. 2008 May 5;52(7):2581–2592. doi: 10.1128/AAC.01540-07

TABLE 1.

ORFs identified in pIP1206

ORF	Gene	G+C (%)	Function	Identity (%)	Pfam^a	Accession no.	Organism (plasmid)
			oriV-1 region	86		AJ851089	Uncult.^b (pRSB107)
1	ccdA	51	Antitoxin	100	07362	AJ851089	Uncult. (pRSB107)
2	ccdB	50	Toxin	100	01845	AJ851089	Uncult. (pRSB107)
3	resD	57	Resolvase	100	00589	AJ851089	Uncult. (pRSB107)
4	repE	47	Replication protein (RepE)	100	01051	AJ851089	Uncult. (pRSB107)
5	sopA	47	Partitioning protein	100	01656	AJ851089	Uncult. (pRSB107)
6	sopB	45	Partitioning protein	100	02195	AJ851089	Uncult. (pRSB107)
7	orf7	55	Hypothetical protein	100	06924	AJ851089	Uncult. (pRSB107)
8	orf8	63	Hypothetical protein	100		AJ851089	Uncult. (pRSB107)
9	orf9	56	DNA methylase	100	01555	AJ851089	Uncult. (pRSB107)
10	orf10	53	Hypothetical protein	100		AJ851089	Uncult. (pRSB107)
11	orf11	57	Hypothetical protein	100	07128	AJ851089	Uncult. (pRSB107)
12	orf12	60	Hypothetical protein	100		AJ851089	Uncult. (pRSB107)
13	orf13	63	Hypothetical protein	98	07339	NC_002134	E. coli (pR100)
14	klcA	55	Hypothetical antirestriction	100	03230	AJ851089	Uncult. (pRSB107)
15	orf15	56	Hypothetical protein	100		AJ851089	Uncult. (pRSB107)
16	orf16	51	Hypothetical protein	100		AJ851089	Uncult. (pRSB107)
17	orf17	49	RNA-directed DNA polymerase	62	08388	NC_008322	Shewanella sp.
18	ydaA	68	Hypothetical protein	100		AJ851089	Uncult. (pRSB107)
19	orf19	61	Hypothetical protein	97		NC_006671	E. coli (pAPEC-O2-R)
20	orf20	58	Hypothetical protein	100		NC_002134	E. coli (pR100)
21	orf21	61	Hypothetical protein	98		NZ_AAJX01000096	E. coli
22	ydbA	56	Hypothetical protein	100		AJ851089	Uncult. (pRSB107)
23	orf23	60	Hypothetical DNA methylase	96		NC_006671	E. coli (pAPEC-O2-R)
24	orf24	61	Hypothetical protein	100		NC_006671	E. coli (pAPEC-O2-R)
25	orf25	49	RNA-directed DNA polymerization	62	08388	NC_008322	Shewanella sp.
26	IS2-orf2	54	Transposase	98	00665	AC_000091	E. coli
27	IS2-orf1	54	Transposase	99	01527	AC_000091	E. coli
28	rafR	48	Transcriptional regulator	89	00356	M29849	E. coli (pRSD2)
29	rafA	51	α-Galactosidase	97	02065	M27273	E. coli (pRSD2)
30	rafB	46	Raffinose permease	97	01306	M27273	E. coli (pRSD2)
31	rafD	51	Raffinose invertase	96	08244	M27273	E. coli (pRSD2)
32	rafY	39	Putative glycoporine	88		U82290	E. coli (pRSD2)
33	IS1-insA	52	Transposase	97	03811	NC_006816	Salmonella enterica serovar Typhimurium (pU302L)
34	IS1-insB	52	Transposase	99	03400	NC_006816	Serovar Typhimurium (pU302L)
35	orf35	47	Stable inheritance protein	30	07885	NC_002483	E. coli (plasmid F)
36	yubN	61	Hypothetical protein	90		NC_002483	E. coli (plasmid F)
37	yubO	52	Hypothetical protein	95		NC_002483	E. coli (plasmid F)
38	yubP	44	Hypothetical protein	99	06067	DQ381420	E. coli (pAPEC-O1-ColBM)
39	orf39	43	Transglycosylation	95	01464	DQ381420	E. coli (pAPEC-O1-ColBM)
40	traM	38	Mating signal	99	05261	NC_009602	E. coli (pSFO157)
41	traJ	33	Regulation	96		M62986	E. coli (IncFI p307)
42	traY	38	oriT nicking	95		M62986	E. coli (IncFI p307)
43	traA	52	F pilin subunit	98	05513	DQ381420	E. coli (pAPEC-O1-ColBM)
44	traL	47	F pilus assembly	100	07178	DQ381420	E. coli (pAPEC-O1-ColBM)
