RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254781000|ref|YP_003065413.1| tRNA (uracil-5-)-methyltransferase [Candidatus Liberibacter asiaticus str. psy62] (371 letters) >gnl|CDD|179917 PRK05031, PRK05031, tRNA (uracil-5-)-methyltransferase; Validated. Length = 362 Score = 670 bits (1730), Expect = 0.0 Identities = 233/365 (63%), Positives = 284/365 (77%), Gaps = 4/365 (1%) Query: 1 MSGTLLIDQYEQQLAEKVDRLRQMMLAFQVPNLQIFRSEPIHYRMRAEFHIWHDGDDLYH 60 L +QYE QLAEKV RL+++ F P ++FRS P HYRMRAEF IWH+GDDLY+ Sbjct: 2 TPECLPPEQYEAQLAEKVARLKELFAPFSAPEPEVFRSPPSHYRMRAEFRIWHEGDDLYY 61 Query: 61 IMFDQQTKERMRIDYFMPGSLLINALMIEMMATIRLEPLLRAKLFQIDYLTSQSDQAIVT 120 MFDQQTK+R+RID F S LINALM ++A +R P+LR KLFQ+D+L++ S + +V+ Sbjct: 62 AMFDQQTKQRIRIDQFPIASELINALMPALLAALRANPVLRHKLFQVDFLSTLSGEILVS 121 Query: 121 LIYHRLLDDAWRECAIRLRDALHARKYQIQLIGRANKTKICLDRDYVDERLTVAGRTLIY 180 L+YH+ LD+ W + A LRDAL + + LIGR+ K KI LD+DYVDERL VAGR IY Sbjct: 122 LLYHKKLDEEWEQAAKALRDAL----FNVHLIGRSRKQKIVLDQDYVDERLPVAGREFIY 177 Query: 181 RQIENSFTQPNAGINVHMLEWVLAATKGIQGDLLELYCGNGNFSLVLARHFDRVLAVEIA 240 RQ+ENSFTQPNA +N MLEW L ATKG +GDLLELYCGNGNF+L LAR+F RVLA EI+ Sbjct: 178 RQVENSFTQPNAAVNEKMLEWALDATKGSKGDLLELYCGNGNFTLALARNFRRVLATEIS 237 Query: 241 KPSVEAARYNIAANHVNNVKIVRMSSKEFTQAMRREREFNRLKDIDIHSYRFKTIFVDPP 300 KPSV AA+YNIAAN ++NV+I+RMS++EFTQAM REFNRLK ID+ SY F TIFVDPP Sbjct: 238 KPSVAAAQYNIAANGIDNVQIIRMSAEEFTQAMNGVREFNRLKGIDLKSYNFSTIFVDPP 297 Query: 301 RSGLDDATVGMVQAYPHILYISCNPDSLCRDLSILSTTHTIERLALFDQFPYTRHMECGV 360 R+GLDD T+ +VQAY ILYISCNP++LC +L LS TH +ER ALFDQFPYT HMECGV Sbjct: 298 RAGLDDETLKLVQAYERILYISCNPETLCENLETLSQTHKVERFALFDQFPYTHHMECGV 357 Query: 361 LLVRK 365 LL +K Sbjct: 358 LLEKK 362 >gnl|CDD|131198 TIGR02143, trmA_only, tRNA (uracil-5-)-methyltransferase. This family consists exclusively of proteins believed to act as tRNA (uracil-5-)-methyltransferase. All members of far are proteobacterial. The seed alignment was taken directly from pfam05958 in Pfam 12.0, but higher cutoffs are used to select only functionally equivalent proteins. Homologous proteins excluded by the higher cutoff scores of this model include other uracil methyltransferases, such as RumA, active on rRNA. Length = 353 Score = 566 bits (1461), Expect = e-162 Identities = 223/357 (62%), Positives = 269/357 (75%), Gaps = 4/357 (1%) Query: 9 QYEQQLAEKVDRLRQMMLAFQVPNLQIFRSEPIHYRMRAEFHIWHDGDDLYHIMFDQQTK 68 QY QLAEKV RL+ + F P ++F S HYRMRAEF IWH+GDDLY+ MFDQQTK Sbjct: 1 QYTAQLAEKVSRLKDLFAPFDAPEPEVFESPDKHYRMRAEFRIWHEGDDLYYAMFDQQTK 60 Query: 69 ERMRIDYFMPGSLLINALMIEMMATIRLEPLLRAKLFQIDYLTSQSDQAIVTLIYHRLLD 128 ++R+D F S LIN LM ++A +R P LR KLFQ+D+LT+ S +A+V+L+YH+ LD Sbjct: 61 SKIRVDQFPAASELINRLMPALIAALRQNPALRHKLFQVDFLTTLSGEALVSLLYHKQLD 120 Query: 129 DAWRECAIRLRDALHARKYQIQLIGRANKTKICLDRDYVDERLTVAGRTLIYRQIENSFT 188 D WR+ A L+D K + LIGRA K KI LD+DYVDE L VAGR IYRQ+ENSFT Sbjct: 121 DEWRQAAEALKDI----KLNVNLIGRARKKKIVLDQDYVDETLPVAGREFIYRQVENSFT 176 Query: 189 QPNAGINVHMLEWVLAATKGIQGDLLELYCGNGNFSLVLARHFDRVLAVEIAKPSVEAAR 248 QPNA +N+ MLEW T+G +GDLLELYCGNGNFSL LA++F RVLA EIAKPSV AA+ Sbjct: 177 QPNAAVNIKMLEWACEVTQGSKGDLLELYCGNGNFSLALAQNFRRVLATEIAKPSVNAAQ 236 Query: 249 YNIAANHVNNVKIVRMSSKEFTQAMRREREFNRLKDIDIHSYRFKTIFVDPPRSGLDDAT 308 YNIAAN+++NV+I+RMS++EFTQAM REF RLK ID+ SY TIFVDPPR+GLD T Sbjct: 237 YNIAANNIDNVQIIRMSAEEFTQAMNGVREFRRLKGIDLKSYNCSTIFVDPPRAGLDPDT 