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= 0523.0006.p (303 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value BH2465 [L] COG4974 Site-specific recombinase XerD 127 3e-29 BS_ripX [L] COG4974 Site-specific recombinase XerD 123 4e-28 CAP0080 [L] COG0582 Integrase 118 1e-26 BS_codV [L] COG4974 Site-specific recombinase XerD 118 1e-26 BH1529 [L] COG4974 Site-specific recombinase XerD 117 2e-26 >BH2465 [L] COG4974 Site-specific recombinase XerD Length = 303 Score = 127 bits (318), Expect = 3e-29, Method: Compositional matrix adjust. Identities = 99/300 (33%), Positives = 153/300 (51%), Gaps = 39/300 (13%) Query: 9 EEELEAFVIWMK-DAGFTPYTQKSYLADVREFLGSLNGKSLEN---VKKLHIISYLTSVR 64 ++ + AF++++K + +P+T +Y D+R F + +S+ + V + YLT + Sbjct: 6 DQWVSAFLLYLKMEKNHSPHTIVNYELDLRHFRDFMEQQSIPSFAAVSYAFVRHYLTVLY 65 Query: 65 ERGVSDATRNRKHASVNCLFKAL------MELELLAANPAAGIKKSKTEKNREPVYLEEH 118 E+ + +T +RK +++ ++ L ME L A+ G+KK P +L E Sbjct: 66 EQEYARSTVSRKLSTLRSFYQFLVREKWVMENPFLLAHTPKGVKKL-------PSFLYEE 118 Query: 119 ELQRFLSAVEGK--YRSRNLAVFLLMSYMGLRVGEVHTLNLSDYNAERLTLRVFGKGRKW 176 E+++ L A+ G + RN A+F + GLRV E L L D + T+ VFGKGRK Sbjct: 119 EMEQLLDALNGDSPLQLRNRALFETIYASGLRVSECCGLKLQDVDLSIGTVFVFGKGRKE 178 Query: 177 RNIPVPAELAPFLEQALSERLEPWRSK----------EEAMFISQKGRRLSIRAIQGIAA 226 R +P+ F A+ E +E R K +F++ +G L+ R ++ I Sbjct: 179 RYVPI----GSFACDAIQEYIENGREKLLKKSKSVDLPGDLFLNYRGGPLTERGVRKILH 234 Query: 227 DTFGRFQAEVPAARRRPYSSHKLRHSFATMLLRKGADLRTVQELLGHSSIQTTTVYTHIT 286 QA AA S H LRHSFAT LL GADLR VQ+LLGH ++ TT VYTH+T Sbjct: 235 ------QALDQAALSTRVSPHSLRHSFATHLLNNGADLRVVQDLLGHENLSTTQVYTHVT 288 >BS_ripX [L] COG4974 Site-specific recombinase XerD Length = 296 Score = 123 bits (308), Expect = 4e-28, Method: Compositional matrix adjust. Identities = 87/287 (30%), Positives = 156/287 (54%), Gaps = 16/287 (5%) Query: 9 EEELEAFVIW-MKDAGFTPYTQKSYLADVREF----LGSLNGKSLENVKKLHIISYLTSV 63 +++++ F+ + M + G + T SY D++ + +L+ +V ++HII YL + Sbjct: 2 KDQIKDFIHYVMVERGLSQNTIVSYERDLKSYSLYLTETLHVTDWNHVTRIHIIQYLKHL 61 Query: 64 RERGVSDATRNRKHASVNCLFKALMELELLAANPAAGIKKSKTEKNREPVYLEEHELQRF 123 ++ G S T R AS+ + L+ ++ +P+ I+ KTE+ P L +E++R Sbjct: 62 KDSGKSGKTSARHLASIRSFHQFLLREKVTDKDPSVHIETQKTERAL-PKVLALNEVERL 120 Query: 124 