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= 0352.0005.p (294 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3K5D8.1 B3K5D8_9BACI Helix-turn-helix-domain containing protein... 262 3e-68 Q65MB5.1 Q65MB5_BACLD YfiF 231 7e-59 B3KIJ0.1 B3KIJ0_9BACI Helix-turn-helix-domain containing protein... 155 3e-36 A6TKQ3.1 A6TKQ3_ALKMQ Helix-turn-helix-domain containing protein... 152 3e-35 B3K424.1 B3K424_9BACI Helix-turn-helix-domain containing protein... 150 2e-34 >B3K5D8.1 B3K5D8_9BACI Helix-turn-helix-domain containing protein AraC type Length = 280 Score = 262 bits (670), Expect = 3e-68, Method: Compositional matrix adjust. Identities = 133/270 (49%), Positives = 178/270 (65%), Gaps = 2/270 (0%) Query: 10 KYHIEEGRYSIQHMKRKGITAMPRPHSHDLTELYYLKQGERVYFVDDRVITVHKGELILI 69 KYHI + +SIQ+M R G ++MPRPH H ELYYL GERVYF+DD V TV KG+L+++ Sbjct: 8 KYHIGDHNFSIQYMSRNGSSSMPRPHEHPYFELYYLLNGERVYFMDDNVFTVKKGDLMIV 67 Query: 70 SSRELHSTASSEIAEFERILINYDPALLPPSLQNEAIWFQGRGYRLFKLNLREQDEAESL 129 + +LHSTASSE FER+LI + + A RL ++ L+ Q E E L Sbjct: 68 NPHDLHSTASSEKLLFERVLIGFSRTFIEQGDAGVANLLDHGTSRLIRIPLKHQPEIERL 127 Query: 130 MSRMLEECRLQRSYYETSIITLFTELMILLQRSENI--SQAGGTKHPLHHLVTDVATYIR 187 + ML EC+ ++++Y + + +L EL+I L R E SQ +HP+H ++++A YI+ Sbjct: 128 LHSMLAECQTEQTHYSSLVRSLMNELLIRLHRIETTLQSQTHEYEHPMHQKISEIAQYIK 187 Query: 188 DHHREALTLEATASNFYISPSYLSRVFHRLTGFHFREYIVHVRVREAERLLAGSTGKIQE 247 + E LTLE A FYISPSYLSRVF RLTGFHFREY+ VR+REA+++L S +Q Sbjct: 188 SNFHEKLTLEQVAKQFYISPSYLSRVFTRLTGFHFREYVQVVRIREAQKMLVSSRDSVQI 247 Query: 248 IASAVGFEHLSHFNKTFKKSTGLTPLQYRK 277 I+ GFEH++HFNKTFKK G TPLQYRK Sbjct: 248 ISELAGFEHIAHFNKTFKKIAGTTPLQYRK 277 >Q65MB5.1 Q65MB5_BACLD YfiF Length = 281 Score = 231 bits (588), Expect = 7e-59, Method: Compositional matrix adjust. Identities = 123/287 (42%), Positives = 177/287 (61%), Gaps = 26/287 (9%) Query: 10 KYHIEEGRYSIQHMKRKGITAMPRPHSHDLTELYYLKQGERVYFVDDRVITVHKGELILI 69 KY I E +SIQ+M+RKG T M PH H+ ELYYL GER YF++ V T KG +I+I Sbjct: 5 KYFIAEHSFSIQYMQRKGFTEMNAPHVHEGYELYYLLSGERTYFINQSVYTAEKGTMIII 64 Query: 70 SSRELHSTASSEIAEFERILINYDPALLPPSLQNEAIWFQGRGYRLF---------KLNL 120 + +LH T+S+E+ EFERILIN+ + P L+ YRL +L Sbjct: 65 NPHDLHRTSSTEVQEFERILINFSHDFIEPLLKCSH-------YRLLPFPENQNFIAFSL 117 Query: 121 