RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780872|ref|YP_003065285.1| 3-demethylubiquinone-9 3-methyltransferase [Candidatus Liberibacter asiaticus str. psy62] (254 letters) >gnl|CDD|179944 PRK05134, PRK05134, bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional. Length = 233 Score = 359 bits (925), Expect = e-100 Identities = 111/239 (46%), Positives = 161/239 (67%), Gaps = 13/239 (5%) Query: 8 YTTKNQDAINQFSNIASEWWEPTGKFKPLHQINPVRIKYIQDKIMQHFQCKSDDTHPFKG 67 + + I +FS +A+ WW+P G+FKPLH+INP+R+ YI++ G Sbjct: 1 MSNVDPAEIAKFSALAARWWDPNGEFKPLHRINPLRLNYIREHA-----------GGLFG 49 Query: 68 LRILDLGCGGGLLSEPMAQMGATVTGIDPSTKNIAIAKNHANMKNINIDYRVSCAEEIA- 126 R+LD+GCGGG+LSE MA++GA VTGID S +NI +A+ HA + IDYR + AEE+A Sbjct: 50 KRVLDVGCGGGILSESMARLGADVTGIDASEENIEVARLHALESGLKIDYRQTTAEELAA 109 Query: 127 ETDEKFDIILNMEVIEHVDNIPYFIKTCCSLLLSNGLMFISTINRNLKAMLLAIIGAEYL 186 E +FD++ ME++EHV + F++ C L+ GL+F ST+NRNLK+ LLAI+GAEY+ Sbjct: 110 EHPGQFDVVTCMEMLEHVPDPASFVRACAKLVKPGGLVFFSTLNRNLKSYLLAIVGAEYV 169 Query: 187 LQWLPKGTHQYDKFIKPTEMECFLAANKVKIIDRVGVVYNVFCNKWQLSAKNMDVNYMV 245 L+ LPKGTH Y KFIKP+E+ +L +++ D G+ YN N+W+LS ++DVNYM+ Sbjct: 170 LRMLPKGTHDYKKFIKPSELAAWLRQAGLEVQDITGLHYNPLTNRWKLS-DDVDVNYML 227 >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 = 316 bits (813), Expect = 3e-87 Identities = 118/231 (51%), Positives = 163/231 (70%), Gaps = 10/231 (4%) Query: 16 INQFSNIASEWWEPTGKFKPLHQINPVRIKYIQDKIMQHFQCKSDDTHPFKGLRILDLGC 75 I +FS +A EWW+P GKFKPLH++NP+R+ YI+D I K+ P GLR+LD+GC Sbjct: 2 IAKFSALAHEWWDPNGKFKPLHKMNPLRLDYIRDTI-----RKNKK--PLFGLRVLDVGC 54 Query: 76 GGGLLSEPMAQMGATVTGIDPSTKNIAIAKNHANMKNIN-IDYRVSCAEEIAETDEK-FD 133 GGGLLSEP+A++GA VTGID S +NI +AK HA + I+YR + E++AE K FD Sbjct: 55 GGGLLSEPLARLGANVTGIDASEENIEVAKLHAKKDPLLKIEYRCTSVEDLAEKGAKSFD 114 Query: 134 IILNMEVIEHVDNIPYFIKTCCSLLLSNGLMFISTINRNLKAMLLAIIGAEYLLQWLPKG 193 ++ MEV+EHV + FI+ C LL G++F STINR K+ LLAI+GAEY+L+ +PKG Sbjct: 115 VVTCMEVLEHVPDPQAFIRACAQLLKPGGILFFSTINRTPKSYLLAIVGAEYILRIVPKG 174 Query: 194 THQYDKFIKPTEMECFLAANKVKIIDRVGVVYNVFCNKWQLSAKNMDVNYM 244 TH ++KFIKP+E+ +L + +++ D G+VYN N+W LS K+ DVNYM Sbjct: 175 THDWEKFIKPSELTSWLESAGLRVKDVKGLVYNPIKNEWTLS-KDTDVNYM 224 >gnl|CDD|178018 PLN02396, PLN02396, hexaprenyldihydroxybenzoate methyltransferase. Length = 322 Score = 245 bits (627), Expect = 7e-66 Identities = 110/241 (45%), Positives = 157/241 (65%), Gaps = 3/241 (1%) Query: 9 TTKNQDAINQFSNIASEWWEPTGKFKPLHQINPVRIKYIQDKIMQHFQCKSDDTHPFKGL 68 T+ N+D + +FS IA WW G FKPLHQ+NP R+ +I+ + +HF PF+GL Sbjct: 74 TSLNEDELAKFSAIADTWWHSEGPFKPLHQMNPTRLAFIRSTLCRHFSKDPSSAKPFEGL 133 Query: 69 RILDLGCGGGLLSEPMAQMGATVTGIDPSTKNIAIAKNHANMKNI--NIDYRVSCAEEIA 126 + +D+GCGGGLLSEP+A+MGATVTG+D KN+ IA+ HA+M + I+Y + AE++A Sbjct: 134 KFIDIGCGGGLLSEPLARMGATVTGVDAVDKNVKIARLHADMDPVTSTIEYLCTTAEKLA 193 Query: 127 ETDEKFDIILNMEVIEHVDNIPYFIKTCCSLLLSNGLMFISTINRNLKAMLLAIIGAEYL 186 + KFD +L++EVIEHV N F K+ +L + NG +STINR ++A I+GAEY+ Sbjct: 194 DEGRKFDAVLSLEVIEHVANPAEFCKSLSALTIPNGATVLSTINRTMRAYASTIVGAEYI 253 Query: 187 LQWLPKGTHQYDKFIKPTEMECFLAANKVKIIDRVGVVYNVFCNKWQLSAKNMDVNYMVL 246 L+WLPKGTHQ+ F+ P E+ L V + + G VYN +W LS ++ VNY+ Sbjct: 254 LRWLPKGTHQWSSFVTPEELSMILQRASVDVKEMAGFVYNPITGRWLLS-DDISVNYIAY 312 Query: 247 G 247 G Sbjct: 313 G 313 >gnl|CDD|149353 pfam08241, Methyltransf_11, Methyltransferase domain. Members of this family are SAM dependent methyltransferases. Length = 95 Score = 83.5 bits (207), Expect = 5e-17 Identities = 32/97 (32%), Positives = 58/97 (59%), Gaps = 3/97 (3%) Query: 71 LDLGCGGGLLSEPMAQM-GATVTGIDPSTKNIAIAKNHANMKNINIDYRVSCAEEIAETD 129 LD+GCG GLL+E +A++ GA VTG+D S + +A+A+ A + + + V AE++ D Sbjct: 1 LDVGCGTGLLTEALARLPGAQVTGVDLSPEMLALARKRA--QEDGLTFVVGDAEDLPFPD 58 Query: 130 EKFDIILNMEVIEHVDNIPYFIKTCCSLLLSNGLMFI 166 E FD++++ V+ H+ + ++ +L G + I Sbjct: 59 ESFDVVVSSLVLHHLPDPERALREIARVLKPGGKLVI 95 >gnl|CDD|181382 PRK08317, PRK08317, hypothetical protein; Provisional. Length = 241 Score = 66.5 bits (163), Expect = 6e-12 Identities = 26/92 (28%), Positives = 47/92 (51%), Gaps = 3/92 (3%) Query: 63 HPFKGLRILDLGCGGGLLSEPMA-QMGAT--VTGIDPSTKNIAIAKNHANMKNINIDYRV 119 G R+LD+GCG G + +A ++G V GID S +A+AK A N+++ Sbjct: 16 AVQPGDRVLDVGCGPGNDARELARRVGPEGRVVGIDRSEAMLALAKERAAGLGPNVEFVR 75 Query: 120 SCAEEIAETDEKFDIILNMEVIEHVDNIPYFI 151 A+ + D FD + + V++H+++ + Sbjct: 76 GDADGLPFPDGSFDAVRSDRVLQHLEDPARAL 107 >gnl|CDD|162663 TIGR02021, BchM-ChlM, magnesium protoporphyrin O-methyltransferase. This model represents the S-adenosylmethionine-dependent O-methyltransferase responsible for methylation of magnesium protoporphyrin IX. This step is essentiasl for the biosynthesis of both chlorophyll and bacteriochlorophyll. This model encompasses two closely related clades, from cyanobacteria (and plants) where it is called ChlM and other photosynthetic bacteria where