LSA--VEGKYRSRNLAVFLLMSYMGLRVGEVHTLNLSDYNAERLTLRVFGKGRKWRNIPV 181 L + + R+ A+ L+ G+RV E+ L +D + +R FGKGRK R +P+ Sbjct: 121 LDTPKLTSPFGYRDKAMLELLYATGIRVSEMIELKTADVHLSMGFIRCFGKGRKERIVPI 180 Query: 182 PAELAPFLEQALSE-RLEPWRSK-EEAMFISQKGRRLSIRAIQGIAADTFGRFQAEVPAA 239 A +E+ +++ R + ++ +A+F++ G+++S QG + + + A Sbjct: 181 GEAAASAIEEYMTKARGKLLKNNVSDALFLNHHGKQISR---QGFWKNLK---KIALEAG 234 Query: 240 RRRPYSSHKLRHSFATMLLRKGADLRTVQELLGHSSIQTTTVYTHIT 286 ++ + H LRHSFAT LL GADLR VQE+LGH+ I TT +YTH+T Sbjct: 235 IKKELTPHTLRHSFATHLLEDGADLRAVQEMLGHADISTTQIYTHVT 281 >CAP0080 [L] COG0582 Integrase Length = 323 Score = 118 bits (296), Expect = 1e-26, Method: Compositional matrix adjust. Identities = 94/317 (29%), Positives = 153/317 (48%), Gaps = 46/317 (14%) Query: 12 LEAFVIWMKDA-GFTPYTQKSYLADVREFLG-------SLNGKSLENV------------ 51 L F+I+M + G + T+ Y D+ L +N +ENV Sbjct: 5 LTGFLIYMTNIKGKSKRTRNEYKNDLILMLKYIKVIKYDINTNGIENVDISDIDNDFIKA 64 Query: 52 ---KKLHI-ISYLTSVRERGVSDATRNRKHASVNCLFKALM-ELELLAANPAAGIKKSKT 106 + L+I + Y R G +R RK A++ F L + ++L NPA ++K K Sbjct: 65 ISLEDLYIFLEYCEDERRNGA--YSRARKVAAIRSFFNYLTTKKKILDYNPAQELEKPKL 122 Query: 107 EKNREPVYLEEHELQRFLSAVE-GKYRSRNLAVFLLMSYMGLRVGEVHTLNLSDYNAERL 165 K R PVYL + FLS ++ K+ RN + L G+RV E+ +N++ + + Sbjct: 123 PK-RNPVYLTIGQANTFLSGIKMNKHYYRNTCIVTLFLNCGMRVSELCNININSIKNDMI 181 Query: 166 TLRVFGKGRKWRNIPVPAELAPFLEQALSERLEPWRS------KEEAMFISQKGRRLSIR 219 + + GKG K R + L A+++ +E RS ++A+FISQKG R+S+R Sbjct: 182 S--IIGKGDKERTV----YLNDMCIDAINKYIEKERSLQKNIKCQQALFISQKGTRISVR 235 Query: 220 AIQGIAADTFGRFQAEVPAARRRPYSSHKLRHSFATMLLRKGADLRTVQELLGHSSIQTT 279 I+ + E + HKLRH+FAT + + G D+ ++Q+LLGHS++ TT Sbjct: 236 TIENLVKKI-----NEDSKLNINKLTPHKLRHTFATTMYQAGTDIISLQQLLGHSNVSTT 290 Query: 280 TVYTHITNREKEEAMAR 296 +YTH+T+ EA + Sbjct: 291 QIYTHVTDDRLREATNK 307 >BS_codV [L] COG4974 Site-specific recombinase XerD Length = 304 Score = 118 bits (295), Expect = 1e-26, Method: Compositional matrix adjust. Identities = 87/287 (30%), Positives = 150/287 (52%), Gaps = 21/287 (7%) Query: 12 LEAFVIWMK-DAGFTPYTQKSYLADVREF-----LGSLNGKSLENVKKLHIISYLTSVRE 65 ++ FV +++ + ++ YT +Y+ + EF + +NG + I +LT E Sbjct: 8 VKLFVEYLQIEKNYSQYTIVNYVDSIEEFETFLRVQGINGFEEAAYQDTRI--FLTEAYE 65 Query: 66 RGVSDATRNRKHASVNCLFKALMELELLAANPAAGIKKSKTEKNREPVYLEEHELQRF-- 