296 Query: 309 VGMVQAYPHILYISCNPDSLCRDLSILSTTHTIERLALFDQFPYTRHMECGVLLVRK 365 +VQAY ILYISCNP++L +L LS TH +ER ALFDQFPYT HMECGVLL RK Sbjct: 297 CKLVQAYERILYISCNPETLKANLEQLSETHRVERFALFDQFPYTHHMECGVLLERK 353 >gnl|CDD|114667 pfam05958, tRNA_U5-meth_tr, tRNA (Uracil-5-)-methyltransferase. This family consists of (Uracil-5-)-methyltransferases EC:2.1.1.35 from bacteria, archaea and eukaryotes. A 5-methyluridine (m(5)U) residue at position 54 is a conserved feature of bacterial and eukaryotic tRNAs. The methylation of U54 is catalysed by the tRNA(m5U54)methyltransferase, which in Saccharomyces cerevisiae is encoded by the nonessential TRM2 gene. It is thought that tRNA modification enzymes might have a role in tRNA maturation not necessarily linked to their known catalytic activity. Length = 353 Score = 566 bits (1461), Expect = e-162 Identities = 223/357 (62%), Positives = 269/357 (75%), Gaps = 4/357 (1%) Query: 9 QYEQQLAEKVDRLRQMMLAFQVPNLQIFRSEPIHYRMRAEFHIWHDGDDLYHIMFDQQTK 68 QY QLAEKV RL+ + F P ++F S HYRMRAEF IWH+GDDLY+ MFDQQTK Sbjct: 1 QYTAQLAEKVSRLKDLFAPFDAPEPEVFESPDKHYRMRAEFRIWHEGDDLYYAMFDQQTK 60 Query: 69 ERMRIDYFMPGSLLINALMIEMMATIRLEPLLRAKLFQIDYLTSQSDQAIVTLIYHRLLD 128 ++R+D F S LIN LM ++A +R P LR KLFQ+D+LT+ S +A+V+L+YH+ LD Sbjct: 61 SKIRVDQFPAASELINRLMPALIAALRQNPALRHKLFQVDFLTTLSGEALVSLLYHKQLD 120 Query: 129 DAWRECAIRLRDALHARKYQIQLIGRANKTKICLDRDYVDERLTVAGRTLIYRQIENSFT 188 D WR+ A L+D K + LIGRA K KI LD+DYVDE L VAGR IYRQ+ENSFT Sbjct: 121 DEWRQAAEALKDI----KLNVNLIGRARKKKIVLDQDYVDETLPVAGREFIYRQVENSFT 176 Query: 189 QPNAGINVHMLEWVLAATKGIQGDLLELYCGNGNFSLVLARHFDRVLAVEIAKPSVEAAR 248 QPNA +N+ MLEW T+G +GDLLELYCGNGNFSL LA++F RVLA EIAKPSV AA+ Sbjct: 177 QPNAAVNIKMLEWACEVTQGSKGDLLELYCGNGNFSLALAQNFRRVLATEIAKPSVNAAQ 236 Query: 249 YNIAANHVNNVKIVRMSSKEFTQAMRREREFNRLKDIDIHSYRFKTIFVDPPRSGLDDAT 308 YNIAAN+++NV+I+RMS++EFTQAM REF RLK ID+ SY TIFVDPPR+GLD T Sbjct: 237 YNIAANNIDNVQIIRMSAEEFTQAMNGVREFRRLKGIDLKSYNCSTIFVDPPRAGLDPDT 296 Query: 309 VGMVQAYPHILYISCNPDSLCRDLSILSTTHTIERLALFDQFPYTRHMECGVLLVRK 365 +VQAY ILYISCNP++L +L LS TH +ER ALFDQFPYT HMECGVLL RK Sbjct: 297 CKLVQAYERILYISCNPETLKANLEQLSETHRVERFALFDQFPYTHHMECGVLLERK 353 >gnl|CDD|129571 TIGR00479, rumA, 23S rRNA (uracil-5-)-methyltransferase RumA. This protein family was first proposed to be RNA methyltransferases by homology to the TrmA family. The member from E. coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA. Length = 431 Score = 106 bits (267), Expect = 8e-24 Identities = 90/381 (23%), Positives = 148/381 (38%), Gaps = 56/381 (14%) Query: 10 YEQQLAEKVDRLRQM---MLAFQVPNLQI---FRSEPIHYRMRAEFHIWHDGDDLYHIMF 63 YE QL K ++ + + F ++ +P YR +A + F Sbjct: 74 YEFQLRSKQQQVIALLERIGKFTSEPIEPLPTIGGDPWGYRNKARLSLGRSPSGQIQAGF 133 Query: 64 DQQTKERMRIDYFMPGSLLINALMIEMMATIRLEPLLRAKL--FQIDYLTSQSDQAIVTL 121 Q+ + + I ++ A L P ++A L F + Sbjct: 134 YQKGSHDI-VP--------IKQCPVQDPALNLLLPKVKAILENFGASIYLEHKELGKARH 184 Query: 122 IYHRLLDDAWRECAIRLRDAL----HARKYQIQLIGRANKTK-ICLD-------RDYVDE 169 R+ E + LR AL H + ++L R K IC + + +E Sbjct: 185 GVLRIGRRT-GELLLVLRTALEGFPHKEELALELQERYPDVKSICQNINPEKTNVIFGEE 243 Query: 170 RLTVAGRTLIYRQIE--------NSFTQPNAGINVHMLEWVLAATKGIQGD--LLELYCG 219 +AG IY + F Q N+G N +++ L A + +QG+ +++ YCG Sbjct: 244 TEQIAGEGPIYEKSGDLSFSLSARDFFQVNSGQNEKLVDRALEALE-LQGEELVVDAYCG 302 Query: 220 