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= 0027.0004.p (367 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3K8Q6.1 B3K8Q6_9BACI Cell envelope-related function transcripti... 414 e-114 Q2BF45.1 Q2BF45_9BACI Membrane-bound transcriptional regulator LytR 171 1e-40 B1HQQ2.1 B1HQQ2_LYSSC Membrane-bound protein 162 4e-38 A3IBM5.1 A3IBM5_9BACI Membrane-bound transcriptional regulator LytR 159 4e-37 C2ZX16.1 C2ZX16_BACCE Membrane-bound protein lytR 158 8e-37 >B3K8Q6.1 B3K8Q6_9BACI Cell envelope-related function transcriptional attenuator, LytR/CpsA family Length = 328 Score = 414 bits (1064), Expect = e-114, Method: Compositional matrix adjust. Identities = 196/310 (63%), Positives = 249/310 (80%), Gaps = 7/310 (2%) Query: 46 FLFQKPLAVLAFDLFLSDRVEDKLKQESYQPLVNDGTTTVKPEPVVYKSDPFSLMLLGTD 105 FLF+ LAV+AFDLF++ VE+ L Q+SY+PL +D T PEPVV +S PFS+MLLG+D Sbjct: 21 FLFRTQLAVVAFDLFMAKDVEESL-QKSYKPLQSDKT----PEPVVLQSKPFSVMLLGSD 75 Query: 106 QRENETARSDTMIYAVIRPEDYKILLISIPRDTYTEIIGHDDNKKDKITHAYAFGGQQMA 165 QRE+E ARSDT+IYAV+RP + K+LLIS+PRDTY +IIG D KKDKI HA+A+GG QMA Sbjct: 76 QREDEPARSDTLIYAVVRPMESKVLLISVPRDTYVDIIGKD--KKDKINHAFAYGGHQMA 133 Query: 166 KDTLENLLGHDIQYYATINFQGLKDAVDAIGGVPLPIKKDIVNKGKDHEKFTIKGGKSNY 225 KDT+E ++ YYA+INFQGLKD VDA+GGV LPI+KDIVNKG+DHEKFTI+ K Y Sbjct: 134 KDTMEAFFDEELDYYASINFQGLKDVVDALGGVELPIRKDIVNKGRDHEKFTIEANKPIY 193 Query: 226 NGEEALNYTRYREDSDFNRTKRQQVFIDVVANKMLSISQIGNIPELLDIMGDNFKTDIQP 285 NGEEALNY RYREDSDFNR KRQQVF+DV A +++ + QIG +PEL++IMGDNF+TD+QP Sbjct: 194 NGEEALNYVRYREDSDFNRAKRQQVFLDVAAKRVMKLDQIGKVPELIEIMGDNFQTDMQP 253 Query: 286 SMIISLAKKFMGGKDMDISSFTVMGEGERIGGIYYDIVDEEDLTEAKAMIDNWMNASTPV 345 II LAK+ + G +D++S+T+MGEG +I GIYY+ D ED+ EA+ +IDNWMN TP Sbjct: 254 KFIIDLAKQMLTGGKVDMTSYTIMGEGMKINGIYYNEADMEDVQEARDLIDNWMNPDTPA 313 Query: 346 DQLIEPGKAQ 355 DQL++P A+ Sbjct: 314 DQLLQPKDAE 323 >Q2BF45.1 Q2BF45_9BACI Membrane-bound transcriptional regulator LytR Length = 308 Score = 171 bits (432), Expect = 1e-40, Method: Compositional matrix adjust. Identities = 98/270 (36%), Positives = 152/270 (56%), Gaps = 11/270 (4%) Query: 74 YQPLVNDGTTTVKPEPVVYKSDPFSLMLLGTDQRENETARSDTMIYAVIRPEDYKILLIS 133 +QP+ + + + + K DPFS+++LG D+R+ + RSDTMI + PE + ++S Sbjct: 46 HQPIEREKSEKRQETVTLEKRDPFSVLMLGVDERDGDKGRSDTMIVLTVNPEKNSVKMLS 105 Query: 134 IPRDTYTEIIGHDDNKKDKITHAYAFGGQQMAKDTLENLLGHDIQYYATINFQGLKDAVD 