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= 0099.0004.p (315 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KCN3.1 B3KCN3_9BACI Helix-turn-helix-domain containing protein... 361 4e-98 B1D825.1 B1D825_9BACL Transcriptional regulator, AraC family 286 2e-75 B0K7N2.1 B0K7N2_THEP3 Transcriptional regulator, AraC family 118 9e-25 B0K6C5.1 B0K6C5_THEPX Helix-turn-helix-domain containing protein... 118 9e-25 B1DAS3.1 B1DAS3_9BACL Transcriptional regulator, AraC family 99 4e-19 >B3KCN3.1 B3KCN3_9BACI Helix-turn-helix-domain containing protein AraC type Length = 315 Score = 361 bits (927), Expect = 4e-98, Method: Compositional matrix adjust. Identities = 175/305 (57%), Positives = 219/305 (71%), Gaps = 9/305 (2%) Query: 13 FEKMFEKQDMLERLDICIEWGHYEIKVLRFHLTSFPAGKVIDFHKHAEFEFHFIPRGRGK 72 +E M E+QD LERLD+ + WG YEI+VLRFHLT+FP GK++ FHKHAE+EFHFIPRG+G Sbjct: 7 YEMMKERQDALERLDLRVYWGRYEIRVLRFHLTTFPPGKIVSFHKHAEYEFHFIPRGKGT 66 Query: 73 VILSGQQYSLSEGMLYLTGPGVIHYQEADAGEAMDELCLHVDITAKERKG---------V 123 VI+ + Y+L EGM YLTGP V+HYQEAD E MDELCLHVDI ++ Sbjct: 67 VIMEDEPYALREGMFYLTGPNVLHYQEADTAEPMDELCLHVDIIPRDEISEPESPALPVS 126 Query: 124 DPWEAAEAEETMVKLRALPVVPAYDYHRAMYCFLEAYEACDGKLLGYYTSIKQLVISILL 183 DPWE AEA++ M KLR LP+ P D HRAM FLEAY+A K G YT+IKQ +I ILL Sbjct: 127 DPWEMAEADDCMEKLRELPMKPTMDIHRAMPYFLEAYQASQEKYSGLYTTIKQCLIQILL 186 Query: 184 KTIRAYDSGDNRAEAPVRNMAAYRYEYAVQYMEANHKTPVTLDNVAEKLHISSRQLQRIF 243 + +RAY+S + AE P R+M AYRY+ A++Y+ AN V LD+VAEKLHISSRQLQRIF Sbjct: 187 RAVRAYESEPSEAELPSRDMKAYRYQLALEYIHANSSGEVVLDDVAEKLHISSRQLQRIF 246 Query: 244 KQVQPERPFSRILEEIRLQAVCRALEENLSSIEQIAQDSGFTNANYLHAVFRKRLGMTPA 303 K+ + FS ILE +RL+AVCR L + SI++IA GF++ +YLH VFRKR G TP Sbjct: 247 KEQAEGQSFSEILEHVRLEAVCRKLIDTNWSIDKIAIHEGFSSGSYLHTVFRKRYGYTPT 306 Query: 304 AFRAL 308 +RA+ Sbjct: 307 TYRAM 311 >B1D825.1 B1D825_9BACL Transcriptional regulator, AraC family Length = 329 Score = 286 bits (732), Expect = 2e-75, Method: Compositional matrix adjust. Identities = 145/301 (48%), Positives = 193/301 (64%), Gaps = 8/301 (2%) Query: 16 MFEKQDMLERLDICIEWGHYEIKVLRFHLTSFPAGKVIDFHKHAEFEFHFIPRGRGKVIL 75 M EK D LERLD+ WG Y I+VL++HLT+F G++I FHKH+EFEFHF+PRG+G V L Sbjct: 27 MKEKMDALERLDLHFRWGRYGIRVLKWHLTTFKPGQLIKFHKHSEFEFHFVPRGKGTVTL 86 Query: 76 SGQQYSLSEGMLYLTGPGVIHYQEADAGEAMDELCLHVDIT------AKERKGVDPWEAA 129 Y L+ GM YLTGPGV+H Q AD M+ELCLHVDIT +E G + WE Sbjct: 87 IDHIYKLNSGMFYLTGPGVVHQQTADNRSGMEELCLHVDITRLPGGEEREEWGSE-WENK 