. 2003 Nov;185(21):6434–6447. doi: 10.1128/JB.185.21.6434-6447.2003

TABLE 2.

ORFs in the genomes of VP16T and VP16C

VP16T			VP16C
ORF/ strand^a	Encoding nucleotides	Function of similar hit and expect value (% identity)^b	ORF/ strand	Encoding nucleotides	Function and expect value (% identity)^b
1/−	<3-116		1/−	<2-85
2/+	115-828	Likely small subunit of terminase^c	2/+	124-837	(70% identical to ORF2C)
3/+	812-2839	Large subunit of phage lambda terminase gpA, 3e-17 (22); closest phage hit bacteriophage WO, 3e-50 (27); closest bacterial hit, R. solanacearum (28)	3/+	821-2842	phi WO, 1e-51 (27)
4/+	2880-3158		4/+	2883-3161
5/+	3224-4861	Portal protein gp4 of phi 21, 6e-13 (22); minor capsid (portal) protein gpB of phage lambda, 6e-10 (19); closest bacterial hit, R. solanacearum, 5e-12 (21)	5/+	3227-4864	gpB of phage lambda, 2e-14 (21)
6/+	4845-6032	Similar to head-tail preconnector protein of Vibrio shiloii, 2e-19 (34); closest phage hit gpC of phage lambda, 4e-9 (27)	6/+	4848-6035	Same (31)
7/+	6047-6451		7/+	6051-6458
8/+	6466-7560	Hypothetical protein gp348 of Sfi11 (S. thermophilus), 5e-4 (25)	8/+	6472-7566	gp348 of Sfi11, 0.005 (24)
9/+	7610-7999		9/+	7954-8046
10/+	8007-8393		10/+	8046-8432
11/+	8603-9064		11/+	8425-9114
12/+	9077-10579	Tail sheath protein L of phage Mu, 3e-12 (24)	12/+	9127-10629	gpL of phage Mu, 1e-21 (27)
13/+	10592-10975		13/+	10815-11024
14/+	11053-11454		14/+	11109-11510
15/+	11550-11654		15/+	11606-11710
16/+	11769-13514	Hypothetical protein (Haemophilus somnus), 6e-52 (31); ORF43, V. harvey phage VHML, 4e-49 (32), putative tail length tape measure protein	16/+	11759-13570	Same, 7e-41 (29)
17/+	13514-14767		17/+	13570-14823
18/+	14760-16013	Putative tail protein, E. coli O157:H7, 3e-10 (25); gpP tail protein of phage Mu, 2e-009 (23)	18/+	14816-16069	43-kDa tail protein, H. influenzae, 6e-9 (24)
19/+	15992-16636	GTG start codon	19/+	16048-16692
20/+	16648-17055	Hypothetical protein NP518999.1 of R. solanacearum, 4e-11 (30)	20/+	16705-17112	Hypothetical protein of R. solanacearum, 3e-5 (26)
21/+	17059-17724		21/+	17116-17781
22/+	17734-18921	Tail protein of phi V (Shigella flexneri), 4e-008 (28); hypothetical protein ymfP (b1152) in prophage e14 region of E. coli K-12, 7e-8 (29)	22/+	17791-18960	Hypothetical protein, E. coli O157:H7, 2e-9 (22)
23/+	18914-19636		23/+	18973-19695
24/+	19649-20983	Hypothetical protein NP519813.1 of R. solanacearum, 3e-10 (71); putative tail fiber-related protein NP520042.1 of R. solanacearum (78)	24/+	19708-21042	Same, 8e-9 (79% identical to ORF24T); putative tail fiber-related protein NP520042.1 of R. solanacearum, 1e-7 (70)
25/+	20986-22320	Hypothetical protein NP519813.1 of R. solanacearum, 5e-10 (43)	25/+	21045-22394	Same, 4e-010 (81% identical to ORF25T); putative tail fiber-related protein NP520042.1 of R. solanacearum, 1e-007 (33)
26/+	22341-22865	Hypothetical protein NMB1012 (imported) of Neisseria meningitidis, 2e-28 (39); secretion activator protein NP539912.1, Bacillus melitensis, 3e-15 (30)
