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= 0016.0006.p (338 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value BS_yacF [J] COG0042 tRNA-dihydrouridine synthase 481 e-136 CAC3199 [J] COG0042 tRNA-dihydrouridine synthase 269 6e-72 PA4852 [J] COG0042 tRNA-dihydrouridine synthase 233 4e-61 ZyhdG [J] COG0042 tRNA-dihydrouridine synthase 231 2e-60 BS_yhdG [E] COG0531 Amino acid transporters 231 2e-60 >BS_yacF [J] COG0042 tRNA-dihydrouridine synthase Length = 247 Score = 481 bits (1238), Expect = e-136, Method: Compositional matrix adjust. Identities = 0/328 (0%), Positives = 0/328 (0%) Query: 1 MLKIGGIEMKNQVVLAPMAGVCNPAFRLIAKEFGTGLVCAEMVSDKAILHGNLRTREMLF 60 M E + + +L A ++ R + Sbjct: 1 MQTQVLFEHPLNEKMRTWLRIEFLIQQLTVNLPIVDHAGALHFFRNVSELLDVFERGEVR 60 Query: 61 VDEREKPLSLQIFGGDRKSLVEAAKVVDKETNADIIDINMGCPVPKVTKCDAGARWLLNP 120 + ++ Q + + + + L+ Sbjct: 61 TELLKELDRQQRKLQTWIGVPGVDQSRIEALIQQLKAAGSVLISAPRIGQFLREDRLIAL 120 Query: 121 DKIYEMVSAVVDAVDKPVTVKMRIGWDSEHIFVEDNARAVERAGGQAVSVHGRTREQLYT 180 + + + D P ++ + A QA+++ Q Sbjct: 121 VRQRLSIPGGCCSFDLPTLHIWLHLPQAQRDSQVETWIASLNPLTQALTMVLDLIRQSAP 180 Query: 181 GHADWKYIRMAKEAVSIPVIGNGDVNTPEDARAMLDQTGCDGVMIGRGALGNPWMLYRTI 240 ++ + +++ + + + + Sbjct: 181 FRKQTSLNGFYQDNGGDADLLRLNLSLDSQLYPQISGHKSRFAIRFMPLDTENGQVPERL 240 Query: 241 QYLNTGELMPEPGPEEKIKVAILHMDRLISLKGEAVAVREMRKHMAWYLKGMKAAARVKD 300 Sbjct: 241 300 Query: 301 VIMEETKRDEMVRILNQFVTQLKEEEEQ 328 Sbjct: 301 328 >CAC3199 [J] COG0042 tRNA-dihydrouridine synthase Length = 321 Score = 269 bits (687), Expect = 6e-72, Method: Compositional matrix adjust. Identities = 133/317 (41%), Positives = 198/317 (62%), Gaps = 1/317 (0%) Query: 2 LKIGGIEMKNQVVLAPMAGVCNPAFRLIAKEFGTGLVCAEMVSDKAILHGNLRTREMLFV 61 +K+G + + V LAPMAGV + FR I K G L EMVS KA+ +G+ T E++ + Sbjct: 1 MKVGNLSFEGNVFLAPMAGVTDIVFRKICKGMGADLTYTEMVSAKALYYGSENTEELMKI 60 Query: 62 DEREKPLSLQIFGGDRKSLVEAAKVVDKETNADIIDINMGCPVPKVTKCDAGARWLLNPD 121 + E+ ++Q+FG + + +A + +++ IIDINMGCP K+ K G+ + +P Sbjct: 61 SDEEEYAAVQMFGSEPDIMAKACEKFNEDDKICIIDINMGCPAHKIVKNGEGSALMKSPK 120 Query: 122 KIYEMVSAVVDAVDKPVTVKMRIGWDSEHIFVEDNARAVERAGGQAVSVHGRTREQLYTG 181 YE+V AV A +KPVTVK R G+D ++I + A+ +E AG ++VHGRTR Q+Y G Sbjct: 121 LAYEIVKAVKKASNKPVTVKFRKGFDEDNINAVEFAKVIEDAGADMITVHGRTRAQMYEG 180 Query: 182 HADWKYIRMAKEAVSIPVIGNGDVNTPEDARAMLDQTGCDGVMIGRGALGNPWMLYRTIQ 241 ADW I+ K++VSIPVIGNGD+ + EDA