it is known as BchM. Length = 219 Score = 66.7 bits (163), Expect = 6e-12 Identities = 47/169 (27%), Positives = 82/169 (48%), Gaps = 14/169 (8%) Query: 64 PFKGLRILDLGCGGGLLSEPMAQMGATVTGIDPSTKNIAIAKNHANMKNI--NIDYRVSC 121 P KG R+LD GCG GLLS +A+ GA V +D S + + +A+N A +++ N+++ V+ Sbjct: 53 PLKGKRVLDAGCGTGLLSIELAKRGAIVKAVDISEQMVQMARNRAQGRDVAGNVEFEVN- 111 Query: 122 AEEIAETDEKFDIILNMEVIEH--VDNIPYFIKTCCSLLLSNGLMFISTINRNLKAMLLA 179 ++ +FDI++ M+V+ H ++ + S L+ + + + L Sbjct: 112 --DLLSLCGEFDIVVCMDVLIHYPASDMAKALGHLAS--LTKERVIFTFAPKTAWLAFLK 167 Query: 180 IIGAEYLLQWLPKGTHQYDKFIKPTEMECFLAANKVKIIDRVGVVYNVF 228 +IG L + T Y T++E L KI+ R G+V F Sbjct: 168 MIGE--LFPGSSRATSAY--LHPMTDLERALGELGWKIV-REGLVSTGF 211 >gnl|CDD|181047 PRK07580, PRK07580, Mg-protoporphyrin IX methyl transferase; Validated. Length = 230 Score = 64.9 bits (159), Expect = 2e-11 Identities = 28/80 (35%), Positives = 42/80 (52%), Gaps = 5/80 (6%) Query: 66 KGLRILDLGCGGGLLSEPMAQMGATVTGIDPSTKNIAIAKNHANMK--NINIDYRVSCAE 123 GLRILD GCG G LS P+A+ GA V D S + + A+ A NI + V Sbjct: 63 TGLRILDAGCGVGSLSIPLARRGAKVVASDISPQMVEEARERAPEAGLAGNITFEVG--- 119 Query: 124 EIAETDEKFDIILNMEVIEH 143 ++ +FD ++ ++V+ H Sbjct: 120 DLESLLGRFDTVVCLDVLIH 139 >gnl|CDD|180466 PRK06202, PRK06202, hypothetical protein; Provisional. Length = 232 Score = 63.9 bits (156), Expect = 4e-11 Identities = 31/124 (25%), Positives = 60/124 (48%), Gaps = 12/124 (9%) Query: 68 LRILDLGCGGGLLSEPMAQMGA------TVTGIDPSTKNIAIAKNHANMKNINIDYRVSC 121 L +LD+GCGGG L+ +A+ VT IDP + +A A+ + + +R + Sbjct: 62 LTLLDIGCGGGDLAIDLARWARRDGLRLEVTAIDPDPRAVAFARANPRRPGVT--FRQAV 119 Query: 122 AEEIAETDEKFDIILNMEVIEHVDN--IPYFIKTCCSLLLSNGLMFISTINRNLKAMLLA 179 ++E+ E+FD++ + + H+D+ + + S L+ L+ + + R+ A L Sbjct: 120 SDELVAEGERFDVVTSNHFLHHLDDAEVVRLLAD--SAALARRLVLHNDLIRSRLAYALF 177 Query: 180 IIGA 183 G Sbjct: 178 WAGT 181 >gnl|CDD|149354 pfam08242, Methyltransf_12, Methyltransferase domain. Members of this family are SAM dependent methyltransferases. Length = 98 Score = 54.7 bits (132), Expect = 2e-08 Identities = 22/97 (22%), Positives = 39/97 (40%), Gaps = 4/97 (4%) Query: 71 LDLGCGGGLLSEPMAQM--GATVTGIDPSTKNIAIAKNHANMKNINI--DYRVSCAEEIA 126 LD+GCG G L + + G TG+D S + A + R+ + I Sbjct: 1 LDIGCGTGTLLRALLEALPGLEYTGVDISPAALEAAAERLAALGLLDAVRVRLDVLDAID 60 Query: 127 ETDEKFDIILNMEVIEHVDNIPYFIKTCCSLLLSNGL 163 FD+++ V+ H+ + ++ LL G+ Sbjct: 61 LDPGSFDVVVASNVLHHLADPRAVLRNLRRLLKPGGV 97 >gnl|CDD|182918 PRK11036, PRK11036, putative S-adenosyl-L-methionine-dependent methyltransferase; Provisional. Length = 255 Score = 52.3 bits (126), Expect = 1e-07 Identities = 47/166 (28%), Positives = 78/166 (46%), Gaps = 13/166 (7%) Query: 68 LRILDLGCGGGLLSEPMAQMGATVTGIDPSTKNIAIAKNHANMKNINIDYRV--SCAEEI 125 LR+LD G G G + +A++G V D S + I AK A K ++ + + A++I Sbjct: 46 LRVLDAGGGEGQTAIKLAELGHQVILCDLSAEMIQRAKQAAEAKGVSDNMQFIHCAAQDI 105 Query: 126 AE-TDEKFDIILNMEVIEHVDNIPYFIKTCCSLLLSNG---LMFISTINRNLKAMLLAII 181 A+ + D+IL V+E V + ++T S+L G LMF N N M + Sbjct: 106 AQHLETPVDLILFHAVLEWVADPKSVLQTLWSVLRPGGALSLMF---YNANGLLMHNMVA 162 Query: 182 GA-EYLLQWLPKG---THQYDKFIKPTEMECFLAANKVKIIDRVGV 223 G +Y+ +PK T D + P ++ +L +I+ + GV Sbjct: 163 GNFDYVQAGMPKRKKRTLSPDYPLDPEQVYQWLEEAGWQIMGKTGV 208 >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 = 51.9 bits (125), Expect = 2e-07 Identities = 28/125 (22%), Positives = 55/125 (44%), Gaps = 9/125 (7%) Query: 47 IQDKIMQHFQCKSDDTHPFKGLRILDLGCGGGLLSEPMAQMG--ATVTGIDPSTKNIAIA 104 + +++ + K F +LD+GCG G L+ + + A +D S +A A Sbjct: 19 MAKRLLALLKEK----GIFIPASVLDIGCGTGYLTRALLKRFPQAEFIALDISAGMLAQA 74 Query: 105 KNHANMKNINIDYRVSCAEEIAETDEKFDIILNMEVIEHVDNIPYFIKTCCSLLLSNGLM 164 K + N+ + AE++ D FD+I++ ++ D++ + +L GL+ Sbjct: 75 KTKL---SENVQFICGDAEKLPLEDSSFDLIVSNLALQWCDDLSQALSELARVLKPGGLL 131 Query: 165 FISTI 169 ST Sbjct: 132 AFSTF 136 >gnl|CDD|183282 PRK11705, PRK11705, cyclopropane fatty acyl phospholipid synthase; Provisional. Length = 383 Score = 51.0 bits (123), Expect = 3e-07 Identities = 32/112 (28%), Positives = 53/112 (47%), Gaps = 14/112 (12%) Query: 67 GLRILDLGCGGGLLSEPMA-QMGATVTGIDPSTKNIAIAKNHANMKNINI---DYRVSCA 122 G+R+LD+GCG G L+ A G +V G+ S + +A+ + I DYR Sbjct: 168 GMRVLDIGCGWGGLARYAAEHYGVSVVGVTISAEQQKLAQERCAGLPVEIRLQDYR---- 223 Query: 123 EEIAETDEKFDIILNMEVIEHV--DNIPYFIKTCCSLLLSNGLMFISTINRN 172 + + +FD I+++ + EHV N + + L +GL + TI N Sbjct: 224 ----DLNGQFDRIVSVGMFEHVGPKNYRTYFEVVRRCLKPDGLFLLHTIGSN 271 >gnl|CDD|162613 TIGR01934, MenG_MenH_UbiE, ubiquinone/menaquinone biosynthesis methyltransferases. Note that a number of non-orthologous genes which are members of pfam03737 have been erroneously annotated as MenG methyltransferases. Length = 223 Score = 49.6 bits (119), Expect = 8e-07 Identities = 24/75 (32%), Positives = 42/75 (56%), Gaps = 4/75 (5%) Query: 64 PFKGLRILDLGCGGGLLSEPMAQMGAT---VTGIDPSTKNIAIAKNHANMKNINIDYRVS 