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= 0260.0028.p (465 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KEX5.1 B3KEX5_9BACI Response regulator receiver 215 9e-54 B1DFU2.1 B1DFU2_9BACL Two component transcriptional regulator, A... 192 7e-47 B1D9Q4.1 B1D9Q4_9BACL Two component transcriptional regulator, A... 141 1e-31 B1D917.1 B1D917_9BACL Two component transcriptional regulator, A... 136 5e-30 C4ZHX9.1 C4ZHX9_9FIRM Two-component response regulator 118 1e-24 >B3KEX5.1 B3KEX5_9BACI Response regulator receiver Length = 474 Score = 215 bits (547), Expect = 9e-54, Method: Compositional matrix adjust. Identities = 154/482 (31%), Positives = 222/482 (46%), Gaps = 37/482 (7%) Query: 1 MIKAVVVDDERLVRKGFISLIDWSSFGVVIVGEAGDGNAALTLLREQEADLLFVDLTMPG 60 MI ++VDD++LVRKG +S + W SFG+ +VGEA +G AL L+ DLL DL MP Sbjct: 1 MIHVLIVDDDKLVRKGLMSFLPWESFGMRVVGEAANGEKALDFLKANRVDLLMTDLAMPV 60 Query: 61 MSGFELIRQVRQRYPAIRCVVLTCHHEFDYVQEALRLGAVDYIVKTLLEVENADETIRRL 120 MSG ELIR VR++YP I VLT H +F+Y+QEALRLGA+DYI K LE E +E +R+ Sbjct: 61 MSGIELIRVVRKQYPNIAIAVLTLHQDFEYIQEALRLGAIDYIAKVELEKEQFEEVFQRI 120 Query: 121 VERVKWEDSTRELLARGEGRVMAADV----ALLYLPQLPDSHEEELFRLSVTKNNPLLAF 176 R+ E+ ++ + V A ALL P P + +S+ Sbjct: 121 HSRI--EEVKQKHKNESDSIVAACPCDTAYALLTYPDEPLTSRMVADCVSLGWTAEADGS 178 Query: 177 QNMWMSP--------------LLSRIPDKETCRELQTVLGAGWQAALVSGLKNQLLQEVE 222 MW++ L +PD TC GW + + E+ Sbjct: 179 ILMWLTDRPKEVQSHGNDEEEPLPPLPDG-TC-------STGWHMVRLRHTADLSPSELL 230 Query: 223 EVLGKAVRHALFYYCGAEDPARLEFGELRRIAGERFSAGEDTLSEAQNL----RWALDRE 278 + + FY C +P +E + + ER GE+ + + L W D E Sbjct: 231 QRIRAYRSRDFFYDCDGNEPYPIE-KSVMELMAERPEPGEEETATVKELLHAFTWVHDDE 289 Query: 279 TWEGFTSGVQQ-RQPAQEQISAFXXXXXXXXXXXXXXXXXXXXXXXXXXGNLNWCHWKSW 337 ++ S +++ R P + + W W Sbjct: 290 AFDKLCSRLKELRIPVSKLMQWIYGCMVDWNRLYRAIQPDDIKMPDTFTC---WREVADW 346 Query: 338 LRQFSGCVQQRMLELGLSKEVVFCLIRAVRFMKAHAGDKINQGDVATEINMSRGYFSQCF 397 L+QF L LS EV ++ AV+ + + DVA +N+SR YF QCF Sbjct: 347 LKQFRENGMTLSGSLQLSPEVSGSIMTAVKIVHDELELPLFAIDVAKRVNLSRSYFYQCF 406 Query: 398 ARFAGETFGECLRGMRLELAKTLLLETYYPIGEIAGRSGFEDDRYFSRLFREHVGKLPSE 457 G +F E LR +R++ A+ L +T PI IA ++G+ED++YFSR FRE G LPSE Sbjct: 407 KEIVGYSFNEYLRKVRIDKAREYLEQTARPIVWIAKQTGYEDEKYFSRTFREQTGMLPSE 466 Query: 458 YR 459 YR Sbjct: 467 YR 468 >B1DFU2.1 B1DFU2_9BACL Two component transcriptional regulator, AraC family Length = 452 Score = 192 bits (487), Expect = 7e-47, Method: Compositional matrix adjust. Identities = 141/481 (29%), Positives = 221/481 (45%), Gaps = 57/481 (11%) Query: 2 IKAVVVDDERLVRKGFISLIDWSSFGVVIVGEAGDGNAALTLLREQEADLLFVDLTMPGM 61 +K ++VDDE VRKG I + W +G IVGEA +G AL L Q D+L DLTMP M Sbjct: 1 MKTLIVDDEHFVRKGLILTVPWKEYGFDIVGEAENGQKALEQLSAQPIDVLITDLTMPKM 60 Query: 62 SGFELIRQVRQRYPAIRCVVLTCHHEFDYVQEALRLGAVDYIVKTLLEVENADETIRRLV 121 SGFEL+++V+Q+YP I