45	traE	47	F pilus assembly	99	05309	DQ381420	E. coli (pAPEC-O1-ColBM)
46	traK	57	F pilus assembly	98	06586	DQ381420	E. coli (pAPEC-O1-ColBM)
47	traB	57	F pilus assembly	99	06447	DQ381420	E. coli (pAPEC-O1-ColBM)
48	traP	49	Conjugal transfer protein	99	07296	DQ381420	E. coli (pAPEC-O1-ColBM)
49	trbG	42		100		DQ381420	E. coli (pAPEC-O1-ColBM)
50	traV	52	F pilus assembly	97		DQ381420	E. coli (pAPEC-O1-ColBM)
51	traC	53	F pilus assembly	98		DQ381420	E. coli (pAPEC-O1-ColBM)
52	trbI	58		98		DQ381420	E. coli (pAPEC-O1-ColBM)
53	traW	60	F pilus assembly	98		DQ381420	E. coli (pAPEC-O1-ColBM)
54	traU	55	F pilus assembly	97	06834	DQ381420	E. coli (pAPEC-O1-ColBM)
55	trbC	55	F pilus assembly	98		DQ381420	E. coli (pAPEC-O1-ColBM)
56	traN	52	Aggregate stability	99	06986	DQ381420	E. coli (pAPEC-O1-ColBM)
57	trbE	41		100		DQ381420	E. coli (pAPEC-O1-ColBM)
58	traF	50	F pilus assembly	99		DQ381420	E. coli (pAPEC-O1-ColBM)
59	trbA	38	Conjugal transfer protein	95		NC_007941	E. coli (pUTI89)
60	artA	33		96		NC_007941	E. coli (pUTI89)
61	traQ	54	F pilin synthesis	95		NC_007941	E. coli (pUTI89)
62	trbB	57		96		DQ381420	E. coli (pAPEC-O1-ColBM)
63	trbJ	47	Conjugal transfer protein	69		DQ381420	E. coli (pAPEC-O1-ColBM)
64	trbF	38		60		NC_007941	E. coli (pUTI89)
65	traH	51	F pilus assembly	99	06122	NC_006671	E. coli (pAPEC-O2-R)
66	traG	50	F pilus assembly	92	07916	DQ381420	E. coli (pAPEC-O1-ColBM)
67	traS	30	Surface exclusion	54		DQ381420	E. coli (pAPEC-O1-ColBM)
68	traT	50	Surface exclusion	99	05818	DQ381420	E. coli (pAPEC-O1-ColBM)
69	traD	52	DNA transport	96	02534	DQ381420	E. coli (pAPEC-O1-ColBM)
70	traI	59	DNA helicase	96	07057	DQ381420	E. coli (pAPEC-O1-ColBM)
71	traX	57	F pilin acetylation	97	05857	AJ851089	Uncult. bact. (pRSB107)
72	finO	55	Fertility inhibition protein	97	05286	DQ381420	E. coli (pAPEC-O1-ColBM)
73	orf73	61	Hypothetical protein	92		DQ381420	E. coli (pAPEC-O1-ColBM)
74	IS1-insB	52	Transposase	99	03400	NC_006816	Serovar Typhimurium (pU302L)
75	IS1-insA	52	Transposase	97	03811	NC_006816	Serovar Typhimurium (pU302L)
76	srnB	49	Postsegregation killing	96		DQ381420	E. coli (pAPEC-O1-ColBM)
77	repA2	46	Regulation of RepA1 expression	84		DQ381420	E. coli (pAPEC-O1-ColBM)
78	repA6	49	Regulation of RepA1 expression	83		AJ851089	Uncult. (pRSB107)
79	ΔrepA1	56	Replication initiation (truncated)	50	02387	AJ851089	Uncult. (pRSB107)
80	orf80	50	Hypothetical protein
81	arcA	53	Arginine deiminase	95	02274	CP000653	Enterobacter sp. strain 638
82	arcC	57	Carbamate kinase	88	00696	CP000653	Enterobacter sp. strain 638
83	arcB	53	Ornithine carbamoyl transferase	91	00185	CP000653	Enterobacter sp. strain 638
84	arcD	54	C-4 dicarboxylate anaerobic carrier	91	03606	CP000653	Enterobacter sp. strain 638
85	argR	48	Arginine repressor	84	01316	CP000653	Enterobacter sp. strain 638
86	orf86	52	Putative transposase	98	05717	NC_002655	E. coli
87	IS1-insB	52	Transposase	99	03400	NC_006816	Serovar Typhimurium (pU302L)
88	IS1-insA	52	Transposase	97	03811	NC_006816	Serovar Typhimurium (pU302L)
89	orf89	52	Truncated hypothetical protein	84		AY545598	E. coli (pAPEC-O2-ColV)