120 FKG ++LD+ CG G L+ +A+ VTG+D S++ + +AK + + NI++ + Sbjct: 37 VFKGQKVLDVACGTGDLAIELAKSAPDRGKVTGVDFSSEMLEVAKKKSELPL-NIEFIQA 95 Query: 121 CAEEIAETDEKFDII 135 AE + D FD + Sbjct: 96 DAEALPFEDNSFDAV 110 >gnl|CDD|178932 PRK00216, ubiE, ubiquinone/menaquinone biosynthesis methyltransferase; Reviewed. Length = 239 Score = 47.5 bits (114), Expect = 3e-06 Identities = 21/93 (22%), Positives = 39/93 (41%), Gaps = 7/93 (7%) Query: 48 QDKIMQHFQCKSDDTHPFKGLRILDLGCGGGLLSEPMAQMG---ATVTGIDPSTKNIAIA 104 ++ + K G ++LDL CG G L+ +A+ V G+D S +A+ Sbjct: 35 LHRVWRRKTIK--WLGVRPGDKVLDLACGTGDLAIALAKAVGKTGEVVGLDFSEGMLAVG 92 Query: 105 KNHANMKNI--NIDYRVSCAEEIAETDEKFDII 135 + + N+++ AE + D FD + Sbjct: 93 REKLRDLGLSGNVEFVQGDAEALPFPDNSFDAV 125 >gnl|CDD|177970 PLN02336, PLN02336, phosphoethanolamine N-methyltransferase. Length = 475 Score = 44.4 bits (105), Expect = 3e-05 Identities = 29/102 (28%), Positives = 49/102 (48%), Gaps = 1/102 (0%) Query: 67 GLRILDLGCGGGLLSEPMAQ-MGATVTGIDPSTKNIAIAKNHANMKNINIDYRVSCAEEI 125 G ++LD+GCG G MA+ V GID S I+ A A + ++++ V+ + Sbjct: 267 GQKVLDVGCGIGGGDFYMAENFDVHVVGIDLSVNMISFALERAIGRKCSVEFEVADCTKK 326 Query: 126 AETDEKFDIILNMEVIEHVDNIPYFIKTCCSLLLSNGLMFIS 167 D FD+I + + I H+ + P ++ L G + IS Sbjct: 327 TYPDNSFDVIYSRDTILHIQDKPALFRSFFKWLKPGGKVLIS 368 >gnl|CDD|178197 PLN02585, PLN02585, magnesium protoporphyrin IX methyltransferase. Length = 315 Score = 44.1 bits (104), Expect = 3e-05 Identities = 22/90 (24%), Positives = 39/90 (43%), Gaps = 9/90 (10%) Query: 60 DDTHPFKGLRILDLGCGGGLLSEPMAQMGATVTGIDPSTKNIAIAKNHAN------MKNI 113 + G+ + D GCG G L+ P+A GA V+ D S +A A+ A + Sbjct: 138 AEDGSLAGVTVCDAGCGTGSLAIPLALEGAIVSASDISAAMVAEAERRAKEALAALPPEV 197 Query: 114 NIDYRVSCAEEIAETDEKFDIILNMEVIEH 143 + + E + K+D + ++V+ H Sbjct: 198 LPKFEANDLESL---SGKYDTVTCLDVLIH 224 >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 = 42.1 bits (100), Expect = 1e-04 Identities = 30/95 (31%), Positives = 41/95 (43%), Gaps = 28/95 (29%) Query: 66 KGLRILDLGCGGG-----LLSE-PMAQMGATVTGIDPSTKNIAIAKNHANMKNINIDYRV 119 LR+LDLG G G L E P A VT +D S + +A+A+ N + +D V Sbjct: 87 GPLRVLDLGTGSGAIALALAKERP----DARVTAVDISPEALAVAR--KNAARLGLD-NV 139 Query: 120 SC-----AEEIAETDEKFDIILNMEVIEHVDNIPY 149 + E + KFD+I V N PY Sbjct: 140 TFLQSDWFEPLP--GGKFDLI--------VSNPPY 164 >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 = 41.0 bits (96), Expect = 3e-04 Identities = 16/72 (22%), Positives = 36/72 (50%), Gaps = 4/72 (5%) Query: 66 KGLRILDLGCGGGLLSEPMAQMGATVTGIDPSTKNIAIAKNHANMKNINIDYRVSCAEEI 125 K +L++G G GL++ + G + D + + + +A + N+ +D ++ ++ Sbjct: 19 KPDDVLEIGAGTGLVAIRLKGKGKCILTTDINPFAVKELRENAKLNNVGLDVVMT---DL 75 Query: 126 AETDE-KFDIIL 136 + KFD+IL Sbjct: 76 FKGVRGKFDVIL 87 >gnl|CDD|181780 PRK09328, PRK09328, N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional. Length = 275 Score = 40.5 bits (96), Expect = 4e-04 Identities = 31/97 (31%), Positives = 42/97 (43%), Gaps = 32/97 (32%) Query: 66 KGLRILDLGCGGG-----LLSE-PMAQMGATVTGIDPSTKNIAIAKNHANMKNINIDYRV 119 + LR+LDLG G G L E P A VT +D S + +A+A+ N K+ RV Sbjct: 108 EPLRVLDLGTGSGAIALALAKERP----DAEVTAVDISPEALAVAR--RNAKHGLGA-RV 160 Query: 120 SCAEEIAETD-------EKFDIILNMEVIEHVDNIPY 149 E + D +FD+I V N PY Sbjct: 161 ----EFLQGDWFEPLPGGRFDLI--------VSNPPY 185 >gnl|CDD|179053 PRK00517, prmA, ribosomal protein L11 methyltransferase; Reviewed. Length = 250 Score = 40.1 bits (95), Expect = 6e-04 Identities = 19/84 (22%), Positives = 34/84 (40%), Gaps = 21/84 (25%) Query: 61 DTHPFKGLRILDLGCGGGLLSEPMAQMGAT-VTGID------PSTK-NIAIAKNHANMKN 112 + G +LD+GCG G+L+ A++GA V +D + + N N + Sbjct: 114 EKLVLPGKTVLDVGCGSGILAIAAAKLGAKKVLAVDIDPQAVEAAREN--AELNGVEL-- 169 Query: 113 INIDYRVSCAEEIAETDEKFDIIL 136 + + D K D+I+ Sbjct: 170 ---------NVYLPQGDLKADVIV 184 >gnl|CDD|184932 PRK14968, PRK14968, putative methyltransferase; Provisional. Length = 188 Score = 39.9 bits (94), Expect = 7e-04 Identities = 24/78 (30%), Positives = 41/78 (52%), Gaps = 12/78 (15%) Query: 66 KGLRILDLGCGGGLLSEPMAQMGATVTGIDPSTKNIAIAKNHANMKNINIDYRVSCAEEI 125 KG R+L++G G G+++ A+ G V G+D + + AK +A + NI + E+ Sbjct: 23 KGDRVLEVGTGSGIVAIVAAKNGKKVVGVDINPYAVECAKCNAKLNNIR-----NNGVEV 77 Query: 126 AETD-------EKFDIIL 136 +D +KFD+IL Sbjct: 78 IRSDLFEPFRGDKFDVIL 95 >gnl|CDD|177887 PLN02244, PLN02244, tocopherol O-methyltransferase. Length = 340 Score = 39.3 bits (92), Expect = 0.001 Identities = 27/79 (34%), Positives = 43/79 (54%), Gaps = 3/79 (3%) Query: 69 RILDLGCGGGLLSEPMAQM-GATVTGIDPSTKNIAIAKNHANMKNIN--IDYRVSCAEEI 125 RI+D+GCG G S +A+ GA V GI S A A A + ++ + ++V+ A Sbjct: 121 RIVDVGCGIGGSSRYLARKYGANVKGITLSPVQAARANALAAAQGLSDKVSFQVADALNQ 180 Query: 126 AETDEKFDIILNMEVIEHV 144 D +FD++ +ME EH+ Sbjct: 181 PFEDGQFDLVWSMESGEHM 199 >gnl|CDD|184931 PRK14967, PRK14967, putative methyltransferase; Provisional. Length = 223 Score = 38.5 bits (90), Expect = 0.002 Identities = 27/85 (31%), Positives = 41/85 (48%), Gaps = 12/85 (14%) Query: 67 GLRILDLGCGGGLLSEPMAQMGA-TVTGIDPSTKNIAIAKNHANMKNINID-YRVSCAEE 124 G R+LDL G G L+ A GA +VT +D S + + A+ +A + +++D R A Sbjct: 37 GRRVLDLCTGSGALAVAAAAAGAGSVTAVDISRRAVRSARLNALLAGVDVDVRRGDWAR- 95 Query: 125 IAETDEKFDIILNMEVIEHVDNIPY 149 A FD++ V N PY Sbjct: 96 -AVEFRPFDVV--------VSNPPY 111 >gnl|CDD|183450 PRK12335, PRK12335, tellurite resistance protein TehB; Provisional. Length = 287 Score = 38.4 bits (90), Expect = 0.002 Identities = 23/70 (32%), Positives = 38/70 (54%), Gaps = 5/70 (7%) Query: 69 RILDLGCGGGLLSEPMAQMGATVTGIDPSTKNIAIAKNHANMKNINIDYRVSCAEEI--A 126 + LDLGCG G S +A +G VT +D + +++ + A +N+NI + +I A Sbjct: 123 KALDLGCGQGRNSLYLALLGFDVTAVDINQQSLENLQEIAEKENLNIRTGL---YDINSA 179 Query: 127 ETDEKFDIIL 136 E++D IL Sbjct: 180 SIQEEYDFIL 189 >gnl|CDD|149213 pfam08003, Methyltransf_9, Protein of unknown function (DUF1698). This family contains many hypothetical proteins. It also includes two putative methyltransferase proteins. Length = 315 Score = 37.8 bits (88), Expect = 0.003 Identities = 30/85 (35%), Positives = 40/85 (47%), Gaps = 8/85 (9%) Query: 64 PFKGLRILDLGCGGGLLSEPMAQMGAT-VTGIDPSTKNIAIAKNHANMKNINIDYRVSC- 121 P KG ILD+GCG G M GA V GIDPS + + + A K + D R Sbjct: 113 PLKGRTILDVGCGNGYHMWRMLGEGAALVVGIDPS--ELFLCQFEAVRKLLGNDQRAHLL 170 Query: 122 ---AEEIAETDEKFDIILNMEVIEH 143 E++ E FD + +M V+ H Sbjct: 171 PLGIEQLPAL-EAFDTVFSMGVLYH 194 >gnl|CDD|183351 PRK11873, arsM, arsenite S-adenosylmethyltransferase; Reviewed. Length = 272 Score = 36.1 bits (84), Expect = 0.009 Identities = 25/82 (30%), Positives = 43/82 (52%), Gaps = 8/82 (9%) Query: 66 KGLRILDLGCGGG---LLSEPMAQMGAT--VTGIDPSTKNIAIAKNHANMKNI-NIDYRV 119 G +LDLG GGG L+ ++G T V G+D + + +A A+ +A N+++R+ Sbjct: 77 PGETVLDLGSGGGFDCFLAAR--RVGPTGKVIGVDMTPEMLAKARANARKAGYTNVEFRL 134 Query: 120 SCAEEIAETDEKFDIILNMEVI 141 E + D D+I++ VI Sbjct: 135 GEIEALPVADNSVDVIISNCVI 156 >gnl|CDD|184509 PRK14103, PRK14103, trans-aconitate 2-methyltransferase; Provisional. Length = 255 Score = 35.8 bits (83), Expect = 0.010 Identities = 15/39 (38%), Positives = 25/39 (64%), Gaps = 2/39 (5%) Query: 69 RILDLGCGGGLLSEPMAQM--GATVTGIDPSTKNIAIAK 105 R++DLGCG G L+ +A+ GA + +D S + +A A+ Sbjct: 32 RVVDLGCGPGNLTRYLARRWPGAVIEALDSSPEMVAAAR 70 >gnl|CDD|161861 TIGR00406, prmA, ribosomal protein L11 methyltransferase. Ribosomal protein L11 methyltransferase is an S-adenosyl-L-methionine-dependent methyltransferase required for the modification of ribosomal protein L11. This protein is found in bacteria and (with a probable transit peptide) in Arabidopsis. Length = 288 Score = 35.6 bits (82), Expect = 0.011 Identities = 30/108 (27%), Positives = 51/108 (47%), Gaps = 10/108 (9%) Query: 66 KGLRILDLGCGGGLLSEPMAQMGA-TVTGIDPSTKNIAIAKNHANMKNINIDYRVSCAEE 124 K ++D+GCG G+LS ++GA V GID + A+ +A + ++ +V Sbjct: 159 KDKNVIDVGCGSGILSIAALKLGAAKVVGIDIDPLAVESARKNAELNQVSDRLQVKLIYL 218 Query: 125 IAETDEKFDIIL-NM--EVIEHVDNIPYFIKTCCSLLLSNGLMFISTI 169 + K D+I+ N+ EVI + P F L+ G + +S I Sbjct: 219 EQPIEGKADVIVANILAEVI--KELYPQFS----RLVKPGGWLILSGI 260 >gnl|CDD|183875 PRK13168, rumA, 23S rRNA m(5)U1939 methyltransferase; Reviewed. Length = 443 Score = 35.5 bits (83), Expect = 0.012 Identities = 12/26 (46%), Positives = 17/26 (65%) Query: 69 RILDLGCGGGLLSEPMAQMGATVTGI 94 R+LDL CG G + P+A+ A V G+ Sbjct: 300 RVLDLFCGLGNFTLPLARQAAEVVGV 325 >gnl|CDD|150895 pfam10294, Methyltransf_16, Putative methyltransferase. Length = 171 Score = 35.4 bits (82), Expect = 0.015 Identities = 30/133 (22%), Positives = 54/133 (40%), Gaps = 23/133 (17%) Query: 42 VRIKYIQDKIMQHFQCKSDDTHPFKGLRILDLGCGGGL----LSEPMAQMGATVTGIDPS 97 V KY++ KI + G +L+LG G GL ++ + T+T ++ + Sbjct: 27 VLSKYLEMKITSGG-------NNLSGKNVLELGSGCGLVGIAVALLLPGASVTITDLEEA 79 Query: 98 ----TKNIAIAKNHANMKNINIDYRV-SCAEEIAE---TDEKFDIILNMEVIEHVDNIPY 149 KNI + K ++ + +V EE+ + D+IL + + + D P Sbjct: 80 IELMKKNIELNKALSSK----VTAKVLDWGEELPDDVFDPHPVDLILAADCVYNEDAFPL 135 Query: 150 FIKTCCSLLLSNG 162 +KT LL Sbjct: 136 LVKTLKDLLGKET 148 >gnl|CDD|178868 PRK00107, gidB, 16S rRNA methyltransferase GidB; Reviewed. Length = 187 Score = 35.1 bits (82), Expect = 0.019 Identities = 24/76 (31%), Positives = 35/76 (46%), Gaps = 8/76 (10%) Query: 66 KGLRILDLGCGGGLLSEPMAQM--GATVTGIDPSTKNIA---IAKNHANMKNINIDYRVS 120 G R+LD+G G G P+A VT +D K IA +KN+ + Sbjct: 45 GGERVLDVGSGAGFPGIPLAIARPELKVTLVDSLGKKIAFLREVAAELGLKNVTV--VHG 102 Query: 121 CAEEIAETDEKFDIIL 136 AEE + +EKFD++ Sbjct: 103 RAEEFGQ-EEKFDVVT 117 >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 = 34.8 bits (80), Expect = 0.022 Identities = 19/104 (18%), Positives = 50/104 (48%), Gaps = 12/104 (11%) Query: 38 QINPVRIKYIQDKIMQHFQCKSDDTHPFKGLRILDLGCGGGLLSEPMAQMGATVTGIDPS 97 Q+N + + + D+ ++ + + ++ ++D CG G + P+A+ +V GI+ Sbjct: 271 QVNSGQNEKLVDRALEALELQGEE-------LVVDAYCGVGTFTLPLAKQAKSVVGIEVV 323 Query: 98 TKNIAIAKNHANMKNI-NIDYRVSCAEEI----AETDEKFDIIL 136 +++ A+ +A + I N+++ E + + D++L Sbjct: 324 PESVEKAQQNAELNGIANVEFLAGTLETVLPKQPWAGQIPDVLL 367 >gnl|CDD|129627 TIGR00536, hemK_fam, HemK family putative methylases. 