Fig 4. Classification of genes encoded by arTVs.

(A) Classification of arTV genes into arCOG functional categories. The homologous gene shared by viruses in the same species is counted as one. The letters represent the following: J, translation, ribosomal structure and biogenesis; K, transcription; L, replication, recombination and repair; D, cell cycle control, cell division, chromosome partitioning; V, defense mechanisms; T, signal transduction mechanisms; M, cell wall/membrane/envelope biogenesis; N, cell motility; O, posttranslational modification, protein turnover, chaperons; G, carbohydrate transport and metabolism; E, amino acid transport and metabolism; F, nucleotide transport and metabolism; H, coenzyme transport and metabolism; I, lipid transport and metabolism; P, inorganic ion transport and metabolism; Q, secondary metabolites biosynthesis, transport and catabolism; R, general function prediction only; S, function unknown; X, virus related. (B) Schematic showing nucleotide-related (partial) metabolic pathways, with a particular enzyme indicated for each reaction. Enzymes that are found encoded by arTVs are in red, otherwise in gray. The number of virus families that harbor the enzyme is indicated next to the enzyme name, with the number of virus species shown in parentheses. NrdA: RnR, MazG: NTP pyrophosphatase, 5′-NCT: 5′-deoxyribonucleotidase, CarA: CP synthase small subunit, Dcd: dCTP deaminase, Tmk: thymidylate kinase, THY1: thymidylate synthase thyX, NDT: nucleoside deoxyribosyltransferase, FolE: GTP cyclohydrolase I, QueC: queuosine biosynthesis protein, QueD: 6-pyruvoyl tetrahydropterin synthase, QueE: 7-carboxy-7-deazaguanine synthase, DpdA: paralog of queuine tRNA-ribosyltransferase, QueFC: NADPH-dependent 7-cyano-7deazaguanine reductase. See S3 and S5 Tables for individual genes classification. arCOG, archaeal clusters of orthologous gene; arTV, archaeal tailed virus; CP, carbamoylphosphate; RnR, ribonucleotide diphosphate reductase.