TABLE 2.

Deduced gene products^a encoded in chromosomal regions flanking ICEF copies in M. fermentans PG18

Gene product or IS	ICEF copy	Sizeb	Closest homolog	% Identity (length)c	Pd	Comment
LepA	IA	599	LepA, M. pulmonis	66 (598)	0	Conserved GTPase
LicA	IA	242	LicA, M. pulmonis	48 (237)	2E-60	Putative choline kinase
ORF228	IIA	228	CysS, M. pulmonis	42 (183)	2E-36	Apparent fusion of conserved hypothetical ORF and cysS in M. pulmonis
ISMf1	IIA, IIB	1,570	IS285 transposase, Yersinia pestis	41 (143)	IE-51	Multiple frameshifts in Tnp reading frame
ORF700	IIA	700	ND			Signal sequence, strain variable among M. fermentans isolates (Fig. 3)
ORF251	IIA	251	OrfD1, M. fermentans	38 (239)	4E-37	ABC transporter, ATP-binding protein; ICEF-IIA insertion at residue 47
Tnp	IIA	136	UU372 integrase, U. urealyticum	68 (119)	6E-41	Fragment of IS3 family transposase gene
ORF349	IIA	349	RC0529, Riskettsia conorii	25 (247)	7E-07	Hypothetical ORF
PdhA	IIA	>101	PdhA, M. pulmonis	67 (101)	1E-32	Pyruvate dehydrogenase E1 α subunit
ORF	IIB	>469	NDe
ORF406	IIB	406	ND
ORF472	IIC	472	CQ002, S. aureus	21 (507)	5E-15	Strain-variable ORF of S. aureus
ORF242	IIC	242	HI1038, Haemophilus influenzae	32 (127)	1E-22	orf242 contains multiple frameshift mutations
ORF375	IIC	375	RC0529 R. conorii	28 (187)	2E-09	Hypothetical ORF

^aThe relative locations and orientations of genes are shown in Fig. 1 or 3.

^bGiven in amino acid residues, except ISMf1 (nucleotides).

^cGiven in identical amino acid residues. Length is the extent of the homologous region.

^dProbability scores from BLASTX.

^eND, no homolog detected in the databases.