breseq  version 0.35.4  revision f352f80f4bc9 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence	position	mutation	freq	annotation	gene	description
RA	958	G→T	48.8%	D208Y (GAC→TAC)	thrA →	Bifunctional aspartokinase/homoserine dehydrogenase 1
RA	3,618	C→A	10.9%	P273Q (CCG→CAG)	thrB →	homoserine kinase
RA	5,144	G→A	93.2%	intergenic (+124/‑90)	thrC → / → yaaX	L‑threonine synthase/DUF2502 family putative periplasmic protein
RA	8,598	G→T	6.1%	D121Y (GAT→TAT)	talB →	transaldolase B
RA	9,946	C→A	11.0%	P183P (CCG→CCT)	satP ←	succinate‑acetate transporter
RA	10,444	G→T	92.6%	F17L (TTC→TTA)	satP ←	succinate‑acetate transporter
RA	11,901	C→A	11.4%	intergenic (‑115/‑262)	yaaI ← / → dnaK	UPF0412 family protein/chaperone Hsp70, with co‑chaperone DnaJ
RA	12,901	G→A	100%	D247N (GAT→AAT)	dnaK →	chaperone Hsp70, with co‑chaperone DnaJ
RA	19,844	G→T	5.1%	I157I (ATC→ATA)	insB1 ←	IS1 transposase B
RA	25,546	G→T	89.1%	D114Y (GAC→TAC)	lspA →	prolipoprotein signal peptidase (signal peptidase II)
RA	28,818	G→T	8.6%	D149Y (GAC→TAC)	dapB →	dihydrodipicolinate reductase
RA	29,139	G→T	100%	G256C (GGT→TGT)	dapB →	dihydrodipicolinate reductase
RA	35,444	G→T	10.0%	S240* (TCG→TAG)	caiD ←	carnitinyl‑CoA dehydratase
RA	35,631	G→T	5.2%	R178S (CGC→AGC)	caiD ←	carnitinyl‑CoA dehydratase
RA	41,442	G→T	12.9%	R164S (CGC→AGC)	caiT ←	putative transporter
RA	42,079	G→A	46.6%	intergenic (‑148/‑324)	caiT ← / → fixA	putative transporter/anaerobic carnitine reduction putative electron transfer flavoprotein subunit
RA	42,150	G→A	67.6%	intergenic (‑219/‑253)	caiT ← / → fixA	putative transporter/anaerobic carnitine reduction putative electron transfer flavoprotein subunit
RA	42,415	A→C	54.6%	T5P (ACT→CCT)	fixA →	anaerobic carnitine reduction putative electron transfer flavoprotein subunit
RA	49,840	G→T	90.4%	A6A (GCG→GCT)	folA →	dihydrofolate reductase
RA	51,352	A→T	6.6%	G85G (GGT→GGA)	apaG ←	protein associated with Co2+ and Mg2+ efflux
RA	54,103	G→T	8.9%	R200R (CGC→CGA)	surA ←	peptidyl‑prolyl cis‑trans isomerase (PPIase)
RA	55,590	G→T	91.9%	T507K (ACG→AAG)	lptD ←	LPS assembly OM complex LptDE, beta‑barrel component
RA	56,677	G→T	93.5%	R145S (CGC→AGC)	lptD ←	LPS assembly OM complex LptDE, beta‑barrel component
RA	69,367	C→A	46.5%	M16I (ATG→ATT)	thiQ ←	thiamine, thiamine pyrophosphate ABC transporter ATPase; ThiBPQ thiamine, thiamine pyrophosphate importer
RA	70,249	A→C	8.4%	C254G (TGC→GGC)	thiP ←	thiamine, thiamine pyrophosphate ABC transporter permease; ThiBPQ thiamine, thiamine pyrophosphate importer
RA	70,465	G→T	43.4%	H182N (CAT→AAT)	thiP ←	thiamine, thiamine pyrophosphate ABC transporter permease; ThiBPQ thiamine, thiamine pyrophosphate importer
RA	76,821	G→T	48.3%	G177G (GGC→GGA)	leuC ←	3‑isopropylmalate dehydratase large subunit
RA	80,123	C→T	92.9%	G25S (GGC→AGC)	leuL ←	leu operon leader peptide
RA	81,562	C→A	91.1%	I236I (ATC→ATA)	leuO →	global transcription factor
RA	82,465	G→T	8.2%	D117Y (GAC→TAC)	ilvI →	acetolactate synthase 3 large subunit
RA	85,890	G→T	13.1%	intergenic (+371/‑231)	cra → / → mraZ	transcriptional repressor‑activator for carbon metabolism/RsmH methytransferase inhibitor
RA	90,252	G→T	52.9%	A200A (GCG→GCT)	murE →	UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate:meso‑ diaminopimelate ligase
RA	92,294	C→A	10.5%	R386R (CGC→CGA)	murF →	UDP‑N‑acetylmuramoyl‑tripeptide:D‑alanyl‑D‑ alanine ligase
RA	92,728	G→T	6.4%	L80L (CTG→CTT)	mraY →	phospho‑N‑acetylmuramoyl‑pentapeptide transferase
RA	93,391	G→T	73.0%	T301T (ACG→ACT)	mraY →	phospho‑N‑acetylmuramoyl‑pentapeptide transferase
RA	97,521	C→A	100%	A90A (GCC→GCA)	murC →	UDP‑N‑acetylmuramate:L‑alanine ligase
RA	97,893	T→A	14.4%	F214L (TTT→TTA)	murC →	UDP‑N‑acetylmuramate:L‑alanine ligase
RA	103,467	G→T	90.6%	D142Y (GAT→TAT)	lpxC →	UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase
RA	104,054	G→T	7.2%	intergenic (+93/‑138)	lpxC → / → secM	UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase/regulator of secA translation
RA	104,561	G→T	93.7%	A124S (GCG→TCG)	secM →	regulator of secA translation
RA	104,582	A→T	17.9%	T131S (ACG→TCG)	secM →	regulator of secA translation
RA	107,298	C→A	36.5%	R845S (CGT→AGT)	secA →	preprotein translocase subunit, ATPase
RA	109,050	C→T	6.4%	E13K (GAA→AAA)	zapD ←	FtsZ stabilizer
RA	109,800	A→T	7.4%	intergenic (‑94/‑131)	coaE ← / → guaC	dephospho‑CoA kinase/GMP reductase
RA	110,883	A→T	6.1%	Y318F (TAC→TTC)	guaC →	GMP reductase
RA	112,729	G→T	43.0%	D286E (GAC→GAA)	hofB ←	T2SE secretion family protein; P‑loop ATPase superfamily protein
RA	118,873	G→T	94.8%	D99Y (GAC→TAC)	pdhR →	pyruvate dehydrogenase complex repressor; autorepressor
RA	120,313	C→A	40.9%	T270T (ACC→ACA)	aceE →	pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding
RA	122,790	G→T	55.5%	A203A (GCG→GCT)	aceF →	pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2
RA	123,784	G→T	6.0%	D535Y (GAC→TAC)	aceF →	pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2
RA	126,488	G→T	5.8%	V420V (GTC→GTA)	yacH ←	uncharacterized protein
RA	126,784	C→A	42.8%	D322Y (GAT→TAT)	yacH ←	uncharacterized protein
RA	132,639	T→A	9.6%	T105S (ACG→TCG)	speE ←	spermidine synthase (putrescine aminopropyltransferase)
RA	134,028	G→T	70.5%	A153A (GCG→GCT)	cueO →	multicopper oxidase (laccase)
RA	134,652	G→T	13.1%	M361I (ATG→ATT)	cueO →	multicopper oxidase (laccase)
RA	137,038	Δ1 bp	10.0%	coding (675/2391 nt)	gcd ←	glucose dehydrogenase
RA	137,779	T→A	8.0%	intergenic (‑67/‑139)	gcd ← / → hpt	glucose dehydrogenase/hypoxanthine phosphoribosyltransferase
RA	142,460	T→A	100%	F298Y (TTC→TAC)	yadE →	putative polysaccharide deacetylase lipoprotein
RA	142,912	G→T	6.0%	F90L (TTC→TTA)	panD ←	aspartate 1‑decarboxylase
RA	145,894	G→T	9.1%	I65I (ATC→ATA)	panB ←	3‑methyl‑2‑oxobutanoate hydroxymethyltransferase
RA	149,697	G→T	9.0%	I739I (ATC→ATA)	htrE ←	putative outer membrane usher protein
RA	153,472	G→T	100%	intergenic (‑102/+268)	yadN ← / ← folK	putative fimbrial‑like adhesin protein/2‑amino‑4‑hydroxy‑6‑hydroxymethyldihyropteridine pyrophosphokinase
RA	158,287	C→A	94.3%	D78Y (GAC→TAC)	ligT ←	2'‑5' RNA ligase
RA	161,068	A→C	11.3%	intergenic (+47/‑149)	hrpB → / → mrcB	putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
RA	162,905	G→T	37.9%	V563V (GTG→GTT)	mrcB →	fused glycosyl transferase and transpeptidase
RA	172,107	G→T	11.1%	E172* (GAA→TAA)	clcA →	H(+)/Cl(‑) exchange transporter
RA	172,979	G→T	7.0%	A462A (GCG→GCT)	clcA →	H(+)/Cl(‑) exchange transporter
RA	176,783	G→T	63.4%	D354Y (GAT→TAT)	dgt →	deoxyguanosine triphosphate triphosphohydrolase
RA	176,864	C→T	7.7%	L381L (CTA→TTA)	dgt →	deoxyguanosine triphosphate triphosphohydrolase
RA	179,424	G→T	9.1%	D159Y (GAT→TAT)	cdaR →	carbohydrate diacid regulon transcriptional regulator; autoregulator
RA	183,820	G→T	6.6%	R440S (CGC→AGC)	glnD ←	uridylyltransferase
RA	186,279	A→T	13.2%	noncoding (81/136 nt)	tff →	novel sRNA, function unknown
RA	192,746	G→T	9.8%	G195C (GGT→TGT)	cdsA →	CDP‑diglyceride synthase
RA	201,962	A→T	69.3%	D117V (GAT→GTT)	dnaE →	DNA polymerase III alpha subunit
RA	215,833	G→T	12.5%	N83K (AAC→AAA)	tsaA ←	tRNA‑Thr(GGU) m(6)t(6)A37 methyltransferase, SAM‑dependent
RA	217,932	A→C	68.0%	I59M (ATT→ATG)	metI ←	DL‑methionine transporter subunit
RA	229,707	G→T	50.2%	R246S (CGT→AGT)	mltD ←	putative membrane‑bound lytic murein transglycosylase D
RA	230,579	C→T	100%	E231K (GAA→AAA)	gloB ←	hydroxyacylglutathione hydrolase
RA	232,860	G→T	93.9%	D103Y (GAT→TAT)	dnaQ →	DNA polymerase III epsilon subunit
RA	233,931	G→A	10.9%	S37N (AGT→AAT)	yafT →	lipoprotein
RA	235,778	C→A	5.2%	pseudogene (186/273 nt)	yafF →	pseudogene, H repeat‑associated protein
RA	236,234	A→T	62.0%	V148E (GTG→GAG)	yafV ←	putative NAD(P)‑binding C‑N hydrolase family amidase
RA	238,195	G→T	90.1%	V532V (GTC→GTA)	fadE ←	acyl coenzyme A dehydrogenase
RA	245,779	C→A	5.5%	pseudogene (779/1713 nt)	lfhA ←	pseudogene, flagellar system protein, promoterless fragment; flagellar biosynthesis
RA	247,002	G→T	6.2%	pseudogene (444/756 nt)	lafU →	pseudogene, lateral flagellar motor protein fragment
RA	249,698	G→T	6.2%	intergenic (+50/‑268)	yafP → / → ykfJ	putative acyl‑CoA transferase/pseudogene
RA	250,722	G→T	6.3%	intergenic (+33/+24)	prfH → / ← pepD	pseudogene, RF‑1 domain family; probable peptide chain release factor/aminoacyl‑histidine dipeptidase (peptidase D)
RA	250,880	G→T	12.0%	P442T (CCG→ACG)	pepD ←	aminoacyl‑histidine dipeptidase (peptidase D)
RA	251,998	T→C	8.1%	K69R (AAA→AGA)	pepD ←	aminoacyl‑histidine dipeptidase (peptidase D)
RA	253,769	C→T	9.2%	V252V (GTC→GTT)	frsA →	fermentation‑respiration switch protein; PTS Enzyme IIA(Glc)‑binding protein; pNP‑butyrate esterase activity
RA	262,114	C→A	74.0%	D51Y (GAT→TAT)	yafY ←	lipoprotein, inner membrane; overproduction stimulates degP expression; CP4‑6 prophage
RA	263,270	C→A	51.5%	V149V (GTG→GTT)	yafZ ←	CP4‑6 prophage; conserved protein
RA	264,812	G→T	5.9%	intergenic (‑141/+188)	ykfA ← / ← perR	CP4‑6 prophage; putative GTP‑binding protein/CP4‑6 prophage; putative DNA‑binding transcriptional regulator
RA	265,159	G→T	8.0%	I245I (ATC→ATA)	perR ←	CP4‑6 prophage; putative DNA‑binding transcriptional regulator
RA	266,127	C→A	5.8%	pseudogene (139/258 nt)	insN →	pseudogene, IS911 transposase A;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related
RA	274,735	A→T	100%	pseudogene (138/348 nt)	afuB ←	pseudogene, CP4‑6 prophage; ABC transporter permease family;Phage or Prophage Related
RA	289,785	C→T	9.7%	W242* (TGG→TGA)	yagM ←	CP4‑6 prophage; uncharacterized protein
RA	295,092	G→T	10.0%	G518G (GGC→GGA)	paoC ←	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
RA	296,308	G→T	5.8%	A113E (GCG→GAG)	paoC ←	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
RA	302,428	G→T	6.2%	P34Q (CCG→CAG)	ecpD ←	polymerized tip adhesin of ECP fibers
RA	307,454	G→A	6.9%	intergenic (‑407/‑369)	ecpR ← / → ykgL	putative transcriptional regulator for the ecp operon/uncharacterized protein
RA	309,785	T→A	10.7%	intergenic (‑269/‑283)	ykgP ← / → eaeH	pseudogene, oxidoreductase family/pseudogene, attaching and effacing protein homology;factor; Not classified
RA	312,532	G→A	91.4%	pseudogene (349/684 nt)	ykgA ←	pseudogene, AraC family;putative regulator; Not classified; putative ARAC‑type regulatory protein
RA	315,372	C→A	9.1%	G114V (GGA→GTA)	rclA ←	reactive chlorine stress species (RCS) resistance protein; pyridine nucleotide‑dependent disulfide oxidoreductase family
RA	317,205	G→A	73.3%	intergenic (+413/‑114)	rclR → / → ykgE	reactive chlorine species (RCS)‑specific activator of the rcl genes/cysteine‑rich LutA family protein; putative electron transport chain YkgEFG component
RA	320,920	G→A	100%	S52S (AGC→AGT)	ykgH ←	putative inner membrane protein
RA	321,223	C→A	92.3%	intergenic (‑148/+65)	ykgH ← / ← betA	putative inner membrane protein/choline dehydrogenase, a flavoprotein