VVLTCH +F YV +A+ GA+DY+VKT +E +E + R+ Sbjct: 61 SGFELMKEVQQQYPHIWIVVLTCHQDFGYVVDAMHAGAIDYLVKTQIEEGKMEEALARIE 120 Query: 122 ERVKWEDSTR-------------ELLARGEGRVMAADVALLYLPQLPD--SHEEELFRLS 166 +R+ D TR EL+ G DV + P P E+ FR+S Sbjct: 121 KRIS--DGTRHRQQAVVQKASCPELILVPSGANGKPDV--IPWPASPTIIPIEQGCFRIS 176 Query: 167 VTKNNPLLAFQNMWMSPLLSRIPDKETCRELQTVLGAGWQAALVSGLKNQLLQEVEEVLG 226 + W ++E E W + + +E + Sbjct: 177 DYGFYDVKPLHKFW---------EEEQLYE-------SWIPVVCESAPEKDFMTTKEWVA 220 Query: 227 KAVRHALFYYCGAEDPARLEFGELRRIAGERFSAGEDTLSEA----QNLRWALDRETWEG 282 + V+ ++FY + P+ + F + A R + G + L + +L W D ++ Sbjct: 221 Q-VKESIFYRFRRDLPSPVRF----QSAVNRSAKGTEQLEKIDRLFHSLHWIFDTGLFQT 275 Query: 283 FTSGVQQRQPAQ----EQISAFXXXXXXXXXXXXXXXXXXXXXXXXXXGNLNWCHWKSWL 338 + V++ +P +++ F NW L Sbjct: 276 WIQLVEETEPNSTYVGDKVGKFLKALSAINGAPAGLDEHKSMMEQR-----NWHELLQSL 330 Query: 339 RQFSGCVQQRMLELGLSKEVVFCLIRAVRFMKAHAGDKINQGDVATEINMSRGYFSQCFA 398 + +QQR +E + +A+ + + +NQ +VA + +SR YF QCF Sbjct: 331 MELRLYLQQR----NFPEETAIGIYKAILLIHDELSENLNQENVAQRVALSRSYFGQCFR 386 Query: 399 RFAGETFGECLRGMRLELAKTLLLETYYPIGEIAGRSGFEDDRYFSRLFREHVGKLPSEY 458 AG +F E L MR+ A+ LL+ T I +A +SGF+D++YFS++F++H LP EY Sbjct: 387 PIAGMSFHELLTEMRIRKAEELLVATNDYIYSVAEQSGFQDEKYFSKVFKQHRHLLPKEY 446 Query: 459 R 459 R Sbjct: 447 R 447 >B1D9Q4.1 B1D9Q4_9BACL Two component transcriptional regulator, AraC family Length = 456 Score = 141 bits (356), Expect = 1e-31, Method: Compositional matrix adjust. Identities = 67/128 (52%), Positives = 91/128 (71%), Gaps = 4/128 (3%) Query: 2 IKAVVVDDERLVRKGFISLIDWSSFGVVIVGEAGDGNAALTLLREQEADLLFVDLTMPGM 61 +K ++VDDE+LVR+G IS++ WS + + +VGEAG+G AL LL E DL+F DL MP M Sbjct: 1 MKVIIVDDEKLVRRGLISMMPWSKYDMEVVGEAGNGRKALELLETLEVDLVFTDLMMPEM 60 Query: 62 SGFELIRQVRQRYPAIRCVVLTCHHEFDYVQEALRLGAVDYIVKTLLEVENADETIRRLV 121 SGFELI ++ +YPA VVL+CH EF + Q+A+RLGA+DYIVK LE + DE + R+ Sbjct: 61 SGFELIEEMNGKYPAASAVVLSCHEEFSFAQKAIRLGAIDYIVKNDLETDVMDEVLERVA 120 Query: 122 ----ERVK 125 E+VK Sbjct: 121 HSYEEKVK 128 Score = 86.7 bits (213), Expect = 5e-15, Method: Compositional matrix adjust. Identities = 39/107 (36%), Positives = 66/107 (61%) Query: 355 SKEVVFCLIRAVRFMKAHAGDKINQGDVATEINMSRGYFSQCFARFAGETFGECLRGMRL 414 S +++ + +A+++M +Q ++A +MSR YFSQCF G++F + +R+ Sbjct: 346 SDDILRVIYKAIQYMHEQEEMDFSQNEIAGIASMSRTYFSQCFKNVTGKSFNDYATEIRM 405 Query: 415 ELAKTLLLETYYPIGEIAGRSGFEDDRYFSRLFREHVGKLPSEYRAE 461 AK LL T PI +IA GF+D++YFS+LF + +G LPS++R + Sbjct: 406 SRAKKLLAHTNTPIYQIAQLVGFKDEKYFSKLFMQEIGVLPSDFRKQ 452 >B1D917.1 B1D917_9BACL Two component transcriptional regulator, AraC family Length = 361 Score = 136 bits (342), Expect = 5e-30, Method: Compositional matrix adjust. Identities = 59/120 (49%), Positives = 89/120 (74%) Query: 1 MIKAVVVDDERLVRKGFISLIDWSSFGVVIVGEAGDGNAALTLLREQEADLLFVDLTMPG 60 MI+ ++VDD++L RKGFIS++ WS+ +V+VGEA +G