# HISTORY 07 Jun 2016: Saved by krc using Paint 2.0-beta19 # molecular_function 20160607: root_PTN000515868 has function S-adenosylmethionine-dependent methyltransferase activity (GO:0008757) 20160607: root_PTN000515868 has function RNA methyltransferase activity (GO:0008173) 20160607: Bacteria _PTN000516061 has function rRNA (cytosine-C5-)-methyltransferase activity (GO:0009383) 20160607: Eukaryota_PTN000515974 has function rRNA (cytosine-C5-)-methyltransferase activity (GO:0009383) 20160607: Archaea_PTN001105891 has function tRNA (cytosine-5-)-methyltransferase activity (GO:0016428) 20160607: Gammaproteobacteria_PTN001867133 has function rRNA (cytosine-C5-)-methyltransferase activity (GO:0009383) # cellular_component 20160607: Eukaryota_PTN000515974 is found in nucleolus (GO:0005730) 20160607: Eukaryota_PTN000515911 is found in nucleolus (GO:0005730) 20160607: Bacteria _PTN000516061 is found in cytosol (GO:0005829) # biological_process 20160607: root_PTN000515868 participates in RNA methylation (GO:0001510) 20160607: Gammaproteobacteria_PTN001867133 participates in rRNA base methylation (GO:0070475) 20160607: Archaea_PTN001105891 participates in tRNA methylation (GO:0030488) 20160607: Eukaryota_PTN000515974 participates in rRNA base methylation (GO:0070475) 20160607: Eukaryota_PTN000515974 participates in ribosomal large subunit biogenesis (GO:0042273) 20160607: Eukaryota_PTN000515974 participates in maturation of LSU-rRNA (GO:0000470) 20160607: Eukaryota_PTN000515911 participates in rRNA base methylation (GO:0070475) 20160607: Bacteria _PTN000516061 participates in rRNA base methylation (GO:0070475) # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES 9ZZZZ:PTN000515868 - PTN000515867 (duplication node) -- Archaea-Eukaryota_PTN000515909 --- PTN001867132 (diamond node) ---- Gammaproteobacteria_PTN001867133 (E. coli rsmF + 3 more seqs) - "rRNA (cytosine-C5-)-methyltransferase activity (GO:0009383)" ---- PTN001867138 (duplication node in Archaea) METJA_trm4 - tRNA (cytosine-5-)-methyltransferase activity "GO:0016428" --- Eukaryota_PTN000515974 - NOP2 [methylates C2870 of the 25S rRNA] - "rRNA (cytosine-C5-)-methyltransferase activity (GO:0009383)" -- PTN001105818 (duplication node) --- Eukaryota_PTN000515968 (plants, dictyostelium, trypanosomes) --- Eukaryota_PTN000515871 (vert NSUN6; no yeast) [targets tRNAs at m5C72] - tRNA (cytosine-5-)-methyltransferase activity "GO:0016428" --- Eukaryota_PTN000515911 (vert NSUN5; Sc RCM1) [methylates C2278 of the 25S rRNA - "rRNA (cytosine-C5-)-methyltransferase activity (GO:0009383)" -- Archaea-Eukaryota_PTN001867219 (Archaea, tetrahymena & plasmodium) - 9ZZZZ:PTN000516069 (duplication node) -- 9BACT:PTN001867222 (3 seqs) -- 9BACT:PTN001897225 (3 seqs) -- 9BACT:PTN000516061 --- 9EMBR:PTN001105908 (Embryophyta - plant sequences) --- 9FIRM:PTN001867242 (Bacillus rsmB & Streptococcus sunL) --- Proteobacteria_PTN000516067 (Ecoli rsmB) - "rRNA (cytosine-C5-)-methyltransferase activity (GO:0009383)" . - Even though it seems odd to have Embryophyta under Eubacteria, the MSA looks really good; maybe these are plastid genes. - Possibly sequences under the diamond node PTN001867132 should be evaluated for proper positioning within the tree. . . NSUN5 & RCM1 ========== PMID:23913415 - Sharma S et al. Yeast Nop2 and Rcm1 methylate C2870 and C2278 of the 25S rRNA, respectively. Nucleic Acids Res. 2013 Oct;41(19):9062-76. . NSUN6 ========== - PMID:26160102 - Haag S et al. NSUN6 is a human RNA methyltransferase that catalyzes formation of m5C72 in specific tRNAs. RNA. 2015 Sep;21(9):1532-43. # REFERENCE Annotation inferences using phylogenetic trees The goal of the GO Reference Genome Project, described in PMID 19578431, is to provide accurate, complete and consistent GO annotations for all genes in twelve model organism genomes. To this end, GO curators are annotating evolutionary trees from the PANTHER database with GO terms describing molecular function, biological process and cellular component. GO terms based on experimental data from the scientific literature are used to annotate ancestral genes in the phylogenetic tree by sequence similarity (ISS), and unannotated descendants of these ancestral genes are inferred to have inherited these same GO annotations by descent. The annotations are done using a tool called PAINT (Phylogenetic Annotation and INference Tool).