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. Both E. coli and H. influenzae have two members rather than one. The members from the Mycoplasmas have an additional C-terminal domain. Length = 284 Score = 34.3 bits (79), Expect = 0.035 Identities = 27/91 (29%), Positives = 42/91 (46%), Gaps = 23/91 (25%) Query: 68 LRILDLGCGGGLLSEPMAQM--GATVTGIDPSTKNIAIAKNHANMKNINIDYRVSCAEEI 125 L ILDLG G G ++ +A A V +D S +A+A+ N + +++RV E Sbjct: 116 LHILDLGTGSGCIALALAYEFPNAEVIAVDISPDALAVAE--ENAEKNQLEHRV----EF 169 Query: 126 AETD-------EKFDIILNMEVIEHVDNIPY 149 +++ +K DII V N PY Sbjct: 170 IQSNLFEPLAGQKIDII--------VSNPPY 192 >gnl|CDD|129569 TIGR00477, tehB, tellurite resistance protein TehB. Part of a tellurite-reducing operon tehA and tehB. Length = 195 Score = 34.1 bits (78), Expect = 0.035 Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 1/73 (1%) Query: 69 RILDLGCGGGLLSEPMAQMGATVTGIDPSTKNIAIAKNHANMKNINIDYRVSCAEEIAET 128 + LDLGCG G S ++ G V D + +IA + +N+ + A Sbjct: 33 KTLDLGCGQGRNSLYLSLAGYDVRAWDHNPASIASVLDMKARENLPLRTDAYDINA-AAL 91 Query: 129 DEKFDIILNMEVI 141 +E +D I + V Sbjct: 92 NEDYDFIFSTVVF 104 >gnl|CDD|185028 PRK15068, PRK15068, tRNA mo(5)U34 methyltransferase; Provisional. Length = 322 Score = 34.1 bits (79), Expect = 0.040 Identities = 30/106 (28%), Positives = 48/106 (45%), Gaps = 19/106 (17%) Query: 44 IKYIQDKIMQHFQCKSDDTHPFKGLRILDLGCGGGLLSEPMAQMGA-TVTGIDPSTKNI- 101 K+ D+++ H P KG +LD+GCG G M GA V GIDPS + Sbjct: 109 WKW--DRVLPHLS-------PLKGRTVLDVGCGNGYHMWRMLGAGAKLVVGIDPSQLFLC 159 Query: 102 ---AIAKNHANMKNINID-YRVSCAEEIAETDEKFDIILNMEVIEH 143 A+ K N + ++ + E++ + FD + +M V+ H Sbjct: 160 QFEAVRKLLGNDQRAHLLPLGI---EQLPA-LKAFDTVFSMGVLYH 201 >gnl|CDD|129544 TIGR00452, TIGR00452, methyltransferase, putative. Known examples to date are restricted to the proteobacteria. Length = 314 Score = 33.4 bits (76), Expect = 0.052 Identities = 27/85 (31%), Positives = 37/85 (43%), Gaps = 8/85 (9%) Query: 64 PFKGLRILDLGCGGGLLSEPMAQMGA-TVTGIDPSTKNI----AIAKNHANMKNINIDYR 118 P KG ILD+GCG G M GA ++ GIDP+ + A+ K N K + Sbjct: 119 PLKGRTILDVGCGSGYHMWRMLGHGAKSLVGIDPTVLFLCQFEAVRKLLDNDKRAIL--- 175 Query: 119 VSCAEEIAETDEKFDIILNMEVIEH 143 E FD + +M V+ H Sbjct: 176 EPLGIEQLHELYAFDTVFSMGVLYH 200 >gnl|CDD|181902 PRK09489, rsmC, 16S ribosomal RNA m2G1207 methyltransferase; Provisional. Length = 342 Score = 33.4 bits (77), Expect = 0.062 Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 5/77 (6%) Query: 62 THPFKGLRILDLGCGGGLLSEPMAQM--GATVTGIDPSTKNIAIAKNHANMKNINIDYRV 119 T KG ++LD+GCG G+LS +A+ +T D S A+ + A + ++ V Sbjct: 193 TPHTKG-KVLDVGCGAGVLSAVLARHSPKIRLTLSDVSA--AALESSRATLAANGLEGEV 249 Query: 120 SCAEEIAETDEKFDIIL 136 + ++ +FD+I+ Sbjct: 250 FASNVFSDIKGRFDMII 266 >gnl|CDD|128898 smart00650, rADc, Ribosomal RNA adenine dimethylases. Length = 169 Score = 32.5 bits (75), Expect = 0.10 Identities = 26/111 (23%), Positives = 42/111 (37%), Gaps = 28/111 (25%) Query: 49 DKIMQHFQCKSDDTHPFKGLRILDLGCGGGLLSEPMAQMGATVTG--IDPS----TKNIA 102 DKI++ + G +L++G G G L+E + + A VT IDP + Sbjct: 3 DKIVRA-------ANLRPGDTVLEIGPGKGALTEELLERAARVTAIEIDPRLAPRLREKF 55 Query: 103 IAKNHANMKNINIDYRVSCAEEIAETDEKFDIILNMEVIEHVDNIPYFIKT 153 A N+ I+ D + + + V N+PY I T Sbjct: 56 AA--ADNLTVIHGDAL-----KFDLPKLQPYKV--------VGNLPYNIST 91 >gnl|CDD|183040 PRK11207, PRK11207, tellurite resistance protein TehB; Provisional. Length = 197 Score = 32.0 bits (73), Expect = 0.13 Identities = 16/37 (43%), Positives = 20/37 (54%) Query: 66 KGLRILDLGCGGGLLSEPMAQMGATVTGIDPSTKNIA 102 K + LDLGCG G S +A G VT D + +IA Sbjct: 30 KPGKTLDLGCGNGRNSLYLAANGFDVTAWDKNPMSIA 66 >gnl|CDD|179319 PRK01683, PRK01683, trans-aconitate 2-methyltransferase; Provisional. Length = 258 Score = 32.2 bits (74), Expect = 0.14 Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 6/43 (13%) Query: 69 RILDLGCGGG----LLSEPMAQMGATVTGIDPSTKNIAIAKNH 107 ++DLGCG G LL E A +TGID S +A A++ Sbjct: 34 YVVDLGCGPGNSTELLVERWPA--ARITGIDSSPAMLAEARSR 74 >gnl|CDD|177877 PLN02233, PLN02233, ubiquinone biosynthesis methyltransferase. Length = 261 Score = 31.8 bits (72), Expect = 0.17 Identities = 27/78 (34%), Positives = 40/78 (51%), Gaps = 9/78 (11%) Query: 66 KGLRILDLGCGGG----LLSEPMAQMGATVTGIDPSTKNIAIAKNHANMKNI----NIDY 117 G R+LDL CG G LLSE + G V G+D S++ +A+A + +K NI++ Sbjct: 73 MGDRVLDLCCGSGDLAFLLSEKVGSDG-KVMGLDFSSEQLAVAASRQELKAKSCYKNIEW 131 Query: 118 RVSCAEEIAETDEKFDII 135 A ++ D FD I Sbjct: 132 IEGDATDLPFDDCYFDAI 149 >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 = 30.7 bits (70), Expect = 0.37 Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 3/71 (4%) Query: 66 KGLRILDLGCGGGLLSEPMAQMGAT-VTGIDPSTKNIAIAKNHANMKNINIDYRVSCAEE 124 G +LD+GCG G+L+ ++GA V G+D + AK +A + + V + Sbjct: 160 PGETVLDVGCGSGILAIAALKLGAKKVVGVDIDPVAVRAAKENAELNGVEAQLEVYLPGD 219 Query: 125 IAETDEKFDII 135 + E K D++ Sbjct: 220 LPE--GKADVV 228 >gnl|CDD|163310 TIGR03533, L3_gln_methyl, protein-(glutamine-N5) methyltransferase, ribosomal protein L3-specific. Members of this protein family methylate ribosomal protein L3 on a glutamine side chain. This family is related to HemK, a protein-glutamine methyltranferase for peptide chain release factors. Length = 284 Score = 30.6 bits (70), Expect = 0.41 Identities = 25/90 (27%), Positives = 39/90 (43%), Gaps = 23/90 (25%) Query: 69 RILDLGCGGGLLSEPMAQM--GATVTGIDPSTKNIAIAKNHANMKNINIDYRVSCAEEIA 126 RILDL G G ++ A A V +D S +A+A N++ ++ RV + Sbjct: 124 RILDLCTGSGCIAIACAYAFPEAEVDAVDISPDALAVA--EINIERHGLEDRV----TLI 177 Query: 127 ETD-------EKFDIILNMEVIEHVDNIPY 149 ++D K+D+I V N PY Sbjct: 178 QSDLFAALPGRKYDLI--------VSNPPY 199 >gnl|CDD|182340 PRK10258, PRK10258, biotin biosynthesis protein BioC; Provisional. Length = 251 Score = 30.5 bits (69), Expect = 0.47 Identities = 14/38 (36%), Positives = 21/38 (55%) Query: 70 ILDLGCGGGLLSEPMAQMGATVTGIDPSTKNIAIAKNH 107 +LD GCG G +S + G+ VT +D S +A A+ Sbjct: 46 VLDAGCGPGWMSRYWRERGSQVTALDLSPPMLAQARQK 83 >gnl|CDD|184744 PRK14560, PRK14560, putative RNA-binding protein; Provisional. Length = 160 Score = 29.4 bits (67), Expect = 0.92 Identities = 15/46 (32%), Positives = 19/46 (41%), Gaps = 9/46 (19%) Query: 108 ANMKNINIDYRVSCAEEIAETDEKFDIILNMEVIEHVDNIPYFIKT 153 ++ID A E ETD+K +I L VD P F K Sbjct: 22 KEKFGVDIDG--KDAVEEVETDKKEEIYL-------VDGEPLFFKV 58 >gnl|CDD|162023 TIGR00755, ksgA, dimethyladenosine transferase. Alternate name: S-adenosylmethionine--6-N',N'-adenosyl (rRNA) dimethyltransferase. Length = 253 Score = 29.2 bits (66), Expect = 1.0 Identities = 23/89 (25%), Positives = 43/89 (48%), Gaps = 10/89 (11%) Query: 66 KGLRILDLGCGGGLLSEPMAQMGATVTGIDPSTKNIAIAKNHANMKNINIDYRVSCAEEI 125 +G +L++G G G L+EP+ + VT I+ + I + ++ R+ E+ Sbjct: 29 EGDVVLEIGPGLGALTEPLLKRAKKVTAIEIDPRLAEILRKLLSLYE-----RL----EV 79 Query: 126 AETDE-KFDIILNMEVIEHVDNIPYFIKT 153 E D K D+ + ++ V N+PY I + Sbjct: 80 IEGDALKVDLPDFPKQLKVVSNLPYNISS 108 >gnl|CDD|150199 pfam09445, Methyltransf_15, RNA cap guanine-N2 methyltransferase. RNA cap guanine-N2 methyltransferases such as Schizosaccharomyces pombe Tgs1 and Giardia lamblia Tgs2 catalyse methylation of the exocyclic N2 amine of 7-methylguanosine. Length = 165 Score = 29.2 bits (66), Expect = 1.1 Identities = 14/48 (29%), Positives = 28/48 (58%) Query: 67 GLRILDLGCGGGLLSEPMAQMGATVTGIDPSTKNIAIAKNHANMKNIN 114 ILD+ CG G + A + +V GID + +++A A+++A + ++ Sbjct: 1 ARIILDVFCGAGGNTIQFANVFCSVIGIDINPEHLACAQHNAEVYGVS 48 >gnl|CDD|166927 PRK00377, cbiT, cobalt-precorrin-6Y C(15)-methyltransferase; Provisional. Length = 198 Score = 29.0 bits (65), Expect = 1.1 Identities = 22/81 (27%), Positives = 35/81 (43%), Gaps = 24/81 (29%) Query: 65 FKGLRILDLGCGGGLLS-EPMAQMGAT--VTGIDPSTKNIAIAKNHANMKNINIDYRVSC 121 KG ILD+GCG G ++ E +G T V +D K I + + +A Sbjct: 39 RKGDMILDIGCGTGSVTVEASLLVGETGKVYAVDKDEKAINLTRRNA------------- 85 Query: 122 AEEIAETDEKFDIILNMEVIE 142 EKF ++ N+ +I+ Sbjct: 86 --------EKFGVLNNIVLIK 98 >gnl|CDD|173391 PTZ00098, PTZ00098, phosphoethanolamine N-methyltransferase; Provisional. Length = 263 Score = 29.2 bits (65), Expect = 1.2 Identities = 30/105 (28%), Positives = 49/105 (46%), Gaps = 10/105 (9%) Query: 69 RILDLGCG-GGLLSEPMAQMGATVTGIDPSTKNIAIAKNHANMKNINIDYRVSCAEEIAE 127 ++LD+G G GG + GA V G+D K + IAK N I++ A +I + Sbjct: 55 KVLDIGSGLGGGCKYINEKYGAHVHGVDICEKMVNIAKLR-NSDKNKIEFE---ANDILK 110 Query: 128 TD---EKFDIILNMEVIEHV--DNIPYFIKTCCSLLLSNGLMFIS 167 D FD+I + + I H+ + + C L NG++ I+ Sbjct: 111 KDFPENTFDMIYSRDAILHLSYADKKKLFEKCYKWLKPNGILLIT 155 >gnl|CDD|129244 TIGR00138, gidB, 16S rRNA methyltransferase GidB. GidB (glucose-inhibited division protein B) appears to be present and in a single copy in nearly all complete eubacterial genomes. It is missing only from some obligate intracellular species of various lineages (Chlamydiae, Ehrlichia, Wolbachia, Anaplasma, Buchnera, etc.). GidB shows a methytransferase fold in its the crystal structure, and acts as a 7-methylguanosine (m(7)G) methyltransferase, apparently specific to 16S rRNA. Length = 181 Score = 29.2 bits (66), Expect = 1.2 Identities = 22/105 (20%), Positives = 45/105 (42%), Gaps = 14/105 (13%) Query: 64 PFKGLRILDLGCGGGLLSEPMAQMG--ATVTGIDPSTKNIA---IAKNHANMKNINI-DY 117 G +++D+G G G P+A +T ++ + K +A K + N+ I + Sbjct: 40 YLDGKKVIDIGSGAGFPGIPLAIARPELKLTLLESNHKKVAFLREVKAELGLNNVEIVNG 99 Query: 118 RVSCAEEIAETDEKFDIILNMEVIEHVDNIPYFIKTCCSLLLSNG 162 R E + +E+FD+I + ++ ++ +LL G Sbjct: 100 