RA	326,385	G→T	12.2%	P404P (CCG→CCT)	betT →	choline transporter of high affinity
RA	329,887	G→T	10.7%	I86I (ATC→ATA)	yahB ←	putative DNA‑bindng transcriptional regulator
RA	332,463	G→T	8.1%	A276A (GCG→GCT)	yahE →	DUF2877 family protein
RA	344,800	G→T	89.1%	E136D (GAG→GAT)	prpB →	2‑methylisocitrate lyase
RA	347,268	G→T	6.3%	D115Y (GAC→TAC)	prpD →	2‑methylcitrate dehydratase
RA	347,382	G→T	13.4%	E153* (GAA→TAA)	prpD →	2‑methylcitrate dehydratase
RA	349,584	G→T	10.1%	E390* (GAA→TAA)	prpE →	propionate‑‑CoA ligase
RA	360,680	C→A	6.6%	R355L (CGA→CTA)	lacI ←	DNA‑binding transcriptional repressor
RA	360,752	A→G	100%	V331A (GTG→GCG)	lacI ←	DNA‑binding transcriptional repressor
RA	361,806	G→A	100%	intergenic (‑63/+14)	lacI ← / ← mhpR	DNA‑binding transcriptional repressor/mhp operon transcriptional activator
RA	362,159	G→T	92.4%	I165I (ATC→ATA)	mhpR ←	mhp operon transcriptional activator
RA	365,572	G→A	7.0%	pseudogene (116/534 nt)	mhpC →	pseudogene, IS30 insertion
RA	365,778	C→T	7.6%	pseudogene (322/534 nt)	mhpC →	pseudogene, IS30 insertion
RA	380,236	C→A	49.2%	intergenic (‑164/‑452)	yaiS ← / → tauA	putative PIG‑L family deacetylase/taurine transporter subunit
RA	381,815	G→T	9.6%	V51V (GTG→GTT)	tauB →	taurine transporter subunit
RA	385,339	A→T	8.5%	intergenic (‑156/‑368)	hemB ← / → yaiT	5‑aminolevulinate dehydratase (porphobilinogen synthase)/pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein
RA	385,485	C→T	49.0%	intergenic (‑302/‑222)	hemB ← / → yaiT	5‑aminolevulinate dehydratase (porphobilinogen synthase)/pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein
RA	385,815	G→T	72.5%	pseudogene (109/1458 nt)	yaiT →	pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein
RA	396,883	A→G	88.7%	Q14Q (CAA→CAG)	iraP →	anti‑RssB factor, RpoS stabilzer during Pi starvation; anti‑adapter protein
RA	397,959	G→A	70.5%	A253T (GCG→ACG)	phoA →	bacterial alkaline phosphatase
RA	402,340	G→T	100%	V160V (GTG→GTT)	aroL →	shikimate kinase II
RA	406,002	G→T	6.1%	G135C (GGC→TGC)	mak →	manno(fructo)kinase
RA	406,075	C→A	92.5%	P159Q (CCG→CAG)	mak →	manno(fructo)kinase
RA	411,027	G→T	100%	L61L (CTC→CTA)	sbcC ←	exonuclease, dsDNA, ATP‑dependent
RA	411,446	C→T	5.5%	Q321Q (CAG→CAA)	sbcD ←	exonuclease, dsDNA, ATP‑dependent
RA	415,042	G→T	7.5%	intergenic (+402/‑5)	phoR → / → brnQ	sensory histidine kinase in two‑component regulatory system with PhoB/branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val
RA	419,985	C→A	10.4%	E130D (GAG→GAT)	acpH ←	acyl carrier protein (ACP) phosphodiesterase; ACP hydrolyase
RA	421,799	C→A	91.8%	I69I (ATC→ATA)	tgt →	tRNA‑guanine transglycosylase
RA	423,068	C→A	8.6%	A109E (GCG→GAG)	yajC →	SecYEG protein translocase auxillary subunit
RA	425,143	G→T	66.1%	T61T (ACG→ACT)	secF →	SecYEG protein translocase auxillary subunit
RA	427,603	C→T	8.0%	intergenic (‑134/+165)	tsx ← / ← yajI	nucleoside channel, receptor of phage T6 and colicin K/putative lipoprotein
RA	433,551	G→T	87.3%	S14Y (TCC→TAC)	yajO ←	2‑carboxybenzaldehyde reductase
RA	434,663	A→C	91.7%	I324S (ATC→AGC)	dxs ←	1‑deoxyxylulose‑5‑phosphate synthase, thiamine triphosphate‑binding, FAD‑requiring
RA	435,336	G→T	94.5%	Q100K (CAG→AAG)	dxs ←	1‑deoxyxylulose‑5‑phosphate synthase, thiamine triphosphate‑binding, FAD‑requiring
RA	437,076	A→T	7.8%	K24N (AAA→AAT)	thiI →	tRNA s(4)U8 sulfurtransferase
RA	437,672	T→A	100%	V223E (GTG→GAG)	thiI →	tRNA s(4)U8 sulfurtransferase
RA	440,793	G→T	5.3%	R444S (CGC→AGC)	yajR ←	putative transporter
RA	441,811	A→C	5.7%	I104M (ATT→ATG)	yajR ←	putative transporter
RA	444,489	G→A	100%	R537C (CGT→TGT)	cyoB ←	cytochrome o ubiquinol oxidase subunit I
RA	446,369	T→G	65.4%	Q233P (CAG→CCG)	cyoA ←	cytochrome o ubiquinol oxidase subunit II
RA	450,228	G→A	7.9%	A101T (GCA→ACA)	bolA →	stationary‑phase morphogene, transcriptional repressor for mreB; also regulator for dacA, dacC, and ampC
RA	450,290	G→A	100%	intergenic (+45/‑299)	bolA → / → tig	stationary‑phase morphogene, transcriptional repressor for mreB; also regulator for dacA, dacC, and ampC/peptidyl‑prolyl cis/trans isomerase (trigger factor)
RA	451,853	C→A	11.7%	T422N (ACC→AAC)	tig →	peptidyl‑prolyl cis/trans isomerase (trigger factor)
RA	453,656	T→A	10.2%	S259T (TCC→ACC)	clpX →	ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease
RA	454,472	G→T	7.7%	A43A (GCG→GCT)	lon →	DNA‑binding ATP‑dependent protease La
RA	456,298	T→A	100%	L652Q (CTG→CAG)	lon →	DNA‑binding ATP‑dependent protease La
RA	456,588	G→T	88.6%	D749Y (GAC→TAC)	lon →	DNA‑binding ATP‑dependent protease La
RA	458,681	C→A	44.1%	I437I (ATC→ATA)	ppiD →	periplasmic folding chaperone, has an inactive PPIase domain
RA	461,710	G→T	5.7%	L353L (CTC→CTA)	ybaE ←	putative ABC superfamily transporter periplasmic‑binding protein
RA	465,341	A→C	18.4%	I339L (ATT→CTT)	mdlA →	putative multidrug transporter subunit of ABC superfamily, ATP‑binding component
RA	469,916	Δ1 bp	8.9%	coding (702/861 nt)	tesB ←	acyl‑CoA thioesterase 2
RA	470,280	G→T	6.9%	A113E (GCG→GAG)	tesB ←	acyl‑CoA thioesterase 2
RA	473,645	G→T	7.9%	Y143* (TAC→TAA)	ylaB ←	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	474,138	G→T	93.4%	intergenic (‑65/+99)	ylaB ← / ← ylaC	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase/DUF1449 family inner membrane protein
RA	475,502	T→A	11.0%	intergenic (‑128/+44)	maa ← / ← hha	maltose O‑acetyltransferase/modulator of gene expression, with H‑NS
RA	475,805	C→A	92.5%	A120A (GCG→GCT)	tomB ←	Hha toxicity attenuator; conjugation‑related protein
RA	477,693	C→A	11.5%	D723Y (GAT→TAT)	acrB ←	multidrug efflux system protein
RA	479,122	G→T	48.2%	F246L (TTC→TTA)	acrB ←	multidrug efflux system protein
RA	479,244	C→A	100%	A206S (GCC→TCC)	acrB ←	multidrug efflux system protein
RA	480,820	C→T	89.5%	D86N (GAC→AAC)	acrA ←	multidrug efflux system
RA	481,667	G→A	100%	A151T (GCG→ACG)	acrR →	transcriptional repressor
RA	486,912	C→A	16.7%	I15I (ATC→ATA)	apt →	adenine phosphoribosyltransferase
RA	488,218	C→A	13.3%	A224E (GCG→GAG)	dnaX →	DNA polymerase III/DNA elongation factor III, tau and gamma subunits
RA	488,839	G→A	7.6%	S431N (AGT→AAT)	dnaX →	DNA polymerase III/DNA elongation factor III, tau and gamma subunits
RA	500,613	G→T	5.3%	G82C (GGT→TGT)	ushA →	bifunctional UDP‑sugar hydrolase/5'‑nucleotidase
RA	509,737	G→A	72.1%	E97K (GAG→AAG)	cueR →	copper‑responsive regulon transcriptional regulator
RA	511,619	A→T	14.4%	Q82L (CAA→CTA)	fetA →	iron exporter, ATP‑binding subunit, ABC transporter FetAB subunit; peroxide resistance protein
RA	512,167	G→T	42.2%	A43A (GCG→GCT)	fetB →	iron exporter permease subunit, ABC transporter FetAB; peroxide resistance protein
RA	521,011	G→T	52.9%	E765D (GAG→GAT)	rhsD →	Rhs family putative polymorphic toxin
RA	523,413	G→T	5.4%	pseudogene (6/708 nt)	rhsH →	pseudogene, Rhs familly protein
RA	524,334:1	+T	100%	pseudogene (239/491 nt)	ybbD →	pseudogene
RA	525,631	C→A	11.2%	R351L (CGC→CTC)	mnmH ←	tRNA 2‑selenouridine synthase, selenophosphate‑dependent
RA	527,186	T→A	9.4%	L164F (TTA→TTT)	allS ←	allD operon transcriptional activator
RA	530,466	C→A	93.6%	F365L (TTC→TTA)	gcl →	glyoxylate carboligase
RA	531,155	G→A	42.1%	intergenic (+2/‑11)	gcl → / → hyi	glyoxylate carboligase/hydroxypyruvate isomerase
RA	531,667	G→T	6.6%	V168F (GTT→TTT)	hyi →	hydroxypyruvate isomerase
RA	531,748	C→A	7.5%	Q195K (CAG→AAG)	hyi →	hydroxypyruvate isomerase
RA	542,200	Δ1 bp	92.7%	coding (65/1668 nt)	fdrA →	putative NAD(P)‑binding acyl‑CoA synthetase
RA	545,542	G→T	6.9%	D154Y (GAC→TAC)	ylbF →	putative anaerobic allantoin catabolic oxamate carbamoyltransferase; DUF2877 family protein
RA	546,491	G→T	88.0%	V199V (GTG→GTT)	ybcF →	putative carbonate kinase
RA	549,397	G→T	94.9%	intergenic (‑1/+2)	lpxH ← / ← ppiB	UDP‑2,3‑diacylglucosamine pyrophosphohydrolase/peptidyl‑prolyl cis‑trans isomerase B (rotamase B)
RA	552,831	A→T	10.7%	F123I (TTC→ATC)	folD ←	bifunctional 5,10‑methylene‑tetrahydrofolate dehydrogenase/ 5,10‑methylene‑tetrahydrofolate cyclohydrolase
RA	555,658	C→T	6.4%	P169L (CCG→CTG)	sfmD →	putative outer membrane export usher protein
RA	557,303	A→T	9.6%	E717D (GAA→GAT)	sfmD →	putative outer membrane export usher protein
RA	557,592	G→T	70.8%	D814Y (GAC→TAC)	sfmD →	putative outer membrane export usher protein
RA	557,784	G→T	50.6%	intergenic (+28/‑8)	sfmD → / → sfmH	putative outer membrane export usher protein/FimA homolog
RA	557,887	A→T	9.4%	S32S (TCA→TCT)	sfmH →	FimA homolog
RA	560,498	A→T	9.4%	F313I (TTC→ATC)	intD ←	DLP12 prophage; putative phage integrase
RA	560,919	G→T	7.8%	V172V (GTC→GTA)	intD ←	DLP12 prophage; putative phage integrase
RA	561,198	A→C	9.3%	D79E (GAT→GAG)	intD ←	DLP12 prophage; putative phage integrase
RA	565,131	G→A	36.7%	G258G (GGG→GGA)	ybcK →	DLP12 prophage; putative recombinase
RA	566,230	C→T	7.4%	intergenic (+346/‑119)	ybcK → / → ybcL	DLP12 prophage; putative recombinase/inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
RA	566,305	G→A	10.6%	intergenic (+421/‑44)	ybcK → / → ybcL	DLP12 prophage; putative recombinase/inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
RA	569,775	G→A	40.5%	V122I (GTT→ATT)	quuD →	DLP12 prophage; putative antitermination protein
RA	576,998	G→T	94.5%	pseudogene (189/309 nt)	aaaD →	pseudogene; DLP12 prophage; tail fiber assembly protein family;Phage or Prophage Related
RA	580,148	C→T	9.6%	K314K (AAG→AAA)	ompT ←	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
RA	580,550	G→T	5.9%	I180I (ATC→ATA)	ompT ←	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
RA	581,203	A→T	93.8%	intergenic (‑114/‑310)	ompT ← / → pauD	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)/tRNA‑OTHER
RA	583,341	T→G	92.9%	S33R (AGT→CGT)	ybcH ←	PRK09936 family protein
RA	593,746	G→T	11.0%	R271L (CGA→CTA)	cusB →	copper/silver efflux system, membrane fusion protein
RA	598,081	G→T	7.7%	G223C (GGC→TGC)	pheP →	phenylalanine transporter
RA	603,207	G→T	56.6%	noncoding (18/59 nt)	sokE →	sRNA at remnant mokE/hokE locus
RA	604,718	G→T	8.0%	intergenic (+85/+197)	insL1 → / ← entD	IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex
RA	607,931	G→A	92.2%	S7F (TCC→TTC)	fepA ←	iron‑enterobactin outer membrane transporter
RA	611,240	G→T	11.9%	R543L (CGC→CTC)	entF →	enterobactin synthase multienzyme complex component, ATP‑dependent
RA	613,755	G→T	42.0%	D16Y (GAT→TAT)	fepE →	regulator of length of O‑antigen component of lipopolysaccharide chains
RA	614,511	G→T	8.8%	D268Y (GAT→TAT)	fepE →	regulator of length of O‑antigen component of lipopolysaccharide chains
RA	616,411	C→A	5.9%	A78A (GCG→GCT)	fepG ←	iron‑enterobactin transporter subunit
RA	617,263	G→T	10.7%	A128E (GCG→GAG)	fepD ←	iron‑enterobactin transporter subunit
RA	619,048	C→A	74.6%	A307S (GCC→TCC)	fepB ←	iron‑enterobactin transporter subunit