ML+ T CDGVM+ R A+GNPW+ Sbjct: 181 KADWDIIKAVKKSVSIPVIGNGDIVSGEDAVRMLEYTNCDGVMVARAAMGNPWIFREIKA 240 Query: 242 YLNTGELMPEPGPEEKIKVAILHMDRLISLKGEAVAVREMRKHMAWYLKGMKAAARVKDV 301 +N+ +++ +P P EK+ + I H + GE AVREMRK++AWY+K +K +K + Sbjct: 241 AINSTQII-KPTPVEKLDMCIFHYKEAVKYYGEKKAVREMRKNIAWYIKSLKNCTDIKCL 299 Query: 302 IMEETKRDEMVRILNQF 318 I E DE++ IL Q+ Sbjct: 300 INSEESSDEVIGILEQY 316 >PA4852 [J] COG0042 tRNA-dihydrouridine synthase Length = 332 Score = 233 bits (594), Expect = 4e-61, Method: Compositional matrix adjust. Identities = 130/321 (40%), Positives = 187/321 (58%), Gaps = 1/321 (0%) Query: 1 MLKIGGIEMKNQVVLAPMAGVCNPAFRLIAKEFGTGLVCAEMVSDKAILHGNLRTREMLF 60 +++IG + N+++LAPMAGV + FR + + G G+V +EMV+ L + ++R L Sbjct: 3 VVRIGPYTLPNRLILAPMAGVTDRPFRQLCRRLGAGMVVSEMVTSDVRLWNSRKSRLRLI 62 Query: 61 VDEREKPLSLQIFGGDRKSLVEAAKVVDKETNADIIDINMGCPVPKVTKCDAGARWLLNP 120 D ++P S+QI GGD L EAA+ + E A IIDINMGCP KV AG+ L + Sbjct: 63 HDGEDEPRSVQIAGGDPAMLAEAAQR-NVELGAQIIDINMGCPAKKVCNKAAGSALLRDE 121 Query: 121 DKIYEMVSAVVDAVDKPVTVKMRIGWDSEHIFVEDNARAVERAGGQAVSVHGRTREQLYT 180 + E++ AVV AVD PVT+K+R GWD ++ A+ E+AG QA++VHGRTR LYT Sbjct: 122 ALVAEILDAVVRAVDVPVTLKIRTGWDRDNRNGVTVAKLAEQAGIQALAVHGRTRADLYT 181 Query: 181 GHADWKYIRMAKEAVSIPVIGNGDVNTPEDARAMLDQTGCDGVMIGRGALGNPWMLYRTI 240 G A+++ I K+AVSIPV NGD+++PE AR +++QTG D ++IGR A G PW+ Sbjct: 182 GEAEYETIAAIKQAVSIPVFANGDIDSPEKARKVIEQTGVDALLIGRAAQGRPWIFREID 241 Query: 241 QYLNTGELMPEPGPEEKIKVAILHMDRLISLKGEAVAVREMRKHMAWYLKGMKAAARVKD 300 YL TGE +P E + + H+ L GE + VR RKH+ WYL + A + Sbjct: 242 HYLRTGEHLPAAPLPEVQSILLEHLAELHLFYGEEMGVRIARKHVGWYLATLPGAREFRA 301 Query: 301 VIMEETKRDEMVRILNQFVTQ 321 D + QF + Sbjct: 302 QFNRLQDTDAQCASVRQFFAE 322 >ZyhdG [J] COG0042 tRNA-dihydrouridine synthase Length = 321 Score = 231 bits (588), Expect = 2e-60, Method: Compositional matrix adjust. Identities = 124/291 (42%), Positives = 182/291 (62%), Gaps = 5/291 (1%) Query: 2 LKIGGIEMKNQVVLAPMAGVCNPAFRLIAKEFGTGLVCAEMVSDKAILHGNLRTR-EMLF 60 ++IG +++N+++ APMAG+ + FR + E G GL +EM+S + + ++R M+ Sbjct: 1 MRIGQYQLRNRLIAAPMAGITDRPFRTLCYEMGAGLTVSEMMSSNPQVWESDKSRLRMVH 60 Query: 61 VDEREKPLSLQIFGGDRKSLVEAAKVVDKETNADIIDINMGCPVPKVTKCDAGARWLLNP 120 +DE ++QI G D K + +AA++ + E+ A IIDINMGCP KV + AG+ L P Sbjct: 61 IDE-PGIRTVQIAGSDPKEMADAARI-NVESGAQIIDINMGCPAKKVNRKLAGSALLQYP 118 Query: 121 DKIYEMVSAVVDAVDKPVTVKMRIGWDSEHIFVEDNARAVERAGGQAVSVHGRTREQLYT 