145 Query: 130 EAEETMVKLRALPVVPAYDYHRAMYCFLEAYEACDGKLLGYYTSIKQLVISILLKTIRAY 189 E+E + L P+ P D H AM CFL+AY A LG YT+I+Q +I ILL+ +A Sbjct: 146 ESEACIQALTDFPLRPFMDQHDAMTCFLQAYMAWRSGELGAYTTIRQSLIQILLRAAKAT 205 Query: 190 DSGDNRAEAPVRNMAAYRYEYAVQYMEANHKTPVTLDNVAEKLHISSRQLQRIFKQVQPE 249 D + P R++ A+R+E A QY+ N+ P+TL VA+++ IS+RQLQR+F + Sbjct: 206 VDRDGQQMLPARDIQAHRFEMAQQYIYDNYARPLTLQEVADRIQISTRQLQRVFHRYGVS 265 Query: 250 RPFSRILEEIRLQAVCRALEENLSSIEQIAQDSGFTNANYLHAVFRKRLGMTPAAFRALR 309 FS LE+ RLQ +C L E +++E IA + GFTN NYL VF+K++GMTP A+R Sbjct: 266 -SFSSYLEDFRLQRICEELVETSNTVESIAVNHGFTNTNYLFQVFKKKMGMTPLAYRQRH 324 Query: 310 Q 310 Q Sbjct: 325 Q 325 >B0K7N2.1 B0K7N2_THEP3 Transcriptional regulator, AraC family Length = 298 Score = 118 bits (295), Expect = 9e-25, Method: Compositional matrix adjust. Identities = 82/296 (27%), Positives = 141/296 (47%), Gaps = 13/296 (4%) Query: 16 MFEKQDMLERLDICIEWGHYEIKVLRFHLTSFPAGKVIDFHKHAEFEFHFIPRGRGKVIL 75 M+ + L +LDI + + I VL F + I H H+ FEFHF+P G VIL Sbjct: 3 MYRASEELSKLDIQVSIDDFIINVLWFRVMVREGEWEIPRHTHSSFEFHFVPEGDSLVIL 62 Query: 76 SGQQYSLSEGMLYLTGPGVIHYQEADAGEAMDELCLHVDITAKERKGVDPWEAAEAEETM 135 +Q+ + +G Y+T PG+ H Q + GE E ++ D E++ +E + Sbjct: 63 DDEQFVVKKGEFYVTAPGIYHEQRS-IGEKYIEYSINCDFKKTEKEVF-----SEIDIIF 116 Query: 136 VKLRALPVVPAYDYHRAMYCFLEAYEACDGKLLGYYTSIKQLVISILLKTIRAYDSGDNR 195 L + P D + AM F A + + +G+Y +IK L++ IL RA DN+ Sbjct: 117 EILSSAKCFPVKDRYGAMKYFELALQEAYAQKIGFYNNIKSLIVMILTMAARAL-VFDNK 175 Query: 196 AEA--PVRNM---AAYRYEYAVQYMEANHKTPVTLDNVAEKLHISSRQLQRIFKQVQPER 250 + PV YR+ +++E N ++++A LH+S +Q+ RI K+ + + Sbjct: 176 ISSYYPVPKKLKETDYRFTLIKKFIEDNISDVRKVEDIANYLHLSPKQINRIVKE-KTNK 234 Query: 251 PFSRILEEIRLQAVCRALEENLSSIEQIAQDSGFTNANYLHAVFRKRLGMTPAAFR 306 ++ ++LQ L+ SI++IA GF++ Y + F++ G P +R Sbjct: 235 STKELINFLKLQEAKEMLKNTNISIKEIANRLGFSSEYYFNQFFKREEGYPPGLYR 290 >B0K6C5.1 B0K6C5_THEPX Helix-turn-helix-domain containing protein, AraC type Length = 298 Score = 118 bits (295), Expect = 9e-25, Method: Compositional matrix adjust. Identities = 82/296 (27%), Positives = 141/296 (47%), Gaps = 13/296 (4%) Query: 16 MFEKQDMLERLDICIEWGHYEIKVLRFHLTSFPAGKVIDFHKHAEFEFHFIPRGRGKVIL 75 M+ + L +LDI + + I VL F + I H H+ FEFHF+P G VIL Sbjct: 3 MYRASEELSKLDIQVSIDDFIINVLWFRVMVREGEWEIPRHTHSSFEFHFVPEGDSLVIL 62 Query: 76 SGQQYSLSEGMLYLTGPGVIHYQEADAGEAMDELCLHVDITAKERKGVDPWEAAEAEETM 135 +Q+ + +G Y+T PG+ H Q + GE E ++ D E++ +E + Sbjct: 63 