RA	623,935	C→A	6.9%	I262I (ATC→ATA)	entB →	isochorismatase
RA	625,364	G→T	100%	G5G (GGG→GGT)	cstA →	carbon starvation protein involved in peptide utilization; APC peptide transporter family protein
RA	629,276	A→T	43.2%	K79* (AAA→TAA)	ybdL →	methionine aminotransferase, PLP‑dependent
RA	631,999	C→A	5.8%	P9P (CCG→CCT)	ybdN ←	PAPS reductase‑like domain protein
RA	638,755	G→T	7.8%	V404V (GTG→GTT)	ybdR →	putative Zn‑dependent NAD(P)‑binding oxidoreductase
RA	639,231	G→A	93.6%	L65F (CTT→TTT)	rnk ←	regulator of nucleoside diphosphate kinase
RA	647,234	C→T	59.4%	E27K (GAA→AAA)	citC ←	[citrate [pro‑3S]‑lyase] ligase
RA	647,422	G→T	94.7%	intergenic (‑110/‑269)	citC ← / → citA	[citrate [pro‑3S]‑lyase] ligase/sensory histidine kinase in two‑component regulatory system with CitB
RA	647,509	T→C	93.4%	intergenic (‑197/‑182)	citC ← / → citA	[citrate [pro‑3S]‑lyase] ligase/sensory histidine kinase in two‑component regulatory system with CitB
RA	648,056	C→A	100%	F122L (TTC→TTA)	citA →	sensory histidine kinase in two‑component regulatory system with CitB
RA	648,368	G→T	7.6%	A226A (GCG→GCT)	citA →	sensory histidine kinase in two‑component regulatory system with CitB
RA	651,654	A→G	9.0%	intergenic (‑230/‑359)	dcuC ← / → pagP	anaerobic C4‑dicarboxylate transport/phospholipid:lipid A palmitoyltransferase
RA	652,465	G→T	6.3%	L151L (CTG→CTT)	pagP →	phospholipid:lipid A palmitoyltransferase
RA	652,865	Δ1 bp	94.2%	coding (118/210 nt)	cspE →	constitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein
RA	654,192	T→A	5.7%	pseudogene (512/594 nt)	ybeM →	pseudogene, C‑N hydrolase superfamily homology;putative enzyme; Not classified; putative amidase
RA	662,108	A→T	86.6%	V522V (GTT→GTA)	mrdA ←	transpeptidase involved in peptidoglycan synthesis (penicillin‑binding protein 2)
RA	662,631	C→A	92.1%	R348L (CGC→CTC)	mrdA ←	transpeptidase involved in peptidoglycan synthesis (penicillin‑binding protein 2)
RA	664,243	C→A	19.7%	D84Y (GAT→TAT)	rsfS ←	ribosomal silencing factor
RA	666,998	G→T	11.6%	L22I (CTT→ATT)	holA ←	DNA polymerase III, delta subunit
RA	667,348	G→T	76.0%	Q99K (CAG→AAG)	lptE ←	LPS assembly OM complex LptDE, lipoprotein component
RA	668,230	C→A	16.9%	L670L (CTG→CTT)	leuS ←	leucyl‑tRNA synthetase
RA	672,142	T→A	67.7%	intergenic (‑139/‑25)	ybeQ ← / → ybeR	Sel1 family TPR‑like repeat protein/uncharacterized protein
RA	690,099	G→T	6.0%	P105T (CCG→ACG)	miaB ←	tRNA‑i(6)A37 methylthiotransferase
RA	692,868	G→T	6.9%	intergenic (‑279/+101)	metT ← / ← asnB	tRNA‑Met/asparagine synthetase B
RA	693,739	G→T	66.4%	H299N (CAC→AAC)	asnB ←	asparagine synthetase B
RA	695,910	G→T	7.4%	R381S (CGC→AGC)	nagC ←	N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor
RA	700,745	T→A	6.8%	V449E (GTG→GAG)	nagE →	fused N‑acetyl glucosamine specific PTS enzyme: IIC, IIB, and IIA components
RA	705,588	C→A	100%	intergenic (+16/+68)	chiQ → / ← fur	chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor
RA	706,097	A→C	73.4%	T2T (ACT→ACG)  *29G (TGA→GGA)	fur ← uof ←	ferric iron uptake regulon transcriptional repressor; autorepressor ryhB‑regulated fur leader peptide
RA	706,185	A→G	7.6%	intergenic (‑4/+206)	uof ← / ← fldA	ryhB‑regulated fur leader peptide/flavodoxin 1
RA	706,479	C→A	51.7%	R148L (CGT→CTT)	fldA ←	flavodoxin 1
RA	715,310	T→A	5.7%	N203Y (AAC→TAC)	speF ←	ornithine decarboxylase isozyme, inducible
RA	716,392	G→A	5.5%	intergenic (+96/+120)	ybfK → / ← kdpE	uncharacterized protein/response regulator in two‑component regulatory system with KdpD
RA	721,412	T→A	6.1%	N361Y (AAC→TAC)	kdpB ←	potassium translocating ATPase, subunit B
RA	723,846	A→C	13.5%	W115G (TGG→GGG)	kdpA ←	potassium translocating ATPase, subunit A
RA	724,813	A→T	100%	intergenic (+17/‑226)	ybfA → / → rhsC	DUF2517 family protein/Rhs family putative polymorphic toxin
RA	725,650	G→T	6.2%	P204P (CCG→CCT)	rhsC →	Rhs family putative polymorphic toxin
RA	729,149	G→A	6.6%	D1371N (GAT→AAT)	rhsC →	Rhs family putative polymorphic toxin
RA	729,456	G→A	64.6%	R75R (AGG→AGA)	ybfB →	putative membrane protein
RA	729,960	G→T	5.4%	pseudogene (372/1521 nt)	rhsO →	pseudogene, Rhs family protein
RA	731,397	G→T	7.0%	A98S (GCC→TCC)	ybfC →	putative periplasmic protein
RA	732,416	G→A	5.2%	pseudogene (136/1137 nt)	ybfL →	pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein
RA	732,494	G→T	76.5%	pseudogene (214/1137 nt)	ybfL →	pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein
RA	734,498	C→A	7.7%	I14I (ATC→ATA)	ybgA →	DUF1722 family protein
RA	735,817	G→T	18.8%	L285L (CTG→CTT)	phr →	deoxyribodipyrimidine photolyase, FAD‑binding
RA	737,846	G→T	8.4%	S56* (TCG→TAG)	dtpD ←	dipeptide and tripeptide permease D
RA	742,840	G→T	6.6%	A129E (GCG→GAG)	abrB ←	regulator of aidB expression; inner membrane protein
RA	743,278	G→A	10.7%	intergenic (‑53/+99)	abrB ← / ← ybgO	regulator of aidB expression; inner membrane protein/putative fimbrial protein
RA	744,267	C→T	9.4%	E58K (GAA→AAA)	ybgO ←	putative fimbrial protein
RA	745,420	C→A	44.0%	G736C (GGT→TGT)	ybgQ ←	putative outer membrane protein
RA	748,382	C→A	6.3%	intergenic (‑131/+259)	ybgD ← / ← gltA	putative fimbrial‑like adhesin protein/citrate synthase
RA	750,112	A→T	10.7%	intergenic (‑188/‑521)	gltA ← / → sdhC	citrate synthase/succinate dehydrogenase, membrane subunit, binds cytochrome b556
RA	751,315	A→T	13.8%	A100A (GCA→GCT)	sdhD →	succinate dehydrogenase, membrane subunit, binds cytochrome b556
RA	753,205	C→A	5.6%	Q21K (CAG→AAG)	sdhB →	succinate dehydrogenase, FeS subunit
RA	754,572	G→T	91.0%	E137D (GAG→GAT)	sucA →	2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding
RA	757,353	A→T	8.0%	N126Y (AAT→TAT)	sucB →	dihydrolipoyltranssuccinase
RA	759,000	C→A	93.6%	F177L (TTC→TTA)	sucC →	succinyl‑CoA synthetase, beta subunit
RA	768,068	G→T	5.3%	P385P (CCG→CCT)	cydA →	cytochrome d terminal oxidase, subunit I
RA	769,421	C→A	9.7%	I308I (ATC→ATA)	cydB →	cytochrome d terminal oxidase, subunit II
RA	779,699	G→T	7.5%	S194* (TCG→TAG)	zitB ←	zinc efflux system
RA	784,901	C→A	6.1%	A179S (GCG→TCG)	galK ←	galactokinase
RA	788,902	G→T	91.7%	R115S (CGT→AGT)	modF ←	fused molybdate transporter subunits of ABC superfamily: ATP‑binding components
RA	789,044	G→T	11.5%	I67I (ATC→ATA)	modF ←	fused molybdate transporter subunits of ABC superfamily: ATP‑binding components
RA	792,351	G→T	13.3%	A114A (GCG→GCT)	modC →	molybdate transporter subunit
RA	796,379	A→T	7.3%	P55P (CCA→CCT)	ybhH →	putative PrpF family isomerase
RA	800,488	G→T	94.3%	V510V (GTG→GTT)	ybhJ →	putative hydratase
RA	800,779	G→T	93.8%	E607D (GAG→GAT)	ybhJ →	putative hydratase
RA	813,435	C→T	10.1%	F312F (TTC→TTT)	moaA →	molybdopterin biosynthesis protein A
RA	815,168	C→A	47.3%	R140R (CGG→AGG)	moaE →	molybdopterin synthase, large subunit
RA	816,152	C→A	10.6%	intergenic (+108/‑97)	ybhL → / → ybhM	UPF0005 family inner membrane protein/UPF0005 family inner membrane protein
RA	816,292	A→T	14.6%	H15L (CAC→CTC)	ybhM →	UPF0005 family inner membrane protein
RA	818,362	G→T	6.5%	G278G (GGC→GGA)	clsB ←	cardiolipin synthase 2
RA	828,374	G→T	100%	V11V (GTC→GTA)	ybiA ←	DUF1768 family protein
RA	828,819	G→T	12.4%	P98P (CCG→CCT)	dinG →	ATP‑dependent DNA helicase
RA	832,445	G→T	89.2%	P213P (CCG→CCT)	ybiC →	putative dehydrogenase
RA	839,397	G→T	6.4%	R514S (CGT→AGT)	ybiO ←	mechanosensitive channel protein, intermediate conductance
RA	839,623	C→A	9.3%	A438A (GCG→GCT)	ybiO ←	mechanosensitive channel protein, intermediate conductance
RA	839,791	C→A	12.5%	A382A (GCG→GCT)	ybiO ←	mechanosensitive channel protein, intermediate conductance
RA	843,299	C→A	92.0%	W54C (TGG→TGT)	glnH ←	glutamine transporter subunit
RA	851,782	A→T	13.0%	K122* (AAA→TAA)	ybiT →	putative transporter subunit of ABC superfamily: ATP‑binding component
RA	853,014	G→T	9.6%	intergenic (+3/+238)	ybiT → / ← ybiU	putative transporter subunit of ABC superfamily: ATP‑binding component/DUF1479 family protein
RA	858,992	C→T	54.6%	intergenic (‑25/‑106)	ybiY ← / → fsaA	putative pyruvate formate lyase activating enzyme/fructose‑6‑phosphate aldolase 1
RA	861,323	T→A	6.2%	S166S (TCA→TCT)	moeA ←	molybdopterin molybdenumtransferase; molybdopterin biosynthesis protein
RA	862,017	G→T	9.6%	intergenic (‑197/‑7)	moeA ← / → iaaA	molybdopterin molybdenumtransferase; molybdopterin biosynthesis protein/Isoaspartyl peptidase
RA	863,481	T→G	16.3%	L169R (CTC→CGC)	gsiA →	glutathione transporter ATP‑binding protein, ABC superfamily
RA	863,745	T→A	13.8%	F257Y (TTT→TAT)	gsiA →	glutathione transporter ATP‑binding protein, ABC superfamily
RA	868,473	A→C	7.9%	I13I (ATA→ATC)	yliE →	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	868,897	G→T	13.4%	D155Y (GAC→TAC)	yliE →	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	874,246	G→T	5.5%	A17S (GCT→TCT)	yliI →	soluble aldose sugar dehydrogenase
RA	876,447	G→A	91.7%	D89N (GAT→AAT)	dacC →	D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 6a)
RA	876,738	G→T	54.4%	D186Y (GAT→TAT)	dacC →	D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 6a)
RA	877,482	C→A	9.8%	D237Y (GAT→TAT)	deoR ←	deoxyribose‑5‑phosphate‑inducible deoxyribose operon transcriptional repressor; repressor of nupG and tsx
RA	879,085	G→T	100%	intergenic (‑241/‑44)	ybjG ← / → mdfA	undecaprenyl pyrophosphate phosphatase/multidrug efflux system protein
RA	884,152	G→T	5.2%	S375* (TCG→TAG)	ybjL ←	putative transporter
RA	888,044	G→T	9.6%	G208C (GGC→TGC)	rimK →	ribosomal protein S6 modification protein
RA	889,044	G→T	18.0%	intergenic (+155/‑196)	ybjN → / → potF	negative regulator of motility; multicopy suppressor of coaA(Ts)/putrescine transporter subunit: periplasmic‑binding component of ABC superfamily
RA	894,579	G→T	5.1%	P202P (CCG→CCT)	rlmC →	23S rRNA m(5)U747 methyltransferase, SAM‑dependent
RA	896,095	C→A	37.0%	intergenic (‑64/+227)	artJ ← / ← artM	arginine binding protein, periplasmic/arginine transporter subunit
RA	899,961	T→A	6.7%	intergenic (‑38/‑88)	ybjP ← / → ybjQ	lipoprotein/UPF0145 family protein
RA	907,596	G→T	11.3%	P4Q (CCA→CAA)	hcr ←	HCP oxidoreductase, NADH‑dependent
RA	920,396	G→T	6.1%	A559A (GCG→GCT)	clpA →	ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity
RA	923,560	G→T	10.1%	N364K (AAC→AAA)	cydC ←	fused glutathione, cysteine exporter subunits of ABC superfamily: membrane component/ATP‑binding component
RA	925,160	G→T	87.5%	S420* (TCA→TAA)	cydD ←	fused glutathione, cysteine exporter subunits of ABC superfamily: membrane component/ATP‑binding component
RA	925,355	A→T	10.4%	L355Q (CTG→CAG)	cydD ←	fused glutathione, cysteine exporter subunits of ABC superfamily: membrane component/ATP‑binding component
RA	925,957	A→T	8.5%	I154I (ATT→ATA)	cydD ←	fused glutathione, cysteine exporter subunits of ABC superfamily: membrane component/ATP‑binding component
RA	943,573	G→T	92.0%	A297S (GCC→TCC)	ycaM →	putative transporter
