TABLE 3.

Localization and description of ORFs and noncoding elements in pMT1

ORF or noncoding element	Position no.	Size (amino acid residues)	Strand or direction	Description (homologue by BLAST)
ORFs
1	87–1109	340	Direct	Transposase
2	1109–1888	259	Direct	Transposase
3	2022–2618	198	Complement	Similar to hypothetical E. coli protein
4	2932–5514	860	Complement	Similar to tail fiber protein gp37
5	5901–6518	205	Complement	Unknown
6	6571–11049	1,492	Complement	Putative protein, similar to lambda host-specific protein J and Northern European squid neurofilament-like protein
7	11188–11739	183	Complement	Unknown
8	11763–12521	252	Complement	Similar to hypothetical Coxiella burnetii protein (motif: RGD cell attachment site)
9	12553–13251	232	Complement	Similar to phage lambda minor tail protein L
10	13341–13676	111	Complement	Unknown
11	13718–18295	1,525	Complement	Putative protein, similar to hypothetical Haemophilus influenzae protein HI1514
12	18653–18970	105	Complement	Unknown
13	19030–19776	248	Complement	Unknown
14	19851–20207	118	Complement	Unknown (Block hit: complement C1Q domain signature)
15	20236–20616	126	Complement	Unknown (Block hit: NSF attachment protein)
16	20700–21044	114	Complement	Unknown (Block hit: geminivirus AR1 coat protein)
17	21142–21975	277	Complement	Unknown (Block hit: histone H5 signature)
18	21975–22274	99	Complement	Unknown
19	22453–22884	143	Complement	Similar to glucan endo-1,3-β-d-glucosidase
20	23190–24065	291	Complement	Unknown
21	24092–24409	105	Complement	Unknown
22	24537–24977	146	Complement	Unknown
23	25015–26253	412	Complement	Unknown
24	26623–27831	402	Complement	Unknown (motif: ATP/GTP binding motif A [P loop])
25	27882–28523	213	Complement	Unknown
26	28719–28985	88	Complement	Unknown (motif: RGD cell attachment site)
27	28995–29885	296	Complement	Unknown
28	30138–30776	212	Complement	Similar to ABC transporter (motif: ATP/GTP binding motif A [P loop])
29	30773–31441	222	Complement	Unknown (motif: aminoacyl-RNA synthetase class II, signature 2)
30	31441–32121	226	Complement	Unknown
31	32285–33763	492	Direct	Unknown
32	33766–34044	92	Direct	Unknown
33	34269–34526	85	Direct	Unknown
34	34531–35058	175	Direct	Similar to S. typhimurium repressor of phase 1 flagellin gene
35	35382–36032	216	Direct	Unknown
36	36982–37464	160	Complement	Unknown
37	37669–37950	93	Complement	Unknown
38	38797–39384	195	Complement	Unknown
39	40132–42015	627	Complement	Unknown (motifs: ABC transporter, aminoacyl-tRNA synthetase class II signature 2, ATP/GTP binding motif A [P loop])
40	42278–43231	317	Complement	Unknown
41	45161–45385	74	Complement	Unknown
42	46550–47614	354	Direct	Similar to E. coli replication protein A (repA)
43	48184–48384	66	Complement	Unknown
44	48396–48656	86	Complement	Unknown
45	49291–49587	98	Complement	Unknown
46	50211–50996	261	Complement	Unknown
47	51336–52412	358	Complement	Similar to recA (motif: ATP/GTP binding motif A [P loop])
48	52681–53550	289	Complement	Similar to Streptococcus pneumoniae DNA Pol Ia
49	53686–54714	342	Complement	Unknown (motif: RGD cell attachment site) (Block hit: T. cruzi P2 protein signature)
50	54834–55265	143	Complement	Unknown
51	55810–56373	187	Direct	Unknown
52	56403–56846	147	Complement	Unknown
53	56843–60250	1135	Complement	Similar to DNA Pol III alpha subunit
54	60548–61783	411	Complement	Similar to CobS protein
55	61881–64235	784	Complement	Similar to CobT protein
56	67074–67588	175	Complement	F1 capsule antigen
57	67669–70170	833	Complement	F1 capsule anchoring protein
58	70195–70971	258	Complement	caf1M
59	71299–72204	301	Direct	caf1R
60	72719–73024	101	Complement	Unknown
61	73545–74582	347	Complement	Similar to DNA ligase
62	74658–75437	259	Complement	Transposase
63	75437–76459	340	Complement	Transposase
64	76861–77118	85	Complement	Unknown
65	77419–78048	209	Complement	Unknown
66	79222–80430	402	Direct	Transposase
67	80899–81921	340	Direct	Transposase
68	82120–82437	105	Complement	Similar to E. coli yhgA
69	82617–82988	123	Complement	Similar to hypothetical protein
70	83297–83752	151	Direct	Similar to E. coli hypothetical protein and reverse transcriptase-like protein
71	83997–85595	532	Complement	Murine toxin
72	87149–87340	63	Direct	Unknown
73	87363–88220	285	Complement	Putative protein, similar to E. coli yhgA
74	90045–91250	401	Direct	Similar to phage P7 parA
75	91247–92218	323	Direct	Similar to phage P7 parB
76	94893–95534	213	Direct	Similar to adenine DNA methyltransferase
77	95766–96185	139	Direct	Unknown (Block hit: NSF attachment site)
78	96239–97018	259	Direct	Unknown
79	97417–97923	168	Direct	Similar to antirestriction protein
80	98635–98865	76	Direct	Similar to E. coli hypothetical protein
81	98938–100947	669	Direct	Similar to Rhizobium meliloti protein and S. sonnei protein
Noncoding elements
	1–1954		Forward	IS100
	38040–38757		Reverse	IS200
	46565–47425		Forward	IncF plasmid RepFIB replicon
	74592–76545		Reverse	IS100

^aPol, polymerase.