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= 0039.0023.p (305 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KDR1.1 B3KDR1_9BACI Helix-turn-helix-domain containing protein... 349 2e-94 B1D7X7.1 B1D7X7_9BACL Transcriptional regulator, AraC family 246 2e-63 Q9KBM0.1 Q9KBM0_BACHD Transcriptional regulator (AraC/XylS family) 217 1e-54 Q0R5R6.1 Q0R5R6_ALIAC AraC/XylS1 199 3e-49 C1I2I2.1 C1I2I2_9CLOT Transcriptional regulator 193 2e-47 >B3KDR1.1 B3KDR1_9BACI Helix-turn-helix-domain containing protein AraC type Length = 292 Score = 349 bits (896), Expect = 2e-94, Method: Compositional matrix adjust. Identities = 156/292 (53%), Positives = 216/292 (73%), Gaps = 2/292 (0%) Query: 1 MDRTSQRLLKEDRVHGDVMFPLAAYWIELPAGTHVLDTHWHEEAEFFMLLEGEILFQVDT 60 MD++ ++ LKE VHG+ FP AYW + G HV+D+HWH+EAE F ++EGE+LFQ+D+ Sbjct: 1 MDQSFRQSLKESTVHGNERFPFGAYWYQFAPGAHVVDSHWHKEAEIFYVMEGEVLFQIDS 60 Query: 61 DYFPLRPGEAVFIESGDIHAAYALQDSPCRFCALVFHPDLLASAQYDTIQQTVILPLLEK 120 +Y P+R GEA+FI+ GD+H +A + C FCA+VF +LAS+ YD +Q+ +I+P E+ Sbjct: 61 EYIPVRAGEAIFIDGGDLHTGHAQGNEGCSFCAMVFDVGMLASSSYDLVQEGMIVPFQER 120 Query: 121 RQSFPRHLTPEMAWQQELLHHLERLMEAYANKMPGFEAFMKGTLLIMLSQIAIEGRSVNH 180 R +FPR +T + LL H++ +M +K G+EA +KG L +ML Q A GR N Sbjct: 121 RAAFPRRMTS--GTDERLLEHIKEMMLLSKHKPAGYEAAIKGHLFLMLFQAASSGRLANR 178 Query: 181 TQSEGADTTKINRLKKVILYIQDNYQEPIRTRDLSELIPMSEGQFCRFFKAMTRKTPVDY 240 ++SE AD T+ RLKKVILYIQ +Y PIR +L++LIPMSEGQFCRFFK+MT +TPVDY Sbjct: 179 SRSEAADMTRTERLKKVILYIQSHYHRPIRLSELADLIPMSEGQFCRFFKSMTGQTPVDY 238 Query: 241 INSYRIRQAADLLQQSERKISDIAMDVGFDNVSYFIKVFRKAMKCSPSEFRK 292 +NSYR+RQAA+LL+ + KISDIA+DVGF ++SYF++VFRK M C+PSE+RK Sbjct: 239 MNSYRVRQAAELLRSPDNKISDIALDVGFGHISYFVRVFRKIMNCTPSEYRK 290 >B1D7X7.1 B1D7X7_9BACL Transcriptional regulator, AraC family Length = 294 Score = 246 bits (627), Expect = 2e-63, Method: Compositional matrix adjust. Identities = 122/291 (41%), Positives = 184/291 (63%), Gaps = 4/291 (1%) Query: 1 MDRTSQRLLKEDRVHGDVMFPLAAYWIELPAGTHVLDTHWHEEAEFFMLLEGEILFQVDT 60 MD++ LLKE R HG+ ++P++ Y I P+ +LD HWH+E E ++ EG +F+VD Sbjct: 1 MDKS---LLKEARKHGNPIYPVSLYEITCPSDAPLLDLHWHDELELLLVTEGTAVFRVDL 57 Query: 61 DYFPLRPGEAVFIESGDIHAAYALQDSPCRFCALVFHPDLLASAQYDTIQQTVILPLLEK 120 + L+ GEA+F+ SG++H+ Y + PC F A+VFH L +S D + I P+LEK Sbjct: 58 QDYELQAGEAIFVNSGELHSGYVVGGKPCSFDAVVFHSSLFSSGSIDYLFDRYISPVLEK 117 Query: 121 