RA	955,568	A→T	58.8%	intergenic (+17/‑152)	aroA → / → ycaL	5‑enolpyruvylshikimate‑3‑phosphate synthetase/putative peptidase‑related chaperone
RA	958,417	A→T	7.7%	N323Y (AAC→TAC)	rpsA →	30S ribosomal subunit protein S1
RA	961,339	C→A	10.2%	L522I (CTC→ATC)	ycaI →	ComEC family inner membrane protein
RA	963,256	G→A	8.0%	D394N (GAT→AAT)	msbA →	fused lipid transporter subunits of ABC superfamily: membrane component/ATP‑binding component
RA	968,415	G→T	100%	S148* (TCG→TAG)	ycbC ←	DUF218 superfamily protein
RA	969,133	T→A	9.8%	R47R (CGT→CGA)	smtA →	putative S‑adenosyl‑L‑methionine‑dependent methyltransferase
RA	976,873	C→A	13.0%	A124E (GCG→GAG)	ldtD →	murein L,D‑transpeptidase
RA	979,844	G→T	12.6%	intergenic (+91/+131)	ycbL → / ← aspC	putative metal‑binding enzyme/aspartate aminotransferase, PLP‑dependent
RA	985,485	G→T	11.2%	R110S (CGT→AGT)	pncB ←	nicotinate phosphoribosyltransferase
RA	987,229	C→A	10.5%	G384G (GGC→GGA)	pepN →	aminopeptidase N
RA	991,460	A→T	9.7%	L314Q (CTG→CAG)	ssuA ←	aliphatic sulfonate binding protein, SsuABC ABC transporter
RA	992,050	T→A	11.0%	E117D (GAA→GAT)	ssuA ←	aliphatic sulfonate binding protein, SsuABC ABC transporter
RA	997,965	G→T	75.2%	D235Y (GAT→TAT)	elfG →	putative fimbrial‑like adhesin protein
RA	1,003,307	C→A	6.9%	S3Y (TCT→TAT)	rlmL →	fused 23S rRNA m(2)G2445 and m(7)G2069 methyltransferase, SAM‑dependent
RA	1,016,392	G→A	12.2%	intergenic (‑17/‑202)	sulA ← / → sxy	SOS cell division inhibitor/CRP‑S‑dependent promoter expression factor
RA	1,020,480	A→C	5.2%	Y185S (TAT→TCT)	helD →	DNA helicase IV
RA	1,024,703	G→T	70.0%	G241G (GGC→GGA)	rlmI ←	23S rRNA m(5)C1962 methyltransferase, SAM‑dependent
RA	1,037,576	G→T	5.0%	G697G (GGC→GGA)	etk ←	tyrosine‑protein kinase, role in O‑antigen capsule formation
RA	1,040,472	A→T	11.3%	V263E (GTG→GAG)	gfcE ←	putative O‑antigen capsule outer membrane auxillary protein export channel
RA	1,042,059	A→T	9.1%	L448Q (CTG→CAG)	gfcD ←	putative O‑antigen capsule production periplasmic protein
RA	1,048,928	C→A	91.1%	E903* (GAA→TAA)	torS ←	hybrid sensory histidine kinase in two‑component regulatory system with TorR
RA	1,049,016	G→A	11.2%	I873I (ATC→ATT)	torS ←	hybrid sensory histidine kinase in two‑component regulatory system with TorR
RA	1,049,407	G→T	90.6%	T743K (ACG→AAG)	torS ←	hybrid sensory histidine kinase in two‑component regulatory system with TorR
RA	1,050,071	G→T	8.4%	R522S (CGC→AGC)	torS ←	hybrid sensory histidine kinase in two‑component regulatory system with TorR
RA	1,051,112	C→A	9.0%	D175Y (GAT→TAT)	torS ←	hybrid sensory histidine kinase in two‑component regulatory system with TorR
RA	1,058,272	A→C	11.8%	C14G (TGC→GGC)	cbpM ←	modulator of CbpA co‑chaperone
RA	1,060,203	G→A	9.7%	V238I (GTT→ATT)	yccE →	uncharacterized protein
RA	1,071,488	G→T	5.1%	R951S (CGC→AGC)	putA ←	fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase
RA	1,073,243	C→A	15.0%	G366C (GGT→TGT)	putA ←	fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase
RA	1,077,911	A→C	91.3%	K71N (AAA→AAC)	efeO →	inactive ferrous ion transporter EfeUOB
RA	1,080,567	T→A	6.1%	C40* (TGT→TGA)	phoH →	ATP‑binding protein; putative PhoH family P‑loop ATPase
RA	1,083,443	G→T	72.7%	S624* (TCG→TAG)	pgaB ←	poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine (PGA) N‑deacetylase outer membrane export lipoprotein
RA	1,084,103	A→T	85.9%	L404* (TTA→TAA)	pgaB ←	poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine (PGA) N‑deacetylase outer membrane export lipoprotein
RA	1,084,932	G→T	5.1%	L128I (CTT→ATT)	pgaB ←	poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine (PGA) N‑deacetylase outer membrane export lipoprotein
RA	1,087,761	G→T	10.3%	intergenic (‑16/‑571)	pgaA ← / → ycdT	biofilm adhesin polysaccharide PGA secretin; OM porin; poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine export protein/diguanylate cyclase, membrane‑anchored
RA	1,088,734	G→T	37.3%	V135F (GTT→TTT)	ycdT →	diguanylate cyclase, membrane‑anchored
RA	1,096,523	G→T	9.3%	F206L (TTC→TTA)	csgG ←	curli production assembly/transport outer membrane lipoprotein
RA	1,099,378	A→C	40.9%	intergenic (‑726/‑29)	csgD ← / → csgB	csgBAC operon transcriptional regulator/curlin nucleator protein, minor subunit in curli complex
RA	1,101,720	G→T	5.3%	A149S (GCT→TCT)	ymdB →	O‑acetyl‑ADP‑ribose deacetylase; RNase III inhibitor during cold shock; putative cardiolipin synthase C regulatory subunit
RA	1,116,601	T→A	6.5%	intergenic (‑190/+97)	bssS ← / ← dinI	biofilm regulator/DNA damage‑inducible protein I
RA	1,116,964	A→G	92.2%	intergenic (‑21/+53)	dinI ← / ← pyrC	DNA damage‑inducible protein I/dihydro‑orotase
RA	1,121,219	G→T	8.7%	E68* (GAA→TAA)	rimJ →	ribosomal‑protein‑S5‑alanine N‑acetyltransferase
RA	1,132,494	T→A	16.8%	I255I (ATT→ATA)	flgI →	putative flagellar basal body protein
RA	1,147,164	G→A	49.0%	D32N (GAC→AAC)	acpP →	acyl carrier protein (ACP)
RA	1,148,953	G→A	8.2%	E66E (GAG→GAA)	pabC →	4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex
RA	1,150,005	G→T	5.9%	A146A (GCG→GCT)	yceG →	septation protein, ampicillin sensitivity
RA	1,150,407	G→T	44.3%	P280P (CCG→CCT)	yceG →	septation protein, ampicillin sensitivity
RA	1,151,750	G→T	85.6%	R178L (CGC→CTC)	holB →	DNA polymerase III, delta prime subunit
RA	1,152,278	G→T	91.2%	E16* (GAA→TAA)	ycfH →	putative DNase
RA	1,153,110	T→A	44.5%	intergenic (+80/‑215)	ycfH → / → ptsG	putative DNase/fused glucose‑specific PTS enzymes: IIB component/IIC component
RA	1,154,905	G→T	46.9%	F701L (TTC→TTA)	fhuE ←	ferric‑rhodotorulic acid outer membrane transporter
RA	1,164,454	G→A	5.6%	intergenic (‑166/‑75)	ycfQ ← / → bhsA	repressor for bhsA(ycfR)/biofilm, cell surface and signaling protein
RA	1,165,425	C→A	10.5%	D136Y (GAC→TAC)	ldtC ←	L,D‑transpeptidase linking Lpp to murein
RA	1,167,371	A→T	5.7%	S684T (TCC→ACC)	mfd ←	transcription‑repair coupling factor
RA	1,172,212	C→A	46.4%	S46S (TCC→TCA)	lolD →	outer membrane‑specific lipoprotein transporter subunit
RA	1,175,193	A→T	17.0%	E36V (GAA→GTA)	cobB →	deacetylase of acs and cheY, chemotaxis regulator
RA	1,191,676	C→T	65.9%	H366H (CAC→CAT)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,688	C→T	63.5%	T370T (ACC→ACT)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,701	T→C	55.9%	L375L (TTA→CTA) ‡	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,703	A→G	57.1%	L375L (TTA→TTG) ‡	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,733	C→T	39.3%	N385N (AAC→AAT)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,736	G→C	39.3%	A386A (GCG→GCC)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,739	A→G	35.5%	K387K (AAA→AAG)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,748	C→T	29.5%	T390T (ACC→ACT)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,760	G→A	12.0%	E394E (GAG→GAA)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,193,516	T→G	27.0%	N60H (AAT→CAT)	ymfE ←	e14 prophage; putative inner membrane protein
RA	1,193,873	G→T	62.3%	intergenic (‑180/‑278)	ymfE ← / → lit	e14 prophage; putative inner membrane protein/e14 prophage; cell death peptidase, inhibitor of T4 late gene expression
RA	1,194,194	C→A	8.0%	S15* (TCA→TAA)	lit →	e14 prophage; cell death peptidase, inhibitor of T4 late gene expression
RA	1,197,664	G→A	6.0%	intergenic (‑124/+51)	ymfJ ← / ← cohE	e14 prophage; uncharacterized protein/e14 prophage; repressor protein phage e14
RA	1,198,429	C→T	14.4%	intergenic (‑40/‑51)	cohE ← / → croE	e14 prophage; repressor protein phage e14/e14 prophage; putative DNA‑binding transcriptional regulator
RA	1,200,194	G→A	5.3%	pseudogene (335/1134 nt)	aaaE →	pseudogene, phage terminase protein A family, e14 prophage;Phage or Prophage Related
RA	1,204,284	C→A	45.2%	D98Y (GAT→TAT)	tfaE ←	e14 prophage; putative tail fiber assembly protein
RA	1,204,620	C→A	18.2%	pseudogene (456/501 nt)	stfE ←	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
RA	1,206,749	A→T	29.4%	intergenic (+114/‑120)	mcrA → / → icdC	putative 5‑methylcytosine/5‑hydroxymethylcytosine‑specific restriction nuclease; 5‑methylcytosine DNA binding protein; e14 prophage gene/pseudogene, isocitrate dehydrogenase C‑terminal gene fragment; idcC' is a 54 codon 3' gene fragment created during e14 prophage insertion
RA	1,211,169	C→A	92.3%	intergenic (‑238/‑76)	bluF ← / → ycgZ	anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; has c‑di‑GMP phosphodiesterase‑like EAL domain, but does not degrade c‑di‑GMP/RcsB connector protein for regulation of biofilm and acid‑resistance
RA	1,219,533	A→G	93.2%	intergenic (+170/+202)	ycgI → / ← minE	pseudogene/cell division topological specificity factor
RA	1,220,996	G→T	100%	R181R (CGG→AGG)	minC ←	cell division inhibitor
RA	1,224,292	G→A	93.1%	D8N (GAT→AAT)	ycgN →	UPF0153 family cysteine cluster protein
RA	1,226,292	T→A	100%	C24S (TGT→AGT)	umuD →	DNA polymerase V, subunit D
RA	1,227,613	C→A	18.5%	N324K (AAC→AAA)	umuC →	DNA polymerase V, subunit C
RA	1,228,033	C→A	42.9%	A152S (GCT→TCT)	dsbB ←	oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I
RA	1,228,591	G→T	94.1%	intergenic (‑105/+41)	dsbB ← / ← nhaB	oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I/sodium:proton antiporter
RA	1,232,912	G→T	5.4%	intergenic (‑215/‑115)	ycgB ← / → dadA	SpoVR family stationary phase protein/D‑amino acid dehydrogenase
RA	1,238,721	C→A	5.8%	A29E (GCG→GAG)	emtA →	lytic murein endotransglycosylase E
RA	1,246,435	T→A	44.0%	intergenic (‑141/‑87)	dhaK ← / → dhaR	dihydroxyacetone kinase, PTS‑dependent, dihydroxyacetone‑binding subunit/dhaKLM operon transcription activator
RA	1,251,120	T→A	15.0%	T97S (ACC→TCC)	ycgV ←	putative adhesin
RA	1,251,539	C→A	6.0%	intergenic (‑131/+638)	ycgV ← / ← ychF	putative adhesin/catalase inhibitor protein; ATPase, K+‑dependent, ribosome‑associated
RA	1,257,465	A→T	11.8%	intergenic (‑134/+17)	prs ← / ← ispE	phosphoribosylpyrophosphate synthase/4‑diphosphocytidyl‑2‑C‑methylerythritol kinase
RA	1,266,292	G→T	7.5%	I338I (ATC→ATA)	chaA ←	calcium/sodium:proton antiporter
RA	1,266,853	C→A	5.7%	A151A (GCG→GCT)	chaA ←	calcium/sodium:proton antiporter
RA	1,276,723	C→A	55.3%	T468T (ACC→ACA)	narG →	nitrate reductase 1, alpha subunit
RA	1,277,786	G→A	93.3%	D823N (GAC→AAC)	narG →	nitrate reductase 1, alpha subunit
RA	1,280,699	G→T	15.7%	L35L (CTG→CTT)	narJ →	molybdenum‑cofactor‑assembly chaperone subunit (delta subunit) of nitrate reductase 1
RA	1,284,124	C→A	49.0%	intergenic (‑44/+6)	purU ← / ← ychJ	formyltetrahydrofolate hydrolase/UPF0225 family protein
RA	1,287,881	C→A	8.6%	intergenic (+60/+84)	galU → / ← hns	glucose‑1‑phosphate uridylyltransferase/global DNA‑binding transcriptional dual regulator H‑NS
RA	1,288,669	A→T	64.7%	intergenic (‑291/‑314)	hns ← / → tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
