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= 0004.0009.p (835 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value BH0078 [TK] COG2208 Serine phosphatase RsbU, regulator of sigma ... 635 0.0 BS_spoIIE [TK] COG2208 Serine phosphatase RsbU, regulator of sig... 615 e-176 BS_rsbU [TK] COG2208 Serine phosphatase RsbU, regulator of sigma... 58 6e-08 >BH0078 [TK] COG2208 Serine phosphatase RsbU, regulator of sigma subunit Length = 346 Score = 635 bits (1637), Expect = 0.0, Method: Compositional matrix adjust. Identities = 0/776 (0%), Positives = 0/776 (0%), Gaps = 8/776 (1%) Query: 61 RAMILDELSPFAAAYFAVIVFMRRDSILPVAAAIILGSL--FTPFPGAVMVAAELIIFFL 118 L+ + R I+ + + A+ I L Sbjct: 57 PRPETQGLTETYVGNWLAKHGSREKLIIASKVSGPSRNNDKGIRPDQALDRK--NIREAL 114 Query: 119 IYKGLESFQKVELSYAPLMVFVSSFM--VGLFKIVMGPSITWYSLMMITLDALLGFVLTL 176 Y + + + L + A + Sbjct: 115 HDSLKRLQTDYLDLYQVHWPQRPTNCFGKLGYSWTDS-APAVSLLDTLDALAEYQRAGKI 173 Query: 177 VFLQALPVFTYKQKSRALRNDEVLCLIILLASVMTGLVGWSVNGLSLEHILSRFXXXXXX 236 ++ + D+ I+ L+ S E Sbjct: 174 RYIGVSNETAFGVMRYLHLADKHDLPRIVTIQNPYSLLNRSFEVGLAEVSQYEGVELLAY 233 Query: 237 XXXXXXXXXXXXXXXXXXXSLADIGAIYQMSLLAFSGMLAGMMQSGRKGAVSIGMLLGST 296 + A + + Sbjct: 234 SCLGFGTLTGKYLNGAKPAGARNTLFSRFTRYSGEQTQKAVAAYVDIARRHGLDPAQMAL 293 Query: 297 ILSVYFLGPGDVMASTWETCAAVVLFLLTPKGMISAIAKYVPGTPDHSRSQHEYARRVRD 356 Sbjct: 294 353 Query: 357 ITADRVTQFSQVFRQLSSSFGQIPRAGEAGKSDREMEDFMNTVTEGACSGCIRRTHCWDA 416 Sbjct: 354 - 412 Query: 417 KFYQTYRYMTDMMTTVEECPNITAAQLPPEWSRICGKTGEVLEVMKGQYELYQHDMRWKR 476 Sbjct: 413 472 Query: 477 QIYDSRQFVAEQLSGVSQVMEDLANEIKREGQAMYRQESQIREALEKLGLSIHSIEILSL 536 Sbjct: 473 532 Query: 537 DPGRVEIEVVHAYTRGFDECRKMIAPLLSDILEENIAVVNETAVHPREGLSMVTFGSAKA 596 Sbjct: 533 592 Query: 597 YEVNTGVAGAAKGGDMLSGDSFSTVELGNGTFAVSISDGMGNGERARMESSAALGMLEKL 656 Sbjct: 593 652 Query: 657 LQSGMDEKLAVKSVNSILLLRSPDEFYATVDMALIDQYSAQTTFMKIASAPSFIRRGSEV 716 Sbjct: 653 712 Query: 717 IPVTASNLPIGIIKEIEVDLVSMQLRPGDILIMMTDGIYDAPGYAVNKEIWMKRLIQELE 776 Sbjct: 713 772 Query: 777 GDDPQELADNLLEKVIRYQGNEIHDDMTIVVSRLDHFHPEWSSLHLPGIGRMERPR 832 Sbjct: 773 828 >BS_spoIIE [TK] COG2208 Serine phosphatase RsbU, regulator of sigma subunit Length = 346 Score = 615 bits (1587), Expect = e-176, Method: Compositional matrix adjust. Identities = 0/767 (0%), Positives = 0/767 (0%), Gaps = 4/767 (0%) Query: 61 RAMILDELSPFAAAYFAVIVFMRRDSILPVAAAIILGSLFTPFPGAVMVAAELIIFFLIY 120 + + L +A+ + S A + Sbjct: 55 VPPRPETQGLTETYVGNWLAKHGSREKLIIASKVSGPSRNNDKGIRPDQALDRKNIREAL 114 Query: 121 KGLESFQKVELSYAPLMVFVS-SFMVGLFKIVMGPSITWYSLMMITLDALLGFVLTLVFL 179 + + + + ++ TLDAL + Sbjct: 115 HDSLKRLQTDYLDLYQVHWPQRPTNCFGKLGYSWTDSAPAVSLLDTLDALAEYQRAGKIR 