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= 0038.0003.p (242 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value ypdB [KT] COG3279 Response regulator of the LytR/AlgR family 288 6e-78 Z3646 [KT] COG3279 Response regulator of the LytR/AlgR family 288 6e-78 ECs3261 [KT] COG3279 Response regulator of the LytR/AlgR family 288 6e-78 BS_lytT [KT] COG3279 Response regulator of the LytR/AlgR family 134 1e-31 CAC1670 [KT] COG3279 Response regulator of the LytR/AlgR family 121 8e-28 >ypdB [KT] COG3279 Response regulator of the LytR/AlgR family Length = 244 Score = 288 bits (736), Expect = 6e-78, Method: Compositional matrix adjust. Identities = 143/244 (58%), Positives = 178/244 (72%), Gaps = 2/244 (0%) Query: 1 MRAIIVEDEVLARQELAFLIGANSAIRIAGEFEDGLDALKYLQTEEVDVIFLDINIPSID 60 M+ IIVEDE LA+QEL++LI +S + I G F+DGLD LK+LQ VD IFLDINIPS+D Sbjct: 1 MKVIIVEDEFLAQQELSWLIKEHSQMEIVGTFDDGLDVLKFLQHNRVDAIFLDINIPSLD 60 Query: 61 GVLLAQNISRFSVKPYIVFITAYKXXXXXXXXXXXXDYILKPYSETRIKAMLHKLEVAFA 120 GVLLAQNIS+F+ KP+IVFITA+K DYILKPY E+RI ML KLE A+ Sbjct: 61 GVLLAQNISQFAHKPFIVFITAWKEHAVEAFELEAFDYILKPYQESRITGMLQKLEAAWQ 120 Query: 121 ARGHQGEEEHV--KLSDKVNLWKNEKIIVVDADEIYYASAQEKTTSVITKGEEYNMALSI 178 + + +D +NL K+E+IIV ++IYYA A EK T V T+ E Y M ++I Sbjct: 121 QQQTSSTPAATVTRENDTINLVKDERIIVTPINDIYYAEAHEKMTFVYTRRESYVMPMNI 180 Query: 179 SEFHSRLPQDRFFRCHRSYLVNLSKIKEIIPWFNNTYLLRLRDLDFEVPVSRSKVKEFRQ 238 +EF S+LP FFRCHRS+ VNL+KI+EI PWFNNTY+LRL+DLDFEVPVSRSKVKEFRQ Sbjct: 181 TEFCSKLPPSHFFRCHRSFCVNLNKIREIEPWFNNTYILRLKDLDFEVPVSRSKVKEFRQ 240 Query: 239 IMRI 242 +M + Sbjct: 241 LMHL 244 >Z3646 [KT] COG3279 Response regulator of the LytR/AlgR family Length = 244 Score = 288 bits (736), Expect = 6e-78, Method: Compositional matrix adjust. Identities = 143/244 (58%), Positives = 178/244 (72%), Gaps = 2/244 (0%) Query: 1 MRAIIVEDEVLARQELAFLIGANSAIRIAGEFEDGLDALKYLQTEEVDVIFLDINIPSID 60 M+ IIVEDE LA+QEL++LI +S + I G F+DGLD LK+LQ VD IFLDINIPS+D Sbjct: 1 MKVIIVEDEFLAQQELSWLIKEHSQMEIVGTFDDGLDVLKFLQHNRVDAIFLDINIPSLD 60 Query: 61 GVLLAQNISRFSVKPYIVFITAYKXXXXXXXXXXXXDYILKPYSETRIKAMLHKLEVAFA 120 GVLLAQNIS+F+ KP+IVFITA+K DYILKPY E+RI ML KLE A+ Sbjct: 61 