RA	1,288,707	G→T	5.9%	intergenic (‑329/‑276)	hns ← / → tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
RA	1,293,293	A→T	11.7%	F95L (TTT→TTA)	adhE ←	fused acetaldehyde‑CoA dehydrogenase/iron‑dependent alcohol dehydrogenase/pyruvate‑formate lyase deactivase
RA	1,299,742	C→A	40.0%	A244A (GCC→GCA)	oppD →	oligopeptide transporter subunit
RA	1,301,604	A→T	7.3%	I433I (ATT→ATA)	clsA ←	cardiolipin synthase 1
RA	1,316,754	G→A	9.2%	F150F (TTC→TTT)	trpE ←	component I of anthranilate synthase
RA	1,322,140	T→A	91.0%	T159S (ACG→TCG)	btuR ←	cob(I)yrinic acid a,c‑diamide adenosyltransferase
RA	1,330,955	G→T	63.3%	D290Y (GAT→TAT)	acnA →	aconitate hydratase 1
RA	1,334,048	G→T	12.0%	E154D (GAG→GAT)	pgpB →	phosphatidylglycerophosphatase B
RA	1,337,533	G→T	87.4%	A18E (GCA→GAA)	osmB ←	lipoprotein
RA	1,340,901	A→T	11.4%	S33S (TCT→TCA)	gmr ←	cyclic‑di‑GMP phosphodiesterase; csgD regulator; modulator of Rnase II stability
RA	1,341,061	C→A	48.5%	Y3* (TAC→TAA)	ymiB →	uncharacterized protein
RA	1,343,867	G→A	7.9%	I166I (ATC→ATT)	yciW ←	putative oxidoreductase
RA	1,344,412	G→A	6.2%	intergenic (‑48/+96)	yciW ← / ← fabI	putative oxidoreductase/enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent
RA	1,351,351	G→T	5.8%	S6* (TCG→TAG)	sapA ←	antimicrobial peptide transport ABC transporter periplasmic binding protein
RA	1,351,378	G→A	5.3%	intergenic (‑11/+302)	sapA ← / ← ymjA	antimicrobial peptide transport ABC transporter periplasmic binding protein/DUF2543 family protein
RA	1,360,489	G→T	12.0%	C228F (TGC→TTC)	puuE →	4‑aminobutyrate aminotransferase, PLP‑dependent
RA	1,362,134	C→A	8.9%	A12A (GCG→GCT)	pspF ←	psp operon transcriptional activator
RA	1,365,283	G→T	92.4%	E271* (GAG→TAG)	ycjM →	alpha amylase catalytic domain family protein
RA	1,369,694	G→A	8.1%	D159N (GAT→AAT)	ycjQ →	putative Zn‑dependent NAD(P)‑binding oxidoreductase
JC JC	1,376,043	IS5 (–) +4 bp	100%	pseudogene (10‑13/126 nt)	ycjV →	pseudogene; putative ATP‑binding component of a transport system
RA	1,377,394	C→T	93.4%	A275A (GCG→GCA)	ycjW ←	LacI family putative transcriptional repressor
RA	1,379,274	G→T	5.0%	D301Y (GAT→TAT)	ycjX →	DUF463 family protein, putative P‑loop NTPase
RA	1,383,189	G→T	10.4%	M1M (ATG→ATT) †	ycjG →	L‑Ala‑D/L‑Glu epimerase
RA	1,386,008	G→T	91.5%	Q35K (CAG→AAG)	ycjY ←	S9 homolog non‑peptidase family protein
RA	1,387,818	C→A	6.2%	A112E (GCG→GAG)	mppA →	murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit
RA	1,388,406	G→T	94.2%	R308L (CGC→CTC)	mppA →	murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit
RA	1,417,454	C→A	10.7%	pseudogene (497/500 nt)	ydaW →	Rac prophage; pseudogene, DNA‑binding protein family;Phage or Prophage Related
RA	1,424,234	C→A	92.9%	S310* (TCA→TAA)	stfR →	Rac prophage; putative tail fiber protein
JC JC	1,428,894	IS2 (–) +5 bp	100%	intergenic (‑413/+317)	ynaE ← / ← ttcC	cold shock protein, Rac prophage/pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related
RA	1,439,430	C→A	6.5%	P708Q (CCG→CAG)	ydbH →	putative membrane‑anchored protein, function unknown
RA	1,439,518	C→A	100%	S737S (TCC→TCA)	ydbH →	putative membrane‑anchored protein, function unknown
RA	1,441,854	C→A	52.1%	R27S (CGT→AGT)	feaB →	phenylacetaldehyde dehydrogenase
RA	1,443,093	C→A	12.6%	L440I (CTC→ATC)	feaB →	phenylacetaldehyde dehydrogenase
RA	1,443,196	A→T	15.7%	Q474L (CAG→CTG)	feaB →	phenylacetaldehyde dehydrogenase
RA	1,444,573	T→A	7.0%	N345I (AAT→ATT)	tynA ←	tyramine oxidase, copper‑requiring
RA	1,444,739	G→A	12.1%	P290S (CCC→TCC)	tynA ←	tyramine oxidase, copper‑requiring
RA	1,445,781	G→T	57.0%	intergenic (‑175/+73)	tynA ← / ← paaZ	tyramine oxidase, copper‑requiring/fused oxepin‑CoA hydrolase/3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase
RA	1,448,131	G→A	49.1%	intergenic (‑232/‑53)	paaZ ← / → paaA	fused oxepin‑CoA hydrolase/3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase/ring 1,2‑phenylacetyl‑CoA epoxidase subunit
RA	1,448,418	C→T	41.9%	L79F (CTC→TTC)	paaA →	ring 1,2‑phenylacetyl‑CoA epoxidase subunit
RA	1,451,422	A→T	56.9%	T246S (ACG→TCG)	paaE →	ring 1,2‑phenylacetyl‑CoA epoxidase, NAD(P)H oxidoreductase component
RA	1,454,724	G→T	85.9%	G472C (GGT→TGT)	paaH →	3‑hydroxyadipyl‑CoA dehydrogenase, NAD+‑dependent
RA	1,460,752	C→T	7.3%	pseudogene (1104/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA	1,460,761	A→G	5.3%	pseudogene (1113/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA	1,460,896	C→T	5.6%	pseudogene (1248/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA	1,477,570	G→A	46.4%	D85N (GAC→AAC)	hrpA →	putative ATP‑dependent helicase
RA	1,483,460	G→T	10.3%	A324A (GCG→GCT)	aldA →	aldehyde dehydrogenase A, NAD‑linked
RA	1,488,630	C→A	13.0%	T233T (ACG→ACT)	ydcI ←	putative DNA‑binding transcriptional regulator
RA	1,489,197	C→T	52.3%	K44K (AAG→AAA)	ydcI ←	putative DNA‑binding transcriptional regulator
RA	1,498,013	C→A	5.9%	R14S (CGT→AGT)	insQ →	IS609 transposase B
RA	1,499,759	G→T	44.1%	V193V (GTC→GTA)	ydcO ←	BenE family inner membrane putative transporter
RA	1,519,349	T→A	100%	K297* (AAA→TAA)	ansP ←	L‑asparagine transporter
RA	1,519,458	C→A	6.4%	V260V (GTG→GTT)	ansP ←	L‑asparagine transporter
RA	1,521,126	G→A	8.4%	intergenic (+5/‑71)	yncG → / → yncH	glutathione S‑transferase homolog/IPR020099 family protein
RA	1,529,506	C→T	5.2%	G204S (GGC→AGC)	yddE ←	PhzC‑PhzF family protein
RA	1,546,535	C→A	7.2%	intergenic (+287/+120)	fdnI → / ← yddM	formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator
RA	1,548,144	G→T	100%	intergenic (‑49/+85)	adhP ← / ← maeA	ethanol‑active dehydrogenase/acetaldehyde‑active reductase/malate dehydrogenase, (decarboxylating, NAD‑requiring) (malic enzyme)
RA	1,552,629	C→A	77.7%	D216Y (GAT→TAT)	ddpD ←	D,D‑dipeptide permease system, ATP‑binding component
RA	1,560,523	C→A	8.8%	R292L (CGC→CTC)	dosC ←	diguanylate cyclase, cold‑ and stationary phase‑induced oxygen‑dependent biofilm regulator
RA	1,561,151	C→A	42.1%	D83Y (GAT→TAT)	dosC ←	diguanylate cyclase, cold‑ and stationary phase‑induced oxygen‑dependent biofilm regulator
RA	1,563,276	G→T	88.7%	H491N (CAC→AAC)	gadC ←	glutamate:gamma‑aminobutyric acid antiporter
RA	1,565,497	G→A	100%	S269L (TCG→TTG)	gadB ←	glutamate decarboxylase B, PLP‑dependent
RA	1,566,392	A→T	8.8%	intergenic (‑90/+272)	gadB ← / ← pqqL	glutamate decarboxylase B, PLP‑dependent/putative periplasmic M16 family zinc metalloendopeptidase
RA	1,575,339	G→T	93.7%	F481L (TTC→TTA)	ydeN ←	putative Ser‑type periplasmic non‑aryl sulfatase
RA	1,578,598	A→T	7.3%	Y716N (TAC→AAC)	ydeP ←	putative oxidoreductase
RA	1,586,871	G→T	5.6%	intergenic (‑172/+51)	hipB ← / ← yneO	antitoxin of HipAB toxin‑antitoxin system/pseudogene, AidA homolog
RA	1,591,894	C→A	5.5%	pseudogene (351/5323 nt)	yneO ←	pseudogene, AidA homolog
RA	1,593,189	T→G	5.5%	A426A (GCA→GCC)	lsrK ←	autoinducer‑2 (AI‑2) kinase
RA	1,602,131	G→T	15.5%	D177Y (GAT→TAT)	tam →	trans‑aconitate methyltransferase
RA	1,603,440	G→A	86.5%	intergenic (‑161/+46)	yneE ← / ← uxaB	bestrophin family putative inner membrane protein/altronate oxidoreductase, NAD‑dependent
RA	1,603,750	C→A	7.3%	L396F (TTG→TTT)	uxaB ←	altronate oxidoreductase, NAD‑dependent
RA	1,608,982	C→A	5.5%	intergenic (‑22/‑79)	sad ← / → yneJ	succinate semialdehyde dehydrogenase, NAD(P)+‑dependent/putative DNA‑binding transcriptional regulator
RA	1,610,766	C→T	42.9%	S249S (AGC→AGT)	yneK →	uncharacterized protein
RA	1,611,158	G→T	51.2%	intergenic (+23/‑127)	yneK → / → ydeA	uncharacterized protein/arabinose efflux transporter, arabinose‑inducible
RA	1,615,440	G→T	10.7%	intergenic (‑46/‑149)	eamA ← / → ydeE	cysteine and O‑acetyl‑L‑serine efflux system/putative transporter
RA	1,620,961	T→G	88.5%	Q226P (CAA→CCA)	dcp ←	dipeptidyl carboxypeptidase II
RA	1,623,050	G→T	6.6%	D148Y (GAC→TAC)	rspR →	transcriptional repressor for rspAB
RA	1,624,474	T→A	5.6%	T233S (ACG→TCG)	ydfI ←	putative NAD‑dependent D‑mannonate oxidoreductase
RA	1,625,116	T→A	6.0%	N19Y (AAC→TAC)	ydfI ←	putative NAD‑dependent D‑mannonate oxidoreductase
RA	1,628,207	G→A	90.8%	G110E (GGA→GAA)	pinQ →	Qin prophage; putative site‑specific recombinase
RA	1,629,460	T→G	10.2%	A215A (GCA→GCC)	stfQ ←	Qin prophage; putative side tail fiber assembly protein
RA	1,646,412	A→T	37.7%	pseudogene (605/1158 nt)	intQ →	pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related
RA	1,654,370	G→T	6.5%	R682L (CGT→CTT)	ynfE →	putative selenate reductase, periplasmic
RA	1,656,349	G→T	46.7%	D513Y (GAT→TAT)	ynfF →	S‑ and N‑oxide reductase, A subunit, periplasmic
RA	1,661,763	C→A	100%	P353P (CCG→CCT)	mlc ←	glucosamine anaerobic growth regulon transcriptional repressor; autorepressor
RA	1,670,193	G→T	9.7%	A142E (GCG→GAG)	pntB ←	pyridine nucleotide transhydrogenase, beta subunit
RA	1,677,054	G→T	12.1%	L213L (CTG→CTT)	rstA →	response regulator of RstAB two‑component system, low Mg‑responsive via PhoQP
RA	1,686,491	T→A	7.5%	A206A (GCA→GCT)	uidC ←	putative outer membrane porin for beta‑glucuronides porin protein
RA	1,689,180	T→G	62.1%	E383D (GAA→GAC)	uidA ←	beta‑D‑glucuronidase
RA	1,690,981	G→T	5.1%	A110E (GCG→GAG)	uidR ←	transcriptional repressor
RA	1,692,573	C→A	75.8%	D289Y (GAT→TAT)	malI ←	transcriptional repressor of Mal regulon
RA	1,696,612	A→T	94.1%	E41D (GAA→GAT)	add →	adenosine deaminase
RA	1,699,862	T→A	71.2%	L119* (TTG→TAG)	ydgK →	DUF2569 family inner membrane protein
RA	1,699,884	C→A	11.1%	T126T (ACC→ACA)	ydgK →	DUF2569 family inner membrane protein
RA	1,701,260	T→A	48.5%	S29T (TCC→ACC)	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,702,966	T→A	8.1%	R597R (CGT→CGA)	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,703,015	G→C	5.4%	E614Q (GAA→CAA)	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,703,071	A→T	8.1%	A632A (GCA→GCT)	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,706,716	C→T	9.6%	intergenic (+301/‑310)	nth → / → dtpA	DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A
RA	1,711,397	C→T	94.2%	R28Q (CGA→CAA)	tyrS ←	tyrosyl‑tRNA synthetase
RA	1,712,820	C→A	7.2%	G347V (GGA→GTA)	anmK ←	anhydro‑N‑acetylmuramic acid kinase
RA	1,721,600	G→T	7.8%	D229Y (GAT→TAT)	nemA →	chromate reductase, quinone reductase, FMN‑linked; N‑Ethylmaleimide reductase; old yellow enzyme
RA	1,722,475	G→T	41.0%	D128Y (GAC→TAC)	gloA →	glyoxalase I, Ni‑dependent
RA	1,723,809	G→T	65.7%	E156* (GAA→TAA)	lhr →	putative ATP‑dependent helicase
RA	1,726,437	C→A	6.8%	L1032I (CTC→ATC)	lhr →	putative ATP‑dependent helicase
RA	1,752,893	T→A	7.8%	P30P (CCA→CCT)	ldtE ←	murein L,D‑transpeptidase
RA	1,754,950	T→A	92.2%	I367F (ATT→TTT)	sufD ←	component of SufBCD Fe‑S cluster assembly scaffold
RA	1,764,150	G→T	71.2%	D274Y (GAT→TAT)	ydiK →	UPF0118 family inner membrane protein
RA	1,764,518	T→A	9.7%	intergenic (+75/‑111)	ydiK → / → rprA	UPF0118 family inner membrane protein/sRNA antisense activator for RpoS translation, Hfq‑dependent