RA----EDFQHEEQFDVI----TSRALASLNVLLELTLNLLKVGG 136 >gnl|CDD|129061 smart00828, PKS_MT, Methyltransferase in polyketide synthase (PKS) enzymes. Length = 224 Score = 28.2 bits (63), Expect = 2.1 Identities = 21/83 (25%), Positives = 32/83 (38%), Gaps = 9/83 (10%) Query: 68 LRILDLGCGGG--LLSEPMAQMGATVTGIDPSTKNIAIAKNHANMK----NINIDYRVSC 121 R+LD GCG G L+ + G S + + + I I YR S Sbjct: 1 KRVLDFGCGYGSDLIDLAERHPHLQLHGYTISPEQAEVGRERIRALGLQGRIRIFYRDSA 60 Query: 122 AEEIAETDEKFDIILNMEVIEHV 144 + +T D++ EVI H+ Sbjct: 61 KDPFPDTY---DLVFGFEVIHHI 80 >gnl|CDD|172452 PRK13943, PRK13943, protein-L-isoaspartate O-methyltransferase; Provisional. Length = 322 Score = 28.3 bits (63), Expect = 2.1 Identities = 23/90 (25%), Positives = 42/90 (46%), Gaps = 11/90 (12%) Query: 66 KGLRILDLGCGGGLLSEPMAQM---GATVTGIDPSTKNIAIAKNHANMKNINIDYRVSCA 122 KG+R+L++G G G + M+++ V ++ S K IAK N++ + I+ + Sbjct: 80 KGMRVLEIGGGTGYNAAVMSRVVGEKGLVVSVEYSRKICEIAKR--NVRRLGIENVIFVC 137 Query: 123 EEIAETDEKF---DIILNMEVIEHVDNIPY 149 + +F D+I V VD +P Sbjct: 138 GDGYYGVPEFAPYDVIF---VTVGVDEVPE 164 >gnl|CDD|180726 PRK06846, PRK06846, putative deaminase; Validated. Length = 410 Score = 28.1 bits (63), Expect = 2.1 Identities = 16/41 (39%), Positives = 25/41 (60%), Gaps = 2/41 (4%) Query: 78 GLLSEPMAQMGAT-VTGIDPSTKNIAIAKNHANMKNINIDY 117 L+ E M +MGA V G+DP++ + AI K+ M I +D+ Sbjct: 179 PLMREAM-KMGAHLVGGVDPASVDGAIEKSLDTMFQIAVDF 218 >gnl|CDD|183320 PRK11805, PRK11805, N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional. Length = 307 Score = 28.2 bits (64), Expect = 2.2 Identities = 25/90 (27%), Positives = 40/90 (44%), Gaps = 23/90 (25%) Query: 69 RILDLGCGGGLLSEPMAQM--GATVTGIDPSTKNIAIAKNHANMKNINIDYRVSCAEEIA 126 RILDL G G ++ A A V +D S +A+A+ N++ ++ RV + Sbjct: 136 RILDLCTGSGCIAIACAYAFPDAEVDAVDISPDALAVAE--INIERHGLEDRV----TLI 189 Query: 127 ETD-------EKFDIILNMEVIEHVDNIPY 149 E+D ++D+I V N PY Sbjct: 190 ESDLFAALPGRRYDLI--------VSNPPY 211 >gnl|CDD|132172 TIGR03128, RuMP_HxlA, 3-hexulose-6-phosphate synthase. at the cost of also yielding formaldehyde. These latter species tend usually have a formaldehyde-activating enzyme to attach formaldehyde to the C1 carrier tetrahydromethanopterin. In these species, the enzyme is viewed as a lyase rather than a synthase and is called D-arabino 3-hexulose 6-phosphate formaldehyde lyase. Note that there is some overlap in specificity with the Escherichia coli enzyme 3-keto-L-gulonate 6-phosphate decarboxylase. Length = 206 Score = 27.7 bits (62), Expect = 2.6 Identities = 19/69 (27%), Positives = 30/69 (43%), Gaps = 12/69 (17%) Query: 68 LRILDLGCGGGLLSEPMAQMGA---TVTGI-DPSTKNIAIAKNHANMKN-----INIDYR 118 L+ +D G +E GA TV G+ D +T A+ + K IN+ + Sbjct: 59 LKTMD---AGEYEAEQAFAAGADIVTVLGVADDATIKGAVKAAKKHGKEVQVDLINVKDK 115 Query: 119 VSCAEEIAE 127 V A+E+ E Sbjct: 116 VKRAKELKE 124 >gnl|CDD|161697 TIGR00080, pimt, protein-L-isoaspartate(D-aspartate) O-methyltransferase. Among the prokaryotes, the gene name is pcm. Among eukaryotes, pimt. Length = 215 Score = 27.9 bits (62), Expect = 2.8 Identities = 18/77 (23%), Positives = 31/77 (40%), Gaps = 10/77 (12%) Query: 29 PTGKFKPLH------QINPVRIKYIQDKIMQHFQCKSDDTHPFK-GLRILDLGCGGGLLS 81 P +F P H P+ I Y Q H + K G+++L++G G G + Sbjct: 33 PREEFVPEHFKEYAYVDTPLEIGYGQTISAPHMVAMMTELLELKPGMKVLEIGTGSGYQA 92 Query: 82 EPMAQM---GATVTGID 95 +A++ V I+ Sbjct: 93 AVLAEIVGRDGLVVSIE 109 >gnl|CDD|130784 TIGR01723, hmd_TIGR, 5,10-methenyltetrahydromethanopterin hydrogenase. This model represents a clade of authenticated coenzyme N(5),N(10)-methenyltetrahydromethanopterin reductases. This enzyme does not use F420. This enzyme acts in methanogenesis and as such is restricted to methanogenic archaeal species. This clade is one of two clades in pfam model pfam03201. Length = 340 Score = 27.6 bits (61), Expect = 3.0 Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 3/26 (11%) Query: 179 AIIGAEYLLQWLPKGTHQ---YDKFI 201 A+ A+ ++ WLPKG Q KFI Sbjct: 136 AVEDADIIITWLPKGNKQPDIIKKFI 161 >gnl|CDD|185604 PTZ00416, PTZ00416, elongation factor 2; Provisional. Length = 836 Score = 27.7 bits (62), Expect = 3.1 Identities = 14/36 (38%), Positives = 17/36 (47%), Gaps = 7/36 (19%) Query: 110 MKNINIDYRVSCAEEIAETDEKFDIILNMEVIEHVD 145 M N +D +I E + D I NM VI HVD Sbjct: 1 MVNFTVD-------QIREIMDNPDQIRNMSVIAHVD 29 >gnl|CDD|182654 PRK10695, PRK10695, hypothetical protein; Provisional. Length = 859 Score = 27.6 bits (62), Expect = 3.1 Identities = 7/23 (30%), Positives = 14/23 (60%) Query: 232 WQLSAKNMDVNYMVLGHLPKTEQ 254 W+L+A + ++ L LP +E+ Sbjct: 82 WRLNADTVTLDSACLSKLPASEE 104 >gnl|CDD|115661 pfam07021, MetW, Methionine biosynthesis protein MetW. This family consists of several bacterial and one archaeal methionine biosynthesis MetW proteins. Biosynthesis of methionine from homoserine in Pseudomonas putida takes place in three