123 +G+S T ++K +++ +K LM +L+ NP + K EK R P +L + EL+ Sbjct: 66 KGLSRRTISKKISALRSFYKFLMREKLIEENPFQLVHLPKQEK-RIPKFLYQKELEELFE 124 Query: 124 LSAVEGKYRSRNLAVFLLMSYMGLRVGEVHTLNLSDYNAERLTLRVFGKGRKWRNIPVPA 183 +S + R+ A+ L+ G+RV E ++ ++D + T+ V GKG+K R IP + Sbjct: 125 VSDISQPAGMRDQALLELLYATGMRVSECCSITINDVDLFMDTVLVHGKGKKQRYIPFGS 184 Query: 184 ----ELAPFLEQALSERLEPWRSKEEAMFISQKGRRLSIRAIQGIAADTFGRFQAEVPAA 239 L ++ L + + +F++Q+G L+ R I+ I + G Q Sbjct: 185 YAREALKVYMNSGRQCLLMKAKEPHDLLFVNQRGGPLTARGIRHILS---GLVQKASSTL 241 Query: 240 RRRPYSSHKLRHSFATMLLRKGADLRTVQELLGHSSIQTTTVYTHIT 286 P H LRH+FAT LL +GADLR+VQELLGHS++ +T +YTH++ Sbjct: 242 HIHP---HMLRHTFATHLLNEGADLRSVQELLGHSNLSSTQIYTHVS 285 >BH1529 [L] COG4974 Site-specific recombinase XerD Length = 200 Score = 117 bits (294), Expect = 2e-26, Method: Compositional matrix adjust. Identities = 0/296 (0%), Positives = 0/296 (0%), Gaps = 16/296 (5%) Query: 12 LEAFVIWMK-DAGFTPYTQKSYLADVREFLGSLNG----KSLENVKKLHIISYLTSVRER 66 ++ D + + L + + + Sbjct: 8 GRDPYLYPGLDIMRNRLNIRQQQRLEQAAYEMTALRAATIELGPLVRGLPHLRTIHRQLY 67 Query: 67 GVSDATRNRKHASVNCLFKALMELELLAANPAAGIKKSKTEKNREPVYLEEHELQRFLSA 126 + + + E+ V LE+ + L+ Sbjct: 68 QDIFDWAGQLREVDIYQGDTPFCHFAYIEKEGNALMQDLEEE-GYLVGLEKAKFVERLAH 126 Query: 127 VEGK--YRSRNLAVFLLMSYMGLRVGEVHTLNLSDYNAERLTLRVFGKGRKWRNIPVPAE 184 + L + +H + + Sbjct: 127 YYCEINVLHPFRVGSGLAQRIFFEQLAIHAGYQLSWQGIEKEAWNQANQSGAMGDLTALQ 186 Query: 185 LAPFLEQALSERLEPWRSKE--EAMFISQKGRRLSIRAIQGIAADTFGRFQAEVPAARRR 242 Sbjct: 187 ------ 240 Query: 243 PYSSHKLRHSFATMLLRKGADLRTVQELLGHSSIQTTTVYTHITNREKEEAMARLQ 298 Sbjct: 241 296 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 0.318 0.132 0.372 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: 20,914,815 Number of extensions: 822697 Number of successful extensions: 1654 Number of sequences better than 1.0e-05: 72 Number of HSP's gapped: 1582 Number of HSP's successfully gapped: 72 Length of query: 303 Length of database: 38,378,431 Length adjustment: 106 Effective length of query: 197 Effective length of database: 26,153,027 Effective search space: 5152146319 Effective search space used: 5152146319 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 (21.7 bits) S2: 115 (48.9 bits)