NGNFSLVLARHFDRVLAVEIAKPSVEAARYNIAANHVNNVKIVRMSSKEFTQAMRREREF 279 G F+L LA+ V+ +E+ SVE A+ N N + NV EF E Sbjct: 303 VGTFTLPLAKQAKSVVGIEVVPESVEKAQQNAELNGIANV--------EFLAG-TLETVL 353 Query: 280 NRLKDIDIHSYRFKTIFVDPPRSGLDDATV-GMVQAYP-HILYISCNPDSLCRDLSILST 337 + + +DPPR G + +++ P I+Y+SCNP +L RDL L Sbjct: 354 PKQPWAGQ---IPDVLLLDPPRKGCAAEVLRTIIELKPERIVYVSCNPATLARDLEFLCK 410 Query: 338 -THTIERLALFDQFPYTRHME 357 + I + D FP+T H+E Sbjct: 411 EGYGITWVQPVDMFPHTAHVE 431 >gnl|CDD|183875 PRK13168, rumA, 23S rRNA m(5)U1939 methyltransferase; Reviewed. Length = 443 Score = 97.5 bits (244), Expect = 5e-21 Identities = 61/183 (33%), Positives = 90/183 (49%), Gaps = 33/183 (18%) Query: 187 FTQPNAGINVHM----LEWVLAATKGIQGD-LLELYCGNGNFSLVLARHFDRVLAVEIAK 241 F Q NA +N M LEW L G D +L+L+CG GNF+L LAR V+ VE + Sbjct: 274 FIQVNAQVNQKMVARALEW-LDPQPG---DRVLDLFCGLGNFTLPLARQAAEVVGVEGVE 329 Query: 242 PSVEAARYNIAANHVNNVKIVRMS-SKEFTQAMRREREFNRLKDIDIHSYRFKTIFVDPP 300 VE AR N N ++NV + ++FT F++ + +DPP Sbjct: 330 AMVERARENARRNGLDNVTFYHANLEEDFTDQPWALGGFDK-------------VLLDPP 376 Query: 301 RSGLDDATVGMVQAYP-----HILYISCNPDSLCRDLSIL-STTHTIERLALFDQFPYTR 354 R+G ++QA I+Y+SCNP +L RD +L + ++R + D FP+T Sbjct: 377 RAG----AAEVMQALAKLGPKRIVYVSCNPATLARDAGVLVEAGYRLKRAGMLDMFPHTG 432 Query: 355 HME 357 H+E Sbjct: 433 HVE 435 >gnl|CDD|179588 PRK03522, rumB, 23S rRNA methyluridine methyltransferase; Reviewed. Length = 315 Score = 84.9 bits (211), Expect = 3e-17 Identities = 46/152 (30%), Positives = 71/152 (46%), Gaps = 18/152 (11%) Query: 216 LYCGNGNFSLVLARHFDRVLAVEIAKPSVEAARYNIAANHVNNVKIVRMSSKEFTQAMRR 275 L+CG G F L A ++ +EI+ ++ A+ + A + NV+ + S +F A Sbjct: 180 LFCGVGGFGLHCATPGMQLTGIEISAEAIACAKQSAAELGLTNVQFQALDSTQFATAQGE 239 Query: 276 EREFNRLKDIDIHSYRFKTIFVDPPRSGLDDATVGMVQ--AYPHILYISCNPDSLCRDLS 333 + + V+PPR G+ + A ILY SCN ++ +DL+ Sbjct: 240 VPDL---------------VLVNPPRRGIGKELCDYLSQMAPRFILYSSCNAQTMAKDLA 284 Query: 334 ILSTTHTIERLALFDQFPYTRHMECGVLLVRK 365 L IER+ LFD FP+T H E LLVR+ Sbjct: 285 HLPGYR-IERVQLFDMFPHTAHYEVLTLLVRQ 315 >gnl|CDD|131140 TIGR02085, meth_trns_rumB, 23S rRNA (uracil-5-)-methyltransferase RumB. This family consists of RNA methyltransferases designated RumB, formerly YbjF. Members act on 23S rRNA U747 and the equivalent position in other proteobacterial species. This family is homologous to the other 23S rRNA methyltransferase RumA and to the tRNA methyltransferase TrmA. Length = 374 Score = 76.0 bits (187), Expect = 1e-14 Identities = 46/154 (29%), Positives = 73/154 (47%), Gaps = 18/154 (11%) Query: 213 LLELYCGNGNFSLVLARHFDRVLAVEIAKPSVEAARYNIAANHVNNVKIVRMSSKEFTQA 272 + +L+CG G F L A ++ +EI ++ A+ + ++N+ + S +F A Sbjct: 237 MWDLFCGVGGFGLHCAGPDTQLTGIEIESEAIACAQQSAQMLGLDNLSFAALDSAKFATA 296 Query: 273 MRREREFNRLKDIDIHSYRFKTIFVDPPRSGL-DDATVGMVQAYPH-ILYISCNPDSLCR 330 E + V+PPR G+ + + Q P ILY SCN ++ + Sbjct: 297 QMSAPEL---------------VLVNPPRRGIGKELCDYLSQMAPKFILYSSCNAQTMAK 341 Query: 331 DLSILSTTHTIERLALFDQFPYTRHMECGVLLVR 364 D++ LS IER+ LFD FP+T H E LLVR Sbjct: 342 DIAELSGYQ-IERVQLFDMFPHTSHYEVLTLLVR 374 >gnl|CDD|163311 TIGR03534, RF_mod_PrmC, protein-(glutamine-N5) methyltransferase, release factor-specific. Members of this protein family are HemK (PrmC), a protein once thought to be involved in heme biosynthesis but now recognized to be a protein-glutamine methyltransferase that modifies the peptide chain release factors. All members