RQSFPRHLTPEMAWQQELLHHLERLMEAYANKMPGFEAFMKGTLLIMLSQIAIEGRSVNH 180 R P HL E ELL L+++ E + N+ E +KG L +L+++ G+ Sbjct: 118 RYEVPAHLRREPGPGMELLAMLDQIFEVHRNEQAASELTIKGLLFSILAKLVSLGKPSVR 177 Query: 181 TQSEGADTTKINRLKKVILYIQDNYQEPIRTRDLSELIPMSEGQFCRFFKAMTRKTPVDY 240 + E + +I RLK VI YI+ NY EPI + L+EL MSE FCRFFK +T K+P++Y Sbjct: 178 VKPE-QEGYRIERLKTVIEYIEQNYAEPIPLQKLAELARMSESYFCRFFKRITTKSPIEY 236 Query: 241 INSYRIRQAADLLQQSERKISDIAMDVGFDNVSYFIKVFRKAMKCSPSEFR 291 +NSYR++QAA L+Q++ KI ++A+DVGF+++SYF VFR+ C+P E+R Sbjct: 237 MNSYRVQQAASRLRQTDAKIMEVALDVGFNSLSYFNTVFRQRFGCTPREYR 287 >Q9KBM0.1 Q9KBM0_BACHD Transcriptional regulator (AraC/XylS family) Length = 299 Score = 217 bits (553), Expect = 1e-54, Method: Compositional matrix adjust. Identities = 108/283 (38%), Positives = 168/283 (59%), Gaps = 4/283 (1%) Query: 11 EDRVHGDVMFPLAAYWIELPAGTHVLDTHWHEEAEFFMLLEGEILFQVDTDYFPLRPGEA 70 E R HGD MFP Y ++ G ++ HWH E E+ + GE FQ+ T +R GE Sbjct: 8 EARAHGDPMFPCNVYRVKEVNGQVIIHCHWHHEMEWIYMEAGEAEFQIGTKMTTVRAGEG 67 Query: 71 VFIESGDIHAAYALQDSPCRFCALVFHPDLLASAQYDTIQQTVILPLLEKRQSFPRHLTP 130 +FI SG +H AY + D P A V HPD ++S YD IQ I P + ++ P L P Sbjct: 68 LFIPSGHLHGAYPVSDKPFSLYATVVHPDFISSFGYDLIQSRYIDPFKDSERTGPIKLCP 127 Query: 131 EMAWQQELLHHLERLMEAYANKMPGFEAFMKGTLLIMLSQIAIEGRSVNHTQSEGADT-T 189 W ++L L+ + + K G+E +K LL M++++ + T+ + T Sbjct: 128 THYWMSDMLTMLQATISQFQQKEEGYELVIKANLLQMMAELV---KHFPRTEEQKTGTPQ 184 Query: 190 KINRLKKVILYIQDNYQEPIRTRDLSELIPMSEGQFCRFFKAMTRKTPVDYINSYRIRQA 249 +I ++KKV+ +I ++Y E + + L+ L+ MSEG F RFFK++ R T V+YI++ R+ +A Sbjct: 185 QIRQIKKVLQFIDEHYDEKLTIKQLANLVQMSEGHFSRFFKSIVRMTAVEYIHTQRLNKA 244 Query: 250 ADLLQQSERKISDIAMDVGFDNVSYFIKVFRKAMKCSPSEFRK 292 A LL++++R I DI+M VGFD+ SYFIK+F++ +C+PSEFR+ Sbjct: 245 ARLLRETDRTIMDISMSVGFDHPSYFIKLFKRHKRCTPSEFRR 287 >Q0R5R6.1 Q0R5R6_ALIAC AraC/XylS1 Length = 310 Score = 199 bits (505), Expect = 3e-49, Method: Compositional matrix adjust. Identities = 109/295 (36%), Positives = 160/295 (54%), Gaps = 2/295 (0%) Query: 9 LKEDRVHGDVMFPLAAYWIELPAGTH--VLDTHWHEEAEFFMLLEGEILFQVDTDYFPLR 66 L E R HGD F + AY + L G H ++ HWH EAEF ++ G + QV + L+ Sbjct: 16 LLEHRQHGDATFHIQAYHVVLTPGPHQQTVNLHWHSEAEFIVVTRGSVCLQVGSHRHLLQ 75 Query: 67 PGEAVFIESGDIHAAYALQDSPCRFCALVFHPDLLASAQYDTIQQTVILPLLEKRQSFPR 126 G+ F+ G++H+ A D P A+VF DLL SA D +QQ + PL ++ FP Sbjct: 76 EGDVAFLSGGELHSMAAPDDKPSECKAIVFGLDLLESAGNDRVQQAYLAPLAARKLRFPG 135 Query: 127 