193 IPRDT TEIIGH DKI HAYAFGG MA DT+EN L I YY IN +G +D VD Sbjct: 106 IPRDTRTEIIGH--GTTDKINHAYAFGGVPMAMDTVENFLDIPIDYYIQINMEGFRDIVD 163 Query: 194 AIGGVPLPIKKDIVNKGKDHEKFTIKGGKSNYNGEEALNYTRYR-ED--SDFNRTKRQQV 250 ++GG+ + D + G + G +G++AL ++R R ED DF R RQ++ Sbjct: 164 SVGGITVNNDLDFDSGG-----YHFPEGTVTMDGKKALAFSRMRYEDPRGDFGRQLRQRM 218 Query: 251 FIDVVANKMLSISQIGNIPELLDIMGDNFKTDIQPSMIISLAKKFMGGKDMDISSFTVMG 310 I V K +S+S + N E+ +G N KT++ ++ + K + DI ++ G Sbjct: 219 IIQAVLKKGVSVSSLANYDEIFSALGKNVKTNLAFGEMVDIQKHYKNAAK-DIEQISIEG 277 Query: 311 EGERIGGIYYDIVDEEDLTEAKAMIDNWMN 340 GERI I+Y +V +E+ ++ + N ++ Sbjct: 278 TGERIDNIWYLMVSDEEKGRIQSEMKNHLS 307 >B1HQQ2.1 B1HQQ2_LYSSC Membrane-bound protein Length = 312 Score = 162 bits (410), Expect = 4e-38, Method: Compositional matrix adjust. Identities = 101/270 (37%), Positives = 153/270 (56%), Gaps = 12/270 (4%) Query: 76 PLVNDGTTTVKPEPVVYKSDPFSLMLLGTDQRENETARSDTMIYAVIRPEDYKILLISIP 135 PL+ E V K +PFS+++LG D+R++++ RSDTMI + PE + ++SIP Sbjct: 50 PLLQTTDAAQLEEKTVIKKEPFSVLMLGVDERKDDSGRSDTMIVITVNPEKQTMKMLSIP 109 Query: 136 RDTYTEIIGHDDNKKDKITHAYAFGGQQMAKDTLENLLGHDIQYYATINFQGLKDAVDAI 195 RDT TEI+GHD DKI HAYAFGG MA DT+EN L I YY IN +G +D + Sbjct: 110 RDTRTEIVGHD--TVDKINHAYAFGGVPMAVDTVENFLNIPIDYYVFINMEGFLQIIDTL 167 Query: 196 GGVPLPIKKDIVNKGKDHEKFTIKGGKSNYNGEEALNYTRYR-ED--SDFNRTKRQQVFI 252 GGV + D+ ++++ G+ +G EAL ++R R ED DF R RQ+ I Sbjct: 168 GGVTINNDMDLT-----YDEYHYPKGEITLDGNEALIFSRIRYEDPRGDFGRQIRQRQII 222 Query: 253 DVVANKMLSISQIGNIPELLDIMGDNFKTDIQPSMIISLAKKFMG-GKDMDISSFTVMGE 311 + V K + S + ++L ++GDN + + +I L + KD++ SF G+ Sbjct: 223 EAVMKKASTPSTLLKATDMLTVLGDNVRMNFSVKELIQLQGIYKKMDKDIEQLSFE-KGD 281 Query: 312 GERIGGIYYDIVDEEDLTEAKAMIDNWMNA 341 GERI I+Y I +EE+L + +A + N + + Sbjct: 282 GERINRIWYYIPNEEELQKIQADLKNHLQS 311 >A3IBM5.1 A3IBM5_9BACI Membrane-bound transcriptional regulator LytR Length = 312 Score = 159 bits (402), Expect = 4e-37, Method: Compositional matrix adjust. Identities = 100/272 (36%), Positives = 152/272 (55%), Gaps = 16/272 (5%) Query: 76 PLVNDGTTTVKPEPVVYKSDPFSLMLLGTDQRENETARSDTMIYAVIRPEDYKILLISIP 135 PL+ E V K +PFS+++LG D+R++++ RSDTMI + PE + ++SIP Sbjct: 50 PLLQTTDAAQLEEKTVIKKEPFSVLMLGVDERKDDSGRSDTMIVITVNPEKQTMKMLSIP 109 Query: 136 RDTYTEIIGHDDNKKDKITHAYAFGGQQMAKDTLENLLGHDIQYYATINFQGLKDAVDAI 195 RDT TEI+GHD DKI HAYAFGG MA DT+EN L I