Table 3. Bacterial group II intron-encoded ORFs and related ORFs^{a, b}.

Species name	ORF namec	Host gene	Locusd	Introne	ORF domains	YxDD	Size (amino acids)	Frame	Accession number
Anabaena sp. (A.s.)	ORF439	Nonef	Tas transposable element	+	RT(0,4-7)-X-Zn	+	439	Free	U13767
Bacillus anthracis (B.a.-07)	PX01–07	PX01–08/PX01–06g	Virulence plasmid PX01	+	RT-X-Zn	+	602	Free	AF065404
Bacillus anthracis (B.a.-23)	PX01–23	PX01–24/ORFXg	Virulence plasmid PX01	+	RT-X	+	461	Free	AF065404
Bacillus halodurans (B.h.)	ORF1	Nonef	Chromosome	+	RT-X	+	418	Free	AB031210
Bacillus megaterium (B.m.)	iepA	Nonef	Class II transposon	+	RT-X-Zn	+	588	Free	AB022308
Calothrix sp. (C.s.)	ORF2	ORF1	Unknown	+	RT-X-Zn	+	584	Free	X71404
Clostridium difficile (C.d.)	Unnamed	ORF14	Conjugative transposon Tn5397	+	RT-X-Zn	+	609	Free	X98606
Escherichia coli (E.c.B)	IntB	ORFH	H-repeat (Rhs)	+	RT-X	+	416	Free	X77508
Escherichia coli (E.c.D)	IntD	IS629h	Chromosome	+h	RT-X	+	448	Free	D37918
Escherichia coli (E.c.-0157)	L7072	None i	Plasmid p0157	+	RT-X-Zn	+	574	Free	AF074613
Lactococcus lactis (L.l.)	LtrA	Relaxase	Conjugative transfer plasmid pRS01	+	RT-X-Zn	+	599	Free	U50902
Pseudomonas alcaligenes (P.a.)	ORFX6	N.D. j	Plasmid RP4	+	RT-X	+	490	Free	U77945
Pseudomonas putida (P.p.)	MatP1	N.D. j	Plasmid PRA500	+	RT-X	+	473	Free	AF101076
Pseudomonas sp. (P.s.)	ORF494	Nonef	κγ element in Tn5040	+	RT-X	+	494	Free	PSY18999
Serratia marcescens (S.ma.)	RetA	Nonef	Plasmid R471a	–k	RT-X	+	495	Free	AF027768
Shigella flexneri (S.f.)	SfiA	IS629-like ORF	She pathogenicity island	+	RT-X	+	431	Free	U97489
Sinorhizobium meliloti (S.me.)	ORF RmInt1	ORF B	ISRm2011–2	+	RT-X	+	415	Free	Y11597
Sphingomonas aromaticivorans (S.a.1)	MatRa	Replication primase	PNL1 plasmid	+	RT-X-Zn	+	633	Free	AF079317
Sphingomonas aromaticivorans (S.a.2)	ORF404	ORF392/ORF416	PNL1 plasmid	+	RT-X-Zn	+	571	Free	AF079317
Streptococcus pneumoniae (S.p.)	Unnamed	Nonef	Capsular polysaccharide biosynthetic locus	+	RT-X	+	425	Free	AF030367

^aFor a general description of column entries see notes to Table 1.

^bSequences omitted from the table were as follows. Highly divergent sequences which may be degenerate remnants were: D90902 [Synechocystis sp., 508 amino acids, RT(0–7)]; and D64002 [Synechocystis sp., 521 amino acids, RT(0–7)]. Fragments corresponding to incompletely sequenced DNA were: S35081 (Azotobacter vinelandii; 86 amino acids); Z47187.1 (Calothrix sp., 120 amino acids); S35080 (Calothrix sp., 161 amino acids); and AAD29837 (Pseudomonas putida, 216 amino acids). Fragments corresponding to (presumably) non-functional remnants of group II intron ORFs were: Z98756 (Mycobacterium leprae, 161 amino acids); AL021428 (Mycobaterium tuberculosis, 235 amino acids); AE000069 (Rhizobium sp. NGR234, 133 amino acids); AL049661 (Streptomyces coelicolor, 145 amino acids); AF0746111 (Yersinia pestis, 156 amino acids); BAA17969 (Synechocystis sp., 150 amino acids); and S43481 (E. coli, 121 amino acids). AF006691 (Pseudomonas putida, ∼210 amino acids) is a fragment found untranslated in the GenBank DNA sequence database.

^cThe ORF name listed in the publication or database entry.

^dThe locus of the ORF, if known.

^eThe presence of an intron structure surrounding the ORF was evaluated by folding the sequence into a consensus group II intron structure (N.Toor and S.Zimmerly, unpublished).

^fThe intron does not appear to be inserted into an ORF although a very small ORF cannot be ruled out.

^gNo host gene is annotated in the GenBank entry, but the intron probably interrupts neighboring ORFs.

^hSequence has not been reported for the 5′ end of the intron, including the upstream exon (IS629-like ORF) and 680 bp of the intron. Otherwise, this sequence is virtually identical to the S.f. intron.

ⁱThe intron is located between ORFs 7070 and 7073; a 5′ extension of the 7073 ORF could include the intron.

^jNo data. Complete flanking sequence was not reported.

^kIntron domains 5 and 6 are clearly not present; the intron structure may be degenerated.