REQDEAESLMSRMLEECRLQRSYYETSIITLFTELMILLQRSENISQAGGTK------HP 174 REQ E ++ M +EC+L++ +E + L +L+ + RS AGG + HP Sbjct: 118 REQAAVEHMLMEMKKECKLKKEGHEDVVRALLFQLLFTIYRS----LAGGGRNQTRPLHP 173 Query: 175 LHHLVTDVATYIRDHHREALTLEATASNFYISPSYLSRVFHRLTGFHFREYIVHVRVREA 234 + ++++A+YI +E +TL+ A FYISPSYLSRVF ++TGFH +EYI H+R+REA Sbjct: 174 MDEKISEIASYINCSFQETMTLDGLAGQFYISPSYLSRVFKKVTGFHLQEYIRHIRIREA 233 Query: 235 ERLLAGSTGKIQEIASAVGFEHLSHFNKTFKKSTGLTPLQYRKEARS 281 ++ L + KI +IA+ GF+H+SHFNK FK+ G+ PLQYRK++R Sbjct: 234 KKRLRDTDEKILDIAADTGFKHISHFNKVFKEIVGIPPLQYRKKSRD 280 >B3KIJ0.1 B3KIJ0_9BACI Helix-turn-helix-domain containing protein AraC type Length = 243 Score = 155 bits (393), Expect = 3e-36, Method: Compositional matrix adjust. Identities = 87/235 (37%), Positives = 139/235 (59%), Gaps = 5/235 (2%) Query: 48 GERVYFVDDRVITVHKGELILISSRELHSTASSEIAEFERILINYDPALLP---PSLQNE 104 GER YF+ +++ ++ G+LILI+ ++H T+ E ERI+IN+ + L P L + Sbjct: 4 GERHYFIKEKLYSIRAGDLILINKFDVHKTSGHGDPEHERIVINFSDSFLGKGHPLLASG 63 Query: 105 AIWFQGRGYRLFKLNLREQDEAESLMSRMLEECRLQRSYYETSIITLFTELMILLQRSEN 164 + + L +L + EQ ++++M +E R + + YE + L TEL+I R + Sbjct: 64 LLGMFNQDRPLLRLTVPEQAIIMQILNKMADEIRERSASYEHMLQVLLTELLIKTYRLTH 123 Query: 165 ISQ--AGGTKHPLHHLVTDVATYIRDHHREALTLEATASNFYISPSYLSRVFHRLTGFHF 222 + A + +PLH +TDV +I H+ + +TL+ + FYISP YLSR+F +TGF Sbjct: 124 SASLPANVSMNPLHQKITDVVKFIHVHYADKITLQGLSETFYISPFYLSRIFKEITGFTI 183 Query: 223 REYIVHVRVREAERLLAGSTGKIQEIASAVGFEHLSHFNKTFKKSTGLTPLQYRK 277 Y+ R+REA+RLL + KI +IA ++GFE L+HF++TFKK +T QYRK Sbjct: 184 INYLNLTRIREAQRLLTDTDLKIVDIAESIGFESLTHFDRTFKKIMNMTASQYRK 238 >A6TKQ3.1 A6TKQ3_ALKMQ Helix-turn-helix-domain containing protein, AraC type Length = 282 Score = 152 bits (385), Expect = 3e-35, Method: Compositional matrix adjust. Identities = 88/256 (34%), Positives = 140/256 (54%), Gaps = 6/256 (2%) Query: 27 GITAMPRPHSHDLTELYYLKQGERVYFVDDRVITVHKGELILISSRELHSTASSEIAEFE 86 G M H HD E+YYL GER YF+ DR+ V G L+LI+ +++H T ++ + Sbjct: 24 GHYTMLSNHFHDQYEIYYLLSGERHYFIKDRIFHVKSGTLVLINRQDVHRTTDADTQDHV 83 Query: 87 RILINYDPALLPPSLQNEAIW---FQGRGYRLFKLNLREQDEAESLMSRMLEECRLQRSY 143 R+L+N+ L S A+ F Y + L+ EQ E L+ +M+ E Q + Sbjct: 84 RVLLNFSKDYLLSSPYVIALLDGLFMNNNYVIPFLS-AEQQYVEVLLDKMIHEIEHQSTG 142 Query: 144 