AL + + E DL+FVDL+MP Sbjct: 1 MIRVLIVDDDKLARKGFISIMPWSNHDMVVVGEAANGAKALEFMEQHEVDLMFVDLSMPV 60 Query: 61 MSGFELIRQVRQRYPAIRCVVLTCHHEFDYVQEALRLGAVDYIVKTLLEVENADETIRRL 120 MSG EL++ RQR+P +R V+L+ H EF+ VQ A R+G +DYI K LE E+ ++ ++R+ Sbjct: 61 MSGMELLQVTRQRFPGLRSVILSFHEEFENVQTAYRMGVLDYISKVRLESEDDEQILKRI 120 Score = 90.5 bits (223), Expect = 3e-16, Method: Compositional matrix adjust. Identities = 46/125 (36%), Positives = 68/125 (54%) Query: 337 WLRQFSGCVQQRMLELGLSKEVVFCLIRAVRFMKAHAGDKINQGDVATEINMSRGYFSQC 396 W+R F V ++ +++AV F++ A ++ VA ++MSR YFSQC Sbjct: 228 WMRDFRKRVYAQVAATTDFTNTTTSILKAVLFIREQASGTLHAEGVADHVHMSRSYFSQC 287 Query: 397 FARFAGETFGECLRGMRLELAKTLLLETYYPIGEIAGRSGFEDDRYFSRLFREHVGKLPS 456 F R G TF + L+ R+ A+ LL ET I +A G+ D +YFS+LF E LPS Sbjct: 288 FKRLTGSTFNDYLKQERIRSAERLLCETNQSIAWVAHAVGYNDSKYFSQLFYEQTRLLPS 347 Query: 457 EYRAE 461 E+RA+ Sbjct: 348 EFRAQ 352 >C4ZHX9.1 C4ZHX9_9FIRM Two-component response regulator Length = 336 Score = 118 bits (295), Expect = 1e-24, Method: Compositional matrix adjust. Identities = 56/137 (40%), Positives = 88/137 (64%), Gaps = 2/137 (1%) Query: 2 IKAVVVDDERLVRKGFISLIDWSSFGVVIVGEAGDGNAALTLLREQEADLLFVDLTMPGM 61 +K +VVDD++L RKG IS++DW +G +VG+ +G AL L++ E D++F D+ MP + Sbjct: 1 MKVLVVDDDKLARKGLISIMDWKKYGFEVVGDVQNGRKALEFLKDNEVDIVFTDIDMPEI 60 Query: 62 SGFELIRQVRQRYPAIRCVVLTCHHEFDYVQEALRLGAVDYIVKTLLEVENADETIRRLV 121 G EL++ ++ YP ++ VV + + +F Y Q ALRLGA+DYI K E + D I LV Sbjct: 61 DGIELMKMCKKEYPEVKFVVFSMYEDFRYAQSALRLGALDYISKISFEGDECDR-ILELV 119 Query: 122 ERVKWEDSTRELLARGE 138 ER K++++ + R E Sbjct: 120 ER-KYKENHSQKETRNE 135 Score = 62.4 bits (150), Expect = 9e-08, Method: Compositional matrix adjust. Identities = 31/122 (25%), Positives = 62/122 (50%), Gaps = 1/122 (0%) Query: 337 WLRQFSGCVQQRMLELGLSKEVVFCLIRAVRFMKAHAGDKINQGDVATEINMSRGYFSQC 396 W++Q+ + Q L+ +K++ + R + + H + + + A +I MSR YFS Sbjct: 207 WVKQWKENLYQTCLQTDKTKDI-YMFARVILYTDEHIEENLKSEEAAAQIGMSRSYFSTR 265 Query: 397 FARFAGETFGECLRGMRLELAKTLLLETYYPIGEIAGRSGFEDDRYFSRLFREHVGKLPS 456 F G+TF + ++ A + + I +IA G+++ YF+++F + G +P+ Sbjct: 266 FKEMTGDTFHNYVISRKMYAAAQKMAKGTENITQIASNLGYDNFYYFTKVFSKEYGCMPT 325 Query: 457 EY 458 EY Sbjct: 326 EY 327 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 0.138 0.416 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: 2,576,918,841 Number of extensions: 100937521 Number of successful extensions: 318559 Number of sequences better than 1.0e-05: 8417 Number of HSP's gapped: 328320 Number of HSP's successfully gapped: 8715 Length of query: 465 Length of database: 3,060,696,203 Length adjustment: 139 Effective length of query: 326 Effective length of database: 1,751,175,118 Effective search space: 570883088468 Effective search space used: 570883088468 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: 133 (55.8 bits)