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= 0493.0008.p (215 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value C3GW80.1 C3GW80_BACTU Two component transcriptional regulator, LuxR 328 2e-88 Q97MM2.1 Q97MM2_CLOAB Response regulator, CheY-like receiver dom... 283 7e-75 A7Z0X2.1 A7Z0X2_BACA2 Two-component response regulator 277 4e-73 B1KTH4.1 B1KTH4_CLOBM Transcriptional regulatory protein DegU (P... 249 1e-64 C4IBW4.1 C4IBW4_CLOBU DNA-binding response regulator 244 3e-63 >C3GW80.1 C3GW80_BACTU Two component transcriptional regulator, LuxR Length = 217 Score = 328 bits (840), Expect = 2e-88, Method: Compositional matrix adjust. Identities = 171/215 (79%), Positives = 186/215 (86%), Gaps = 3/215 (1%) Query: 2 VDIMIVDDQQIVREGLKMILSLHEEINVIGEASNGEEALELLSYTSPEVILMDIKMPVMN 61 +D++IVDDQQIVREGLKM+LSLHEEIN++GEASNGEE LELLS+T E+ILMDI+MP+M+ Sbjct: 1 MDVVIVDDQQIVREGLKMVLSLHEEINIVGEASNGEELLELLSHTYAEIILMDIRMPIMD 60 Query: 62 GIEATKLVKAKYPGIKVIILTTFNDSEYIFTGLKNGADGYILKDSGSQEIISSIKTACEG 121 GI ATKLVK KYP IKVIILTTFNDSEYIFTGLKNGADGYILKDS SQEII SIKTA EG Sbjct: 61 GIVATKLVKEKYPEIKVIILTTFNDSEYIFTGLKNGADGYILKDSDSQEIIESIKTAFEG 120 Query: 122 NILLNPKITREVVNALNSVNNAGT---ENLRNEQILQLLTPRELEVAKCIMEGKSNKEIS 178 NILLNPKIT +VV ALNS N T E N+Q LLTPRELEVAK IMEGKSNK IS Sbjct: 121 NILLNPKITLKVVKALNSANYKETVKAEFNENKQPSNLLTPRELEVAKHIMEGKSNKAIS 180 Query: 179 SDLFITEGTVKNYVSRMLEKLELKNRTELTLCLQK 213 +LFITEGTVKNYVSR+LEKLEL NRTELTL LQK Sbjct: 181 KELFITEGTVKNYVSRILEKLELNNRTELTLYLQK 215 >Q97MM2.1 Q97MM2_CLOAB Response regulator, CheY-like receiver domain and HTH DNA-binding domain Length = 213 Score = 283 bits (724), Expect = 7e-75, Method: Compositional matrix adjust. Identities = 138/215 (64%), Positives = 179/215 (83%), Gaps = 2/215 (0%) Query: 1 MVDIMIVDDQQIVREGLKMILSLHEEINVIGEASNGEEALELLSYTSPEVILMDIKMPVM 60 M+D++IVDDQ+IVREGLKMIL L+ E NVIGEASNG E L LL + SP VILMDI+MPVM Sbjct: 1 MIDVIIVDDQEIVREGLKMILGLNNEFNVIGEASNGAELLTLLEHQSPNVILMDIRMPVM 60 Query: 61 NGIEATKLVKAKYPGIKVIILTTFNDSEYIFTGLKNGADGYILKDSGSQEIISSIKTACE 120 +GIEAT+LVK YP +KVIILTTFN+ E+IF LKNGADGY+LKD+GS+EI +SIK ACE Sbjct: 61 DGIEATRLVKENYPDLKVIILTTFNEDEFIFDVLKNGADGYVLKDAGSKEIFNSIKAACE 120 Query: 121 GNILLNPKITREVVNALNSVNNAGTENLRNEQILQLLTPRELEVAKCIMEGKSNKEISSD 180 G++LLNP++T ++VNALN+++ + L+ + +L LLTPRE++VA +++GKSN+ I+ Sbjct: 121 GSVLLNPQVTLKLVNALNTLDK--KKPLQEKNLLHLLTPREMDVANHVLKGKSNRAIAEA 178 Query: 181 LFITEGTVKNYVSRMLEKLELKNRTELTLCLQKSL 215 LF+TEGT+KNYVS++LEKLEL NR+EL L LQ L Sbjct: 179 LFLTEGTIKNYVSKILEKLELGNRSELILYLQNYL 213 >A7Z0X2.1 A7Z0X2_BACA2 Two-component response regulator Length = 214 Score = 277 bits (709), Expect = 4e-73, Method: Compositional matrix adjust. Identities = 137/214 (64%), Positives = 170/214 (79%) Query: 2 VDIMIVDDQQIVREGLKMILSLHEEINVIGEASNGEEALELLSYTSPEVILMDIKMPVMN 61 +++M+ DDQ IVREGLKMILSLHE I + GEAS GEE L LLS T +VILMDI+MP M+ Sbjct: 1 MNVMVADDQSIVREGLKMILSLHEGIQISGEASCGEEVLRLLSQTETDVILMDIRMPGMD 60 Query: 62 GIEATKLVKAKYPGIKVIILTTFNDSEYIFTGLKNGADGYILKDSGSQEIISSIKTACEG 121 GIE TK VKA+YP +KVIILTTF D YIF GLK+GADGY+LKD+ S E+I+S++ EG Sbjct: 61 GIETTKAVKARYPSVKVIILTTFEDDHYIFAGLKSGADGYLLKDADSDEMIASLQAVYEG 120 Query: 122 NILLNPKITREVVNALNSVNNAGTENLRNEQILQLLTPRELEVAKCIMEGKSNKEISSDL 181 ++LNPKIT VV ALN++ + ++ ++LTPREL+VAK IMEGKSNK I++DL Sbjct: 121 KMMLNPKITVSVVKALNNMEIPAVQKEPRTKLKEILTPRELDVAKHIMEGKSNKRIAADL 180 Query: 182 FITEGTVKNYVSRMLEKLELKNRTELTLCLQKSL 215 F+TEGTVKNYVSR+L+KLE+ NRTELTL LQK L Sbjct: 181 FLTEGTVKNYVSRILDKLEVSNRTELTLYLQKLL 214 >B1KTH4.1 B1KTH4_CLOBM Transcriptional regulatory protein DegU (Protease production enhancerprotein) Length = 219 Score = 249 bits (636), Expect = 1e-64, Method: Compositional matrix adjust. Identities = 125/218 (57%), Positives = 170/218 (77%), Gaps = 5/218 (2%) Query: 1 MVDIMIVDDQQIVREGLKMILSLHEEINVIGEASNGEEALELLSYTSPEVILMDIKMPVM 60 M+++++ DDQ+IVR+G+ MILSL+EEIN+IGEA NG+E + LL + P+VILMDI+MP+M Sbjct: 1 MINVIVADDQKIVRDGITMILSLYEEINIIGEAENGKELIMLLEKSLPDVILMDIRMPIM 60 Query: 61 NGIEATKLVKAKYPGIKVIILTTFNDSEYIFTGLKNGADGYILKDSGSQEIISSIKTACE 120 +G+EATK+VK KY +KVIILTTFN+ EYIF +K GADGY+LKD+GS+ II +IK+ Sbjct: 61 DGVEATKIVKEKYKNVKVIILTTFNEDEYIFKPIKYGADGYLLKDAGSEYIIEAIKSVYN 120 Query: 121 GNILLNPKITREVVNALNSVNNAGTENLRN----EQILQLLTPRELEVAKCIMEGKSNKE 176 G +LL+P++T +VV A NS+ T++ N + L LTPRE EVAK + +GKSNK+ Sbjct: 121 GAMLLDPEVTVKVVKAFNSITEK-TQSFTNFNKIKYELDALTPREREVAKLVSQGKSNKD 179 Query: 177 ISSDLFITEGTVKNYVSRMLEKLELKNRTELTLCLQKS 214 I + LF+TEGTVKNYV+R+LEKLEL NRTEL L + + Sbjct: 180 ICNILFLTEGTVKNYVTRILEKLELNNRTELALFINQD 217 >C4IBW4.1 C4IBW4_CLOBU DNA-binding response regulator Length = 216 Score = 244 bits (624), Expect = 3e-63, Method: Compositional matrix adjust. Identities = 119/214 (55%), Positives = 166/214 (77%), Gaps = 2/214 (0%) Query: 1 MVDIMIVDDQQIVREGLKMILSLHEEINVIGEASNGEEALELLSYT-SPEVILMDIKMPV 59 M++++I DDQ+IVREGLKMILSL EI VIGE NG++ +ELL P+VILMDI+MP+ Sbjct: 1 MINVIIADDQKIVREGLKMILSLDNEIKVIGEVDNGQDLIELLKKNIYPDVILMDIRMPI 60 Query: 60 MNGIEATKLVKAKYPGIKVIILTTFNDSEYIFTGLKNGADGYILKDSGSQEIISSIKTAC 119 +NG++ATK++K K+ IK+IILTTFN+ EYIFTG++NGADGYILKD+G EI +IKTAC Sbjct: 61 INGVDATKIIKEKFSHIKIIILTTFNEDEYIFTGIRNGADGYILKDAGFDEISKAIKTAC 120 Query: 120 EGNILLNPKITREVVNALNSVNNAGTENLRNEQILQLLTPRELEVAKCIMEGKSNKEISS 179 GNILLNP++ +++ N ++ N E+ L LLT RE++VA + +GKSNK+I + Sbjct: 121 AGNILLNPEVASKIIKEFNKLSPNKAINYNKEK-LNLLTKREMDVAILVGQGKSNKDICN 179 Query: 180 DLFITEGTVKNYVSRMLEKLELKNRTELTLCLQK 213 +LF+TEGT+KNY++++ EKL L +RTEL L + + Sbjct: 180 ELFLTEGTIKNYLTKIFEKLNLASRTELALFIDQ 213 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 0.314 0.133 0.353 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: 1,133,716,183 Number of extensions: 43363827 Number of successful extensions: 185458 Number of sequences better than 1.0e-05: 19468 Number of HSP's gapped: 185935 Number of HSP's successfully gapped: 19486 Length of query: 215 Length of database: 3,060,696,203 Length adjustment: 130 Effective length of query: 85 Effective length of database: 1,835,964,253 Effective search space: 156056961505 Effective search space used: 156056961505 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 128 (53.9 bits)