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Table 4 Gene function prediction results for bacteriophage genomes.

From: Gene function prediction based on genomic context clustering and discriminative learning: an application to bacteriophages

Gene (Phage abbrev.: CDS location) Existing function annotation Predicted function Supporting phages (phage abbrev.) SS
69: 4704..5324 Uncharacterised Prohead protease PVL N
phi-105: 7918..8520 Uncharacterised Major tail protein Cherry, Gamma, 3A, 47 Y
Tuc2009: 23727..24224 Uncharacterised Major tail protein bIL285, bIL286, bIL309, ul36, phiSLT Y
A118: 4590..5159 determines size and shape of viral capsid, putative scaffolding protein Prohead protease PVL N
71: 4149..4748 Phage minor structural protein, GP20 Prohead protease PVL N
phi ETA: 21172..21768 minor capsid protein Prohead protease phi 13 N
phi 11: 21115..21750 phi Mu50B-like protein Prohead protease phi 13 N
P22: 38551..38991 lysozyme, endolysin_autolysin Lysin V N
Sf6: 3975..4859 putative scaffolding protein Prohead protease ST64B, V N
HK620: 23655..24539 scaffold protein Prohead protease P27 N
sk1: 8582..11581 Mu-like prophage protein, phage-related protein [function unknown] Tape measure bIL170 Y
77: 19572..21026 CHAP domain, Ami_3, SH3 domain Lysin phi-105 N
77: 3291..4028 Clp protease Prohead protease Cherry, Gamma, phi-105 N
phiSLT: 20002..20775 protease, clp protease Prohead protease bIL285, bIL309, phiPV83 N
phiSLT: 38923..40377 amidase, CHAP, Ami_3, SH3b Lysin bIL285, bIL286, bIL309, ul36, 315.5, 315.6 Y
bIL286: 21258..21965 protease, clp protease Prohead protease bIL285, bIL309, phiPV83 N
  1. Full names of the phages are as follows with abbreviations in bold: Staphylococcus aureus bacteriophage PVL, Bacteriophage 69, Bacteriophage A118, Bacteriophage 71, Bacteriophage phi ETA, Staphylococcus aureus phage phi 11, Staphylococcus aureus phage phi 13, Enterobacteria phage P22, Enterobacteria phage Sf6, Salmonella typhimurium bacteriophage ST64B, Shigella flexneri bacteriophage V, Bacteriophage HK620, Bacteriophage P27, Bacteriophage sk1, Bacteriophage bIL170, Bacillus anthracis phage Cherry, Bacillus anthracis phage Gamma, Bacteriophage 3A, Bacteriophage 47, Bacteriophage phi-105, Bacteriophage 77, Bacteriophage bIL285, Bacteriophage bIL286, Bacteriophage bIL309, Bacteriophage Tuc2009, Lactococcus phage ul36, Staphylococcus aureus prophage phiPV83, Staphylococcus aureus temperate phage phiSLT, Streptococcus pyogenes phage 315.5, Streptococcus pyogenes phage 315.6.
  2. This is a subset of the predictions generated by SynFPS. SS refers to Sequence Similarity: N indicates there is no significance in sequence similarity between the target gene (first column) and any of the corresponding genes in the supporting phages (second last column) within the same cluster; Y indicates at least one of the corresponding genes show significant similarity. BLAST-P with Blosum45 has been used to test for similarity significance.