HLTPEMAWQQELLHHLERLMEAYANKMPGFEAFMKGTLLIMLSQIAIEGRSVNHTQSEGA 186 L + + EL L + EA + G+E +KG L +L+Q+ V + Sbjct: 136 ALPHDHPLRDELARRLCEIAEALEEQPVGYELAVKGCLYDVLAQLFRAKLLVEDSPRREM 195 Query: 187 DTTKINRLKKVILYIQDNYQEPIRTRDLSELIPMSEGQFCRFFKAMTRKTPVDYINSYRI 246 D + + LK V+ YI + + +R DL+ + MSEG F RFFK MT + P+ Y+N R+ Sbjct: 196 DDRRADTLKAVLTYIDAHLSDKLRLADLARVANMSEGHFFRFFKEMTHRKPMQYVNERRV 255 Query: 247 RQAADLLQQSERKISDIAMDVGFDNVSYFIKVFRKAMKCSPSEFRKGAVQGAGQS 301 +AADLL+ R I+ I MD+GF +VSYFIKVFR C+P +RK ++ +S Sbjct: 256 ARAADLLKDPNRSITAIGMDLGFHDVSYFIKVFRSYKHCTPLAYRKALLKKPPRS 310 >C1I2I2.1 C1I2I2_9CLOT Transcriptional regulator Length = 295 Score = 193 bits (490), Expect = 2e-47, Method: Compositional matrix adjust. Identities = 103/296 (34%), Positives = 160/296 (54%), Gaps = 2/296 (0%) Query: 1 MDRTSQRLLKEDRVHGDVMFPLAAYWIELPAGTHVLDTHWHEEAEFFMLLEGEILFQVDT 60 MD S LKE HG++ PL Y +E +HWH+E EF +L G +D Sbjct: 1 MDNKSYLQLKEQVNHGNMQLPLEVYNVEFRNSADFY-SHWHDEMEFIYILNGSAEICIDF 59 Query: 61 DYFPLRPGEAVFIESGDIHAAYALQDSPCRFCALVFHPDLLASAQYDTIQQTVILPLLEK 120 F + G+ + I +G IH ++S + ALVF+ L+ D Q + P+++ Sbjct: 60 KIFSVTTGDFIIIPNGSIHYMIGKENSKISYVALVFNLSLIEGNTLDYSQINFVNPIMKN 119 Query: 121 RQSFPRHLTPEMAWQQELLHHLERLMEAYANKMPGFEAFMKGTLLIMLSQIAIEGR-SVN 179 + F + ++++ ++E+Y NK GF+ +KG+L + S I EG S+N Sbjct: 120 KLFFKNIIRTSNVGHAKIVNSFNNIIESYNNKSYGFQLEIKGSLFSIFSTIFKEGYISLN 179 Query: 180 HTQSEGADTTKINRLKKVILYIQDNYQEPIRTRDLSELIPMSEGQFCRFFKAMTRKTPVD 239 +D K+ LK+VI YIQ NY+ PI ++L+++ SE F RFFKA T KT Sbjct: 180 LNSENYSDLIKVENLKEVIKYIQTNYKNPISIKELADIAQYSEYHFLRFFKAQTGKTCTQ 239 Query: 240 YINSYRIRQAADLLQQSERKISDIAMDVGFDNVSYFIKVFRKAMKCSPSEFRKGAV 295 YIN +RI++A LL + I++IA +VGF +VSYFIK F+K + SP+++RK + Sbjct: 240 YINYFRIQKATLLLFDTNLSITEIAYEVGFGDVSYFIKTFKKFLSISPTKYRKSNL 295 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 0.137 0.409 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: 1,744,798,155 Number of extensions: 69590658 Number of successful extensions: 174649 Number of sequences better than 1.0e-05: 4293 Number of HSP's gapped: 174928 Number of HSP's successfully gapped: 4294 Length of query: 305 Length of database: 3,060,696,203 Length adjustment: 135 Effective length of query: 170 Effective length of database: 1,788,859,178 Effective search space: 304106060260 Effective search space used: 304106060260 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: 131 (55.1 bits)