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= 0542.0005.p (304 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value Q5WKX6.1 Q5WKX6_BACSK Putative uncharacterized protein 264 7e-69 B1DGG5.1 B1DGG5_9BACL Transcriptional regulator, AraC family 257 1e-66 B3KC02.1 B3KC02_9BACI Helix-turn-helix-domain containing protein... 228 5e-58 Q5WIZ4.1 Q5WIZ4_BACSK Putative uncharacterized protein 227 1e-57 B1DB31.1 B1DB31_9BACL Transcriptional regulator, AraC family 111 8e-23 >Q5WKX6.1 Q5WKX6_BACSK Putative uncharacterized protein Length = 289 Score = 264 bits (675), Expect = 7e-69, Method: Compositional matrix adjust. Identities = 136/285 (47%), Positives = 182/285 (63%), Gaps = 2/285 (0%) Query: 16 MEPIRRHFDHQLPFTLLLDYKETKSPQRELPDHQHDWYEFIYVYGGKGSFFIDQTFYEMH 75 +EP+R+ FD + F + YK+TK+P RELPDH HDWYE +YVY GKG+FFIDQ ++ Sbjct: 4 LEPVRKTFDSENDFPFFIAYKDTKTPNRELPDHLHDWYEIVYVYQGKGTFFIDQNLFQAE 63 Query: 76 PGDIIVVPGNTVHRGFPDNEEPVTSSALFFSPALIHNHTYSESYPYLKLFDAAKTNKQYK 135 GDII +PGNT+HR P E +TS+A+FFSP L+ + +S+ YL+LF+ K K Y+ Sbjct: 64 QGDIITIPGNTIHRVIPTAENLITSTAIFFSPVLLQRSVFWDSHSYLRLFEEGKGRKNYR 123 Query: 136 YTLSPEHAEILQNDIEEIHREREQNQQDGGQAXXXXXXXXXXXXNRYCLPQTAEPVASSP 195 + L P++ L+ I+++ E ++ + D Q NR CL +E V Sbjct: 124 HRLEPKNRAQLELYIDQLWEEEKEKRIDQRQMLALLLQQILLFLNRNCL--KSEHVGHHN 181 Query: 196 LLPEWFREALSYINDHLDQPLELGTLAGRAAISPAHFSRVFKQRLGMNVTDYIATKRIFA 255 P W + L YI +L+ LEL LA AA+SPAHFSRVFK+ +GMNVT+YI TKRI Sbjct: 182 AGPVWINQVLDYIELNLENELELNNLAKIAAVSPAHFSRVFKKLIGMNVTEYITTKRIIM 241 Query: 256 AKDSLLQSSYTIEQIAMACGFESLPHFYRTFKRITSMTPAAYRKS 300 AK+ L + I IA CGF S+PHFYRTFKR+TS+TPAAYR S Sbjct: 242 AKNLLQKQKENIALIAEQCGFNSMPHFYRTFKRLTSVTPAAYRSS 286 >B1DGG5.1 B1DGG5_9BACL Transcriptional regulator, AraC family Length = 287 Score = 257 bits (656), Expect = 1e-66, Method: Compositional matrix adjust. Identities = 129/288 (44%), Positives = 174/288 (60%), Gaps = 2/288 (0%) Query: 16 MEPIRRHFDHQLPFTLLLDYKETKSPQRELPDHQHDWYEFIYVYGGKGSFFIDQTFYEMH 75 M+ I + F+ F L Y++TKSPQRELPDH HDWYE ++VY G G+FFI+ +FYEM+ Sbjct: 1 MQTIHKRFEETDKFPFSLVYRDTKSPQRELPDHLHDWYEIVFVYSGTGTFFINHSFYEMN 60 Query: 76 PGDIIVVPGNTVHRGFPDNEEPVTSSALFFSPALIHNHTYSESYPYLKLFDAAKTNKQYK 135 PGD ++PGNTVHR FPD PVTSSA+FF+P I + ES+ L+ F+ A+ +K YK Sbjct: 61 PGDAFLIPGNTVHRAFPDEFSPVTSSAIFFAPRFIQPMEFGESHSLLRCFEQARKSKSYK 120 Query: 136 YTLSPEHAEILQNDIEEIHREREQNQQDGGQAXXXXXXXXXXXXNRYCLPQTAEPVASSP 