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= 0541.0098.p (344 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value ML0354 [EH] COG0028 Thiamine pyrophosphate-requiring enzymes [ac... 404 e-113 STM0821 [KL] COG1199 Rad3-related DNA helicases 331 9e-91 AGc4439 [K] COG0568 DNA-directed RNA polymerase, sigma subunit (... 315 7e-86 AGc4432 [J] COG0564 Pseudouridylate synthases, 23S RNA-specific 315 7e-86 YFL022c [J] COG0016 Phenylalanyl-tRNA synthetase alpha subunit 137 2e-32 >ML0354 [EH] COG0028 Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase] Length = 346 Score = 404 bits (1039), Expect = e-113, Method: Compositional matrix adjust. Identities = 189/324 (58%), Positives = 244/324 (75%), Gaps = 1/324 (0%) Query: 19 VTDPQLLNDLRVKYLGKKGELTEVLRGMGGLSAEERPVIGQVANLVRSAIEEIISTKQEA 78 V D + LN+LR LGKKGELTE+L+GM L+ EERPVIG +AN R K+ Sbjct: 21 VADEKTLNNLRTVMLGKKGELTEILKGMKDLTNEERPVIGALANAFRDEFGAKFEAKKVE 80 Query: 79 FQQQETLNRLNAEKVDVTLPGRRLPQGGIHPVSRVVREIEDIFIGMGYRVAEGPEVETDY 138 +Q L +E +DVTLPG+ +G H +++ EIE+IF+GMGY + +G EVETD+ Sbjct: 81 IEQAVMNAALESETLDVTLPGKAQKKGSRHILTQTQEEIEEIFLGMGYEIVDGYEVETDH 140 Query: 139 YNFEALNLPKNHPARDMQDSFYLTEDILMRTQTSPVQIRTMQAMK-GETPVKIICPGKVF 197 YNFE +NLPK+HPARDMQD+FY+T ++L+RT TSP+Q RTM A + +++I PG+V+ Sbjct: 141 YNFERMNLPKDHPARDMQDTFYITNEVLLRTHTSPMQARTMDAHDFSKGGLRMIAPGRVY 200 Query: 198 RRDDDDATHSFQFHQIEGLVIGRHIRMSDLKGTLQQFVQEMFGPNTGIRLRPSFFPFTEP 257 RRD DDATHS QFHQIEGLV+ ++I M+DLKGTL +++MFG + +R RPS+FPFTEP Sbjct: 201 RRDTDDATHSHQFHQIEGLVVDKNITMADLKGTLDLVMKKMFGQDRELRWRPSYFPFTEP 260 Query: 258 SVEVDVSCFKCGGHGCRLCKQSGWLEILGAGMVHPNVLEKGGYDPAEYSGFAFGMGVERI 317 SVEVD+SCFKCGG GC +CK +GW+EILGAGMVHPNVLE G D + YSGFAFG+G ERI Sbjct: 261 SVEVDISCFKCGGKGCNVCKHTGWIEILGAGMVHPNVLEMSGLDSSVYSGFAFGLGQERI 320 Query: 318 AMLKYGIDDIRYFYTNDMAFVKQF 341 AML+YGI+DIR FY D+ F++QF Sbjct: 321 AMLRYGINDIRGFYQGDVRFLEQF 344 >STM0821 [KL] COG1199 Rad3-related DNA helicases Length = 714 Score = 331 bits (849), Expect = 9e-91, Method: Compositional matrix adjust. Identities = 17/323 (5%), Positives = 56/323 (17%), Gaps = 14/323 (4%) Query: 19 VTDPQLLNDLRVKYLGKKGELTEVLRGMGGLSAEERPVIGQVANLVRSAIEEIISTKQEA 78 Q+ + + + V + I I ++E Sbjct: 17 ALQDQIPDFIPRAPQRQMIADVARTLAGEEGRHLAIEAPTGVGKTLSYLIPGIAIAREEQ 76 Query: 79 FQQQETLNRLNAEKVDVTLPGRRLPQGGIHPVSRVVREIEDIFIGMGYRVAEGPEVETDY 