YY IN +G +D + Sbjct: 110 RDTRTEIVGHD--TVDKINHAYAFGGVPMAVDTVENFLNIPIDYYVFINMEGFLQIIDTL 167 Query: 196 GGVPLPIKKDIVNKGKDHEKFTIKGGKSNYNGEEALNYTRYR-ED--SDFNRTKRQQVFI 252 GGV + D+ ++++ G+ +G EAL ++R R ED DF R RQ+ I Sbjct: 168 GGVTINNDMDLT-----YDEYHYPKGEITLDGNEALIFSRIRYEDPRGDFGRQIRQRQII 222 Query: 253 DVVANKMLSISQIGNIPELLDIMGDNFKTDIQPSMIISLAKKFMGGKDMD--ISSFTV-M 309 + V K + + + ++L ++GDN + + +I L + K MD I + Sbjct: 223 EAVMKKASTPATLLKATDMLTVLGDNVRMNFSVKELIQLQGIY---KKMDKGIEQLSFEQ 279 Query: 310 GEGERIGGIYYDIVDEEDLTEAKAMIDNWMNA 341 G+GERI I+Y I +EE+L + +A + N + + Sbjct: 280 GDGERINRIWYYIPNEEELQKIQADLKNHLQS 311 >C2ZX16.1 C2ZX16_BACCE Membrane-bound protein lytR Length = 304 Score = 158 bits (399), Expect = 8e-37, Method: Compositional matrix adjust. Identities = 92/257 (35%), Positives = 145/257 (56%), Gaps = 11/257 (4%) Query: 74 YQPLVNDGTTTVKPEPVVYKSDPFSLMLLGTDQRENETARSDTMIYAVIRPEDYKILLIS 133 + PL D +T + + S P S++LLG D+R + RSD+++ + P+D + ++S Sbjct: 39 HTPLERDHSTKRSTDVKLGNSQPVSILLLGADERGADKGRSDSIMLLTLNPKDSSMKMVS 98 Query: 134 IPRDTYTEIIGHDDNKKDKITHAYAFGGQQMAKDTLENLLGHDIQYYATINFQGLKDAVD 193 IPRDTYTEI+G KKDKI HAYAFGG +M+ +T+EN L + YY +N +G +D VD Sbjct: 99 IPRDTYTEIVGK--GKKDKINHAYAFGGIEMSVNTVENFLDVPVDYYIEVNMEGFQDIVD 156 Query: 194 AIGGVPLPIKKDIVNKGKDHEKFTIKGGKSNYNGEEALNYTRYRED---SDFNRTKRQQV 250 A+GGV + +G+ EK TI + NGE+AL YTR R++ DF R RQ+ Sbjct: 157 AVGGVDVNNDLAFTLEGQTFEKGTI-----HLNGEQALKYTRMRKEDPRGDFGRQMRQRQ 211 Query: 251 FIDVVANKMLSISQIGNIPELLDIMGDNFKTDIQPSMIISLAKKFMGGKDMDISSFTVMG 310 ++ V ++ +IS I + +L+ + N KT++ + L + + + G Sbjct: 212 VLEAVISQGANISSITKLGTMLEAVEKNVKTNLNQDQMWDLQSNYKAAMNKK-EEIQIPG 270 Query: 311 EGERIGGIYYDIVDEED 327 +G + GI+Y V E+D Sbjct: 271 DGRKQDGIWYYFVSEKD 287 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 0.316 0.135 0.382 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: 2,030,337,849 Number of extensions: 86802070 Number of successful extensions: 204973 Number of sequences better than 1.0e-05: 1908 Number of HSP's gapped: 200607 Number of HSP's successfully gapped: 1908 Length of query: 367 Length of database: 3,060,696,203 Length adjustment: 137 Effective length of query: 230 Effective length of database: 1,770,017,148 Effective search space: 407103944040 Effective search space used: 407103944040 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 132 (55.5 bits)