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Table 2 Methyltransferases predicted to encode pyrrolysine by UAG read-through in a set of methanogenic archaea

From: A computational method to predict genetically encoded rare amino acids in proteins

Organism Computationally identified pyrrolysine-proteins* annotated by their homologs
Methanosarcina acetivorans (AE010299) 1. gi|56678713|gb|AAV95379.1| trimethylamine methyltransferase family protein [Silicibacter pomeroyi DSS-3]
  2. gi|14247242|dbj|BAB57633.1| menaquinone biosynthesis methyltransferase [Staphylococcus aureus subsp. Aureus Mu50]
  3. gi|36785418|emb|CAE14364.1| protein methyltranferase [Photorhabdus luminescens subsp. laumondii TTO1]
  4. gi|56679325|gb|AAV95991.1| trimethylamine methyltransferase family protein [Silicibacter pomeroyi DSS-3]
  5. i|20904823|gb|AAM30145.1| SAM-dependent methyltransferases [Methanosarcina mazei Goe1]
  6. gi|56312282|emb|CAI06927.1| predicted methyltransferase [Azoarcus sp. EbN1]
  7. gi|45047608|emb|CAF30735.1| generic methyltransferase [Methanococcus maripaludis]
  8. gi|20905508|gb|AAM30766.1| methylcobalamin: Coenzyme M methyltransferase [Methanosarcina mazei Goe1]
  9. Predicted ORF monomethylamine methyltransferase [Methanosarcina mazei Goe1]
  10. Predicted ORF monomethylamine methyltransferase [Methanosarcina mazei Goe1]
  11. Predicted ORF dimethylamine methyltransferase [Methanosarcina mazei Goe1]
  12. Predicted ORF dimethylamine methyltransferase [Methanosarcina mazei Goe1]
  13. Predicted ORF dimethylamine methyltransferase [Methanosarcina mazei Goe1]
Methanosarcina mazei (AE008384) 1. gi|19914316|gb|AAM03972.1| trimethylamine methyltransferase [Methanosarcina acetivorans str. C2A]
  2. gi|19914320|gb|AAM03976.1| dimethylamine methyltransferase [Methanosarcina acetivorans str. C2A]
  3. gi|19914753|gb|AAM04365.1| trimethylamine methyltransferase [Methanosarcina acetivorans str. C2A]
  4. gi|19913899|gb|AAM03597.1| monomethylamine methyltransferase [Methanosarcina acetivorans str. C2A]
  5. gi|19914755|gb|AAM04366.1| dimethylamine methyltransferase [Methanosarcina acetivorans str. C2A]
  6. gi|19914320|gb|AAM03976.1| dimethylamine methyltransferase [Methanosarcina acetivorans str. C2A]
  7. gi|19913899|gb|AAM03597.1| monomethylamine methyltransferase [Methanosarcina acetivorans str. C2A]
Methanosarcina barkeri (draft genome) 1. gi|19914320|gb|AAM03976.1| dimethylamine methyltransferase [Methanosarcina acetivorans str. C2A]
  2. gi|19913899|gb|AAM03597.1| monomethylamine methyltransferase [Methanosarcina acetivorans str. C2A]
  3. gi|19914316|gb|AAM03972.1| trimethylamine methyltransferase [Methanosarcina acetivorans str. C2A]
  4. gi|19914320|gb|AAM03976.1| dimethylamine methyltransferase [Methanosarcina acetivorans str. C2A]
  5. gi|19914334|gb|AAM03988.1| protein-L-isoaspartate (D-aspartate) O-methyltransferase [Methanosarcina acetivorans str. C2A]
  6. gi|19913899|gb|AAM03597.1| monomethylamine methyltransferase [Methanosarcina acetivorans str. C2A]
  7. gi|19913899|gb|AAM03597.1| monomethylamine methyltransferase [Methanosarcina acetivorans str. C2A]
Methanococcoides burtonii (draft genome) 1. gi|19914320|gb|AAM03976.1| dimethylamine methyltransferase [Methanosarcina acetivorans str. C2A]
  2. gi|19914753|gb|AAM04365.1| trimethylamine methyltransferase [Methanosarcina acetivorans str. C2A]
  3. gi|5458504|emb|CAB49992.1| methlytransferase, putative [Pyrococcus abyssi]
  4. gi|5458504|emb|CAB49992.1| methlytransferase, putative [Pyrococcus abyssi] (overlaps with #3)
  5. gi|19914320|gb|AAM03976.1| dimethylamine methyltransferase [Methanosarcina acetivorans str. C2A]
  6. gi|19914753|gb|AAM04365.1| trimethylamine methyltransferase [Methanosarcina acetivorans str. C2A]
  7. gi|19913899|gb|AAM03597.1| monomethylamine methyltransferase [Methanosarcina acetivorans str. C2A
  1. *Each entry corresponds to a computationally identified read-through protein in the organism indicated to the left. FASTA files for these recoded protein sequences are provided in the Additional data files. For each recoded protein, the GI number and the functional annotation for a homologous protein are given. These open reading frames (ORFs) in M. acitovorans were predicted during a repeat search using a BLAST database containing putative methylamine methyltransferase ORFs in M. mazei as identified by our method. Although the M. acitovorans genome was annotated for several pyrrolysine-containing methylamine methyltranferases, this was not the case with the M. mazei genome. Thus, several methyltransferases that are specific to these methanosarcina species could not be detected in our original calculation due to the lack of read-through homologs. Such repeat searches were not performed for the two unfinished genomes.