DDEQFVVKKGEFYVTAPGIYHEQRS-IGEKYIEYSINCDFKKTEKEVF-----SEIDIIF 116 Query: 136 VKLRALPVVPAYDYHRAMYCFLEAYEACDGKLLGYYTSIKQLVISILLKTIRAYDSGDNR 195 L + P D + AM F A + + +G+Y +IK L++ IL RA DN+ Sbjct: 117 EILSSAKCFPVKDRYGAMKYFELALQEAYAQKIGFYNNIKSLIVMILTMAARAL-VFDNK 175 Query: 196 AEA--PVRNM---AAYRYEYAVQYMEANHKTPVTLDNVAEKLHISSRQLQRIFKQVQPER 250 + PV YR+ +++E N ++++A LH+S +Q+ RI K+ + + Sbjct: 176 ISSYYPVPKKLKETDYRFTLIKKFIEDNISDVRKVEDIANYLHLSPKQINRIVKE-KTNK 234 Query: 251 PFSRILEEIRLQAVCRALEENLSSIEQIAQDSGFTNANYLHAVFRKRLGMTPAAFR 306 ++ ++LQ L+ SI++IA GF++ Y + F++ G P +R Sbjct: 235 STKELINFLKLQEAKEMLKNTNISIKEIANRLGFSSEYYFNQFFKREEGYPPGLYR 290 >B1DAS3.1 B1DAS3_9BACL Transcriptional regulator, AraC family Length = 314 Score = 99.4 bits (246), Expect = 4e-19, Method: Compositional matrix adjust. Identities = 76/291 (26%), Positives = 136/291 (46%), Gaps = 9/291 (3%) Query: 24 ERLDICIEWGHYEIKVLRFHLTSFPAGKVIDFHKHAEFEFHFIPRGRGKVILSGQQYSLS 83 + LD+ I G + VL F H + +E H+IP G+G++I G+++ LS Sbjct: 9 DNLDLKILLGKLVLNVLYIKSGYFYRSMPEHRHSNGSYELHYIPSGQGRLIAEGKEFPLS 68 Query: 84 EGMLYLTGPGVIHYQEADAGEAMDELCLHVDITAKERKG---VDPWEAAEAEETMVKLRA 140 G LY+TGP V H Q D+ + M E C+ + R ++ ++E+T R Sbjct: 69 PGSLYMTGPCVDHEQITDSSDPMFEYCIFFEALPSGRTNHGKLNGRSGCDSEDTSEIARL 128 Query: 141 LPVVPAY---DYHRAMYCFLEAYEACDGKLLGYYTSIKQLVISILLKTIRAYDSGDNRAE 197 P + D + F + + + +GY SI + I++ +R Y + + Sbjct: 129 FLNTPFWIGQDSQQLQLVFEKLAWEINTRAIGYRRSITIQLEHIVIGLVRNYTNNQPTLQ 188 Query: 198 -APVRNMAAYRYEYAVQYMEANHKTPVTLDNVAEKLHISSRQLQRIFKQVQPERPFSRIL 256 AP++ + R + N+K +T+ +A++L +S RQ +R ++ Q L Sbjct: 189 TAPLKTLDDKRMVLIENSILYNYKH-ITITTLADQLGLSIRQTERAVRK-QYGMSLREKL 246 Query: 257 EEIRLQAVCRALEENLSSIEQIAQDSGFTNANYLHAVFRKRLGMTPAAFRA 307 +E R+Q R L+ +L +I +IA G+ ++ F+K G TP+A+R Sbjct: 247 QEARMQEAARLLDASLLTIGEIAVQVGYHSSESFATHFKKWHGATPSAYRV 297 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 0.322 0.136 0.403 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: 1,826,830,894 Number of extensions: 72864266 Number of successful extensions: 181604 Number of sequences better than 1.0e-05: 655 Number of HSP's gapped: 186352 Number of HSP's successfully gapped: 655 Length of query: 315 Length of database: 3,060,696,203 Length adjustment: 135 Effective length of query: 180 Effective length of database: 1,788,859,178 Effective search space: 321994652040 Effective search space used: 321994652040 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)