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= 0026.0003.p (257 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value RSc2024 [R] COG1279 Lysine efflux permease 68 2e-11 RSc0385 [R] COG1279 Lysine efflux permease 55 2e-07 Rv1986 [R] COG1279 Lysine efflux permease 54 2e-07 MT2040 [R] COG1279 Lysine efflux permease 54 2e-07 Rv0488 [R] COG1279 Lysine efflux permease 50 3e-06 >RSc2024 [R] COG1279 Lysine efflux permease Length = 202 Score = 67.8 bits (164), Expect = 2e-11, Method: Compositional matrix adjust. Identities = 59/191 (30%), Positives = 90/191 (47%), Gaps = 13/191 (6%) Query: 54 LEAIVHGILLAFGLILPLGVQNIFVFNQGALQPRFRRVVPVVLTAAVCDTLLIAAAVGGI 113 + A G++L F LIL +G QN F+ QG L R V + A+ D LLI A V G Sbjct: 1 MNAATQGLILGFSLILAIGSQNAFILRQGILG---RHVFVLCSVCALSDALLIVAGVSGF 57 Query: 114 SLVLLSVEWVTPIVYGAGILFLCIMGW-KIWNAAPGE------RDREARVLSLKGQVGYA 166 +++ ++ + G F+ G ++ +A G+ + +EA SL + Sbjct: 58 FVLVKHTPYIVDVARYGGAAFILWYGISRLLSALRGDSQMDISKAKEAD--SLPKALLSC 115 Query: 167 LSVSLLNPHALLDTVGVIGTNSLQYTGAERWXXXXXXXGISWMWFLSLAAAGRVLGRLDS 226 L+ + LNPH LDTV +IG+ S Q+ G E W S ++F L +L L S Sbjct: 116 LAFTFLNPHVYLDTVFLIGSISAQF-GDESWKFGVGASAASLIFFFCLGYGAALLRPLFS 174 Query: 227 SGRVIRLLNTV 237 S R+L+ V Sbjct: 175 SPVAWRILDFV 185 >RSc0385 [R] COG1279 Lysine efflux permease Length = 212 Score = 54.7 bits (130), Expect = 2e-07, Method: Compositional matrix adjust. Identities = 62/206 (30%), Positives = 95/206 (46%), Gaps = 9/206 (4%) Query: 49 RSRRMLEAIVHGILLAFGLILPLGVQNIFVFNQGALQPRFRRVVPVVLTAAVCDTLLIAA 108 S ++ A + G L LI+ +G QN +V QG R V+ VVL A+CD LIA Sbjct: 7 ESAPLIGAALSGFGLGASLIVAIGAQNAYVLRQGL---RREYVLGVVLICALCDMALIAL 63 Query: 109 AVGGI-SLVLLSVEWVTPIVYGAGILFLCIMGWKI----WNAAPGERDREARVLSLKGQV 163 V G+ +L+ W+T + + AG FL G + W A + R S + Sbjct: 64 GVAGMGTLISAHPAWLTAVRW-AGAAFLLAYGARAFRAAWRGAERLQARNGDKASHAQVL 122 Query: 164 GYALSVSLLNPHALLDTVGVIGTNSLQYTGAERWXXXXXXXGISWMWFLSLAAAGRVLGR 223 AL++SLLNPH LDTV ++G +Y S +WF L R+L Sbjct: 123 ASALALSLLNPHVYLDTVVLLGAIGGRYAMPANVAFAGGAMCASILWFSLLGFGARLLEP 182 Query: 224 LDSSGRVIRLLNTVSALLIWGIAVYM 249 + + R+L+ + ++W IA+ + Sbjct: 183 VFARPVAWRVLDALIGAVMWAIALTL 208 >Rv1986 [R] COG1279 Lysine efflux permease Length = 199 Score = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust. Identities = 58/205 (28%), Positives = 95/205 (46%), Gaps = 13/205 (6%) Query: 53 MLEAIVHGILLAFGLILPLGVQNIFVFNQGALQPRFRRVVPVVLTAAVCDTLLIAAAVGG 112 M +V G L F LI +G QN FV QG + V+PVV V D +LIAA + G Sbjct: 1 MNSPLVVGFLACFTLIAAIGAQNAFVLRQGIQR---EHVLPVVALCTVSDIVLIAAGIAG 57 Query: 113 ISLVLLSVEWVTPIVYGAGILFLCIMGWKIWNAAPGER-----DREARVLSLKGQVGYAL 167 ++ + +V G FL +G+ + A R A + L + Sbjct: 58 FGALIGAHPRALNVVKFGGAAFL--IGYGLLAARRAWRPVALIPSGATPVRLAEVLVTCA 115 Query: 168 