TABLE 2.

Bacteriophage φKO2 gene analysis

Gene	Predicted protein size (no. of amino- acids)	Predicted function	Phages with best matchesa	Extent of best match (% identity/length of region [no. of aminoacids])
1	143	Small terminase subunit	PY54, DT1, CP-933C, φST64B	64/143
2	568	Large terminase subunit	PY54, ΦP27, SfV, φST64B, φE125	71/568
3	59	Unknown (head assembly?)	PY54f, e14, ΦP27, φST64B, φE125	42/59
4	422	Portalb	PY54, φE125, φST64B, ΦP27	75/422
5	306	Maturation protease/scaffold	PY54, φE125, Gifsy-1, λc	64/306
6	428	Major head shell (coat) proteinb	PY54c, φE125	76/366
7	152	No matches (head assembly?)	PY54	43/86
8	98	Unknown (head assembly?)	PY54, SfV, φST64B	50/98
9	112	No matches (virion assembly?)	PY54	59/112
10	129	No matches (virion assembly?)	PY54	56/129
11	133	Unknown (tail assembly?)	PY54, D3, λSo, φE125, HK97	68/133
12	155	Major tail shaft proteinb	PY54	70/143
13	122	Tail chaperone?	PY54	62/122
14e	202	Frameshifted tail chaperone?	PY54f	52/202
15	1,118	Tail “tape measure”	PY54, HK022, TP901-1c	56/1,118
16	112	Tail tip structure (λ gpM)	HK97, HK022, φE125, N15, λc	67/112
17	251	Tail tip structure (λ gpL)	HK022, N15, HK97, λc	74/251
18	236	Tail tip structure (λ gpK)	HK97, N15, HK022, λc	86/333
19	111	Moron gene	Xanthomonas prophage XccP1	33/99
20	197	Tail tip structure (λ gpI)	N15, HK022, φE125, λc	69/194
21	3,433	Tail tip fiber (λ gpJ)	HK022, N15, λSo, λc	69/941
22	80	DinI SOS response regulator	Stm6d, Gifsy-2	76/67
23	127	UmuD′ DNA polymerase subunit	Stm6d, N15, P1c	68/129
24	323	Plasmid partitioning (SopB)	N15c, PY54, P1c	76/320
25	387	Plasmid partitioning (SopA)	N15c, PY54, P7	92/387
26	640	Protelomerase	N15c, PY54c, VHML	75/640
27	260	Auxiliary antirepressor	N15c, CP-933N, φP27, φ11, A118	74/262
28	76	Antirepressor	N15c, PY54c	78/76
29	54	Inhibitor of cell division	N15c, PY54, P4c, φR73	85/54
306	58	Control of genes 27 to 29?	φR73, P4, N15	60/43
31	75	No matches	None
32	111	Unknown	N15, PY54	69/116
33	182	Unknown	P22, PY54	35/110
34	82	Unknown	N15	81/82
35	1,328	Replicase	N15c, PY54	92/1,318
36	202	Prophage repressor	N15c, PY54c	88/202
37	69	Cro repressor	N15, PY54c	87/65
38	245	Q-like antiterminator	N15, PY54, Gifsy-1	70/248
39	202	Exonuclease III; Pol III ɛ	N15, 186	62/197
40	44	No matches	None
41	110	No matches	None
42	226	No matches	None
43	97	Unknown	N15	61/94
44	203	Unknown	CP-933P, N15, ST64T	30/109
45	108	Unknown	N15, ɛ15 plasmid pKM101	77/108
46	79	Unknown	N15, PY54	73/73
47	68	No matches	None
48	95	Possible Cro-like repressor	N15	85/95
49	104	Unknown	N15, Xylella prophage XfP3	93/104
50	73	Unknown	N15	80/73
51	75	Unknown	N15	71/75
52	353	DNA adenine methylase	PY54, SfV, φP27, VMHL, N15	77/353
53	101	No matches	None
54	163	No matches	None
55	154	No matches	None
56	57	No matches	None
57	32	No matches	None
58	99	Unknown	N15, PY54, λSo, Omega, TM4	90/99
59	241	Unknown	φ80	66/74
60	120	Holin?	PY54, φP27, ST64T, SfV, φE125	65/120
61	96	No matches	None
62	146	Unknown	Salmonella plasmid pHCM2	33/130
63	127	Unknown	S. enterica serovar Typhi prophage Sti1d	68/127
64	66	No matches	None

^aMatches are listed in descending order of extent of similarity. The matching genes (names not shown) of the indicated phages typically occupy very similar positions on those genomes. Unless denoted by a footnote, they have not been shown by direct experimentation to have the function indicated, but they have sequence similarities to ones that have been so studied.

^bPresence in φKO2 confirmed by N-terminal amino acid analysis (see text).

^cThis phage's gene has been shown directly to have the indicated function.

^dThe names of S. enterica serovar Typhimurium and Typhi defective prophages Stm6 and Sti1, respectively, are provisional (13).

^eNote that gene 14 is likely expressed as a frameshifted protein whose N terminus is identical to that of the gene 13 protein but whose C terminus has extra sequence; gene 30 may not be an authentic gene.

^fGene not annotated in original genome sequence publication.