180 D + +++ VV+AVD PVT+K+R GW EH E+ A+ E G QA+++HGRTR L+ Sbjct: 119 DVVKSILTEVVNAVDVPVTLKIRTGWAPEHRNCEEIAQLAEDCGIQALTIHGRTRACLFN 178 Query: 181 GHADWKYIRMAKEAVSIPVIGNGDVNTPEDARAMLDQTGCDGVMIGRGALGNPWMLYRTI 240 G A++ IR K+ VSIPVI NGD+ P ARA+LD TG D +MIGR A G PW+ Sbjct: 179 GEAEYDSIRAVKQKVSIPVIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQ 238 Query: 241 QYLNTGELMPEPGPEEKIK-VAILHMDRLISLKGEAVAVREMRKHMAWYLK 290 YL+TGEL+P P P ++K + H+ L G A R RKH++WYL+ Sbjct: 239 HYLDTGELLP-PLPLAEVKRLLCAHVRELHDFYGPAKGYRIARKHVSWYLQ 288 >BS_yhdG [E] COG0531 Amino acid transporters Length = 321 Score = 231 bits (588), Expect = 2e-60, Method: Compositional matrix adjust. Identities = 124/291 (42%), Positives = 182/291 (62%), Gaps = 5/291 (1%) Query: 2 LKIGGIEMKNQVVLAPMAGVCNPAFRLIAKEFGTGLVCAEMVSDKAILHGNLRTR-EMLF 60 ++IG +++N+++ APMAG+ + FR + E G GL +EM+S + + ++R M+ Sbjct: 1 MRIGQYQLRNRLIAAPMAGITDRPFRTLCYEMGAGLTVSEMMSSNPQVWESDKSRLRMVH 60 Query: 61 VDEREKPLSLQIFGGDRKSLVEAAKVVDKETNADIIDINMGCPVPKVTKCDAGARWLLNP 120 +DE ++QI G D K + +AA++ + E+ A IIDINMGCP KV + AG+ L P Sbjct: 61 IDE-PGIRTVQIAGSDPKEMADAARI-NVESGAQIIDINMGCPAKKVNRKLAGSALLQYP 118 Query: 121 DKIYEMVSAVVDAVDKPVTVKMRIGWDSEHIFVEDNARAVERAGGQAVSVHGRTREQLYT 180 D + +++ VV+AVD PVT+K+R GW EH E+ A+ E G QA+++HGRTR L+ Sbjct: 119 DVVKSILTEVVNAVDVPVTLKIRTGWAPEHRNCEEIAQLAEDCGIQALTIHGRTRACLFN 178 Query: 181 GHADWKYIRMAKEAVSIPVIGNGDVNTPEDARAMLDQTGCDGVMIGRGALGNPWMLYRTI 240 G A++ IR K+ VSIPVI NGD+ P ARA+LD TG D +MIGR A G PW+ Sbjct: 179 GEAEYDSIRAVKQKVSIPVIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQ 238 Query: 241 QYLNTGELMPEPGPEEKIK-VAILHMDRLISLKGEAVAVREMRKHMAWYLK 290 YL+TGEL+P P P ++K + H+ L G A R RKH++WYL+ Sbjct: 239 HYLDTGELLP-PLPLAEVKRLLCAHVRELHDFYGPAKGYRIARKHVSWYLQ 288 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 0.319 0.135 0.397 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: 25,051,640 Number of extensions: 1015057 Number of successful extensions: 2208 Number of sequences better than 1.0e-05: 82 Number of HSP's gapped: 2038 Number of HSP's successfully gapped: 82 Length of query: 338 Length of database: 38,378,431 Length adjustment: 107 Effective length of query: 231 Effective length of database: 26,037,693 Effective search space: 6014707083 Effective search space used: 6014707083 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 (21.7 bits) S2: 116 (49.3 bits)