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= 0520.0009.p (307 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KIS6.1 B3KIS6_9BACI PRD domain protein 360 7e-98 B1D7P7.1 B1D7P7_9BACL Transcriptional antiterminator, BglG 266 2e-69 C0ZH78.1 C0ZH78_BREBN Probable transcriptional antiterminator 243 1e-62 C3E7Z3.1 C3E7Z3_BACTU Transcription antiterminator 176 3e-42 C2YEU7.1 C2YEU7_BACCE Transcription antiterminator 176 3e-42 >B3KIS6.1 B3KIS6_9BACI PRD domain protein Length = 295 Score = 360 bits (925), Expect = 7e-98, Method: Compositional matrix adjust. Identities = 174/288 (60%), Positives = 224/288 (77%), Gaps = 3/288 (1%) Query: 21 FEVLRVIGNNVVMVQGGRKGKEYVIIGKGIGFAVKDTGFIDANDQRIEKLFRLEDRDEWS 80 F V+RVIGNNVVMV GG+K EYVI+GKGIGF K G I ++D+RIEKLFRLEDR++WS Sbjct: 7 FTVVRVIGNNVVMVTGGKKESEYVILGKGIGFGAKIGGTIASDDKRIEKLFRLEDREQWS 66 Query: 81 QYQILLEDIDPKVMKITDDIIADIAHEFSGKLNDKIYLALPSHIQFTIYRLRGGMDIVXX 140 Q LLE+ DP+VM+ITD I+ I EF G LNDK+YLALPSHIQFTIYR+R GMDI+ Sbjct: 67 QAHHLLEEFDPQVMEITDQILNLIGQEFPGTLNDKVYLALPSHIQFTIYRIRKGMDII-- 124 Query: 141 XXFLQETKMSFPKEFEIAYRAAEKISAEFNVQIPEDEVGFLTYHVYSAVSNVPVGQLVKA 200 FL+ET++SFPKE++IA +AAE I F++++PEDE+GFLTYHVYSAVS+VPVG LVKA Sbjct: 125 NPFLEETRISFPKEYDIAAKAAELIGKTFDIEVPEDEIGFLTYHVYSAVSHVPVGHLVKA 184 Query: 201 SNIVSELLDMIREERKVTFVYGSMNHIRLMIHLRFSIERILQGSL-IDNPFVKHIQKEYK 259 SN+V L+ I EER+V F GSM+++RL++HLRFS++RIL + +DNPF + I+ ++ Sbjct: 185 SNVVGSLVKYIEEERQVAFDRGSMDYVRLLMHLRFSVDRILNQEIHVDNPFAEQIRSKFT 244 Query: 260 EEYKLAQKLGKVMQNSLGTEVPEEEICFLAMHLRRLFQTLDQQHKQKQ 307 +EY LA +L +M+ LG +VPE E+CFLAMHL RLF QQ Q + Sbjct: 245 QEYGLATRLSGMMEKELGKKVPEAEVCFLAMHLYRLFTGRLQQKNQPR 292 >B1D7P7.1 B1D7P7_9BACL Transcriptional antiterminator, BglG Length = 286 Score = 266 bits (679), Expect = 2e-69, Method: Compositional matrix adjust. Identities = 128/283 (45%), Positives = 195/283 (68%), Gaps = 2/283 (0%) Query: 20 QFEVLRVIGNNVVMVQGGRKGKEYVIIGKGIGFAVKDTGFIDANDQRIEKLFRLEDRDEW 79 Q + R++GNNV++ + +EYV+ GKGIGF+ K FIDA D RIEK +RL+DRD+ Sbjct: 6 QLRIDRIVGNNVILTMEPKSSREYVLFGKGIGFSCKGQKFIDAEDPRIEKRYRLDDRDKA 65 Query: 80 SQYQILLEDIDPKVMKITDDIIADIAHEFSGKLNDKIYLALPSHIQFTIYRLRGGMDIVX 139 Y LLE++DP+V++I++ II +I ++ K+Y ALPSHIQF +YRLR GM+IV Sbjct: 66 LHYHSLLEELDPEVVQISEQIIDEIRERLGTPVDPKVYFALPSHIQFVVYRLRNGMEIVN 125 Query: 140 XXXFLQETKMSFPKEFEIAYRAAEKISAEFNVQIPEDEVGFLTYHVYSAVSNVPVGQLVK 