of the seed alignment are encoded next to the release factor 1 gene (prfA) and confirmed by phylogenetic analysis. SIMBAL analysis (manuscript in prep.) shows the motif [LIV]PRx[DE]TE (in Escherichia coli, IPRPDTE) confers specificity for the release factors rather than for ribosomal protein L3. Length = 251 Score = 43.2 bits (103), Expect = 9e-05 Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 2/69 (2%) Query: 197 HMLEWVLAATKGIQGDLLELYCGNGNFSLVLARHFD--RVLAVEIAKPSVEAARYNIAAN 254 ++E L K +L+L G+G +L LA+ RV AV+I+ ++ AR N A Sbjct: 75 ELVEAALERLKKGPLRVLDLGTGSGAIALALAKERPDARVTAVDISPEALAVARKNAARL 134 Query: 255 HVNNVKIVR 263 ++NV ++ Sbjct: 135 GLDNVTFLQ 143 >gnl|CDD|181780 PRK09328, PRK09328, N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional. Length = 275 Score = 37.5 bits (88), Expect = 0.006 Identities = 19/67 (28%), Positives = 32/67 (47%), Gaps = 3/67 (4%) Query: 200 EWVLAATKGIQGD-LLELYCGNGNFSLVLARHFD--RVLAVEIAKPSVEAARYNIAANHV 256 EW L A + +L+L G+G +L LA+ V AV+I+ ++ AR N Sbjct: 98 EWALEALLLKEPLRVLDLGTGSGAIALALAKERPDAEVTAVDISPEALAVARRNAKHGLG 157 Query: 257 NNVKIVR 263 V+ ++ Sbjct: 158 ARVEFLQ 164 >gnl|CDD|181902 PRK09489, rsmC, 16S ribosomal RNA m2G1207 methyltransferase; Provisional. Length = 342 Score = 36.1 bits (84), Expect = 0.013 Identities = 18/53 (33%), Positives = 32/53 (60%), Gaps = 2/53 (3%) Query: 206 TKGIQGDLLELYCGNGNFSLVLARHFD--RVLAVEIAKPSVEAARYNIAANHV 256 T +G +L++ CG G S VLARH R+ +++ ++E++R +AAN + Sbjct: 193 TPHTKGKVLDVGCGAGVLSAVLARHSPKIRLTLSDVSAAALESSRATLAANGL 245 >gnl|CDD|149353 pfam08241, Methyltransf_11, Methyltransferase domain. Members of this family are SAM dependent methyltransferases. Length = 95 Score = 35.4 bits (82), Expect = 0.027 Identities = 11/45 (24%), Positives = 21/45 (46%), Gaps = 1/45 (2%) Query: 214 LELYCGNGNFSLVLARHFD-RVLAVEIAKPSVEAARYNIAANHVN 257 L++ CG G + LAR +V V+++ + AR + + Sbjct: 1 LDVGCGTGLLTEALARLPGAQVTGVDLSPEMLALARKRAQEDGLT 45 >gnl|CDD|162363 TIGR01444, fkbM_fam, methyltransferase, FkbM family. Members of this family are characterized by two well-conserved short regions separated by a variable in both sequence and length. The first of the two regions is found in a large number of proteins outside this subfamily, a number of which have been characterized as methyltransferases. One member of the present family, FkbM, was shown to be required for a specific methylation in the biosynthesis of the immunosuppressant FK506 in Streptomyces strain MA6548. Length = 143 Score = 34.6 bits (80), Expect = 0.045 Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 2/47 (4%) Query: 218 CGNGNFSLVLARHFD--RVLAVEIAKPSVEAARYNIAANHVNNVKIV 262 G+ SL AR RV+A E + E N+ N++ NV ++ Sbjct: 7 ANIGDTSLYFARKGAEGRVIAFEPLPDAYEILEENVKLNNLPNVVLL 53 >gnl|CDD|181047 PRK07580, PRK07580, Mg-protoporphyrin IX methyl transferase; Validated. Length = 230 Score = 33.7 bits (78), Expect = 0.082 Identities = 14/41 (34%), Positives = 21/41 (51%) Query: 218 CGNGNFSLVLARHFDRVLAVEIAKPSVEAARYNIAANHVNN 258 CG G+ S+ LAR +V+A +I+ VE AR + Sbjct: 72 CGVGSLSIPLARRGAKVVASDISPQMVEEARERAPEAGLAG 112 >gnl|CDD|184932 PRK14968, PRK14968, putative methyltransferase; Provisional. Length = 188 Score = 33.7 bits (78), Expect = 0.083 Identities = 15/48 (31%), Positives = 29/48 (60%) Query: 214 LELYCGNGNFSLVLARHFDRVLAVEIAKPSVEAARYNIAANHVNNVKI 261 LE+ G+G ++V A++ +V+ V+I +VE A+ N N++ N + Sbjct: 28 LEVGTGSGIVAIVAAKNGKKVVGVDINPYAVECAKCNAKLNNIRNNGV 75 >gnl|CDD|134556 PRK01424, PRK01424, S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional. Length = 366 Score = 32.6 bits (74), Expect = 0.17 Identities = 19/47 (40%), Positives = 24/47 (51%), Gaps = 4/47 (8%) Query: 179 IYRQIENSFTQPNAGINVHMLEWVL--AATKGIQGDLLELYCGNGNF 223 +Y QIE S P AG+ H + +L KGIQ L L+ G G F Sbjct: 190 VYSQIEGSVAAPTAGL--HFTKDILDKLKAKGIQTAFLTLHVGAGTF 234 >gnl|CDD|148126 pfam06325, PrmA, Ribosomal protein L11 methyltransferase (PrmA). This family consists of several Ribosomal protein L11 methyltransferase (EC:2.1.1.-) sequences. Length = 294 Score = 32.2 bits (74), Expect = 0.22 Identities = 9/26 (34%), Positives = 14/26 (53%) Query: 233 RVLAVEIAKPSVEAARYNIAANHVNN 258 +V+ V+I +V AA+ N N V Sbjct: 185 KVVGVDIDPVAVRAAKENAELNGVEA 210 >gnl|CDD|128898 smart00650, rADc, Ribosomal RNA adenine dimethylases. Length = 169 Score = 32.1 bits (74), Expect = 0.23 Identities = 10/27 (37%), Positives = 14/27 (51%) Query: 213 LLELYCGNGNFSLVLARHFDRVLAVEI 239 +LE+ G G + L RV A+EI Sbjct: 17 VLEIGPGKGALTEELLERAARVTAIEI 43 >gnl|CDD|149354 pfam08242, Methyltransf_12, Methyltransferase domain. Members of this family are SAM dependent methyltransferases. Length = 98 Score = 32.0 bits (73), Expect = 0.25 Identities = 14/52 (26%), Positives = 23/52 (44%), Gaps = 2/52 (3%) Query: 214 LELYCGNGNFSLVLARHFD--RVLAVEIAKPSVEAARYNIAANHVNNVKIVR 263 L++ CG G L V+I+ ++EAA +AA + + VR Sbjct: 1 LDIGCGTGTLLRALLEALPGLEYTGVDISPAALEAAAERLAALGLLDAVRVR 52 >gnl|CDD|162639 TIGR01983, UbiG, ubiquinone biosynthesis O-methyltransferase. This model represents an O-methyltransferase believed to act at two points in the ubiquinone biosynthetic pathway in bacteria (UbiG) and fungi (COQ3). A separate methylase (MenG/UbiE) catalyzes the single C-methylation step. The most commonly used names for genes in this family do not indicate whether this gene is an O-methyl, or C-methyl transferase. Length = 224 Score = 31.5 bits (72), Expect = 0.40 Identities = 15/84 (17%), Positives = 36/84 (42%), Gaps = 5/84 (5%) Query: 194 INVHMLEWVLAATKGIQGDLLELY-----CGNGNFSLVLARHFDRVLAVEIAKPSVEAAR 248 +N L+++ + + L L CG G S LAR V ++ ++ ++E A+ Sbjct: 25 MNPLRLDYIRDTIRKNKKPLFGLRVLDVGCGGGLLSEPLARLGANVTGIDASEENIEVAK 84 Query: 249 YNIAANHVNNVKIVRMSSKEFTQA 272 + + + ++ S ++ + Sbjct: 85 LHAKKDPLLKIEYRCTSVEDLAEK 108 >gnl|CDD|178880 PRK00121, trmB, tRNA (guanine-N(7)-)-methyltransferase; Reviewed. Length = 202 Score = 31.3 bits (72), Expect = 0.47 Identities = 14/62 (22%), Positives = 28/62 (45%), Gaps = 2/62 (3%) Query: 214 LELYCGNGNFSLVLARHF--DRVLAVEIAKPSVEAARYNIAANHVNNVKIVRMSSKEFTQ 271 LE+ G G F + +A+ + +E+ +P V A I + N++++ + E Sbjct: 45 LEIGFGKGEFLVEMAKANPDINFIGIEVHEPGVGKALKKIEEEGLTNLRLLCGDAVEVLL 104 Query: 272 AM 273 M Sbjct: 105 DM 106 >gnl|CDD|162684 TIGR02072, BioC, biotin biosynthesis protein BioC. This enzyme, which is found in biotin biosynthetic gene clusters in proteobacteria, firmicutes, green-sulfur bacteria, fusobacterium and bacteroides, is believed to carry out an enzymatic step prior to the formation of pimeloyl-CoA (although attribution of this annotation is not traceable). The enzyme appears related to methyltransferases by homology. Length = 240 Score = 30.3 bits (69), Expect = 0.82 Identities = 12/63 (19%), Positives = 28/63 (44%), Gaps = 2/63 (3%) Query: 194 INVHMLEWVLAATKGIQGDLLELYCGNGNFSLVLARHF--DRVLAVEIAKPSVEAARYNI 251 + +L + I +L++ CG G + L + F +A++I+ + A+ + Sbjct: 19 MAKRLLALLKEKGIFIPASVLDIGCGTGYLTRALLKRFPQAEFIALDISAGMLAQAKTKL 78 Query: 252 AAN 254 + N Sbjct: 79 SEN 81 >gnl|CDD|161703 TIGR00091, TIGR00091, tRNA (guanine-N(7)-)-methyltransferase. In E. coli, this protein flanks the DNA repair protein MutY, also called micA. Length = 194 Score = 29.6 bits (67), Expect = 1.2 Identities = 20/89 (22%), Positives = 34/89 (38%), Gaps = 12/89 (13%) Query: 213 LLELYCGNGNFSLVLARHF--DRVLAVEIAKPSVEAARYNIAANHVNNVKIVRMSSKEFT 270 LE+ CG G F + +A+ L +EI P V AA + N+ ++ + E Sbjct: 20 HLEIGCGKGRFLIDMAKQNPDKNFLGIEIHTPIVLAANNKANKLGLKNLHVLCGDANELL 79 Query: 271 QAMRREREFNRLKDIDIHSYRFKTIFVDP 299 + L + ++ F DP Sbjct: 80 DKFFPD---GSLSKVFLN-------FPDP 98 >gnl|CDD|183040 PRK11207, PRK11207, tellurite resistance protein TehB; Provisional. Length = 197 Score = 28.9 bits (65), Expect = 2.0 Identities = 23/64 (35%), Positives = 32/64 (50%), Gaps = 3/64 (4%) Query: 202 VLAATKGIQ-GDLLELYCGNGNFSLVL-ARHFDRVLAVEIAKPSVEAARYNIAANHVNNV 259 VL A K ++ G L+L CGNG SL L A FD V A + S+ AA +++N+ Sbjct: 22 VLEAVKVVKPGKTLDLGCGNGRNSLYLAANGFD-VTAWDKNPMSIANLERIKAAENLDNL 80 Query: 260 KIVR 263 Sbjct: 81 HTAV 84 >gnl|CDD|181382 PRK08317, PRK08317, hypothetical protein; Provisional. Length = 241 Score = 28.7 bits (65), Expect = 2.2 Identities = 15/62 (24%), Positives = 25/62 (40%), Gaps = 4/62 (6%) Query: 200 EWVLAATKGIQGDL-LELYCGNGNFSLVLARHFD---RVLAVEIAKPSVEAARYNIAANH 255 GD L++ CG GN + LAR RV+ ++ ++ + A+ A Sbjct: 9 ARTFELLAVQPGDRVLDVGCGPGNDARELARRVGPEGRVVGIDRSEAMLALAKERAAGLG 68 Query: 256 VN 257 N Sbjct: 69 PN 70 >gnl|CDD|184890 PRK14896, ksgA, 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Provisional. Length = 258 Score = 28.7 bits (65), Expect = 2.3 Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 2/51 (3%) Query: 212 DLLELYCGNGNFSLVLARHFDRVLAVEIAKPSVEAARYNIAANHVNNVKIV 262 +LE+ G G + LA+ +V A+E+ E R + A NV+I+ Sbjct: 32 PVLEIGPGKGALTDELAKRAKKVYAIELDPRLAEFLRDDEIA--AGNVEII 80 >gnl|CDD|150417 pfam09741, DUF2045, Uncharacterized conserved protein (DUF2045). This entry is the conserved 250 residues of proteins of approximately 450 amino acids. It contains several highly conserved motifs including a CVxLxxxD motif.The function is unknown. Length = 237 Score = 28.7 bits (64), Expect = 2.6 Identities = 13/53 (24%), Positives = 25/53 (47%) Query: 282 LKDIDIHSYRFKTIFVDPPRSGLDDATVGMVQAYPHILYISCNPDSLCRDLSI 334 LKD+ +T++ P R +D AYP+I ++ + D + D+ + Sbjct: 100 LKDLSPIYKVSQTVYASPSRFHMDSKGEVETIAYPNICFMVDDFDEVFDDVVV 152 >gnl|CDD|147829 pfam05891, Hydroxy-O-Methy, Putative hydroxyindole-O-methyltransferase. This family of proteins is a putative hydroxyindole-O-methyltransferase and by homology, is expected to catalyse the conversion of N-acetyl serotonin to melatonin. The protein is expressed in the tail neuron PVT and in uterine cells [worm-base]. Length = 217 Score = 28.5 bits (64), Expect = 3.0 Identities = 10/50 (20%), Positives = 19/50 (38%) Query: 226 VLARHFDRVLAVEIAKPSVEAARYNIAANHVNNVKIVRMSSKEFTQAMRR 275 +L F +V VE + + A+ +A + ++FT R Sbjct: 73 LLLPLFSKVDLVEPVEDFLAKAKEYLAEEKKKVGNFFCVGLQDFTPEEGR 122 >gnl|CDD|173405 PTZ00113, PTZ00113, proliferating cell nuclear antigen; Provisional. Length = 275 Score = 28.3 bits (63), Expect = 3.4 Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 2/65 (3%) Query: 232 DRVLAVEIAKPSVEAARYNIAANHVNNVKIVRMSSKEFTQAMRREREF-NRLK-DIDIHS 289 D+V + + S+E +I N V +SSKE T R+ EF + +K +ID +S Sbjct: 109 DKVSSFSLKLMSIEQDALSIPENEEGFDAEVTLSSKELTNICRQMNEFSDTVKIEIDSNS 168 Query: 290 YRFKT 294 +F T Sbjct: 169 IKFTT 173 >gnl|CDD|184931 PRK14967, PRK14967, putative methyltransferase; Provisional. Length = 223 Score = 28.1 bits (63), Expect = 3.8 Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 6/83 (7%) Query: 197 HMLEWVLAATKGIQG-DLLELYCGNGNFSLVLARH-FDRVLAVEIAKPSVEAARYNIAAN 254 +L LAA G +L+L G+G ++ A V AV+I++ +V +AR N Sbjct: 23 QLLADALAAEGLGPGRRVLDLCTGSGALAVAAAAAGAGSVTAVDISRRAVRSARLNALLA 82 Query: 255 HVNNVKIVRMSSKEFTQAMRRER 277 V+ V + ++ +A+ Sbjct: 83 GVD----VDVRRGDWARAVEFRP 101 >gnl|CDD|184963 PRK15001, PRK15001, SAM-dependent 23S ribosomal RNA mG1835 methyltransferase; Provisional. Length = 378 Score = 27.7 bits (61), Expect = 4.5 Identities = 24/97 (24%), Positives = 48/97 (49%), Gaps = 22/97 (22%) Query: 209 IQGDLLELYCGNGNFSL-VLARHFD-RVLAVEIAKPSVEAARYNIAANHVNNVKIVRMSS 266 ++G++++L CGNG L +L ++ +V+ V+ + +V ++R N+ N Sbjct: 228 LEGEIVDLGCGNGVIGLTLLDKNPQAKVVFVDESPMAVASSRLNVETN------------ 275 Query: 267 KEFTQAMRREREF---NRLKDIDIHSYRFKTIFVDPP 300 +A+ R EF N L ++ +RF + +PP Sbjct: 276 --MPEALDRC-EFMINNALSGVE--PFRFNAVLCNPP 307 >gnl|CDD|152815 pfam12380, Peptidase_C62, Gill-associated viral 3C-like peptidase. a positive-stranded RNA virus of prawns, that has been called yellow head virus protease and gill-associated virus 3C-like peptidase. The GAV cysteine protease is predicted to be the key enzyme in the processing of the GAV replicase polyprotein precursors, pp1a and pp1ab. This protease employs a Cys(2968)-His(2879) catalytic dyad. Length = 284 Score = 27.7 bits (61), Expect = 4.6 Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 6/80 (7%) Query: 281 RLKDIDIH---SYRFKTIFVDPPRSGLDDATVGMVQAYPHILYISCNPDSLCRDLSIL-- 335 R++D++ H YR + V R L+ G +P ++ SC ++L R + + Sbjct: 17 RVEDLNKHPYNKYRKNIVRVYGERGDLNGFLSGKFLHFPRHIFDSCTDNTLTRHIRVTKG 76 Query: 336 STTHTIERLA-LFDQFPYTR 354 TH IE L+ +D P+ + Sbjct: 77 EETHDIELLSEEYDATPFIK 96 >gnl|CDD|181982 PRK09602, PRK09602, translation-associated GTPase; Reviewed. Length = 396 Score = 27.9 bits (63), Expect = 4.8 Identities = 19/57 (33%), Positives = 25/57 (43%), Gaps = 19/57 (33%) Query: 282 LKDIDIHSYRFKTIFVDPPRSGLDDATVGMVQAY-----PHI-LYISCNP-DSLCRD 331 L D++I +Y F TI D VG+ AY P L + CNP + C D Sbjct: 23 LADVEIANYPFTTI----------DPNVGV--AYVRVECPCKELGVKCNPRNGKCID 67 >gnl|CDD|171521 PRK12467, PRK12467, peptide synthase; Provisional. Length = 3956 Score = 27.4 bits (61), Expect = 6.4 Identities = 9/34 (26%), Positives = 18/34 (52%), Gaps = 5/34 (14%) Query: 98 PLLRAKLFQIDYLTSQSDQAIVTLIYHRLLDDAW 131 PLLR +L ++ D+ ++ + H ++ D W Sbjct: 161 PLLRVRLLRLA-----DDEHVLVVTLHHIISDGW 189 >gnl|CDD|129628 TIGR00537, hemK_rel_arch, HemK-related putative methylase. The gene hemK from E. coli was found to contribute to heme biosynthesis and originally suggested to be protoporphyrinogen oxidase (Medline 95189105). Functional analysis of the nearest homolog in Saccharomyces cerevisiae, YNL063w, finds it is not protoporphyrinogen oxidase and sequence analysis suggests that HemK homologs have S-adenosyl-methionine-dependent methyltransferase activity (Medline 99237242). Homologs are found, usually in a single copy, in nearly all completed genomes, but varying somewhat in apparent domain architecture. This model represents an archaeal and eukaryotic protein family that lacks an N-terminal domain found in HemK and its eubacterial homologs. It is found in a single copy in the first six completed archaeal and eukaryotic genomes. Length = 179 Score = 27.1 bits (60), Expect = 6.6 Identities = 20/79 (25%), Positives = 32/79 (40%), Gaps = 12/79 (15%) Query: 179 IYRQIENSFTQPNAGINVHMLEWVLAATKGIQGDLLELYCGNGNFSLVLARHFDRVLAVE 238 +Y E+S +LE L K D+LE+ G G ++ L +L + Sbjct: 1 VYEPAEDSL----------LLEANLRELKP--DDVLEIGAGTGLVAIRLKGKGKCILTTD 48 Query: 239 IAKPSVEAARYNIAANHVN 257 I +V+ R N N+V Sbjct: 49 INPFAVKELRENAKLNNVG 67 >gnl|CDD|179053 PRK00517, prmA, ribosomal protein L11 methyltransferase; Reviewed. Length = 250 Score = 27.4 bits (62), Expect = 6.9 Identities = 13/26 (50%), Positives = 16/26 (61%) Query: 233 RVLAVEIAKPSVEAARYNIAANHVNN 258 +VLAV+I +VEAAR N N V Sbjct: 144 KVLAVDIDPQAVEAARENAELNGVEL 169 >gnl|CDD|132493 TIGR03452, mycothione_red, mycothione reductase. Mycothiol, a glutathione analog in Mycobacterium tuberculosis and related species, can form a disulfide-linked dimer called mycothione. This enzyme can reduce mycothione to regenerate two mycothiol molecules. The enzyme shows some sequence similarity to glutathione-disulfide reductase, trypanothione-disulfide reductase, and dihydrolipoamide dehydrogenase. The characterized protein from M. tuberculosis, a homodimer, has FAD as a cofactor, one per monomer, and uses NADPH as a substrate. Length = 452 Score = 27.4 bits (61), Expect = 6.9 Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 10/73 (13%) Query: 234 VLAVEIAKPSVEAARYNIAANHVNNVKIVRMSSKEF-------TQAMRREREFNRLKDID 286 V A E+A+ E+AR I A +++V+ + S+ F R + +ID Sbjct: 50 VYAAEVAQSIGESARLGIDA-EIDSVRWPDIVSRVFGDRIDPIAAGGEDYRRGDETPNID 108 Query: 287 IHSYRFKTIFVDP 299 + Y FV P Sbjct: 109 V--YDGHARFVGP 119 >gnl|CDD|178974 PRK00312, pcm, protein-L-isoaspartate O-methyltransferase; Reviewed. Length = 212 Score = 27.1 bits (61), Expect = 8.7 Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 1/50 (2%) Query: 214 LELYCGNGNFSLVLARHFDRVLAVEIAKPSVEAARYNIAANHVNNVKIVR 263 LE+ G+G + VLA RV +VE K A+ + ++NV VR Sbjct: 83 LEIGTGSGYQAAVLAHLVRRVFSVERIKTLQWEAKRRLKQLGLHNV-SVR 131 >gnl|CDD|162023 TIGR00755, ksgA, dimethyladenosine transferase. Alternate name: S-adenosylmethionine--6-N',N'-adenosyl (rRNA) dimethyltransferase. Length = 253 Score = 26.9 bits (60), Expect = 8.9 Identities = 9/27 (33%), Positives = 15/27 (55%) Query: 213 LLELYCGNGNFSLVLARHFDRVLAVEI 239 +LE+ G G + L + +V A+EI Sbjct: 33 VLEIGPGLGALTEPLLKRAKKVTAIEI 59 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.327 0.139 0.418 Gapped Lambda K H 0.267 0.0858 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 6,275,756 Number of extensions: 410951 Number of successful extensions: 1082 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1062 Number of HSP's successfully gapped: 44 Length of query: 371 Length of database: 5,994,473 Length adjustment: 95 Effective length of query: 276 Effective length of database: 3,941,713 Effective search space: 1087912788 Effective search space used: 1087912788 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 58 (25.9 bits)