Figure 4
From: Crystal structure of AFV3-109, a highly conserved protein from crenarchaeal viruses
Genomic context of the AFV3-109 ortholog in Firmicutes. The yddF gene (big red arrow) from Bacillus subtilis has homologues in several genomes of Archaeal viruses (small red arrows), such as: the SFV0026 gene in Sulfolobus islandicus filamentous virus, the ORF108 in Acidianus rod-shaped virus 1, the B116 gene in Sulfolobus turreted icosahedral virus, the ORF114a in Sulfolobus islandicus rudivirus 1 variant XX, the ORF117 in Acidianus two-tailed virus, the ORF114 in Sulfolobus islandicus rod-shaped virus 2, and the AFV1p37 gene in Acidianus filamentous virus 1. The yddF gene is found inside an integrated pro-virus in the Bacillus subtilis genome. This pro-virus starts with the ydcL gene (yellow arrow), which codes for an integrase and is next to a leucine tRNA gene (black arrow). The ydcL and sacV (pink arrow) genes have homologues in the Clostridium phage φ 36262 genome; the ydcM (orange arrow) and rapI (brown arrow) genes have homologues in the Bacillus phage φ 105 genome, the ydcN (light green arrow) gene in the Lactobacillus gasseri phage KC5a, and the ydcN (light green arrow) gene in the Bacillus cerus E33L Plasmid pE33L466. Nine out of the twenty-four genes in this pro-virus: ydcL, ydcM, ydcN, sacV, ydcQ (dark blue arrow), ydcR (blue green arrow), yddE (purple arrow), yddH (dark green arrow), and rapI, have homologues in other probable integrated pro-viruses (light blue rectangles; the grey rectangles represent the genome genes outside the probable inserted pro-virus) in several genomes of Firmicutes. The names of the species have the following annotation: B.su is Bacillus subtilis, B.cz is Bacillus cerus E33L, B.ld is Bacillus licheniformis ATCC 14580, B.li is Bacillus licheniformis DSM13, E.fa is Enterococcus faecalis, L.mo is Listeria monocytogenes EGD-e, M.ta is Moorella thermoacetica, S.ao is Staphylococcus aureus NCTC8325, S.av is Staphylococcus aureus Mu50, S.aa is Staphylococcus aureus USA300, S.ac is Staphylococcus aureus COL, S.ar is Staphylococcus aureus MRSA252, S.an is Streptococcus agalactiae NEM316 (serotype III), and S.ag is S.agalactiae 2603 (serotype V). The size and the genomic location of the probable integrated pro-virus is also indicated.