GVLLAQNISQFAHKPFIVFITAWKEHAVEAFELEAFDYILKPYQESRITGMLQKLEAAWQ 120 Query: 121 ARGHQGEEEHV--KLSDKVNLWKNEKIIVVDADEIYYASAQEKTTSVITKGEEYNMALSI 178 + + +D +NL K+E+IIV ++IYYA A EK T V T+ E Y M ++I Sbjct: 121 QQQTSSTPAATVTRENDTINLVKDERIIVTPINDIYYAEAHEKMTFVYTRRESYVMPMNI 180 Query: 179 SEFHSRLPQDRFFRCHRSYLVNLSKIKEIIPWFNNTYLLRLRDLDFEVPVSRSKVKEFRQ 238 +EF S+LP FFRCHRS+ VNL+KI+EI PWFNNTY+LRL+DLDFEVPVSRSKVKEFRQ Sbjct: 181 TEFCSKLPPSHFFRCHRSFCVNLNKIREIEPWFNNTYILRLKDLDFEVPVSRSKVKEFRQ 240 Query: 239 IMRI 242 +M + Sbjct: 241 LMHL 244 >ECs3261 [KT] COG3279 Response regulator of the LytR/AlgR family Length = 244 Score = 288 bits (736), Expect = 6e-78, Method: Compositional matrix adjust. Identities = 143/244 (58%), Positives = 178/244 (72%), Gaps = 2/244 (0%) Query: 1 MRAIIVEDEVLARQELAFLIGANSAIRIAGEFEDGLDALKYLQTEEVDVIFLDINIPSID 60 M+ IIVEDE LA+QEL++LI +S + I G F+DGLD LK+LQ VD IFLDINIPS+D Sbjct: 1 MKVIIVEDEFLAQQELSWLIKEHSQMEIVGTFDDGLDVLKFLQHNRVDAIFLDINIPSLD 60 Query: 61 GVLLAQNISRFSVKPYIVFITAYKXXXXXXXXXXXXDYILKPYSETRIKAMLHKLEVAFA 120 GVLLAQNIS+F+ KP+IVFITA+K DYILKPY E+RI ML KLE A+ Sbjct: 61 GVLLAQNISQFAHKPFIVFITAWKEHAVEAFELEAFDYILKPYQESRITGMLQKLEAAWQ 120 Query: 121 ARGHQGEEEHV--KLSDKVNLWKNEKIIVVDADEIYYASAQEKTTSVITKGEEYNMALSI 178 + + +D +NL K+E+IIV ++IYYA A EK T V T+ E Y M ++I Sbjct: 121 QQQTSSTPAATVTRENDTINLVKDERIIVTPINDIYYAEAHEKMTFVYTRRESYVMPMNI 180 Query: 179 SEFHSRLPQDRFFRCHRSYLVNLSKIKEIIPWFNNTYLLRLRDLDFEVPVSRSKVKEFRQ 238 +EF S+LP FFRCHRS+ VNL+KI+EI PWFNNTY+LRL+DLDFEVPVSRSKVKEFRQ Sbjct: 181 TEFCSKLPPSHFFRCHRSFCVNLNKIREIEPWFNNTYILRLKDLDFEVPVSRSKVKEFRQ 240 Query: 239 IMRI 242 +M + Sbjct: 241 LMHL 244 >BS_lytT [KT] COG3279 Response regulator of the LytR/AlgR family Length = 241 Score = 134 bits (337), Expect = 1e-31, Method: Compositional matrix adjust. Identities = 80/248 (32%), Positives = 130/248 (52%), Gaps = 14/248 (5%) Query: 1 MRAIIVEDEVLARQELAFLIGANSAIRIAGEFEDGLDALKYLQTEEVDVIFLDINIPSID 60 +R +IV+DE+LAR ELA+L+ + E E+ A + ++ D++FLD+++ + Sbjct: 2 LRVLIVDDEMLARDELAYLLKRTNDEMEINEAENIESAFDQMMDQKPDLLFLDVDLSGEN 61 Query: 61 GVLLAQNISRFSVKPYIVFITAYKXXXXXXXXXXXXDYILKPYSETRIKAMLHKLE---- 116 G +A+ + + P IVF TAY DY+ KP+ E RI+ L K + Sbjct: 62 GFDIAKRLKKMKHPPAIVFATAYDQYALKAFEVDALDYLTKPFDEERIQQTLKKYKKVNR 