steps. The first step is the acylation of homoserine to yield an acyl-L-homoserine. This reaction is catalysed by the products of the metXW genes and is equivalent to the first step in enterobacteria, gram-positive bacteria and fungi, except that in these microorganisms the reaction is catalysed by a single polypeptide (the product of the metA gene in Escherichia coli and the met5 gene product in Neurospora crassa). In Pseudomonas putida, as in gram-positive bacteria and certain fungi, the second and third steps are a direct sulfhydrylation that converts the O-acyl-L-homoserine into homocysteine and further methylation to yield methionine. The latter reaction can be mediated by either of the two methionine synthetases present in the cells. Length = 193 Score = 27.8 bits (62), Expect = 3.1 Identities = 13/37 (35%), Positives = 18/37 (48%), Gaps = 1/37 (2%) Query: 67 GLRILDLGCGGGLLSEPMA-QMGATVTGIDPSTKNIA 102 G R+LDLGCG G L + + GI+ +A Sbjct: 14 GSRVLDLGCGDGSLLYLLQEEKQVDGRGIELDAAGVA 50 >gnl|CDD|162689 TIGR02081, metW, methionine biosynthesis protein MetW. This protein is found alongside MetX, of the enzyme that acylates homoserine as a first step toward methionine biosynthesis, in many species. It appears to act in methionine biosynthesis but is not fully characterized. Length = 194 Score = 27.3 bits (61), Expect = 3.8 Identities = 10/14 (71%), Positives = 11/14 (78%) Query: 67 GLRILDLGCGGGLL 80 G R+LDLGCG G L Sbjct: 14 GSRVLDLGCGDGEL 27 >gnl|CDD|182954 PRK11088, rrmA, 23S rRNA methyltransferase A; Provisional. Length = 272 Score = 26.8 bits (60), Expect = 5.2 Identities = 19/98 (19%), Positives = 38/98 (38%), Gaps = 21/98 (21%) Query: 48 QDKIMQHFQCK-SDDTHPFKGLRILDLGCGGGLLSEPMA-----QMGATVTGIDPSTKNI 101 +D + + + +LD+GCG G + +A + G+D S + Sbjct: 71 RDAVANLLAERLDEKAT-----ALLDIGCGEGYYTHALADALPEITTMQLFGLDIS--KV 123 Query: 102 AI---AKNHANMKNINIDYRVSCAEEIAETDEKFDIIL 136 AI AK + + + V+ + + D+ D I+ Sbjct: 124 AIKYAAKRYP-----QVTFCVASSHRLPFADQSLDAII 156 >gnl|CDD|152698 pfam12263, DUF3611, Protein of unknown function (DUF3611). This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 180 and 205 amino acids in length. There are two completely conserved residues (W and G) that may be functionally important. Length = 183 Score = 26.5 bits (59), Expect = 6.4 Identities = 19/58 (32%), Positives = 25/58 (43%), Gaps = 15/58 (25%) Query: 158 LLSNGLMFISTINRNLKAMLLAIIGAEYLLQWL-------PKGTHQYD--KFIKPTEM 206 LL GL+ NL M LA+IGA+ + L P G YD K I ++ Sbjct: 103 LLRLGLII------NLLGMFLALIGAQATVGILLAKALSQPPGIAVYDPNKAITALDV 154 >gnl|CDD|183597 PRK12564, PRK12564, carbamoyl phosphate synthase small subunit; Reviewed. Length = 360 Score = 26.6 bits (60), Expect = 6.6 Identities = 8/57 (14%), Positives = 19/57 (33%) Query: 85 AQMGATVTGIDPSTKNIAIAKNHANMKNINIDYRVSCAEEIAETDEKFDIILNMEVI 141 A G T + + + A+ + +++ VS E ++ + I Sbjct: 127 AMKGVIATEDFDAEELLEKARAFPGLLGLDLVKEVSTKEPYPWPGPGGELKYKVVAI 183 >gnl|CDD|178277 PLN02672, PLN02672, methionine S-methyltransferase. Length = 1082 Score = 26.3 bits (58), Expect = 7.8 Identities = 14/47 (29%), Positives = 27/47 (57%), Gaps = 5/47 (10%) Query: 63 HP---FKGLRILDLGCGGGLLSEPMAQ--MGATVTGIDPSTKNIAIA 104 HP F+ + +LGCG G +S +A+ + + V G+D + + + +A Sbjct: 112 HPDSIFRDKTVAELGCGNGWISIAIAEKWLPSKVYGLDINPRAVKVA 158 >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 = 26.1 bits (58), Expect = 8.0 Identities = 10/38 (26%), Positives = 16/38 (42%), Gaps = 2/38 (5%) Query: 70 ILDLGCGGGLLSEPMAQMGA--TVTGIDPSTKNIAIAK 105 ++D+G G S A+ GA V +P I + Sbjct: 2 VIDVGANIGDTSLYFARKGAEGRVIAFEPLPDAYEILE 39 >gnl|CDD|179184 PRK00961, PRK00961, H(2)-dependent methylenetetrahydromethanopterin dehydrogenase; Provisional. Length = 342 Score = 26.3 bits (58), Expect = 9.1 Identities = 10/26 (38%), Positives = 15/26 (57%), Gaps = 3/26 (11%) Query: 179 AIIGAEYLLQWLPKGTHQ---YDKFI 201 A+ A+ ++ WLPKG Q +KF Sbjct: 138 AVADADIVITWLPKGGMQPDIIEKFA 163 >gnl|CDD|178418 PLN02823, PLN02823, spermine synthase. Length = 336 Score = 26.2 bits (58), Expect = 9.9 Identities = 9/32 (28%), Positives = 18/32 (56%), Gaps = 1/32 (3%) Query: 106 NHANMKNINIDYRVSCA-EEIAETDEKFDIIL 136 N + ++ ++ A E+ + DEKFD+I+ Sbjct: 150 NREAFCDKRLELIINDARAELEKRDEKFDVII 181 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 0.321 0.136 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: 4,105,377 Number of extensions: 255647 Number of successful extensions: 540 Number of sequences better than 10.0: 1 Number of HSP's gapped: 512 Number of HSP's successfully gapped: 77 Length of query: 254 Length of database: 5,994,473 Length adjustment: 91 Effective length of query: 163 Effective length of database: 4,028,145 Effective search space: 656587635 Effective search space used: 656587635 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: 56 (25.1 bits)