RA	1,766,617	A→T	10.8%	intergenic (+75/‑152)	ydiM → / → ydiN	MFS superfamily sugar transport 1 family protein/MFS transporter superfamily protein
RA	1,770,281	T→A	100%	D146E (GAT→GAA)	ydiF →	putative acetyl‑CoA:acetoacetyl‑CoA transferase: alpha subunit/beta subunit
RA	1,775,744	C→A	40.3%	V31V (GTC→GTA)	ydiS →	putative oxidoreductase
RA	1,777,451	C→A	74.3%	A55E (GCG→GAG)	fadK →	short chain acyl‑CoA synthetase, anaerobic
RA	1,788,981	A→T	5.5%	S143R (AGT→AGA)	btuC ←	vitamin B12 transporter subunit: membrane component of ABC superfamily
RA	1,791,509	C→A	17.4%	P231P (CCG→CCT)	pheT ←	phenylalanine tRNA synthetase, beta subunit
RA	1,795,267	A→T	10.1%	F521I (TTC→ATC)	thrS ←	threonyl‑tRNA synthetase
RA	1,798,834	G→A	13.3%	pseudogene (1060/1476 nt)	arpB →	pseudogene, ankyrin repeats
RA	1,800,416	C→T	52.0%	intergenic (‑76/‑211)	ydiY ← / → pfkB	acid‑inducible putative outer membrane protein/6‑phosphofructokinase II
RA	1,801,813	A→T	8.1%	T53S (ACT→TCT)	ydiZ →	uncharacterized protein
RA	1,802,047	G→A	100%	intergenic (+100/‑6)	ydiZ → / → yniA	uncharacterized protein/fructosamine kinase family protein
RA	1,803,109	C→T	55.5%	A128T (GCC→ACC)	yniB ←	putative inner membrane protein
RA	1,807,214	G→T	5.7%	A59D (GCC→GAC)	ydjO ←	uncharacterized protein
RA	1,813,263	C→A	13.3%	E148* (GAG→TAG)	chbR ←	repressor of chb operon for N,N'‑diacetylchitobiose utilization
RA	1,819,917	C→T	6.5%	intergenic (‑35/+295)	spy ← / ← astE	periplasmic ATP‑independent protein refolding chaperone, stress‑induced/succinylglutamate desuccinylase
RA	1,821,696	A→T	68.0%	L274Q (CTG→CAG)	astB ←	succinylarginine dihydrolase
RA	1,825,763	C→A	91.0%	A159A (GCG→GCT)	astC ←	succinylornithine transaminase, PLP‑dependent
RA	1,832,413	C→A	92.8%	L315L (CTC→CTA)	ynjC →	inner membrane putative ABC superfamily transporter permease
RA	1,833,730	C→A	94.0%	R3S (CGT→AGT)	ynjE →	molybdopterin synthase sulfurtransferase
RA	1,850,797	C→A	6.0%	R130L (CGG→CTG)	ydjH ←	putative kinase
RA	1,850,880	C→A	60.3%	V102V (GTG→GTT)	ydjH ←	putative kinase
RA	1,857,750	T→A	5.3%	V241V (GTT→GTA)	gapA →	glyceraldehyde‑3‑phosphate dehydrogenase A
RA	1,862,404	G→T	9.4%	E414* (GAA→TAA)	yeaG →	protein kinase, endogenous substrate unidentified; autokinase
RA	1,865,422	C→A	94.6%	R261R (CGA→AGA)	yeaI →	putative membrane‑anchored diguanylate cyclase
RA	1,868,749	A→C	6.4%	E47D (GAA→GAC)	yeaL →	UPF0756 family putative inner membrane protein
RA	1,872,520	G→T	92.1%	P183P (CCG→CCT)	yeaP →	diguanylate cyclase
RA	1,873,569	C→A	6.0%	intergenic (‑57/+91)	yeaQ ← / ← yoaG	UPF0410 family protein/uncharacterized protein
RA	1,884,367	T→A	5.6%	V141V (GTA→GTT)	yeaY ←	Slp family lipoprotein, RpoE‑regulated
RA	1,894,208	A→T	7.3%	K509* (AAA→TAA)	yoaD →	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase, regulator of cellulose production
RA	1,899,495	G→A	6.0%	K146K (AAG→AAA)	yobD →	UPF0266 family inner membrane protein
RA	1,902,115	C→A	6.1%	intergenic (‑267/+403)	yobF ← / ← yebO	DUF2527 family heat‑induced protein/putative inner membrane protein
RA	1,904,572	C→A	6.3%	R14R (CGA→AGA)	yebQ →	putative transporter
RA	1,905,599	C→A	10.6%	A356E (GCG→GAG)	yebQ →	putative transporter
RA	1,909,342	T→A	100%	E150D (GAA→GAT)	proQ ←	RNA chaperone, putative ProP translation regulator
RA	1,913,996	T→G	8.1%	Y744D (TAC→GAC)	yebT →	MCE domain protein
RA	1,932,701	C→A	5.9%	Q266K (CAG→AAG)	pykA →	pyruvate kinase II
RA	1,941,921	A→T	7.5%	V163E (GTG→GAG)	yebC ←	UPF0082 family protein
RA	1,942,066	G→T	18.9%	H115N (CAT→AAT)	yebC ←	UPF0082 family protein
RA	1,943,414	C→A	7.0%	D456Y (GAT→TAT)	aspS ←	aspartyl‑tRNA synthetase
RA	1,944,177	C→A	93.4%	L201L (CTG→CTT)	aspS ←	aspartyl‑tRNA synthetase
RA	1,944,879	C→A	9.0%	intergenic (‑100/‑210)	aspS ← / → yecD	aspartyl‑tRNA synthetase/isochorismatase family protein
RA	1,948,050	C→A	5.7%	L118I (CTT→ATT)	cmoB →	tRNA (cmo5U34)‑carboxymethyltransferase, carboxy‑SAM‑dependent
RA	1,957,975	C→A	6.3%	A445S (GCT→TCT)	flhA ←	putative flagellar export pore protein
RA	1,959,915	C→A	64.2%	P178P (CCG→CCT)	flhB ←	flagellin export apparatus, substrate specificity protein
RA	1,960,721	C→A	7.3%	D192Y (GAT→TAT)	cheZ ←	chemotaxis regulator, protein phosphatase for CheY
RA	1,969,291	G→T	100%	I97I (ATC→ATA)	cheA ←	fused chemotactic sensory histidine kinase in two‑component regulatory system with CheB and CheY: sensory histidine kinase/signal sensing protein
RA	1,973,690	A→G	5.1%	A468A (GCT→GCC)	otsA ←	trehalose‑6‑phosphate synthase
RA	1,975,265	C→A	5.8%	D202Y (GAT→TAT)	otsB ←	trehalose‑6‑phosphate phosphatase, biosynthetic
RA	1,977,138	C→A	7.2%	V471V (GTG→GTT)	araG ←	fused L‑arabinose transporter subunits of ABC superfamily: ATP‑binding components
RA	1,980,402	A→C	7.8%	intergenic (‑793/‑4)	araF ← / → ftnB	L‑arabinose transporter subunit/ferritin B, putative ferrous iron reservoir
RA	1,982,943	A→T	14.2%	L10* (TTA→TAA)	yecH ←	DUF2492 family protein
RA	1,984,987	C→A	69.5%	T38T (ACG→ACT)	yecA ←	UPF0149 family protein
RA	1,986,289	T→A	90.3%	N4Y (AAT→TAT)	pgsA ←	phosphatidylglycerophosphate synthetase
RA	1,991,843	G→A	7.1%	L40F (CTC→TTC)	yecS ←	ABC family putative inner membrane permease
RA	1,997,314	G→T	93.1%	intergenic (‑227/‑39)	fliC ← / → fliD	flagellar filament structural protein (flagellin)/flagellar filament capping protein
RA	1,999,098	C→A	9.5%	V105V (GTC→GTA)	fliS →	flagellar protein potentiates polymerization
RA	1,999,632	G→T	90.3%	intergenic (+73/‑5)	fliT → / → amyA	putative flagellar synthesis and assembly chaperone/cytoplasmic alpha‑amylase
RA	2,007,547	C→A	15.6%	R280S (CGC→AGC)	fliF →	flagellar basal‑body MS‑ring and collar protein
RA	2,020,166	C→A	89.9%	D445Y (GAC→TAC)	yedQ ←	putative membrane‑anchored diguanylate cyclase
RA	2,022,182	C→A	5.9%	L222F (TTG→TTT)	yedI ←	DUF808 family inner membrane protein
RA	2,030,998	C→A	9.5%	P212P (CCG→CCT)	yedV ←	putative sensory kinase in two‑component regulatory system with YedW
RA	2,034,714	C→T	12.0%	intergenic (+115/‑142)	yedZ → / → zinT	inner membrane heme subunit for periplasmic YedYZ reductase/zinc and cadmium binding protein, periplasmic
RA	2,035,090	C→A	91.9%	Q79K (CAG→AAG)	zinT →	zinc and cadmium binding protein, periplasmic
RA	2,036,511	C→T	6.9%	intergenic (+132/+438)	yodB → / ← serU	cytochrome b561 homolog/tRNA‑Ser
RA	2,038,769	C→A	13.3%	V117V (GTC→GTA)	yeeJ →	putative adhesin
RA	2,039,694	C→T	49.8%	R426C (CGC→TGC)	yeeJ →	putative adhesin
RA	2,040,800	C→A	17.9%	T794T (ACC→ACA)	yeeJ →	putative adhesin
RA	2,041,982	A→T	10.3%	S1188S (TCA→TCT)	yeeJ →	putative adhesin
RA	2,065,158	T→A	12.1%	S47T (TCA→ACA)	flu →	CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
RA	2,066,503	C→A	6.1%	S495* (TCA→TAA)	flu →	CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
RA	2,074,680	A→T	94.0%	W22R (TGG→AGG)	sbmC ←	DNA gyrase inhibitor
RA	2,077,212	A→T	70.1%	N326Y (AAT→TAT)	sbcB →	exodeoxyribonuclease I; exonuclease I
RA	2,090,880	C→A	8.4%	L301L (CTG→CTT)	wzzB ←	regulator of length of O‑antigen component of lipopolysaccharide chains
RA	2,098,995	C→A	94.5%	G182* (GGA→TGA)	wbbI ←	d‑Galf:alpha‑d‑Glc beta‑1,6‑galactofuranosyltransferase
RA	2,102,205	C→A	9.1%	V287V (GTG→GTT)	wzxB ←	putative polisoprenol‑linked O‑antigen transporter
RA	2,108,219:1	+A	100%	coding (1159/1395 nt)	wcaM ←	colanic acid biosynthesis protein
RA	2,110,346	G→A	70.0%	T88I (ACC→ATC)	wcaL ←	putative glycosyl transferase
RA	2,113,761	C→A	5.2%	E425D (GAG→GAT)	wcaJ ←	colanic biosynthesis UDP‑glucose lipid carrier transferase
RA	2,114,911	A→T	90.4%	L42Q (CTG→CAG)	wcaJ ←	colanic biosynthesis UDP‑glucose lipid carrier transferase
RA	2,115,361	C→A	14.8%	R367L (CGC→CTC)	cpsG ←	phosphomannomutase
RA	2,131,206	C→T	9.5%	intergenic (‑482/‑177)	wza ← / → yegH	colanic acid export protein; outer membrane auxillary lipoprotein/inner membrane protein
RA	2,135,016	C→A	5.8%	V26V (GTG→GTT)	asmA ←	suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic protein
RA	2,139,910	G→T	92.3%	R1055L (CGA→CTA)	yegE →	putative diguanylate cyclase
RA	2,142,983	C→A	9.3%	R495L (CGC→CTC)	yegI ←	protein kinase‑related putative non‑specific DNA‑binding protein
RA	2,144,474	C→A	94.4%	intergenic (‑8/‑192)	yegI ← / → yegJ	protein kinase‑related putative non‑specific DNA‑binding protein/uncharacterized protein
RA	2,146,030	T→A	47.0%	S194C (AGT→TGT)	yegL ←	VMA domain protein
RA	2,146,863	C→A	5.2%	noncoding (74/143 nt) V9V (GTG→GTT)	sibA → ibsA ←	sRNA antisense regulator of toxic IbsA protein toxic membrane protein
RA	2,148,615	C→A	6.1%	R373R (CGC→CGA)	mdtA →	multidrug efflux system, subunit A
RA	2,149,603	A→T	92.8%	E287V (GAA→GTA)	mdtB →	multidrug efflux system, subunit B
RA	2,154,431	G→T	6.9%	L855L (CTG→CTT)	mdtC →	multidrug efflux system, subunit C
RA	2,163,087	C→A	13.7%	R299S (CGT→AGT)	yegS →	phosphatidylglycerol kinase, metal‑dependent
RA	2,168,487	A→T	27.2%	D14E (GAT→GAA)	gatA ←	galactitol‑specific enzyme IIA component of PTS
RA	2,168,795	C→A	90.8%	D336Y (GAT→TAT)	gatZ ←	D‑tagatose 1,6‑bisphosphate aldolase 2, subunit
RA	2,175,796	C→A	5.4%	S155S (TCG→TCT)	yegW ←	putative DNA‑binding transcriptional regulator
RA	2,176,158	C→T	8.0%	A35T (GCC→ACC)	yegW ←	putative DNA‑binding transcriptional regulator
RA	2,176,481	G→T	10.2%	A217D (GCT→GAT)	yegX ←	putative family 25 glycosyl hydrolase
RA	2,179,205	G→T	90.1%	A24E (GCG→GAG)	rcnR ←	transcriptional repressor of rcnA
RA	2,181,645	A→G	92.8%	N83N (AAT→AAC)	yehA ←	putative fimbrial‑like adhesin protein
RA	2,189,071	A→T	7.2%	E431D (GAA→GAT)	metG →	methionyl‑tRNA synthetase
RA	2,189,888	C→A	5.6%	intergenic (+76/‑65)	metG → / → yehH	methionyl‑tRNA synthetase/DUF4132 family pseudogene; defective yehI paralog; molybdate metabolism regulator, first fragment; molybdate metabolism regulator, second fragment 2; yehI' molR mutations have phenotypes and the N‑terminal molR fragment of yehI' may be expressed and may have retained or evolved MolR function
RA	2,191,159	C→A	7.8%	pseudogene (1207/2847 nt)	yehH →	DUF4132 family pseudogene; defective yehI paralog; molybdate metabolism regulator, first fragment; molybdate metabolism regulator, second fragment 2; yehI' molR mutations have phenotypes and the N‑terminal molR fragment of yehI' may be expressed and may have retained or evolved MolR function
RA	2,191,496	C→A	13.7%	pseudogene (1544/2847 nt)	yehH →	DUF4132 family pseudogene; defective yehI paralog; molybdate metabolism regulator, first fragment; molybdate metabolism regulator, second fragment 2; yehI' molR mutations have phenotypes and the N‑terminal molR fragment of yehI' may be expressed and may have retained or evolved MolR function
RA	2,192,748	T→A	5.3%	pseudogene (2796/2847 nt)	yehH →	DUF4132 family pseudogene; defective yehI paralog; molybdate metabolism regulator, first fragment; molybdate metabolism regulator, second fragment 2; yehI' molR mutations have phenotypes and the N‑terminal molR fragment of yehI' may be expressed and may have retained or evolved MolR function
