 277 IS EVGF SSSRFY FF K+ G TPLEWR++ Sbjct: 239 ISAEVGFHSSSRFYDFFFKSVGMTPLEWRRQC 270 >B3KBD7.1 B3KBD7_9BACI Helix-turn-helix-domain containing protein AraC type Length = 260 Score = 96.3 bits (238), Expect = 3e-18, Method: Compositional matrix adjust. Identities = 75/246 (30%), Positives = 118/246 (47%), Gaps = 15/246 (6%) Query: 33 SHEYDELTLILEGEGYYSSAEQNIKVSKGDLILIPSRLHHGFVCTEPWQ-GISVHFYHDK 91 SH+ E+TLI+EG G + + ++ +V G+++LIPS + H F P + G+ D+ Sbjct: 22 SHQELEITLIMEGSGRFCAHGRDARVESGNVVLIPSEVPHSFHALSPIRFGV---LLADR 78 Query: 92 LPAYCQYLFHNAEREQDRIRSAYLSEEDMRWAEISLIQLEKEW-KLESYNADSYVLMRVA 150 +P+ + LF ++ R R LS D E +L +EW ++ S + Sbjct: 79 IPSEVKELFDRLIQD-GRTRIIALSRLDRDRYE----RLFREWLRIRSAPLKDPIRNYAV 133 Query: 151 LETILLLFQRNRVTMLLPHVLNDQFTIQEVLKEIHAGYHTQITVSELASRYFLSESNLRK 210 +LLLF H + +I + I + VS LA LSE RK Sbjct: 134 WVELLLLFLNEHA-----HSDHQALSISFIGDYIRQYIRDPMHVSTLAEMAGLSEDGFRK 188 Query: 211 KFTELIGVSPKQYIINLRLREAKRLLQQTDKAVEIISHEVGFTSSSRFYHFFVKAAGATP 270 +F ++ G++PKQY RL EAK LL +DK ++ ++ VGF+ F +F K G P Sbjct: 189 QFAKIYGMTPKQYQQQCRLAEAKWLLSSSDKDLQSLAESVGFSQLHSFSLWFKKMEGCPP 248 Query: 271 LEWRKK 276 EWR + Sbjct: 249 SEWRNR 254 >B5EUY9.1 B5EUY9_VIBFM Transcriptional regulator, AraC family Length = 259 Score = 87.0 bits (214), Expect = 2e-15, Method: Compositional matrix adjust. Identities = 68/256 (26%), Positives = 122/256 (47%), Gaps = 35/256 (13%) Query: 32 HSHEYDELTLILEGEGYYSSAEQNIKVSKGDLILIPSRLHHGFVCTEPWQGISVHF---- 87 HSH+Y +L + L+G+ + + + G + +IP+ H F+ + + ++F Sbjct: 21 HSHDYHQLVIGLKGQAEFEINNKINVIYTGKVAIIPAAQEHAFLSLYQSEILVLNFPQVF 80 Query: 88 YHDKLPAYCQYLFHNAEREQDRIRSAYLSEEDMRWAEISLIQLEKEWKLESYNADSYVLM 147 D+L + + LF + Y + I L+ E + N D ++L Sbjct: 81 TDDELASRVKKLF---------CKMGYYQLDSQIQHLIQLLVCEIQS-----NVDDHLLS 126 Query: 148 RVALETILLLFQRN--------RVTMLLPHVLNDQFTIQEVLKEIHAGYHTQITVSELAS 199 R TI+ L +R+ ++ L P V+++ T+ H G T+IT+++LAS Sbjct: 127 RSCSNTIISLLERHLIDENSAKKIKRLNPDVIDNFITL-------HLG--TKITIAQLAS 177 Query: 200 RYFLSESNLRKKFTELIGVSPKQYIINLRLREAKRLLQQTDKAVEIISHEVGFTSSSRFY 259 FL ES F + G++P QYI+ R+ AK+LL++++ V I+ + GF + S F Sbjct: 178 TVFLGESQFYAIFKQEFGLTPHQYIVTKRIDYAKQLLRESNFTVGEIAQQTGFANQSAFS 237 Query: 260 HFFVKAAGATPLEWRK 275 H F+K G +P +R Sbjct: 238 HAFMKKVGHSPSHYRN 253 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 0.399 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: 1,741,290,353 Number of extensions: 67932269 Number of successful extensions: 180611 Number of sequences better than 1.0e-05: 2501 Number of HSP's gapped: 181458 Number of HSP's successfully gapped: 2501 Length of query: 302 Length of database: 3,060,696,203 Length adjustment: 135 Effective length of query: 167 Effective length of database: 1,788,859,178 Effective search space: 298739482726 Effective search space used: 298739482726 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)