			26/+	22557-22808
27/+	22862-23458		27/+	22810-23406
28/+	23566-23802		28/+	23525-23758
29/+	23804-25897		29/+	23763-26282	Probable HA-related protein NP519008 of R. solanacearum, 0.011 (28)
30/+	25901-29173		30/+	26287-27408
31/+	29411-29884		31/+	27638-28117
32/+	29899-30168		32/−	28126-28392
33/−	30182-30433		33/−	28411-28722
34/−	30408-30647		34/−	28712-28936
35/−	30619-31185	eac protein of phage P22, 0.027 (19)	35/−	28908-29468	No similarity (70% identical to ORF35T)
36/−	31178-31705		36/−	29461-29640
			37/−	29633-30187
			38/−	30193-30678
37; 38/−	31763-31951; 31948-34092	DNA, polymerase of phi SPO2 of B. subtitis, 4e-70 (35 and 31)	39/−	30737-32797	Same, 3e-57 (31)
39/−	34089-34602		40/−	32857-33582	First 520 of 726 nucleotides are similar to ORF39T
40/−	34667-35680		41/−	33653-34714
41/−	35692-36744		42/−	34732-35859	Phage-related protein of X. fastidiosa 9a5c, 8e-004 (26)
42/−	36823-37686		43/+	35863-36714
42.1/−	37785-37858	Same as ORF44C, not called by GeneMark	44/+	36801-37004	90% likelihood of HTH domain
43+	37969-38226
44/+	38219-39871	Hypothetical protein of phi A2 (Lactobacillus casei), 6e-50 (32); helicase, phi PSA (Listeria monocytogenes), 7e-47 (32); putative DEAH family helicase, Lactobacillus phage phi adh, 3e-46 (29)	45/+	36997-39153	Same, 9e-49 (34)
45/+	39868-40374	Hypothetical protein NP416862 of E. coli K-12, 1e-19 (45); closest phage hit, unknown protein, phi V (S. flexneri), 3e-19 (44)
46/+	40374-40886		46/+	39153-39662
47/+	40932-41267	Putative transcriptional regulator NP 335121, M. tuberculosis CDC1551, 2e-5 (33)	47/+	39708-40043	Same, 4e-5 (34)
48/−	41324-41575
49/+	41628-41840
			48/+	40031-40216
50/+	41837-41995		49/+	40402-40560
51/+	41982-42344		50/+	40580-40912
52/+	42341-42781
53/+	42778-43266		51/+	40909-41361
54/+	43280-43480		52/+	41365-41574
55/+	43483-43674		53/+	41578-41766
56/+	43676-43909		54/+	41823-42002
57/+	43969-44112
58/−	44109-44387		55/−	41999-42265
59/−	44384-44731		56/−	42262-42570
60/−	44728-45141	Putative polypeptide deformylase, S. coelicolor, 3e-015 (37)	57/−	42704-43117	Polypeptide deformylase, Aquifex aeolicus, 2e-13 (38)
61/−	45138-45422		58/−	43114-43416
62/−	45371-45778		59/−	43413-43784
63/−	45805-48180	Hypothetical protein NP489430 of Nostoc sp. PCC7120, 2e-19 (27); virulence-associated protein E of D. nodosus, 3e-15 (28)	60/−	43781-46156	Same, 3e-20 (27)
			61/+	46198-46371
64/+	48776-49468		62/+	46690-47442	(86% identical to ORF64T)

ORFs of the two phages whose nucleotide sequences are similar or which encode similar amino acid sequences are on the same line. ORFs that are not similar to each other are on different lines.

The first function is the most closely related GenBank entry. The other function(s) is the most closely related phage hit, if it is not the top hit. The percentages of identity are the percentages of identical residues between the ORFs and each GenBank gene.

See text.