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

Table 4 Gene function prediction results for bacteriophage genomes.

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

† 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.
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.

ISSN: 1471-2105