RA	2,194,695	T→A	90.5%	L313Q (CTA→CAA)	yehI →	DUF4132 domain‑containing protein
RA	2,195,449	A→T	100%	E564D (GAA→GAT)	yehI →	DUF4132 domain‑containing protein
RA	2,197,797	A→T	14.0%	intergenic (+29/‑278)	yehK → / → yehL	uncharacterized protein/putative ABC superfamily transporter ATP‑binding subunit
RA	2,198,012	C→A	14.6%	intergenic (+244/‑63)	yehK → / → yehL	uncharacterized protein/putative ABC superfamily transporter ATP‑binding subunit
RA	2,204,432	G→T	46.2%	pseudogene (1854/2001 nt)	yehQ →	pseudogene
RA	2,209,074	T→A	8.3%	*244K (TAA→AAA)	mlrA →	transcriptional activator of csgD and csgBA
RA	2,209,162	C→A	71.3%	I9I (ATC→ATA)	yohO →	putative membrane protein
RA	2,216,296	C→A	92.0%	I211I (ATC→ATA)	dld →	D‑lactate dehydrogenase, FAD‑binding, NADH independent
RA	2,216,446	G→T	10.5%	A261A (GCG→GCT)	dld →	D‑lactate dehydrogenase, FAD‑binding, NADH independent
RA	2,220,503	C→T	13.0%	V83M (GTG→ATG)	yohF ←	putative oxidoreductase
RA	2,223,247	C→T	74.5%	W206* (TGG→TGA)	dusC ←	tRNA‑dihydrouridine synthase C
RA	2,225,190	C→T	90.0%	G231G (GGC→GGT)	yohK →	LrgB family inner membrane protein
RA	2,225,260	C→T	7.3%	intergenic (+67/‑63)	yohK → / → cdd	LrgB family inner membrane protein/cytidine/deoxycytidine deaminase
RA	2,225,529	G→T	6.2%	S69S (TCG→TCT)	cdd →	cytidine/deoxycytidine deaminase
RA	2,233,142	A→T	8.5%	V229E (GTG→GAG)	mglB ←	methyl‑galactoside transporter subunit
RA	2,237,098	G→T	100%	H12N (CAT→AAT)	folE ←	GTP cyclohydrolase I
RA	2,238,975	T→A	5.8%	Q425L (CAA→CTA)	cirA ←	colicin IA outer membrane receptor and translocator; ferric iron‑catecholate transporter
RA	2,240,937	A→T	10.2%	C359S (TGC→AGC)	lysP ←	lysine transporter
RA	2,243,089	G→T	8.4%	I3I (ATC→ATA)	yeiE ←	putative DNA‑binding transcriptional regulator
RA	2,259,580	C→A	7.8%	intergenic (+79/‑144)	yeiP → / → yeiQ	elongation factor P‑like protein/putative NAD‑dependent D‑mannonate oxidoreductase
RA	2,259,689	C→A	9.4%	intergenic (+188/‑35)	yeiP → / → yeiQ	elongation factor P‑like protein/putative NAD‑dependent D‑mannonate oxidoreductase
RA	2,263,137	C→A	70.9%	intergenic (+91/‑321)	lpxT → / → mepS	lipid A 1‑diphosphate synthase; undecaprenyl pyrophosphate:lipid A 1‑phosphate phosphotransferase/murein DD‑endopeptidase, space‑maker hydrolase, mutational suppressor of prc thermosensitivity, outer membrane lipoprotein
RA	2,263,171	T→C	6.3%	intergenic (+125/‑287)	lpxT → / → mepS	lipid A 1‑diphosphate synthase; undecaprenyl pyrophosphate:lipid A 1‑phosphate phosphotransferase/murein DD‑endopeptidase, space‑maker hydrolase, mutational suppressor of prc thermosensitivity, outer membrane lipoprotein
RA	2,264,143	G→A	94.9%	intergenic (+119/‑62)	mepS → / → rtn	murein DD‑endopeptidase, space‑maker hydrolase, mutational suppressor of prc thermosensitivity, outer membrane lipoprotein/resistance protein for phages lambda and N4, putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	2,270,338	T→A	10.7%	L187Q (CTG→CAG)	yejF →	microcin C transporter, ATP‑binding subunit; ABC family
RA	2,276,667	C→A	7.8%	E254* (GAA→TAA)	yejK ←	spermidine nucleoid‑associated protein
RA	2,287,829	C→A	64.6%	S185S (TCG→TCT)	ccmF ←	heme lyase, CcmF subunit
RA	2,289,043	C→A	70.4%	W8L (TGG→TTG)	ccmD ←	cytochrome c biogenesis protein
RA	2,289,374	C→A	87.8%	V142V (GTG→GTT)	ccmC ←	heme exporter subunit
RA	2,292,271	A→T	14.8%	C263S (TGC→AGC)	napH ←	ferredoxin‑type protein essential for electron transfer from ubiquinol to periplasmic nitrate reductase (NapAB)
RA	2,298,128	C→T	6.5%	intergenic (+256/+459)	eco → / ← mqo	ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA	2,298,492	A→G	6.8%	intergenic (+620/+95)	eco → / ← mqo	ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA	2,299,044	C→A	10.1%	R397L (CGT→CTT)	mqo ←	malate dehydrogenase, FAD/NAD(P)‑binding domain
RA	2,303,070	T→G	94.2%	Q272P (CAG→CCG)	ada ←	fused DNA‑binding transcriptional dual regulator/O6‑methylguanine‑DNA methyltransferase
RA	2,305,116	C→A	93.5%	intergenic (‑103/+9)	apbE ← / ← ompC	putative thiamine‑synthetic flavin transferase lipoprotein/outer membrane porin protein C
RA	2,305,135	T→C	94.1%	Y365C (TAC→TGC)	ompC ←	outer membrane porin protein C
RA	2,309,824	C→A	9.5%	L57I (CTC→ATC)	rcsB →	response regulator in two‑component regulatory system with RcsC and YojN
RA	2,310,604	C→A	40.0%	G918C (GGT→TGT)	rcsC ←	hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA	2,311,008	T→A	7.2%	H783L (CAC→CTC)	rcsC ←	hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA	2,313,924	C→A	18.4%	R135S (CGC→AGC)	atoS →	sensory histidine kinase in two‑component regulatory system with AtoC
RA	2,321,041	G→T	42.8%	F194L (TTC→TTA)	yfaP ←	DUF2135 family protein, putative host defense protein
RA	2,323,370	G→T	6.5%	pseudogene (4512/4605 nt)	yfaS ←	pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein
RA	2,327,738	C→A	7.8%	pseudogene (144/4605 nt)	yfaS ←	pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein
RA	2,329,729	G→T	56.2%	A132E (GCG→GAG)	yfaA ←	DUF2138 family protein, putative host defense protein
RA	2,330,502	C→A	92.4%	D800Y (GAT→TAT)	gyrA ←	DNA gyrase (type II topoisomerase), subunit A
RA	2,331,288	C→T	6.8%	D538N (GAT→AAT)	gyrA ←	DNA gyrase (type II topoisomerase), subunit A
RA	2,339,051	C→A	12.0%	S236S (TCC→TCA)	nrdA →	ribonucleoside‑diphosphate reductase 1, alpha subunit
RA	2,344,807	G→T	11.3%	V349V (GTC→GTA)	glpT ←	sn‑glycerol‑3‑phosphate transporter
RA	2,345,023	C→A	13.5%	P277P (CCG→CCT)	glpT ←	sn‑glycerol‑3‑phosphate transporter
RA	2,348,894	T→A	60.9%	V384E (GTG→GAG)	glpB →	sn‑glycerol‑3‑phosphate dehydrogenase (anaerobic), membrane anchor subunit
RA	2,352,082	C→A	35.8%	P81P (CCG→CCT)	rhmA ←	2‑keto‑3‑deoxy‑L‑rhamnonate aldolase
RA	2,352,573	C→A	100%	P353P (CCG→CCT)	rhmT ←	putative L‑rhamnonate transporter
RA	2,353,889	C→A	9.8%	V335V (GTG→GTT)	rhmD ←	L‑rhamnonate dehydratase
RA	2,359,673	G→T	93.3%	M89I (ATG→ATT)	arnB →	uridine 5'‑(beta‑1‑threo‑pentapyranosyl‑4‑ulose diphosphate) aminotransferase, PLP‑dependent
RA	2,362,338	T→A	94.5%	L274Q (CTG→CAG)	arnA →	fused UDP‑L‑Ara4N formyltransferase/UDP‑GlcA C‑4'‑decarboxylase
RA	2,370,361:1	+G	100%	coding (711/759 nt)	menH ←	2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
RA	2,370,837	Δ1 bp	9.8%	coding (235/759 nt)	menH ←	2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
RA	2,370,987	C→A	91.6%	E29* (GAA→TAA)	menH ←	2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
RA	2,378,963	A→T	9.4%	L80* (TTG→TAG)	yfbK ←	Von Willebrand factor domain putative lipoprotein
RA	2,380,078	C→T	68.0%	S247F (TCT→TTT)	yfbL →	putative peptidase
RA	2,383,897	C→A	48.7%	R363L (CGC→CTC)	nuoN ←	NADH:ubiquinone oxidoreductase, membrane subunit N
RA	2,387,701	C→A	10.0%	M275I (ATG→ATT)	nuoL ←	NADH:ubiquinone oxidoreductase, membrane subunit L
RA	2,395,041	C→A	12.4%	R164L (CGG→CTG)	nuoE ←	NADH:ubiquinone oxidoreductase, chain E
RA	2,395,151	C→A	49.5%	T127T (ACG→ACT)	nuoE ←	NADH:ubiquinone oxidoreductase, chain E
RA	2,399,210	G→T	94.1%	S304* (TCA→TAA)	lrhA ←	transcriptional repressor of flagellar, motility and chemotaxis genes
RA	2,405,946	T→G	100%	Q43P (CAG→CCG)	yfbU ←	UPF0304 family protein
RA	2,407,678	T→A	14.4%	S244T (TCT→ACT)	ackA →	acetate kinase A and propionate kinase 2
RA	2,408,000	T→A	9.5%	V351E (GTG→GAG)	ackA →	acetate kinase A and propionate kinase 2
RA	2,412,205	C→A	66.8%	D151Y (GAT→TAT)	yfcD ←	putative NUDIX hydrolase
RA	2,415,498	G→T	5.4%	T104T (ACG→ACT)	yfcH →	putative NAD‑dependent nucleotide‑sugar epimerase
RA	2,416,101	C→A	90.4%	intergenic (+21/+27)	yfcH → / ← yfcI	putative NAD‑dependent nucleotide‑sugar epimerase/transposase_31 family protein
RA	2,417,358	C→A	51.3%	E211* (GAA→TAA)	hisP ←	histidine/lysine/arginine/ornithine transporter subunit
RA	2,418,065	G→A	8.8%	V216V (GTC→GTT)	hisM ←	histidine/lysine/arginine/ornithine transporter subunit
RA	2,422,841	C→A	90.6%	D293Y (GAT→TAT)	purF ←	amidophosphoribosyltransferase
RA	2,424,074	C→T	91.0%	D57N (GAC→AAC)	cvpA ←	colicin V production membrane protein
RA	2,426,731	G→T	8.5%	I225I (ATC→ATA)	accD ←	acetyl‑CoA carboxylase, beta (carboxyltransferase) subunit
RA	2,428,760	C→A	7.8%	R119L (CGC→CTC)	truA ←	tRNA pseudouridine(38‑40) synthase
RA	2,434,701	C→A	11.6%	A128A (GCG→GCT)	fabB ←	3‑oxoacyl‑[acyl‑carrier‑protein] synthase I
RA	2,441,382	C→A	14.0%	G180C (GGT→TGT)	prmB ←	N5‑glutamine methyltransferase
RA	2,442,770	A→C	15.0%	D253E (GAT→GAG)	yfcO ←	DUF2544 family putative outer membrane protein
RA	2,442,790	C→A	6.6%	D247Y (GAT→TAT)	yfcO ←	DUF2544 family putative outer membrane protein
RA	2,442,971	C→A	46.0%	E186D (GAG→GAT)	yfcO ←	DUF2544 family putative outer membrane protein
RA	2,443,918	T→G	10.7%	Y51S (TAT→TCT)	yfcP ←	putative fimbrial‑like adhesin protein
RA	2,450,335	C→T	93.0%	intergenic (‑44/+159)	sixA ← / ← fadJ	phosphohistidine phosphatase/fused enoyl‑CoA hydratase and epimerase and isomerase/3‑hydroxyacyl‑CoA dehydrogenase
RA	2,450,346	G→T	92.0%	intergenic (‑55/+148)	sixA ← / ← fadJ	phosphohistidine phosphatase/fused enoyl‑CoA hydratase and epimerase and isomerase/3‑hydroxyacyl‑CoA dehydrogenase
RA	2,452,454	G→T	100%	P62Q (CCG→CAG)	fadJ ←	fused enoyl‑CoA hydratase and epimerase and isomerase/3‑hydroxyacyl‑CoA dehydrogenase
RA	2,454,297	T→G	93.8%	E39D (GAA→GAC)	yfcZ ←	UPF0381 family protein
RA	2,455,524	G→T	11.4%	R247L (CGC→CTC)	fadL →	long‑chain fatty acid outer membrane transporter
RA	2,456,282	C→A	10.2%	intergenic (+157/‑209)	fadL → / → yfdF	long‑chain fatty acid outer membrane transporter/uncharacterized protein
RA	2,456,723	A→C	8.6%	D78A (GAT→GCT)	yfdF →	uncharacterized protein
RA	2,474,418	G→T	100%	S413* (TCA→TAA)	emrY ←	putative multidrug efflux system
RA	2,475,290	C→A	9.7%	P122P (CCG→CCT)	emrY ←	putative multidrug efflux system
RA	2,487,163	C→T	6.0%	intergenic (‑430/+83)	frc ← / ← yfdX	formyl‑CoA transferase, NAD(P)‑binding/uncharacterized protein
RA	2,491,279	G→T	37.4%	R166S (CGT→AGT)	alaC ←	valine‑pyruvate aminotransferase 3
RA	2,494,747	G→T	6.7%	D47Y (GAT→TAT)	ypdC →	putative DNA‑binding protein
RA	2,495,918	C→A	10.2%	V683F (GTT→TTT)	fryA ←	putative PTS enzyme, Hpr component/enzyme I component/enzyme IIA component
RA	2,498,834	C→A	12.6%	E65* (GAA→TAA)	ypdE ←	aminopeptidase
RA	2,498,906	C→A	7.7%	G41C (GGT→TGT)	ypdE ←	aminopeptidase
RA	2,501,358	G→T	7.4%	R6S (CGC→AGC)	fryC ←	putative enzyme IIC component of PTS
RA	2,503,015	C→A	7.2%	intergenic (‑110/‑94)	glk ← / → yfeO	glucokinase/putative ion channel protein
RA	2,504,065	C→T	16.8%	G319G (GGC→GGT)	yfeO →	putative ion channel protein
RA	2,511,317	C→A	50.5%	intergenic (‑6/+203)	yfeA ← / ← alaX	putative diguanylate cyclase/tRNA‑Ala