121 Query: 117 --VAFAARGHQGEEEHVKLSDKVNLWKNEKIIVVDADEIYYASAQEKTTSVITKGEEYNM 174 V H G+ K+ L E I++VD +I YA ++ +V T Y + Sbjct: 122 DIVETEQNSHAGQH-------KLALSVGESIVIVDTKDIIYAGTEDGHVNVKTFDHSYTV 174 Query: 175 ALSISEFHSRLPQDRFFRCHRSYLVNLSKIKEIIPWFNNTYLLRLRDLDFEVPVSRSKVK 234 + ++ +LP F R HRS++VN IKEI PWFN+TY L ++D ++PVSR+ K Sbjct: 175 SDTLVVIEKKLPDSDFIRVHRSFVVNTEYIKEIQPWFNSTYNLIMKD-GSKIPVSRTYAK 233 Query: 235 EFRQIMRI 242 E ++++ I Sbjct: 234 ELKKLLHI 241 >CAC1670 [KT] COG3279 Response regulator of the LytR/AlgR family Length = 253 Score = 121 bits (304), Expect = 8e-28, Method: Compositional matrix adjust. Identities = 81/257 (31%), Positives = 133/257 (51%), Gaps = 21/257 (8%) Query: 1 MRAIIVEDEVLARQELAFLIGANSAIRIAG---EFEDGLDALKYLQTEEVDVIFLDINIP 57 ++ I++EDE+ +EL F++ I I G ++G+D +K L+ + V FLDIN+P Sbjct: 3 IKCILIEDEISNEKELYFILRRYDDIEIVGMVQNTDEGIDLVKKLRPQAV---FLDINVP 59 Query: 58 SIDGVLLAQNISRFSVKPYIVFITAYKXXXXXXXXXXXXDYILKPYSETRIKAMLHKLEV 117 + +G+ LA+ I ++F+TAY DYILKP+S RI+ + +L+ Sbjct: 60 NFNGIKLAEEIKDVDSTIAVIFVTAYDKYAVAAFEIKALDYILKPFSIARIEKAVERLKE 119 Query: 118 AFAARGHQGEE-----------EHVKLSDKVNLWKNEKIIVVDADEIYYASAQEKTTSVI 166 E+ E + +K+ KI++VD ++IY+ + + T V Sbjct: 120 YINVNKSMKEKLFELICEFNNMERKYIINKIPCENKGKIVLVDVNDIYFFYIKSEKTYVK 179 Query: 167 TKGEEYNMALSISEFHSRLPQDRFFRCHRSYLVNLSKIKEIIPWFNNTYLLRLRDL-DFE 225 Y + ++++ + FFR HRSYLVNL+KI EI WFN TY L + D E Sbjct: 180 LNDIIYVTSSTLNDMEKKTG---FFRAHRSYLVNLNKIFEIYSWFNGTYKLIMSDYRKSE 236 Query: 226 VPVSRSKVKEFRQIMRI 242 +PVSR V++ ++I+ I Sbjct: 237 IPVSRGNVRKLKEIINI 253 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 0.322 0.138 0.388 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: 15,305,271 Number of extensions: 600845 Number of successful extensions: 1646 Number of sequences better than 1.0e-05: 42 Number of HSP's gapped: 1707 Number of HSP's successfully gapped: 42 Length of query: 242 Length of database: 38,378,431 Length adjustment: 103 Effective length of query: 139 Effective length of database: 26,499,029 Effective search space: 3683365031 Effective search space used: 3683365031 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: 114 (48.5 bits)