90	orf90	43	Hypothetical protein	69		NC_008253	E. coli
91	orf91	49	Transposase	95	02371	AF389912	S. marcescens
92	repA2	47	Regulation of RepA1 expression	97		NC_007635	E. coli (pCoo)
93	repA6	49	Regulation of RepA1 expression	83		AJ851089	Uncult. (pRSB107)
94	repA1	56	Replication initiation	96	02387	AJ851089	Uncult. (pRSB107)
95	repA4	58	Replication protein	99		V00351	E. coli (pRSC13)
96	tir	52	Transfer inhibition	100	02517	AJ851089	Uncult. (pRSB107)
97	pemI	53	Plasmid stable inheritance	100	04014	AJ851089	Uncult. (pRSB107)
98	pemK	55	Plasmid stable inheritance	100	02452	AJ851089	Uncult. (pRSB107)
99	IS1-insA	52	Transposase	97	03811	NC_006816	Serovar Typhimurium (pU302L)
100	ΔIS1-insB	52	Transposase (truncated)	64	03400	NC_006816	Serovar Typhimurium (pU302L)
101	IS26-tnpA	52	Transposase	100	00665	NC_006856	S. enterica
102	IS1-insA	52	Transposase	97	03811	NC_006816	Serovar Typhimurium (pU302L)
103	IS1-insB	52	Transposase	99	03400	NC_006816	Serovar Typhimurium (pU302L)
104	tetD	35	Tetracycline resistance	100	00165	AJ851089	Uncult. (pRSB107)
105	tetC	32	Tetracycline transcriptional regulator	100	00440	AJ851089	Uncult. (pRSB107)
106	tetA	43	MFS efflux pump	99	07690	AJ851089	Uncult. (pRSB107)
107	tetR	40	Tetracycline repressor protein	100	02909	AJ851089	Uncult. (pRSB107)
108	jemC	41	Transcriptional regulator	100	01022	AJ851089	Uncult. (pRSB107)
109	orf109	37	Hypothetical protein	100		AJ851089	Uncult. (pRSB107)
110	IS1-insB	52	Transposase	99	03400	NC_006816	Serovar Typhimurium (pU302L)
111	IS1-insA	52	Transposase	97	03811	NC_006816	Serovar Typhimurium (pU302L)
112	catA	44	Chloramphenicol resistance	100	00302	AP000342	E. coli (pR100)
113	ybjA	48	Acetyltransferase	100	00583	AP000342	E. coli (pR100)
114	tnpA-Tn21	63	Transposase	100	01526	AP000342	E. coli (pR100)
115	tnpR-Tn21	57	Resolvase	100	02796	AP000342	E. coli (pR100)
116	IS26-tnpA	52	Transposase	100	00665	NC_006856	S. enterica
117	ΔchrA	58	Chromate ion transport (truncated)	100	02417	AJ698325	Uncult. (pRSB101)
118	orf118	62	Hypothetical protein	100		DQ390454	E. coli (pLEW517)
119	sulI	62	Sulfonamide resistance	99	00809	AP000342	E. coli (pR100)
120	qacEΔ1	50	Quaternary ammonium compound resistance	100	00893	AP000342	E. coli (pR100)
121	aadA4	58	Streptomycin-spectinomycin resistance	100	01909	AY214164	E. coli (pAPEC-O2-R)
122	dfrA17	36	Trimethoprim resistance	100	00186	AY828551	E. coli
123	int	61	Integrase	100	02899	AP000342	E. coli (pR100)
124	ΔtnpM	63	Transposase (truncated)	81	00563	AJ851089	Uncult. (pRSB107)
125	IS26-tnpA	52	Transposase	100	00665	NC_006856	S. enterica
126	orf126	55	Hypothetical protein	100	03551	AJ698325	Uncult. (pRSB101)
127	IS26-tnpA	52	Transposase	100	00665	NC_006856	S. enterica
128	ΔtnpA-Tn3	51	Transposase (truncated)	99	01526	CP000057	H. influenzae
129	tnpR-Tn3	51	Resolvase	99	02796	CP000057	H. influenzae
130	bla_TEM-1	49	β-Lactam resistance	100	00144	AB070224	S. marcescens
131	rmtB	56	Aminoglycoside resistance	100	07091	AB103506	S. marcescens
132	orf132	59	Hypothetical protein
133	orf133	69	Transposase	99	04986	CT025832	A. baumannii
134	qepA	72	Fluoroquinolone resistance	56	07690	CP000316	Polaromonas sp.