195 SP+ E I+ ++ E A NR L +T E SS Sbjct: 121 LETSPDKREAFSGLIDVMNEEWLNRLPSYRAAIAVRLYDFLIALNRMALTET-EHTRSSS 179 Query: 196 LLPEWFREALSYINDHL-DQPLELGTLAGRAAISPAHFSRVFKQRLGMNVTDYIATKRIF 254 P W R L YI+ H+ Q + L L+ +A+++ AHFSRVFKQ GMNV++YI K+I Sbjct: 180 AEPSWIRTILDYIDAHIGSQEMSLADLSSKASVTYAHFSRVFKQHTGMNVSEYILIKKIM 239 Query: 255 AAKDSLLQSSYTIEQIAMACGFESLPHFYRTFKRITSMTPAAYRKSNR 302 AK+ L+ + TI + +ACGFES +FY+ FK IT MTP YR+S R Sbjct: 240 LAKEKLMLTGDTIASVCLACGFESESYFYKKFKLITGMTPVEYRRSCR 287 >B3KC02.1 B3KC02_9BACI Helix-turn-helix-domain containing protein AraC type Length = 291 Score = 228 bits (581), Expect = 5e-58, Method: Compositional matrix adjust. Identities = 113/285 (39%), Positives = 169/285 (59%), Gaps = 1/285 (0%) Query: 16 MEPIRRHFDHQLPFTLLLDYKETKSPQRELPDHQHDWYEFIYVYGGKGSFFIDQTFYEMH 75 M P+R+ F F + + Y+ KSPQ ELP H HD YE +YVY GKG+FFI+ E Sbjct: 1 MTPLRKPFQGDPLFPMEMVYRTKKSPQLELPHHLHDLYELVYVYQGKGTFFIENKLMEKK 60 Query: 76 PGDIIVVPGNTVHRGFPDNEEPVTSSALFFSPALIHNHTYSE-SYPYLKLFDAAKTNKQY 134 GD+ ++PGNT+H FPD ++P+ SSALFF+P+L+ S+ Y L F+ A+ Y Sbjct: 61 EGDLFIIPGNTIHSSFPDPDQPIVSSALFFAPSLVLGANGSDLQYSVLSCFEYAQKTGSY 120 Query: 135 KYTLSPEHAEILQNDIEEIHREREQNQQDGGQAXXXXXXXXXXXXNRYCLPQTAEPVASS 194 ++ L + +++ ++ I E Q +A NRY +AE A S Sbjct: 121 RHQLPESNQAYIEDMLKGISEEIRLAQLGFREALVLQLRSLLLHINRYISTLSAEQTAHS 180 Query: 195 PLLPEWFREALSYINDHLDQPLELGTLAGRAAISPAHFSRVFKQRLGMNVTDYIATKRIF 254 + P W +++ +I++HLDQP+ L L+ +AA+ PAHFSR+FK+ G++VT Y+ KRI Sbjct: 181 QIGPAWLMDSIQWIHEHLDQPIGLAALSAQAAVDPAHFSRMFKKYTGLHVTGYMHAKRIA 240 Query: 255 AAKDSLLQSSYTIEQIAMACGFESLPHFYRTFKRITSMTPAAYRK 299 AK+ L ++ QIA CG+ +L HF+R FK++T MTP AYR+ Sbjct: 241 RAKELLRNHEASVGQIAEICGYATLTHFHRNFKKLTGMTPGAYRR 285 >Q5WIZ4.1 Q5WIZ4_BACSK Putative uncharacterized protein Length = 283 Score = 227 bits (578), Expect = 1e-57, Method: Compositional matrix adjust. Identities = 117/288 (40%), Positives = 172/288 (59%), Gaps = 7/288 (2%) Query: 16 MEPIRRHFD--HQLPFTLLLDYKETKSPQRELPDHQHDWYEFIYVYGGKGSFFIDQTFYE 73 M PIR+ F+ H +PF L+ + +TKS ELP H H+W+E I V+ G +FFID F+E Sbjct: 1 MGPIRKCFNQSHIVPFQLV--HNKTKSCDDELPHHLHEWHEIIMVHQGTCTFFIDDCFFE 58 Query: 74 MHPGDIIVVPGNTVHRGFPDNEEPVTSSALFFSPALIHNHTYSESYPYLKLFDAAKTNKQ 133 + GDI++VPGN++H D + VT+SAL+F P+L+ + SES LF AKT KQ Sbjct: 59 LASGDIVIVPGNSIHCSLLDKGKTVTTSALYFCPSLLASMIGSESDSLHSLFTTAKTTKQ 118 Query: 