199 FL ETKM +P+EF+IA +AA+ IS +F++ IPEDEVGFLTYHVYSA +V GQ+V+ Sbjct: 126 P--FLYETKMCYPQEFKIAAKAAKMISEKFDITIPEDEVGFLTYHVYSAAGSVTAGQMVQ 183 Query: 200 ASNIVSELLDMIREERKVTFVYGSMNHIRLMIHLRFSIERILQGSLIDNPFVKHIQKEYK 259 + +++E+++ I R+ S ++ RL++HLR+ +ERILQ +NPF I+ + Sbjct: 184 LTELMNEIVERIEGWREAPLSKKSSDYARLIMHLRYMMERILQNKETENPFSAEIKDKIP 243 Query: 260 EEYKLAQKLGKVMQNSLGTEVPEEEICFLAMHLRRLFQTLDQQ 302 E++ A+ + +++ L +V +EI +LAMHL RLF+++D + Sbjct: 244 TEHQKAELIAQMIGERLNVKVSSDEIGYLAMHLYRLFRSVDAE 286 >C0ZH78.1 C0ZH78_BREBN Probable transcriptional antiterminator Length = 285 Score = 243 bits (620), Expect = 1e-62, Method: Compositional matrix adjust. Identities = 118/277 (42%), Positives = 182/277 (65%), Gaps = 2/277 (0%) Query: 21 FEVLRVIGNNVVMVQGGRKGKEYVIIGKGIGFAVKDTGFIDANDQRIEKLFRLEDRDEWS 80 + + RV+ +NVV+V+ G+E V+ GKGIGF K I A+D R+EK FRLE+ Sbjct: 9 YAITRVLNHNVVLVEEPGSGQEIVLFGKGIGFGAKPGNTIPAHDLRVEKRFRLENESHQK 68 Query: 81 QYQILLEDIDPKVMKITDDIIADIAHEFSGKLNDKIYLALPSHIQFTIYRLRGGMDIVXX 140 QYQ +L +DP V+ I ++IIA IA E + +LN+ +++ALP HIQF IYRL GM+IV Sbjct: 69 QYQNILSQVDPAVVGIAEEIIALIASEITPELNEHVHVALPDHIQFAIYRLNNGMEIVNP 128 Query: 141 XXFLQETKMSFPKEFEIAYRAAEKISAEFNVQIPEDEVGFLTYHVYSAVSNVPVGQLVKA 200 FL E + + KE+ +A RAA+ I F++ IP+ E+GFL H++SA+S VPV + V+ Sbjct: 129 --FLFEIQTLYTKEYALANRAADMIKNAFDLDIPDSEIGFLALHIHSAISYVPVKKAVQF 186 Query: 201 SNIVSELLDMIREERKVTFVYGSMNHIRLMIHLRFSIERILQGSLIDNPFVKHIQKEYKE 260 +NI++EL+ +I E+ +T +++++RL+ HLRF++ERI Q I NP + ++ E Sbjct: 187 TNIITELVSLIEEQTAITIERSTIDYVRLITHLRFAVERIRQQKFIKNPLLDRVKTTMPE 246 Query: 261 EYKLAQKLGKVMQNSLGTEVPEEEICFLAMHLRRLFQ 297 Y+LA +L + + L VPE+E+ ++A+HL RL Q Sbjct: 247 AYQLATELAQYISTRLEIAVPEDEVGYMALHLYRLLQ 283 >C3E7Z3.1 C3E7Z3_BACTU Transcription antiterminator Length = 282 Score = 176 bits (445), Expect = 3e-42, Method: Compositional matrix adjust. Identities = 98/280 (35%), Positives = 170/280 (60%), Gaps = 7/280 (2%) Query: 21 FEVLRVIGNNVVMVQGGRKGKEYVIIGKGIGFAVKDTGFIDANDQRIEKLFRLEDRDEWS 80 E+ +V+ NNV+ + + +E V+IGKGIGF K ++ ++IEK+F L++ + Sbjct: 5 LEIKKVLNNNVI-IASHPEHEEVVVIGKGIGFGKKAKDVLE--QEQIEKMFVLKNERDRE 61 Query: 81 QYQILLEDIDPKVMKITDDIIADIAHEFSGKLNDKIYLALPSHIQFTIYRLRGGMDIVXX 140 QY++L+ I K++++ +DI+ I + LN+ I++AL HI F I RL+ G+ I Sbjct: 62 QYKLLVPHISEKLIELMNDIMLYIQGKAKSPLNEHIHIALTDHISFAIKRLKQGLTI--D 119 Query: 