TABLE 2.

Data on genes found in D3 DNA

Gene	Position		Initiation codon	Size of protein (kDa)	pI	Sequence similarity
	Left end	Right end
1	37	417	ATG	14.1	8.7
2	419	2110	ATG	63.3	5.2	D3 terminase large subunitE. coli hypothetical 50.9-kDa protein; 3e-77; P75978 (YMFN_ECOLI) Phage φ105 ORF22; 8e-43; BAA36628 Phage A2 ORF5; 4e-35; CAA66178 Phage HK97 terminase large subunit; e-33; AAF31098 Phage HK022 terminase large subunit; e-33; AAF30354 Phage φPVL ORF2; 2e-28; BAA31875
3	2107	2271	ATG	5.5	8.3
4	2264	3568	GTG	47.3	8.8	D3 portal protein Phage HK022 portal protein; 6e-57; AAF30355 Phage HK97 gp3 portal protein; 3e-56; P49859 (VP3_BPHK7) Phage φC21 gp34; 7e-35; CAA07104
5	3572	4462	ATG	31.9	4.7	D3 capsid protease Phage φadh hypothetical protein; 3e-23; CAB52520 Phage φ7201 ORF25; 5e-18; AAF43518 Phage DT1 scaffolding protein; 6e-18; AAD21883 Phage Sfi21 orf-221 Clp protease; e-15; AF115103
6	4459	5646	ATG	42.9	4.8	D3 major capsid protein Phage HK97 major capsid protein precursor GP5; 2e-69; P49861 (COAT_BPHK7)
7	5691	5978	ATG	10.2	9.7
8	6005	6409	ATG	15.0	8.5
9	6390	6710	ATG	11.6	4.2
10	6711	7067	ATG	13.7	5.6	Phage HK022 gp9; 6e-11; AAF30361
11	7184	7684	ATG	18.9	8.8	Phage HK97 gp73; 6e-24; AAF31121
12	7763	8575	ATG	30.2	9.0
13	8586	9143	ATG	21.2	5.6
14	9136	9630	ATG	17.8	9.9	Phage HK022 gp10; 9e-21; AAF30362
15	9633	9998	ATG	13.3	4.9	Phage HK022 gp11; 7e-31; AAF30363
16	10074	10595	ATG	18.7	4.3	D3 major tail protein Pseudomonas aeruginosa prophage 28 (similar to V gene of lambda and gene13 of N15) major tail protein; 1e-55; BAA83172 Phage HK022 gp12 (major tail protein); 8e-53; AAF30364
17	10605	10964	ATG	12.3	4.6	D3 tail protein Phage HK022 gp13 (lambda gpG analog); 2e-47; AAF30365
18	10970	11242	GTG	10.3	8.0	D3 tail protein Phage HK022 gp14 (lambda gpT analog); 1e-10; AAF30366
19	11292	13796	ATG	87.8	4.9	D3 tail tape measure protein Phage HK022 gp15 (tail length tape measure protein); e-82; AAF30367 Phage HK97 (tail length tape measure protein) gp16; 2e-25; AAF31092
21	13793	14272	ATG	18.4	5.4
22	14256	14747	ATG	18.1	4.8	Phage MB78 hypothetical protein; 4e-04; CAB36891
23	14837	15208	ATG	13.2	4.5
24	15219	15413	ATG	7.4	8.2
25	15468	15875	ATG	14.9	8.4
26	15847	18576	GTG	99.5	5.0
27	18636	20879	ATG	80.3	5.3
28	21282	23345	ATG	75.5	9.1	D3 acetylase Salmonella serotype Typhimurium O-antigen acetylase; 2e-53; U65941
29	23383	23715	ATG	12.5	8.8
30	24857	25180	GTG	11.3	4.5
31	25505	25987	ATG	17.3	9.0	D3 endolysin Phage HK97 lysin; 2e-41; AAF31145 Phage HK022 lysin; 2e-41; AAF31145 Phage lambda endolysin (gpR); 5e-41; P03706 (LYCV_LAMBD) Phage 186 P protein; 3e-32; AAC34155 Phage P2 lysozyme; 3e-32; P51771 (LYCV_BPP2)
32	25984	26352	GTG	12.6	6.9	P. aeruginosa prophage hypothetical protein; 1e-16; BAA83169
33	26349	26609	ATG	9.4	9.9	P. aeruginosa prophage hypothetical protein; 2e-14; BAA83170
34	26600	26908	ATG	11.4	6.3
35	27104	28213C	ATG	41.4	9.8	D3 integrase Phage Sfx integrase; 8e-33; AAD10295E. coli prophage DLP12 integrase; 4e-31; P24218 (INTD_ECOLI) Phage V integrase; 1e-30; AAB72135 Phage P22 integrase; 2e-30; CAA27685 Phage APSE-1 integrase; e-29; AAF03981 Phage SfII integrase; 2e-19; AAC39270
