Table 1.

Open reading frames of ϕYS61 examined in this study

ORFa	Ribosomal binding site and start codon sequenceb	Position (nt)c		Predicted protein
				Size (aa)	Mol mass (kDa)	pI	Putative functiond	Closest homologe					Reference and/or accession no.
		Start	Stop					Description	Extent	Identity (%)	% positives	% gaps
1	AGGAGGTAAAAATTTATG	129	257	42	5.0	9.35		None
2	AGGAGGGTAATTGAATATG	287	1048	253	29.5	9.00		None
3	AAGGAGAAACAAAATG	1032	1817	261	30.0	10.06	Terminal protein	None					This study
4	AGGAGAAACAAATG	1829	3904	691	79.6	5.04	DNA polymerase (PHA02563, 1E−09)	Streptococcus phage Cp-1, p05	523/568	18	32	14	NP_044817
5	GAAAGGTTTATAAACCATG	3994	5082	362	42.2	8.88	DNA encapsidation protein (PHA00149, 2E−51)	Bacillus phage B103, gene 16	303/321	33	53	11	NP_690650
6	AGGGTGGCATTGACTTGTG	5113	5214	33	3.8	6.74		None
7	AGGAGGATAACAATG	5330	6061	243	27.3	8.75	NMN transporter (PF04973, 1E−18)	Lactococcus phage KSY1, gp052	229/249	53	73	0	YP_001469050
8	GAAAGGACGGTCAATTATG	6393	6854	153	16.5	4.79		None
9	AGGAGTCTAATAATG	6960	7304	114	12.0	3.74	Structural protein	None					This study
10	AGGAGAAACACAATG	7447	7821	124	14.4	4.81		None
11	GGAGGAATTGAATAACAATG	7811	8200	129	14.8	4.18		None
12A	AGGAGAAATATTATG	8383	9618	411	45.4	5.02	Major capsid protein (PHA00144, 1E−37)	Enterococcus phage EF62ϕ, ORF40	421/469	31	52	5	This study, ADX81364
12B	AGGAGAAATATTATG	8383	9881	500	53.9	5.31	Major capsid protein with bacterial Ig-like domain (PF02368, 1E−6)	Bacillus phage ϕ29, major head protein	483/448	25	42	17	This study, YP_002004536
13	TGGAACATCAAGCACTTATG	10160	10669	169	18.2	5.42		None
14	AGGGGCACAGCATG	10680	10931	83	10.0	6.58		None
15	AGGAGGAATTATG	10975	11172	65	7.7	4.47		None
16	AGTAGAAAGGAGATG	11208	11768	186	21.1	9.95		None
17	AGGAGGCCATACAAAATG	11847	12458	203	21.1	6.76		None
18	GAAAGGAAATAGATTAAATG	12513	13400	295	32.7	6.40	Lysin, N-acetyl-l-alanine amidase (PF01510, 7E−4)	Weissella paramesenteroides ATCC 33313, LytA	270/305	50	61	12	ZP_04782183
19	AGGAGAACAAACATG	13440	13967	175	17.1	9.48		None
20	GGAGGAAAATAATTTTG	14126	15472	448	49.4	4.75	Tail lysin	Bacillus phage B103, gene 13	303/365	28	44	13	NP_690647
21	AGGAGAAATTCAAATG	15535	17730	731	82.1	5.84	Tail protein (PHA00380, 3E−16)	Bacillus phage PZA, gp9	731/599	23	39	24	P07534
22	ATTTTGCAAGCAAAATTATG	18052	19422	456	49.8	4.69	Upper collar connector (PHA00147, 9E−27)	Enterococcus faecalis T2, EFBG_02899	328/333	33	53	12	ZP_05423975
23	AGGAGGAGAAATGTAATG	19422	20330	302	34.5	4.46	Lower collar protein (PHA01077, 6E−13)	Enterococcus phage EF62ϕ, ORF33	245/255	32	51	12	ADX81357
24	AAACCGCAAATAATTCAATG	20396	21760	454	47.5	4.96	Tail fiber protein (PF01391, 9E−9)	Mycobacterium phage Bxz2, gp4	108/344	62	72	10	NP_817595
25	GCATTATTTAGCGCCTGATG	21812	22120	102	11.8	6.40		None
26	GCGGTATACAGCACATG	22333	24312	659	74.6	5.01	Structural protein	Escherichia coli MS 60-1, HMPREF9533_04376	419/712	24	41	6	This study, EGB80821
27	AGGAGAGAAAATAGTG	24328	24681	117	13.0	5.65	Phage holin 4 (PF05105, 8E−11)	Leuconostoc phage 1-A4, LM1A4_024	106/123	33	55	0	ADD71747
28	AGGAGGCAGAGCATG	24800	25087	95	11.0	6.72		None
29	AGAGGGTCTTTTTTG	25059	25550	163	18.8	5.10		None
30	AGGAGACTAAGGAATG	25581	25820	79	9.2	4.78		Lactobacillus acidophilus 30SC, LAC30SC_06460	66/67	36	50	0	YP_004292355
31	AGGAGGGTTTTAAATTATG	25824	26291	155	17.3	5.81		None
32	TTGCTTTATCGTGCGAGGTG	26263	26526	87	10.2	8.77		None
33	AGGAGGCGGCTTATG	26516	26689	57	6.5	4.11		None
34	AGGAGGCAGGCGTTTAATG	26823	26933	36	4.0	5.99		None
35	AGGGGAAAGATAATG	26933	27208	91	10.3	4.11		None
36	GGAGGACAAGTAACATG	27201	27518	105	12.0	4.28		None
37	AGGAGGACAAGTAACATG	27520	28491	323	36.4	6.36		None
38	GAAAGGATTTTATAATG	28493	29017	174	19.9	5.30		Listeria phage B025, ORF62	169/212	24	38	25	YP_001468701
39	AGGAGGCTTGACATG	29091	29186	31	3.6	5.89		None
40	GAAAGGAAGCATAATG	29300	29998	232	24.3	4.63		None
41	AGGAGGATATAACATG	29998	30321	107	11.5	9.00		Lactobacillus acidophilus 30SC, LAC30SC_00610	98/227	29	41	1	YP_004286453
42	GAGAGGAAATGCAATG	30504	30986	160	18.8	10.04	HNH endonuclease	Enterococcus phage EFRM31, gp11	120/173	38	60	4	YP_004306639
43	GGAACGCTATG	30983	31102	39	4.8	9.58		None
44	GGGGTGGAAATTATG	31125	31334	69	8.1	4.23		None
45	GAGGTGGAAATTATG	31487	31648	53	6.2	6.71		None
46	GAGGTATGGAAATATG	31887	32144	85	9.7	4.71		Lactobacillus phage Lb338-1, ORF13	57/102	35	65	4	YP_002790692
47	GAGGAAATTATCATG	32233	32577	114	13.4	3.79		None

^aStructural proteins identified by MS analysis are shown in boldface.

^bPredicted ribosomal binding sites and start codons are underlined. nt, nucleotide.

^cORF positions on the complement strand are shown in italics.

^dBest hits in the Conserved Domains Database. Accession numbers and E values are shown in parentheses. PHA, CDD accession; PF, Pfam accession.

^eClosest homolog determined by BLAST searches. Extent, alignment length/hit sequence length (aa). Percentages of identical positions, positive positions, and gap positions in each BLAST alignment are shown in separate columns.