YETSIITLFTELMILLQR--SENISQAGGTKHPLHHLVTDVATYIRDHHREALTLEATAS 201 ++ ++ L +L++ R N +H ++ + YI +++ LTL + A Sbjct: 143 FQVALQALLMDLLVYTSRYIESNRHDVLAPPSQVHEKISQIVQYINTNYQTPLTLSSVAQ 202 Query: 202 NFYISPSYLSRVFHRLTGFHFREYIVHVRVREAERLLAGSTGKIQEIASAVGFEHLSHFN 261 NF++S YLSR F + TGF F EYI ++R+REA+RLL + K+ +I+ AVGF +SHF Sbjct: 203 NFFVSQYYLSRTFKQATGFTFVEYINNIRIREAQRLLRETNHKVIDISEAVGFGSISHFG 262 Query: 262 KTFKKSTGLTPLQYRK 277 + FK+ T +PL YR+ Sbjct: 263 RVFKEVTRFSPLNYRR 278 >B3K424.1 B3K424_9BACI Helix-turn-helix-domain containing protein AraC type Length = 288 Score = 150 bits (378), Expect = 2e-34, Method: Compositional matrix adjust. Identities = 93/277 (33%), Positives = 145/277 (52%), Gaps = 7/277 (2%) Query: 11 YHIEEGRYSIQHMKRKGITAMPRPHSHDLTELYYLKQGERVYFVDDRVITVHKGELILIS 70 YH G S+++ +R G +M H HD ELYYL GER+YF+ DR V G+L+ + Sbjct: 9 YHDPTGYLSMEYDRRIGYFSMSADHLHDHYELYYLLSGERIYFIKDRSYRVRAGDLVFVD 68 Query: 71 SRELHSTASSEIAEFERILINYDPAL-----LPPSLQNEAIWFQGRGYRLFKLNLREQDE 125 +H T S + +R+++ +P L +PP L G + +L + Sbjct: 69 RNAVHKTLDSGRPDHDRLVLYINPELFADLAVPPELAEGLKEPFGWDVPILRLPSPASEA 128 Query: 126 AESLMSRMLEECRLQRSYYETSIITLFTELMILLQRSENIS--QAGGTKHPLHHLVTDVA 183 E ++ M+ E ++ + EL++ RS ++ ++ T+ LH V Sbjct: 129 VERMVGDMVNEMIHPQAGSSWLLRHRTVELLLFAYRSRHLGMVRSADTEPVLHPKTQAVV 188 Query: 184 TYIRDHHREALTLEATASNFYISPSYLSRVFHRLTGFHFREYIVHVRVREAERLLAGSTG 243 Y+ D++R+ALTL A F ISP YLSR+F + TGF F +Y+ +RV+EA+RLL S Sbjct: 189 RYLNDNYRQALTLPEVAEAFRISPHYLSRLFKQTTGFTFSDYLNLLRVKEAQRLLRESDD 248 Query: 244 KIQEIASAVGFEHLSHFNKTFKKSTGLTPLQYRKEAR 280 I +IA GF + SHF K FK++ L+P YR++ R Sbjct: 249 SITDIAWRSGFSNFSHFGKMFKRTVQLSPRAYRQQYR 285 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 0.134 0.389 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: 1,653,570,305 Number of extensions: 63131805 Number of successful extensions: 170827 Number of sequences better than 1.0e-05: 4786 Number of HSP's gapped: 171156 Number of HSP's successfully gapped: 4787 Length of query: 294 Length of database: 3,060,696,203 Length adjustment: 134 Effective length of query: 160 Effective length of database: 1,798,280,193 Effective search space: 287724830880 Effective search space used: 287724830880 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: 130 (54.7 bits)