36	28099	28440C	ATG	12.5	8.9
37	28588	28749C	ATG	6.1	3.8
38	28746	28979C	ATG	8.5	6.1
39	28979	29305C	ATG	11.8	6.6
40	29302	29991C	ATG	25.8	4.9
41	30192	30503C	ATG	11.7	4.6
42	31282	31641C	ATG	13.4	5.1
43	31634	32356C	ATG	26.5	4.5
44	32492	33772C	GTG	47.7	5.4
45	33769	33942C	GTG	6.3	9.7
46	33911	34195C	GTG	10.4	5.4
47	34135	34266C	ATG	5.0	9.8
48	34294	34551C	ATG	10.2	11.8
49	34611	34787C	GTG	6.7	8.7
50	34780	35115C	ATG	12.7	9.5	P. aeruginosa regulatory protein AlgR; 4e-10; P26275 (ALGR_PSEAE) P. putida PprA; 9e-10; CAA56559
51	35112	35738C	ATG	23.3	5.0	D3 exonuclease Phage VT-Sa exonuclease; 5e-06; BAA84296 Phage lambda exonuclease; 8e-06; P03697 (EXO_LAMBD) Phage 933W exonuclease; 8e-06; AAD25418
52	35742	36569C	ATG	29.9	6.7
53	36503	37567C	ATG	40.2	5.4
54	37615	37752C	ATG	4.8	10.3
55	38086	38268C	ATG	6.6	10.2
56	38265	38639C	ATG	14.1	5.1
57	38636	39244C	ATG	22.8	5.1
58	39237	39407C	ATG	6.5	9.1
59	39410	39895C	ATG	18.1	5.6
60	39880	40026C	GTG	5.5	4.5
61	40161	40430C	ATG	10.0	5.7
62	40423	41079C	ATG	25.0	5.5
63	41083	41580C	GTG	19.1	8.6
64	41630	42418C	ATG	29.5	4.5
65	42415	42963C	ATG	20.6	4.6
66	42960	43385C	ATG	15.6	4.5
67	43628	43921C	ATG	11.1	8.8
68	44080	44829C	ATG	27.4	7.7
69	45369	46040C	ATG	24.6	5.6	D3 C1 repressor Phage D3112 repressor; e-14; S13498
70	46128	46349	ATG	7.9	7.9	D3 Cro
71	46351	46659	ATG	11.4	5.7	D3 CII Phage lambda CII protein; e-04; P03042 (RPC2_LAMBD) Phage 434 CII protein; 2e-04; P03043 (RPC2_BP434)
72	46659	46922	ATG	9.6	10.2
73	46919	47908	ATG	37.0	8.9	D3 DNA replication protein O Phage HK97 gp54; e-06; AAF31132 Phage lambda replication protein O; 3e-05; AAA96584
74	47905	49245	ATG	48.9	5.4	D3 DNA helicaseBacillus subtilis helicase; e-75; P37469 Phage P1 Ban protein; e-69; CAA09719
75	49245	49364	ATG	4.6	7.9
76	49361	49870	GTG	19.0	7.9
77	49872	50075	ATG	7.8	4.5	Phage φCTX ORF39; 6e-09; AB008550
78	50065	50697	ATG	24.1	9.7	Phage APSE-1 P46; 4e-23; AAF03989 Phage φadh ORF188; 3e-16; CAB52497
79	50690	51277	ATG	22.1	6.6
80	51274	51582	ATG	11.5	5.3
81	51579	51692	ATG	4.1	5.7
82	51689	52330	ATG	23.9	9.9	D3 NinG Phage P22 NinG; 2e-21; CAA55163 Phage lambda ORF204; e-20; P03770 (Y204_LAMBD) Phage 21 NinG; 2e-20; CAB39991 Phage 933W ORF15; 2e-15; CAB39297 Phage H-19B ORF204; 4e-15; AAD04653
83	52330	52647	ATG	11.8	9.5
84	52715	53293	ATG	21.5	9.5
85	53398	53473				Met-tRNA (CAU)
86	53980	54055				Gly-tRNA (UCC)
87	54068	54142				Asn-tRNA (GUU)
88	54147	54222				Thr-tRNA (UGU)
89	54241	54645	ATG	14.0	6.5
90	54638	54922	ATG	10.5	10.0	Phage φCTX ORF10; 4e-6; AB008550
91	54922	55155	ATG	8.3	5.1
92	55155	55280	ATG	4.6	10.0
93	55273	55434	ATG	5.9	3.8
94	55434	55685	ATG	9.4	9.7
95	55682	55942	ATG	9.2	6.7

^aEmphasis is given to phage homologs. The similar protein is followed by the BLAST E value and the GenBank accession number (and in some cases sequence designation) of that protein. Proteins clearly identifiable by experimental or BLAST analysis are in boldface.