141 XXFLQETKMSFPKEFEIAYRAAEKISAEFNVQIPEDEVGFLTYHVYSAVSNVPVGQLVKA 200 FL ETKM +PKE+EIA E +++ + +PE E+GF+ H+YS+++N + + + Sbjct: 120 NPFLVETKMLYPKEYEIAEGVVELLNSRLQITLPEGEIGFIALHIYSSLTNSDLSSVNQN 179 Query: 201 SNIVSELLDMIREERKVTFVYGSMNHIRLMIHLRFSIERILQGSLID--NPFVKHIQKEY 258 S ++++L+ +I ++T S++++RL+ HL+++IER+ +G ++ F ++ EY Sbjct: 180 SRLIAQLVSLIETNLQITLDQESIHYLRLIRHLQYAIERVKKGEKVEESQSFADLLKAEY 239 Query: 259 KEEYKLAQKLGKVMQNSLGTEVPEEEICFLAMHLRRLFQT 298 Y LA KL KVMQ L V E E +L MHL+RL + Sbjct: 240 PACYNLAWKLVKVMQKELQLPVYEAESIYLTMHLQRLVKA 279 >C2YEU7.1 C2YEU7_BACCE Transcription antiterminator Length = 282 Score = 176 bits (445), Expect = 3e-42, Method: Compositional matrix adjust. Identities = 98/280 (35%), Positives = 170/280 (60%), Gaps = 7/280 (2%) Query: 21 FEVLRVIGNNVVMVQGGRKGKEYVIIGKGIGFAVKDTGFIDANDQRIEKLFRLEDRDEWS 80 E+ +V+ NNV+ + + +E V+IGKGIGF K ++ ++IEK+F L++ + Sbjct: 5 LEIKKVLNNNVI-IASHPEHEEVVVIGKGIGFGKKAKDVLE--QEQIEKMFVLKNERDRE 61 Query: 81 QYQILLEDIDPKVMKITDDIIADIAHEFSGKLNDKIYLALPSHIQFTIYRLRGGMDIVXX 140 QY++L+ I K++++ +DI+ I + LN+ I++AL HI F I RL+ G+ I Sbjct: 62 QYKLLVPHISEKLIELMNDIMLYIQGKAKSPLNEHIHIALTDHISFAIKRLKQGLTI--D 119 Query: 141 XXFLQETKMSFPKEFEIAYRAAEKISAEFNVQIPEDEVGFLTYHVYSAVSNVPVGQLVKA 200 FL ETKM +PKE+EIA E +++ + +PE E+GF+ H+YS+++N + + + Sbjct: 120 NPFLVETKMLYPKEYEIAEGVVELLNSRLQITLPEGEIGFIALHIYSSLTNSDLSSVNQN 179 Query: 201 SNIVSELLDMIREERKVTFVYGSMNHIRLMIHLRFSIERILQGSLID--NPFVKHIQKEY 258 S ++++L+ +I ++T S++++RL+ HL+++IER+ +G ++ F ++ EY Sbjct: 180 SRLIAQLVSLIETNLQITLDQESIHYLRLIRHLQYAIERVKKGEKVEESQSFADLLKAEY 239 Query: 259 KEEYKLAQKLGKVMQNSLGTEVPEEEICFLAMHLRRLFQT 298 Y LA KL KVMQ L V E E +L MHL+RL + Sbjct: 240 PACYNLAWKLVKVMQKELQLPVYEAESIYLTMHLQRLVKA 279 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 0.140 0.399 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: 1,626,511,648 Number of extensions: 64672823 Number of successful extensions: 173271 Number of sequences better than 1.0e-05: 907 Number of HSP's gapped: 170690 Number of HSP's successfully gapped: 943 Length of query: 307 Length of database: 3,060,696,203 Length adjustment: 135 Effective length of query: 172 Effective length of database: 1,788,859,178 Effective search space: 307683778616 Effective search space used: 307683778616 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)