138 + + + + L + E Sbjct: 77 KTLVVSTANVALQDQIFSKDLPLLRKIIPDLRFTAAFGRGRYVCPRNLAALASSEPTQQD 136 Query: 139 YNFEALNLPKNHPARDMQDSFYLTEDILMRTQTSPVQIRTMQAMKGETPVKIICPGKVFR 198 + + + + L D+ + + + + K Sbjct: 137 LLAFLDDELTPNNQEEQKRCARLKGDLDGYKWDGLRDHTDI--AIDDDLWRRLSTDKASC 194 Query: 199 RDDDDATHSFQFHQIEGLVIGRHIRMSDLKGTLQQFVQEMFGPNTGIRLRPSFFPFTEPS 258 + + + + + + L E + Sbjct: 195 L-NRNCHYYRECPFFVARREIQEAEVVVANHALVMAAMESEAVLPEPKHLLLVLDEGHHL 253 Query: 259 VEVDVSCFKCGGHGCRLCKQSGWLEILGAGMVHPNVLEKGGYDPAEYSGFAFGMGVERIA 318 +V + ++ K E + Sbjct: 254 PDVARD---ALEM--------SAEITASWYRLQLDLFSKLVATCMEQFRPKTTPPLANPE 302 Query: 319 MLKYGIDDIRYFYTNDMAFVKQF 341 L +++ + A + + Sbjct: 303 RLNAHCEEVYELIASLNAILNLY 325 >AGc4439 [K] COG0568 DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) Length = 301 Score = 315 bits (807), Expect = 7e-86, Method: Compositional matrix adjust. Identities = 0/331 (0%), Positives = 0/331 (0%), Gaps = 12/331 (3%) Query: 19 VTDPQLLNDLRVKYLGKKGELTEVLRGMGGLSAEERPVIGQVANLVRSAIEEIISTKQEA 78 L + + + + E Sbjct: 18 NVGKSTLLNKLLGQKISITSRKAQTTRHRIVGIHTEGAYQAIYVDTPGLHMEEKRAINRL 77 Query: 79 FQQQETLNRLNAEKVDVTLPGRRLP--QGGIHPVSRVVREIEDIFIGMGYRVAEGPEVET 136 + + + + E V + G R + R + + + V E ++ Sbjct: 78 MNKAASSSIGDVELVIFVVEGTRWTPDDEMVLNKLREGKAPVILAVNKVDNVQEKADLLP 137 Query: 137 DYYNFEALNLPKNHPARDMQDSFYLTED-----ILMRTQTSPVQIRTMQAMKGETPVKII 191 + + + + + T + Sbjct: 138 HLQFLASQMNFLDIVPISAETGLNVDTIAAIVRKHLPEATHHFPEDYITDRS--QRFMAS 195 Query: 192 CPGKVFRRDDDDATHSFQFHQIEGLVIGRHIRMSDLKGTLQQFVQEMFGPNTGI-RLRPS 250 + +E + R L +E + Sbjct: 196 EIIREKLMRFL-GAELPYSVTVEIERFVSNERGGYDINGLILVEREGQKKMVIGNKGAKI 254 Query: 251 FFPFTEPSVEVDVSCFKCGGHGCRLCKQSGWLEILGAGMVHPNVLEKGGYDPAEYSGFAF 310 E ++ Sbjct: 255 KTIGIEARKDMQEMFEAPVHL- 313 Query: 311 GMGVERIAMLKYGIDDIRYFYTNDMAFVKQF 341 Sbjct: 314 344 >AGc4432 [J] COG0564 Pseudouridylate synthases, 23S RNA-specific Length = 340 Score = 315 bits (807), Expect = 7e-86, Method: Compositional matrix adjust. Identities = 0/331 (0%), Positives = 0/331 (0%), Gaps = 12/331 (3%) Query: 19 VTDPQLLNDLRVKYLGKKGELTEVLRGMGGLSAEERPVIGQVANLVRSAIEEIISTKQEA 78 D + D+ + L+ + A + + + Sbjct: 18 GEDAEGRIDVWLVGEVGSDLSRSRLKALIEQGAVLLNGQPVTEPKKKVHPGDRVEIVMPE 77 Query: 79 FQQQETLNRLNAEKVDVTLPGRRLP--QGGIHPVSRVVREIEDIFIGMGYRVAEGPEVET 136 + V+ + G+ + + Y + Sbjct: 78 PEDPVPQGEDIPLDVEYEDEDLIVLVKPAGLVVHPGAGNWTGTLVNALIYHCGDSLSGIG 137 Query: 137 DYYNFEALNLPKNHPARDMQDSFYLTED-----ILMRTQTSPVQIRTMQAMKGETPVKII 191 ++ + M + + R +A+ Sbjct: 138 GVKRPGIVHRLDKETSGVMVVAKNDNAHRHLAAQFADHGRTGPLERAYKAVV--WGRPRT 195 Query: 192 CPGKVFRRDDDDATHSFQFHQIEGLVIGRHIRMSDLKGTLQQFVQEMFGPNTGI-RLRPS 250 G V T + ++ + + + + R Sbjct: 196 LRGTVDAALGR-GTDRTKRAVKNEDSFDAREAITHYEVMERFHEKPDASCLASMVECRLE 254 Query: 251 FFPFTEPSVEVDVSCFKCGGHGCRLCKQSGWLEILGAGMVHPNVLEKGGYDPAEYSGFAF 310 + V + G L V Y Sbjct: 255 TGRTHQIRVHMAHIGHPLIGD-PEYGAAFRTKANLLDEPARSTVNRFPRQALHAYLLAFE 313 Query: 311 GMGVERIAMLKYGIDDIRYFYTNDMAFVKQF 341 Sbjct: 314 344 >YFL022c [J] COG0016 Phenylalanyl-tRNA synthetase alpha subunit Length = 346 Score = 137 bits (346), Expect = 2e-32, Method: Compositional matrix adjust. Identities = 0/352 (0%), Positives = 0/352 (0%), Gaps = 73/352 (20%) Query: 21 DPQLLNDLRVKYLGKKGELTE--VLRGMGGLSAEERPVIGQVANLVRSAIEEIISTKQEA 78 L + + G++ V + + I+ S + Sbjct: 155 VSLLDTLDALAEYQRAGKIRYIGVSNETAFGVMRYLHLADKHDLPRIVTIQNPYSLLNRS 214 Query: 79 FQQQETLNRLNAEKVDVTLPGRRLPQGGIHPVSRVVREIEDIFIGMGY-RVAEGPEVETD 137 F+ + Q + G T Sbjct: 215 FEVG----------------LAEVSQYEGVELLAYSCLGFGTLTGKYLNGAKPAGARNTL 258 Query: 138 YYNFEALNLPKNHPARDMQDSFY----LTEDI---------------------------- 165 + F + + A L Sbjct: 259 FSRFTRYSGEQTQKAVAAYVDIARRHGLDPAQMALAFVRRQPFVASTLLGATTMDQLKTN 318 Query: 166 --------LMRTQTSPVQIRTMQAM-KGETPVKIICPGKVFRRDDDDATHSFQFHQIEGL 216 + + Sbjct: 319 IESLHLELSEDVLAEIEAVHQVYTYP 378 Query: 217 VIGRHIRMSDLKGTLQQFVQEMFGPNTGIRLRPSFFPFTEPSVEVDVSCFKCGGHGCRLC 276 Sbjct: 379 --------- 429 Query: 277 KQSGWLEILGAGMVHPNVLEKGGYDPAEYSGFAFGMGVERIAMLKYGIDDIR 328 Sbjct: 430 ---- 477 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 0.140 0.418 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: 25,750,457 Number of extensions: 1176967 Number of successful extensions: 1644 Number of sequences better than 1.0e-05: 8 Number of HSP's gapped: 1615 Number of HSP's successfully gapped: 11 Length of query: 344 Length of database: 38,378,431 Length adjustment: 107 Effective length of query: 237 Effective length of database: 26,037,693 Effective search space: 6170933241 Effective search space used: 6170933241 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: 116 (49.3 bits)