174 Query: 180 QALPVFTYKQKSRALRNDEVLCLIILLASVMTGLVGWSVNGLSLEHILSRFXXXXXXXXX 239 + + + ++ + + +S++ Sbjct: 175 YIGVSNETAFGVMRYLHLADKHDLPRIVTIQNPYSLLNRSFEVGLAEVSQYEGVELLAYS 234 Query: 240 XXXXXXXXXXXXXXXXSLADIGAIYQMSLLAFSGMLAGMMQSGRKGAVSIGMLLGSTILS 299 ++ + + A G+ L+ Sbjct: 235 CLGFGTLTGKYLNGAKPAGARNTLFSRFTRYSGEQTQKAVAAYVDIARRHGLDPAQMALA 294 Query: 300 VYFLGPGDVMASTWETCAAVVLFLLTPKGMISAIAKYVPGTPDHSRSQHEYARRVRDITA 359 Sbjct: 295 354 Query: 360 DRVTQFSQVFRQLSSSFGQIPRAGEAGKSDREMEDFMNTVTEGACSGCIRRTHCWDAKFY 419 Sbjct: 355 414 Query: 420 QTYRYMTDMMTTVEECPNITAAQLPPEWSRICGKTGEVLEVMKGQYELYQHDMRWKRQIY 479 Sbjct: 415 474 Query: 480 DSRQFVAEQLSGVSQVMEDLANEIKREGQAMYRQESQIREALEKLGLSIHSIEILSLDPG 539 Sbjct: 475 534 Query: 540 RVEIEVVHAYTRGFDECRKMIAPLLSDILEENIAVVNET-AVHPREGLSMVTFGSAKAYE 598 Sbjct: 535 -- 592 Query: 599 VNTGVAGAAKGGDMLSGDSFSTVELGNGTFAVSISDGMGNGERARMESSAALGMLEKLLQ 658 Sbjct: 593 652 Query: 659 SGMDEKLAVKSVNSILLLRSPDEFYATVDMALIDQYSAQTTFMKIASAPSFIRRGSEVIP 718 Sbjct: 653 712 Query: 719 VTASNLPIGIIKEIEVDLVSMQLRPGDILIMMTDGIYDAPGYAVNKEIWMKRLIQELEGD 778 Sbjct: 713 772 Query: 779 DPQELADNLLEKVIRYQGNEIHDDMTIVVSRLDHFHPEWSSLHLPGI 825 Sbjct: 773 819 >BS_rsbU [TK] COG2208 Serine phosphatase RsbU, regulator of sigma subunit Length = 346 Score = 58.2 bits (139), Expect = 6e-08, Method: Compositional matrix adjust. Identities = 15/202 (7%), Positives = 40/202 (19%), Gaps = 8/202 (3%) Query: 613 LSGDSFSTVELGNGTFAVSISDGMGNGERARMESSAALGMLEKLLQSGMDEKLAVKSVNS 672 + + ++ S + G + + S ++ ++ Sbjct: 134 PQRPTNCFGK-LGYSWTDSAPAVSLLDTLDALAEYQRAGKIRYIGVSNETAFGVMRYLHL 192 Query: 673 ILLLRSPDEFYATVDMALIDQYSAQTTFMKIASAPSFI--RRGSEVIPVTASNLPIGIIK 730 P +L+++ + +T L Sbjct: 193 ADKHDLPRIVTIQNPYSLLNRSFEVGLAEVSQYEGVELLAYSCLGFGTLTGKYLNGAKPA 252 Query: 731 EIEVDLVSMQLRPGDILIMMTDGIYDA---PGYAVNKEIWMKRLIQELEGDDPQELADNL 787 L S R Y + M + L Sbjct: 253 GARNTLFSRFTRYSGEQTQKAVAAYVDIARRHGLDPAQ--MALAFVRRQPFVASTLLGAT 310 Query: 788 LEKVIRYQGNEIHDDMTIVVSR 809 ++ +H +++ V Sbjct: 311 TMDQLKTNIESLHLELSEDVLA 332 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 0.321 0.136 0.396 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: 56,980,522 Number of extensions: 2252470 Number of successful extensions: 6342 Number of sequences better than 1.0e-05: 4 Number of HSP's gapped: 6339 Number of HSP's successfully gapped: 4 Length of query: 835 Length of database: 38,378,431 Length adjustment: 115 Effective length of query: 720 Effective length of database: 25,115,021 Effective search space: 18082815120 Effective search space used: 18082815120 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: 120 (50.8 bits)