134 YKYTLSPEHAEILQNDIEEIHREREQNQQDGGQAXXXXXXXXXXXXNRYCLPQTAEPVAS 193 Y+Y + E L +EI +E G+ +R C TA+ Sbjct: 119 YRYYMEREKQAFLAGLFDEIAKETAIADLYSGETVALLIRYAIVFVSRNC--GTAQE-KL 175 Query: 194 SPLLPEWFREALSYINDHLDQPLELGTLAGRAAISPAHFSRVFKQRLGMNVTDYIATKRI 253 SPL+P W +E+L+YI+ HL + L+L LA A + P++FS+ FK +G+ +++ +KR+ Sbjct: 176 SPLVPAWIKESLAYIDAHLHEELDLKMLAAHACVHPSYFSKKFKASIGLTYIEFLKSKRL 235 Query: 254 FAAKDSLLQSSYTIEQIAMACGFESLPHFYRTFKRITSMTPAAYRKSN 301 AKD L + +I+ IA ACG+ S+PHFYRTF+ T TPAAYRK++ Sbjct: 236 VKAKDLLKTTDLSIQAIAEACGYHSMPHFYRTFRAATGTTPAAYRKNS 283 >B1DB31.1 B1DB31_9BACL Transcriptional regulator, AraC family Length = 289 Score = 111 bits (278), Expect = 8e-23, Method: Compositional matrix adjust. Identities = 87/298 (29%), Positives = 130/298 (43%), Gaps = 27/298 (9%) Query: 6 IFRFDSGGDVMEPIRRHFDHQLPFTLLLDYKETKSPQRELPDHQHDWYEFIYVYGGKGSF 65 I RF G + EP+ FD ++ Y + H H YEF Y+Y G+ F Sbjct: 9 ILRF---GSISEPLWIEFDRRI------GYHSMDT------THYHRSYEFFYLYSGERKF 53 Query: 66 FIDQTFYEMHPGDIIVVPGNTVHR----GFPDNEEPVTSSALFFSPALIHNHTYSESYPY 121 FI + Y++ GD+I+V N VHR P++E V L F L T P+ Sbjct: 54 FIRDSVYQIQSGDLILVNTNDVHRTSELSQPNHERIVLHYDLPFFDGLSREETELLLSPF 113 Query: 122 LKLFDAAKTNKQYKYTLSPEHAEILQNDIEEIHREREQNQQDGGQAXXXXXXXXXXXXNR 181 K N Q + H E L E + RE ++ R Sbjct: 114 ASAHPIIKLNLQERM-----HLEAL---FESLLRELQECPPGYQLHVRNMATEILLFTAR 165 Query: 182 YCLPQTAEPVASSPLLPEWFREALSYINDHLDQPLELGTLAGRAAISPAHFSRVFKQRLG 241 + L + + P + + + + +IN H +PL L LA + IS H SRVFK+ G Sbjct: 166 HALKRKSLPSIELTPVQQKVTDIIRHINQHFREPLPLDELAKQFFISKGHLSRVFKEVTG 225 Query: 242 MNVTDYIATKRIFAAKDSLLQSSYTIEQIAMACGFESLPHFYRTFKRITSMTPAAYRK 299 + YI RI A+ L ++ ++I QI+ CGFE+ HF + FK ++ ++P YRK Sbjct: 226 FGFSQYINVTRIKEAELLLKETDWSITQISERCGFENFSHFGKVFKELSGLSPRDYRK 283 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 0.418 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: 1,858,332,027 Number of extensions: 76617380 Number of successful extensions: 201024 Number of sequences better than 1.0e-05: 4750 Number of HSP's gapped: 201252 Number of HSP's successfully gapped: 4750 Length of query: 304 Length of database: 3,060,696,203 Length adjustment: 135 Effective length of query: 169 Effective length of database: 1,788,859,178 Effective search space: 302317201082 Effective search space used: 302317201082 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)