135	Δint	61	Integrase (truncated)	100	02899	DQ390454	E. coli (pLEW517)
136	IS26-tnpA	52	Transposase	100	00665	NC_006856	S. enterica
137	nqrc	47	NADH-ubiquinone oxidoreductase	100	04205	AJ851089	Uncult. (pRSB107)
138	orf138	55	Hypothetical protein	99	03239	AJ851089	Uncult. (pRSB107)
139	orf139	53	Hypothetical protein	100		AJ851089	Uncult. (pRSB107)
140	orf140	57	Hypothetical protein	100	04945	AJ851089	Uncult. (pRSB107)
141	orf141	59	Hypothetical protein	100	02687	AJ851089	Uncult. (pRSB107)
142	orf142	58	Hypothetical protein	100	02687	AJ851089	Uncult. (pRSB107)
143	orf143	57	ABC transporter ATP binding protein	100	00005	AJ851089	Uncult. (pRSB107)
144	orf144	58	Hypothetical protein	100	08534	AJ851089	Uncult. (pRSB107)
145	orf145	49	Hypothetical protein	100		AJ851089	Uncult. (pRSB107)
146	orf146	57	Glucose-1-phosphatase	100	00328	AJ851089	Uncult. (pRSB107)
147	IS26-tnpA	52	Transposase	100	00665	CT025832	A. baumannii
148	orf148	54	Hypothetical protein	100	01402	AJ851089	Uncult. (pRSB107)
149	orf149	48	Plasmid stabilization system	100	05016	AJ851089	Uncult. (pRSB107)
150	orf150	38	Hypothetical protein	100		AJ851089	Uncult. (pRSB107)
151	orf151	33	Hypothetical protein	100		AJ851089	Uncult. (pRSB107)
152	orf152	49	Hypothetical protein	100		NC_006816	Serovar Typhimurium (pU302L)
153	orf153	45	Hypothetical protein
154	int	57	Integrase	99	00589	AJ851089	Uncult. bact. (pRSB107)
155	repA	51	Replication	99	01051	AJ851089	Uncult. bact. (pRSB107)
156	IS1-insA	52	Transposase	97	03811	NC_006816	Serovar Typhimurium (pU302L)
157	IS1-insB	52	Transposase	99	03400	NC_006816	Serovar Typhimurium (pU302L)
158	mmuM	60	Homocysteine S-methyltransferase	100	02574	U70214	E. coli
159	mmuP	54	S-methylmethionine permease	99	00324	U70214	E. coli
160	IS5-tnpA	55	Transposase	99	01609	AJ001620	E. coli
161	doc	52	Death on curing protein	99	05012	AF234173	Bacteriophage P1
162	phd	51	Prevent host death protein	100	02604	AF234173	Bacteriophage P1
163	hsdM	45	Type I restriction enzyme, methylase	99	02384	X13145	E. coli (pR124/3)
164	hsdS	39	Type I restriction enzyme, specificity	57	01420	CP000447	S. frigidimarina
165	hsdR	43	Type I restriction enzyme, nuclease	97	04313	X13145	E. coli (pR124/3)
166	IS1-insA	52	Transposase	97	03811	NC_006816	Serovar Typhimurium (pU302L)
167	IS1-insB	52	Transposase	99	03400	NC_006816	Serovar Typhimurium (pU302L)
168	orf168	48	Hypothetical protein	23		AAMR01000022	V. splendidus
169	orf169	49	Hypothetical protein	41		AAMR01000022	V. splendidus
170	orf170	49	Hypothetical protein	100		DQ381420	E. coli (pAPEC-O1-ColBM)
171	vagD	59	Virulence-associated protein	99	01850	DQ381420	E. coli (pAPEC-O1-ColBM)
172	vagC	54	Virulence-associated protein	100	04014	DQ381420	E. coli (pAPEC-O1-ColBM)
173	orf173	44	Hypothetical protein	89		DQ449578	Klebsiella pneumoniae (pK245)
174	orf174	50	Hypothetical protein	100		DQ381420	E. coli (pAPEC-O1-ColBM)
175	korC	57	Hypothetical protein	100		DQ381420	E. coli (pAPEC-O1-ColBM)
176	orf176	45	Hypothetical protein	100		DQ381420	E. coli (pAPEC-O1-ColBM)

Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families.

Uncult., uncultured bacterium.