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= 0521.0006.p (234 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B1BBE3.1 B1BBE3_CLOBO Regulatory protein VanR 254 4e-66 A0PXH1.1 A0PXH1_CLONN Transcriptional regulatory protein 250 7e-65 C3IC79.1 C3IC79_BACTU Two-component response regulator 246 1e-63 C2P8N5.1 C2P8N5_BACCE Two-component response regulator 244 4e-63 C2N4G9.1 C2N4G9_BACCE Two-component response regulator 244 4e-63 >B1BBE3.1 B1BBE3_CLOBO Regulatory protein VanR Length = 235 Score = 254 bits (649), Expect = 4e-66, Method: Compositional matrix adjust. Identities = 128/233 (54%), Positives = 175/233 (75%), Gaps = 3/233 (1%) Query: 1 MYTILIADDELEIVELLQLYLEKE-YNILQAQNGNEALKLMQSHTVDLAILDIMMPGMDG 59 M ILIADDE EI+ELL LYLEK+ + I A NG EA +++ ++ VD+AI+DIMMP +DG Sbjct: 1 MAEILIADDEEEIIELLSLYLEKDKHCIYSAVNGLEAFEIISNNKVDIAIIDIMMPKIDG 60 Query: 60 LQLLKRIRENDHFPVLFLSAKSQYHDKILGLELGADDYISKPFNPLEIVARVGSMLRRVH 119 L+K+IRE P++ LSAKS+Y DKILGL+LGADDY++KPFN +E+VARV + LRR + Sbjct: 61 YHLIKKIREKYDIPIIMLSAKSEYSDKILGLDLGADDYVTKPFNAMEVVARVNAQLRRYN 120 Query: 120 EF--DAPAVQEKKKEQIVLGRLLLDRSSCQVEVDGEPVALTSTEYKILELLMEQPGRVFT 177 + + ++KK + G L L+ ++C + D V LTSTEYKI+ L+E GRVFT Sbjct: 121 KLKKNTYVNLKEKKSYLECGNLRLNINTCTLYKDNVEVYLTSTEYKIISYLLENKGRVFT 180 Query: 178 RKKIYEAVWEDFYVYEDNSIMVHISNIRDKIERDSKKPEYLKTIRGLGYKIEA 230 +K+I+E VWE+ + +DN+IMVHISN+RDK+E DSK P+Y+KTIRGLGYK++A Sbjct: 181 KKQIFEYVWEEPFYGDDNAIMVHISNLRDKVEDDSKNPKYIKTIRGLGYKLDA 233 >A0PXH1.1 A0PXH1_CLONN Transcriptional regulatory protein Length = 232 Score = 250 bits (639), Expect = 7e-65, Method: Compositional matrix adjust. Identities = 129/234 (55%), Positives = 181/234 (77%), Gaps = 4/234 (1%) Query: 1 MYTILIADDELEIVELLQLYLEKE-YNILQAQNGNEALKLMQSHTVDLAILDIMMPGMDG 59 M +LIADDE EI+ELL LYLEK+ + I A NG EAL+++ ++ VD+AI+DIMMP +DG Sbjct: 1 MARVLIADDEEEIIELLSLYLEKDGHCIYSAVNGLEALQIINNNEVDIAIIDIMMPQIDG 60 Query: 60 LQLLKRIRENDHFPVLFLSAKSQYHDKILGLELGADDYISKPFNPLEIVARVGSMLRRVH 119 L+++IREN PV+ LSAKS+Y DKILGL+LGADDYI+KPFN +E++ARV + LRR + Sbjct: 61 YHLVRKIRENYDMPVIMLSAKSEYCDKILGLDLGADDYITKPFNAMEVLARVKAQLRRYN 120 Query: 120 EFDAPAVQEKKKEQIV-LGRLLLDRSSCQVEVDGEPVALTSTEYKILELLMEQPGRVFTR 178 + + + +EK ++Q + G+L L+ ++C + + V LTSTEYKIL L+E G+VFT+ Sbjct: 121 K--SMSEKEKCEKQYLECGKLRLNINTCTLYKENIEVYLTSTEYKILFYLLENKGKVFTK 178 Query: 179 KKIYEAVWEDFYVYEDNSIMVHISNIRDKIERDSKKPEYLKTIRGLGYKIEAPV 232 K+I+E VWE+ + +DN+IMVHISN+RDKIE DSK P Y+KTIRGLGYK+++ + Sbjct: 179 KQIFEYVWEEPFYGDDNAIMVHISNLRDKIEDDSKNPHYIKTIRGLGYKLDSNI 232 >C3IC79.1 C3IC79_BACTU Two-component response regulator Length = 238 Score = 246 bits (628), Expect = 1e-63, Method: Compositional matrix adjust. Identities = 121/226 (53%), Positives = 168/226 (74%), Gaps = 2/226 (0%) Query: 3 TILIADDELEIVELLQLYLEKE-YNILQAQNGNEALKLMQSHTVDLAILDIMMPGMDGLQ 61 TILI DD+ +I+ELL+L+LE E + +L+A +G ALK ++ + +DLAI+DIMMP MDG Q Sbjct: 4 TILIVDDDTDIIELLKLFLEIEGFLVLEASDGEAALKYVKENHIDLAIVDIMMPKMDGYQ 63 Query: 62 LLKRIRENDHFPVLFLSAKSQYHDKILGLELGADDYISKPFNPLEIVARVGSMLRRVHEF 121 L+K++RE FP+L LSAK+Q DKI+GL LGADD+I KPF+PLEI+ARV + LRR +EF Sbjct: 64 LIKKVRETLKFPILILSAKTQEIDKIMGLGLGADDFIVKPFSPLEIIARVQAHLRRSYEF 123 Query: 122 DAPAVQEKKKEQIVLGRLLLDRSSCQVEVDGEPVALTSTEYKILELLMEQPGRVFTRKKI 181 + + E QI +G L+LD SC + + + L++ EYK+L L ME PGR+FT+K+I Sbjct: 124 NKNTL-ESTVNQIHIGNLILDHHSCMLYKYNKSITLSAIEYKLLTLFMEDPGRIFTKKQI 182 Query: 182 YEAVWEDFYVYEDNSIMVHISNIRDKIERDSKKPEYLKTIRGLGYK 227 +E VW D Y +DN+IMVHIS +R+K+E + P Y+KTIRGLGY+ Sbjct: 183 FERVWSDHYYSDDNAIMVHISRLREKLEDSPRNPVYIKTIRGLGYR 228 >C2P8N5.1 C2P8N5_BACCE Two-component response regulator Length = 238 Score = 244 bits (623), Expect = 4e-63, Method: Compositional matrix adjust. Identities = 117/210 (55%), Positives = 161/210 (76%), Gaps = 2/210 (0%) Query: 20 YLEKE-YNILQAQNGNEALKLMQSHTVDLAILDIMMPGMDGLQLLKRIRENDHFPVLFLS 78 +LE E + +++A NG ALK ++ + +DLAI+DIMMP MDG QL+K+IRE FP+L LS Sbjct: 21 FLEMENFFVVEASNGEVALKCLEENHIDLAIVDIMMPKMDGYQLIKKIRETLQFPILILS 80 Query: 79 AKSQYHDKILGLELGADDYISKPFNPLEIVARVGSMLRRVHEFDAPAVQEKKKEQIVLGR 138 AKSQ DKI+GL +GADD+I+KPF+ LEI+ARV + LRR +EF+ AV+ K+K QI +G Sbjct: 81 AKSQEVDKIIGLGIGADDFITKPFSALEIIARVQAHLRRSYEFNDKAVKGKEK-QIHMGD 139 Query: 139 LLLDRSSCQVEVDGEPVALTSTEYKILELLMEQPGRVFTRKKIYEAVWEDFYVYEDNSIM 198 L+LD SC + E + L++TEYKIL L ME+PGR+FT+K+I+E+VW D+Y +DN+IM Sbjct: 140 LVLDHHSCTLYKSSETITLSATEYKILTLFMEEPGRIFTKKQIFESVWSDYYCADDNTIM 199 Query: 199 VHISNIRDKIERDSKKPEYLKTIRGLGYKI 228 VHIS +R+K+E K P Y+KTIRGLGY+ Sbjct: 200 VHISRLREKLEDSPKNPVYIKTIRGLGYRF 229 >C2N4G9.1 C2N4G9_BACCE Two-component response regulator Length = 238 Score = 244 bits (623), Expect = 4e-63, Method: Compositional matrix adjust. Identities = 117/210 (55%), Positives = 161/210 (76%), Gaps = 2/210 (0%) Query: 20 YLEKE-YNILQAQNGNEALKLMQSHTVDLAILDIMMPGMDGLQLLKRIRENDHFPVLFLS 78 +LE E + +++A NG ALK ++ + +DLAI+DIMMP MDG QL+K+IRE FP+L LS Sbjct: 21 FLEMENFFVVEASNGEVALKCLEENHIDLAIVDIMMPKMDGYQLIKKIRETLQFPILILS 80 Query: 79 AKSQYHDKILGLELGADDYISKPFNPLEIVARVGSMLRRVHEFDAPAVQEKKKEQIVLGR 138 AKSQ DKI+GL +GADD+I+KPF+ LEI+ARV + LRR +EF+ AV+ K+K QI +G Sbjct: 81 AKSQEVDKIIGLGIGADDFITKPFSALEIIARVQAHLRRSYEFNDKAVKGKEK-QIHMGD 139 Query: 139 LLLDRSSCQVEVDGEPVALTSTEYKILELLMEQPGRVFTRKKIYEAVWEDFYVYEDNSIM 198 L+LD SC + E + L++TEYKIL L ME+PGR+FT+K+I+E+VW D+Y +DN+IM Sbjct: 140 LVLDHHSCTLYKSSETITLSATEYKILTLFMEEPGRIFTKKQIFESVWSDYYCADDNTIM 199 Query: 199 VHISNIRDKIERDSKKPEYLKTIRGLGYKI 228 VHIS +R+K+E K P Y+KTIRGLGY+ Sbjct: 200 VHISRLREKLEDSPKNPVYIKTIRGLGYRF 229 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 0.319 0.139 0.387 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: 1,371,091,410 Number of extensions: 55451154 Number of successful extensions: 250047 Number of sequences better than 1.0e-05: 30414 Number of HSP's gapped: 218398 Number of HSP's successfully gapped: 30573 Length of query: 234 Length of database: 3,060,696,203 Length adjustment: 131 Effective length of query: 103 Effective length of database: 1,826,543,238 Effective search space: 188133953514 Effective search space used: 188133953514 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 (21.7 bits) S2: 129 (54.3 bits)