TABLE 1.

ORFs identified in Y. pestis pMT1 DNA sequence by classification^a

ORF class	Designation	Function or comments	Organism or element (gene if known)	Accession no.	Location (bp)
DNA metabolism	ORF1	IS100	Y. pestis IS100 (orfB)	U59875	73885–74661
	ORF2	Ligase	Bacteriophage T3	X05031	74680–75777
	ORF12	Integrase	Vibrio cholera	U39068	82931–84109
	ORF16	DNA Pol III	E. coli	M19334	88955–92479
	ORF26	RecA	Bacteroides fragilis	M63029	96910–97986
	ORF34	RepA	E. coli plasmid ColV	L01250	Complement, 717–1781
	ORF41	exoA	Bacteriophage T4	X01804	4968–6053
	ORF43	exoB	Bacteriophage T4	X01804	6271–8199
	ORF46	IS200	IS200	U22457	9675–10184
	ORF60	Rep-like	Coxiella burnetti	L34077	16197–16895
	ORF61	SpoJ-like	Streptococcus pneumoniae	AF000658	16862–17563
	ORF69	Gene 17-like	Bacteriophage T4	X52394	20457–21713
	ORF93	IS100	Y. pestis IS100 (orfB)	U59875	Complement, 46449–47231
	ORF94	IS100	Y. pestis IS100 (orfA)	U59875	Complement, 47228–48250
	ORF101	IS285	Y. pestis IS285 (orf2)	X78303	51013–52221
	ORF102	Transposase	Enterobacter	U60777	52648–53712
	ORF108	Membrane endonuclease	E. coli plasmid-pKM101 (nuc)	U09868	Complement, 57629–58117
	ORF111	Resolvase	Pseudomonas syringae (stbA)	L48985	Complement, 60161–60781
	ORF113	ParA	Bacteriophage P1	X02954	61767–63041
	ORF114	ParB	Bacteriophage P1	K02380	63038–64009
	ORF123	Adenine-specific DNA methylase	E. coli pEC156 EcoVIII methylase	U48806	66648–67325
	ORF128	Antirestriction	E. coli	Z34467	69208–69714
	ORF135	DNA partitioning	Rhizobium meliloti (Orf1 and Orf2 of pRmeGR4a)	X69105	70730–72739
			Shigella sonnei (psiB)	U82272
			Streptococcus pneumoniae (spoOJ)	AF000658
	ORF136	IS100	Y. pestis IS100 (orfA)	U59875	72863–73882
Protein metabolism	ORF28	HflC-like	Vibrio parahaemolyticus	U09005	98281–99111
	ORF63	ABC transporter/ATP binding	Archaeglobus fulgidus (AF1064)	AE001029	17500–18198
	ORF75	L12 ribosomal protein L12e	Haloferax volcanii	X58924	25927–26361
Gene regulation	ORF5	Caf1R	Y. pestis (caf1R)	X61996	Complement, 77118–78041
	ORF22	PrpB-like	Pseudomonas putida	X80272	94557–95636
	ORF56	Repressor of flagellum synthesis	Salmonella abony (fljA)	D26167	Complement, 13278–13841
Known virulence	ORF6	Caf1M	Y. pestis (caf1M)	X61996	78318–79127
	ORF8	Caf1A	Y. pestis (caf1A)	X61996	79152–81653
	ORF9	Caf1	Y. pestis (caf1)	X61996	81734–82246
	ORF107	Murine toxin	Y. pestis (ymt)	X92727	Complement, 55788–57551
Lambda-like	ORF80a	V major tail fiber	Bacteriophage lambda	P03733	28560–29303
		Intimin	E. coli O157:H7 (eae)	P43261
	ORF84	H tail fiber	Bacteriophage lambda	AF007380	30041–34618
	ORF85	M minor tail fiber	Bacteriophage lambda	P03737	34660–34995
	ORF86	L minor tail fiber	Bacteriophage lambda	P03738	35052–35783
	ORF87a	K tail assembly	Bacteriophage lambda	P03729	35815–36570
	ORF88	I tail assembly	Bacteriophage lambda	P03730	36561–37148
	ORF89	J host specificity	Bacteriophage lambda	P03749	37164–41801
	ORF91	Hypothetical protein ORF314	Bacteriophage lambda	P03745	42469–45405
	ORF92	Tail fiber assembly	Bacteriophage lambda (tfa)	225931	45707–46315
Hypothetical in databaseb	ORF15	CobT	Pseudomonas denitrificans (cobT)	P29934	85075–87441
	ORF15a	CobS	Pseudomonas denitrificans (cobS)	P29933	87539–88771
	ORF29	Hypothetical	Bacteriophage P22	X78401	99265–99636
	ORF33a	Hypothetical regulatory	Bacteriophage P1	76816	100922–147
	ORF38	Hypothetical lipoprotein	Bacillus subtilis (orfK yzeA)	L16808, Z93102	Complement, 3530–4552
	ORF59	Long hypothetical protein	Pyrococcus horikoshii (PHBW005)	AB009472	Complement, 14573–16132
	ORF73	SRPI hypothetical protein	Synechococcus PCC7942 pANL	Q55032	24271–25146
	ORF104	Hypothetical protein	E. coli	U70214	Complement, 54408–54803
	ORF105	Hypothetical protein	E. coli	U70214	Complement, 54694–55002
	ORF116	Hypothetical	Sphingomonas S88	U51197	64388–65785
	ORF131	Hypothetical	E. coli	AE000133	70427–70657
Fragmentsc	ORF23	DNA polymerase	Lactococcus lactis	U78771	95646–96641
	ORF33	Type II	Helicobacter pylori	AE000647	100590–100925
	ORF99	Hypothetical protein	Methanobacterium thermo-autotrophicum	AE000913	Complement, 49210–50004
	ORF103	Hypothetical transposase	Salmonella typhimurium	Z29513	Complement, 53911–54234
	ORF103a	IS600	Shigella sonnei	X05952	54281–54481
	ORF106	Hypothetical	Shigella flexneri	U97489	55073–55543
	ORF106a	IS801	Pseudomonas syringae	X57269	55589–55729
	ORF110	Hypothetical	Salmonella typhimurium	Z29513	Complement, 59154–60140
	ORF115a	SamB-like	Salmonella typhimurium	D90202	87539–88771

^aORFs listed were assigned a putative function according to our criteria outlined in the general overview section of Results and Discussion. Classification then was based on these putative functions. 

^bHomology above our criteria with proteins in the database that have not been assigned a function. 

^cORFs that appear to be remnants of larger proteins in the database.