SVSLLNPHALLDTVGVIGTNSLQYTGAERWXXXXXXXGISWMWFLSLA-AAGRVLGRLDS 226 + + LNPH LDTV ++G + +++ +RW S +WF +L AGR+ G + Sbjct: 116 AFTFLNPHVYLDTVVLLGALANEHSD-QRWLFGLGAVTASAVWFATLGFGAGRLRGLFTN 174 Query: 227 SGRVIRLLNTVSALLIWGIAVYMGV 251 G R+L+ + A+++ + + + V Sbjct: 175 PGS-WRILDGLIAVMMVALGISLTV 198 >MT2040 [R] COG1279 Lysine efflux permease Length = 199 Score = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust. Identities = 58/205 (28%), Positives = 95/205 (46%), Gaps = 13/205 (6%) Query: 53 MLEAIVHGILLAFGLILPLGVQNIFVFNQGALQPRFRRVVPVVLTAAVCDTLLIAAAVGG 112 M +V G L F LI +G QN FV QG + V+PVV V D +LIAA + G Sbjct: 1 MNSPLVVGFLACFTLIAAIGAQNAFVLRQGIQR---EHVLPVVALCTVSDIVLIAAGIAG 57 Query: 113 ISLVLLSVEWVTPIVYGAGILFLCIMGWKIWNAAPGER-----DREARVLSLKGQVGYAL 167 ++ + +V G FL +G+ + A R A + L + Sbjct: 58 FGALIGAHPRALNVVKFGGAAFL--IGYGLLAARRAWRPVALIPSGATPVRLAEVLVTCA 115 Query: 168 SVSLLNPHALLDTVGVIGTNSLQYTGAERWXXXXXXXGISWMWFLSLA-AAGRVLGRLDS 226 + + LNPH LDTV ++G + +++ +RW S +WF +L AGR+ G + Sbjct: 116 AFTFLNPHVYLDTVVLLGALANEHSD-QRWLFGLGAVTASAVWFATLGFGAGRLRGLFTN 174 Query: 227 SGRVIRLLNTVSALLIWGIAVYMGV 251 G R+L+ + A+++ + + + V Sbjct: 175 PGS-WRILDGLIAVMMVALGISLTV 198 >Rv0488 [R] COG1279 Lysine efflux permease Length = 201 Score = 50.4 bits (119), Expect = 3e-06, Method: Compositional matrix adjust. Identities = 54/182 (29%), Positives = 84/182 (46%), Gaps = 11/182 (6%) Query: 71 LGVQNIFVFNQGALQPRFRRVVPVVLTAAVCDTLLIAAAVGGISLVLLSVEWVTPIVYGA 130 +G QN FV QG R V+ +V + D LIAA VGG + ++ + +T + Sbjct: 8 IGPQNAFVLRQGI---RREYVLVIVALCGIADGALIAAGVGGFAALIHAHPNMTLVARFG 64 Query: 131 GILFLCIMGWKIWNA-----APGERDREARVLSLKGQVGYALSVSLLNPHALLDTVGVIG 185 G FL +G+ + A G E+ +L G V L V+ LNPH LDTV +IG Sbjct: 65 GAAFL--IGYALLAARNAWRPSGLVPSESGPAALIGVVQMCLVVTFLNPHVYLDTVVLIG 122 Query: 186 TNSLQYTGAERWXXXXXXXGISWMWFLSLAAAGRVLGRLDSSGRVIRLLNTVSALLIWGI 245 + + + RW S +WF L + L ++ R+L+ + A+ + G+ Sbjct: 123 ALANEESD-LRWFFGAGAWAASVVWFAVLGFSAGRLQPFFATPAAWRILDALVAVTMIGV 181 Query: 246 AV 247 AV Sbjct: 182 AV 183 Database: COG Posted date: Aug 3, 2010 9:58 AM Number of letters in database: 38,378,431 Number of sequences in database: 115,334 Lambda K H 0.327 0.140 0.447 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 115334 Number of Hits to DB: 18,562,627 Number of extensions: 763239 Number of successful extensions: 1878 Number of sequences better than 1.0e-05: 7 Number of HSP's gapped: 1867 Number of HSP's successfully gapped: 7 Length of query: 257 Length of database: 38,378,431 Length adjustment: 104 Effective length of query: 153 Effective length of database: 26,383,695 Effective search space: 4036705335 Effective search space used: 4036705335 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 114 (48.5 bits)