TABLE 2.

E. coli K-12 genes containing AGG_AGG or AGA_AGA sequences

Gene name	Protein function	Gene length (nt)	Positions of tandem codons (nt)	No. of sense codons after +1 shift	Conservation of tandem codona	Protein conservationa
AGG_AGG-containing genes
ninE	Unknown	171	154, 160	113	K-12, O157, phage 82	K-12, O157, bacteriophages
yhaC	Unknown	1,188	409, 415	1	E.c., S.f.	E.c., S.f.
smf	Putative Rossmann-fold nucleotide-binding protein	1,125	1084, 1090	471	E.c., S.f., S.t., Y.p.	Conserved
fecC	Citrate-dependent iron(III) transport	999	985, 991	90	K-12	Conserved
AGA_AGA-containing genes
intE	Prophage e14 integrase	1,128	556, 561	7	K-12	Conserved
rfbX	Putative O-antigen transporter	1,248	25, 30	24	K-12	Conserved
yagM	CP4-6 prophage	855	685, 690	45	K-12	Conserved
yacH	Putative membrane protein	1,854	1837, 1842	8	K-12	Conserved
ydaU	Rac prophage	858	370, 375	15	K-12	K-12
ymfK	e14 prophage, putative phage repressor	675	652, 657	10	K-12	K-12
rfaS	Lipopolysaccharide core biosynthesis	936	640, 645	2	K-12	K-12
ymfH	e14 prophage	312	196, 201	7	K-12	K-12
ydfO	Qin prophage	426	289, 294	46	K-12, CFT073	E.c.
gspA	Putative export protein A	1,470	10, 15	40	K-12, CFT073	Conserved
ycdF	Unknown	231	199, 204	44	K-12, CFT073, S.f.	K-12, CFT073, S.f.
ygeP	Unknown	300	280, 285	5	K-12, O157	K-12, O157
yjcF	Unknown	1,293	325, 330	17	K-12, O157, S.f.	K-12, O157, S.f.
yhiJ	Unknown	1,623	799, 804	4	K-12, O157, S.f.	K-12, O157, S.f.
t150	IS150 putative transposase	852	586, 591	33	K-12, S.f.	Conserved
t150	IS150 putative transposase	852	778, 783	3	K-12, S.f.	Conserved
ylbH	Unknown	711	307, 312	5	E.c.	E.c.
b1459	Unknown	201	181, 186	5	E.c.	Conserved
ydeN	Putative sulfatase	1,716	19, 24	4	E.c.	Conserved
emrK	Multidrug resistance protein K	1,164	37, 42	8	E.c.	Conserved
intC	Putative prophage Sf6-like integrase	1,158	484, 489	26	E.c.	Conserved
sfmF	Putative fimbria-like protein	516	4, 9	15	E.c.	Conserved
yfcC	Putative S-transferase	1,542	52, 57	8	E.c.	Conserved
ygeH	Putative invasion protein	1,377	1210, 1215	5	E.c.	Conserved
yhiU	Putative membrane protein	1,158	7, 13 + 11, 16	3 or 4	E.c.	Conserved
ybcK	DLP12 prophage, putative recombinase	1,527	73, 78	5	E.c.	Conserved
ybcK	DLP12 prophage, putative recombinase	1,527	1000, 1005	8	E.c.	Conserved
ybfL	Putative receptor	858	694, 699	17	E.c.	Conserved
ydcC	H repeat-associated protein	1,137	973, 978	17	E.c.	Conserved
yhhI	H repeat-associated protein	1,137	973, 978	17	E.c.	Conserved
yjgR	Putative nucleotide triphosphate hydrolase	1,503	1492, 1497	60	E.c.	Conserved
yqeI	Putative sensory transducer	810	292, 297	14	E.c.	Conserved
intR	Rac prophage, putative transposase	1,236	757, 7632	2	E.c., S.f.	Conserved
ynbB	Putative phosphatidate cytidiltransferase	897	577, 582	15	E.c., S.f.	Conserved
lhr	Enzyme; DNA replication and repair	4,617	2797, 2802	15	E.c., S.f.	Conserved
yddW	Unknown	1,320	37, 42	4	E.c., S.f.	Conserved
yifQ	Unknown	726	703, 708	12	E.c., S.f.	Conserved
mdoC	Membrane protein for succinylation of osmoregulated periplasmic glucans	1,158	580, 585	10	E.c., S.f.	Conserved
ybjR	N-Acetylmuramoyl-l-alanine amidase	831	4, 9	45	E.c., S.f.	Conserved
recF	Gap repair protein	1,074	394, 399	35	E.c., S.f., S.t.	Conserved
trmD	tRNA (guanine-1-)-methyltransferase	768	655, 660	9	E.c., S.f., S.t., Y.p.	Conserved
yjbFb	Putative membrane-associated protein	669	22, 27	2	E.c., S.f.	Conserved
pnpb	Polynucleotide phosphorylase	2,205	7, 12	7	E.c., S.f.	Conserved

^aBacterial names are abbreviated as follows: K-12, E. coli K-12; O157, E. coli O157:H7; CFT073, E. coli CFT073; E.c. includes all three E. coli species (K-12, O157:H7, and CFT073); S.f., Shigella flexneri 2a strain 301; S.t., Salmonella enterica serovar Typhimurium LT2; Y.p., Yersinia pestis KIM. A protein is considered conserved if its homologues are present in at least four different genera.

^bThe genes yjbF and pnp were excluded from the total count of the AGA_AGA occurrences and all other considerations in the text for the reasons discussed in the text.