RA	2,514,152	G→T	5.5%	intergenic (‑1/‑258)	gltX ← / → valU	glutamyl‑tRNA synthetase/tRNA‑Val
RA	2,516,553	T→G	5.6%	E264D (GAA→GAC)	xapB ←	xanthosine transporter
RA	2,520,652	C→A	90.4%	I116I (ATC→ATA)	yfeH →	putative inorganic ion transporter
RA	2,526,023	T→A	9.2%	Y86N (TAC→AAC)	cysK →	cysteine synthase A, O‑acetylserine sulfhydrolase A subunit
RA	2,526,851	A→T	43.5%	intergenic (+112/‑272)	cysK → / → ptsH	cysteine synthase A, O‑acetylserine sulfhydrolase A subunit/phosphohistidinoprotein‑hexose phosphotransferase component of PTS system (Hpr)
RA	2,536,986	G→A	11.2%	intergenic (‑99/+205)	cysP ← / ← ucpA	thiosulfate‑binding protein/furfural resistance protein, putative short‑chain oxidoreductase
RA	2,538,683	C→A	7.4%	D96Y (GAT→TAT)	murR ←	repressor for murPQ, MurNAc 6‑P inducible
RA	2,542,627	T→G	73.1%	I389M (ATT→ATG)	yfeW →	penicillin binding protein PBP4B; weak DD‑carboxypeptidase activity
RA	2,549,676	C→A	90.7%	L28L (CTG→CTT)	eutL ←	putative ethanol utilization carboxysome structural protein
RA	2,550,123	G→A	6.2%	Y178Y (TAC→TAT)	eutC ←	ethanolamine ammonia‑lyase, small subunit (light chain)
RA	2,552,999	A→T	6.8%	A261A (GCA→GCT)	intZ →	CPZ‑55 prophage; putative phage integrase
RA	2,556,367	G→T	9.3%	R162L (CGA→CTA)	yffP →	CPZ‑55 prophage; uncharacterized protein
RA	2,559,092	C→A	6.7%	A384A (GCG→GCT)	eutA ←	reactivating factor for ethanolamine ammonia lyase
RA	2,559,860	G→T	7.6%	S128S (TCC→TCA)	eutA ←	reactivating factor for ethanolamine ammonia lyase
RA	2,564,894	C→A	5.1%	D73Y (GAT→TAT)	eutE ←	aldehyde oxidoreductase, ethanolamine utilization protein
RA	2,568,332	G→T	5.7%	R11S (CGT→AGT)	eutQ ←	RmlC‑like cupin domain protein
RA	2,568,720	C→T	90.2%	A33T (GCC→ACC)	eutP ←	putative P‑loop NTPase ethanolamine utilization protein
RA	2,573,363	C→A	13.8%	V123V (GTC→GTA)	tktB →	transketolase 2, thiamine triphosphate‑binding
RA	2,576,325	C→A	93.2%	E171D (GAG→GAT)	nudK ←	GDP‑mannose pyrophosphatase
RA	2,576,879	G→T	8.1%	intergenic (‑42/+26)	nudK ← / ← aegA	GDP‑mannose pyrophosphatase/putative oxidoreductase, FeS binding subunit/NAD/FAD‑binding subunit
RA	2,586,791	G→T	14.0%	G113G (GGC→GGA)	ypfH ←	palmitoyl‑CoA esterase activity, uncertain physiological substrate
RA	2,587,029:1	+G	89.9%	coding (101/699 nt)	ypfH ←	palmitoyl‑CoA esterase activity, uncertain physiological substrate
RA	2,589,808	G→T	46.9%	Q97K (CAG→AAG)	ypfJ ←	putative neutral zinc metallopeptidase
RA	2,589,933	G→A	92.2%	T55I (ACC→ATC)	ypfJ ←	putative neutral zinc metallopeptidase
RA	2,597,173	T→G	67.9%	L666R (CTG→CGG)	hyfB →	hydrogenase 4, membrane subunit
RA	2,601,404	C→T	50.9%	L377F (CTC→TTC)	hyfF →	hydrogenase 4, membrane subunit
RA	2,605,661	C→A	8.3%	L135I (CTC→ATC)	hyfR →	hydrogenase‑4 transcriptional activator
RA	2,606,516	G→T	89.6%	D420Y (GAC→TAC)	hyfR →	hydrogenase‑4 transcriptional activator
RA	2,610,619	C→A	12.6%	G389G (GGC→GGA)	bepA →	periplasmic metalloprotease and chaperone for OM protein maintenance and assembly
RA	2,610,919	C→A	92.4%	intergenic (+3/‑18)	bepA → / → yfgD	periplasmic metalloprotease and chaperone for OM protein maintenance and assembly/putative oxidoreductase
RA	2,614,168	C→A	94.4%	D22Y (GAT→TAT)	upp ←	uracil phosphoribosyltransferase
RA	2,617,515	T→G	5.5%	I371M (ATT→ATG)	ppk →	polyphosphate kinase, component of RNA degradosome
RA	2,618,693	G→T	63.7%	E74* (GAA→TAA)	ppx →	exopolyphosphatase
RA	2,619,125	G→T	6.9%	G218C (GGT→TGT)	ppx →	exopolyphosphatase
RA	2,625,926	A→T	7.2%	intergenic (‑32/+37)	guaA ← / ← guaB	GMP synthetase (glutamine aminotransferase)/IMP dehydrogenase
RA	2,632,012	C→A	71.7%	intergenic (‑1/+10)	bamB ← / ← yfgM	BamABCDE complex OM biogenesis lipoprotein/putative anti‑RcsB factor
RA	2,645,592	C→A	10.7%	D19Y (GAC→TAC)	yfhM ←	bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein
RA	2,646,327	G→T	9.1%	D159Y (GAT→TAT)	sseA →	3‑mercaptopyruvate sulfurtransferase
RA	2,648,521	C→A	8.1%	A399A (GCG→GCT)	pepB ←	aminopeptidase B
RA	2,651,665	G→T	92.3%	G210G (GGC→GGA)	hscA ←	DnaK‑like molecular chaperone specific for IscU
RA	2,665,693	C→A	7.5%	G96G (GGC→GGA)	hcaD →	phenylpropionate dioxygenase, ferredoxin reductase subunit
RA	2,666,401	C→A	5.5%	G332G (GGC→GGA)	hcaD →	phenylpropionate dioxygenase, ferredoxin reductase subunit
RA	2,669,978	C→A	60.5%	A69A (GCG→GCT)	yphD ←	inner membrane putative ABC superfamily sugar transporter permease
RA	2,670,769	C→A	38.7%	E318* (GAA→TAA)	yphE ←	putative sugar transporter subunit of ABC superfamily, ATP‑binding component
RA	2,671,274	C→A	100%	T149T (ACG→ACT)	yphE ←	putative sugar transporter subunit of ABC superfamily, ATP‑binding component
RA	2,678,030	C→A	10.6%	A279A (GCG→GCT)	glyA ←	serine hydroxymethyltransferase
RA	2,678,647	C→A	12.8%	V74F (GTT→TTT)	glyA ←	serine hydroxymethyltransferase
RA	2,680,862	C→A	16.6%	R434L (CGA→CTA)	glrR ←	response regulator regulating glmY sRNA in two‑component system with sensor protein GlrK
RA	2,681,873	T→A	89.3%	Q97L (CAG→CTG)	glrR ←	response regulator regulating glmY sRNA in two‑component system with sensor protein GlrK
RA	2,683,829	C→A	90.0%	R210L (CGT→CTT)	glrK ←	sensor protein kinase regulating glmY sRNA in two‑component system with response regulator GlrR
RA	2,692,793	C→A	72.2%	H226N (CAT→AAT)	yfhH →	putative DNA‑binding transcriptional regulator
RA	2,694,843	G→T	70.6%	I82I (ATC→ATA)	pdxJ ←	pyridoxine 5'‑phosphate synthase
RA	2,699,380	C→A	72.1%	P368P (CCG→CCT)	lepA ←	back‑translocating elongation factor EF4, GTPase
RA	2,711,249	G→T	8.1%	G213G (GGC→GGA)	yfiF ←	putative methyltransferase
RA	2,715,643	G→T	92.4%	E778* (GAA→TAA)	pka →	protein lysine acetyltransferase
RA	2,719,426	T→C	100%	intergenic (‑321/+2)	kgtP ← / ← rrfG	alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon
RA	2,724,678	C→A	5.5%	intergenic (‑162/+281)	rrsG ← / ← clpB	16S ribosomal RNA of rrnG operon/protein disaggregation chaperone
RA	2,725,657	C→A	8.6%	D626Y (GAC→TAC)	clpB ←	protein disaggregation chaperone
RA	2,726,786	C→A	93.2%	A249A (GCG→GCT)	clpB ←	protein disaggregation chaperone
RA	2,727,116	C→A	7.9%	A139A (GCG→GCT)	clpB ←	protein disaggregation chaperone
RA	2,733,753	C→T	100%	E253K (GAG→AAG)	aroF ←	3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tyrosine‑repressible
RA	2,735,293	A→T	11.7%	I20I (ATA→ATT)	yfiR →	putative periplasmic inhibitor of YfiN activity
RA	2,742,753	C→A	6.5%	I207I (ATC→ATA)	yfjD →	UPF0053 family inner membrane protein
RA	2,749,134	C→A	11.5%	intergenic (+397/‑384)	smpB → / → intA	trans‑translation protein/CP4‑57 prophage; integrase
RA	2,753,424	G→T	41.1%	G361* (GGA→TGA)	yfjI →	CP4‑57 prophage; uncharacterized protein
JC	2,758,770	+GCACTATG	33.6%	intergenic (‑258/+102)	yfjL ← / ← yfjM	CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein/CP4‑57 prophage; uncharacterized protein
RA	2,761,733	T→A	11.2%	V222E (GTA→GAA)	yfjP →	CP4‑57 prophage; 50S ribosome‑binding GTPase family protein
RA	2,767,365	A→T	5.7%	Y230F (TAT→TTT)	yfjW →	CP4‑57 prophage; putative inner membrane protein
RA	2,771,358	G→A	92.6%	intergenic (+217/+147)	ypjF → / ← ypjA	CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter
RA	2,771,366	G→A	9.0%	intergenic (+225/+139)	ypjF → / ← ypjA	CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter
RA	2,774,902	G→T	6.3%	T395K (ACG→AAG)	ypjA ←	adhesin‑like autotransporter
RA	2,776,219	C→A	48.1%	intergenic (‑134/+205)	ypjA ← / ← pinH	adhesin‑like autotransporter/pseudogene, invertase resolvase family
RA	2,778,281	C→T	5.3%	pseudogene (90/1374 nt)	ypjC ←	pseudogene
RA	2,779,067	C→A	86.5%	intergenic (‑697/+54)	ypjC ← / ← ileY	pseudogene/tRNA‑Ile
RA	2,787,915	T→A	6.7%	W102R (TGG→AGG)	gabP →	gamma‑aminobutyrate transporter
RA	2,790,370	G→T	6.8%	I6I (ATC→ATA)	yqaE ←	cyaR sRNA‑regulated protein
RA	2,790,428	G→T	11.2%	intergenic (‑41/‑142)	yqaE ← / → ygaV	cyaR sRNA‑regulated protein/tributyltin‑inducible repressor of ygaVP
RA	2,803,846	C→A	7.4%	I48I (ATC→ATA)	ygaH →	putative L‑valine exporter, norvaline resistance protein
RA	2,805,420	C→A	47.8%	A212E (GCG→GAG)	emrA →	multidrug efflux system
RA	2,806,531	T→G	6.4%	L186R (CTG→CGG)	emrB →	multidrug efflux system protein
RA	2,808,646	G→T	6.0%	R385S (CGC→AGC)	gshA ←	glutamate‑cysteine ligase
RA	2,808,987	G→T	6.3%	S271* (TCG→TAG)	gshA ←	glutamate‑cysteine ligase
RA	2,809,404	C→A	9.2%	R132L (CGT→CTT)	gshA ←	glutamate‑cysteine ligase
RA	2,825,160	A→T	33.2%	I163I (ATT→ATA)	norR ←	anaerobic nitric oxide reductase DNA‑binding transcriptional activator
RA	2,825,783	C→T	91.5%	intergenic (‑135/‑52)	norR ← / → norV	anaerobic nitric oxide reductase DNA‑binding transcriptional activator/anaerobic nitric oxide reductase flavorubredoxin
RA	2,828,952	C→A	88.1%	T611T (ACG→ACT)	hypF ←	carbamoyl phosphate phosphatase and maturation protein for [NiFe] hydrogenases
RA	2,831,086	C→A	61.0%	E127* (GAA→TAA)	hydN ←	formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit
RA	2,833,710	C→A	7.3%	S276R (AGC→AGA)	ascF →	fused cellobiose/arbutin/salicin‑specific PTS enzymes: IIB component/IC component
RA	2,835,094	C→A	67.2%	P249Q (CCG→CAG)	ascB →	cryptic 6‑phospho‑beta‑glucosidase
RA	2,840,562	C→A	58.5%	V70V (GTG→GTT)	hycD ←	hydrogenase 3, membrane subunit
RA	2,841,044	C→A	94.0%	A519A (GCG→GCT)	hycC ←	hydrogenase 3, membrane subunit
RA	2,846,112	C→A	60.5%	I206I (ATC→ATA)	hypD →	hydrogenase maturation protein
RA	2,846,721	G→T	32.4%	D37Y (GAT→TAT)	hypE →	carbamoyl dehydratase, hydrogenases 1,2,3 maturation protein
RA	2,846,933	G→T	5.5%	E107D (GAG→GAT)	hypE →	carbamoyl dehydratase, hydrogenases 1,2,3 maturation protein
RA	2,850,790	C→A	88.5%	I113I (ATC→ATA)	mutS →	methyl‑directed mismatch repair protein
RA	2,860,460	G→T	14.5%	R151S (CGC→AGC)	rpoS ←	RNA polymerase, sigma S (sigma 38) factor
JC	2,871,516	Δ124 bp	6.4%	intergenic (+539/+289)	iap → / ← ygbF	aminopeptidase in alkaline phosphatase isozyme conversion/CRISPR adaptation ssRNA endonuclease
RA	2,873,087	G→T	100%	V15V (GTC→GTA)	ygbT ←	multifunctional endonuclease Cas1, CRISPR adaptation protein; DNA repair enzyme
RA	2,876,760	C→T	93.3%	G246G (GGG→GGA)	casA ←	CRISP RNA (crRNA) containing Cascade antiviral complex protein
RA	2,878,668	G→T	93.2%	V637V (GTC→GTA)	ygcB ←	R‑loop helicase‑annealase Cas3 needed for Cascade anti‑viral activity
RA	2,879,449	G→T	87.4%	S377* (TCA→TAA)	ygcB ←	R‑loop helicase‑annealase Cas3 needed for Cascade anti‑viral activity
RA	2,880,202	G→T	5.7%	S126* (TCA→TAA)	ygcB ←	R‑loop helicase‑annealase Cas3 needed for Cascade anti‑viral activity
RA	2,886,199	C→A	9.8%	H62N (CAT→AAT)	ygcN →	putative oxidoreductase
RA	2,888,584	G→T	90.7%	I185I (ATC→ATA)	ygcQ ←	putative flavoprotein
RA	2,893,446	T→A	68.9%	K63* (AAA→TAA)	ygcW ←	putative dehydrogenase
RA	2,899,073	C→A	10.9%	R2S (CGC→AGC)	ygcG →	uncharacterized protein
RA	2,902,059	C→T	6.6%	V323I (GTC→ATC)	pyrG ←	CTP synthetase
RA	2,927,355	A→C	5.8%	intergenic (‑308/‑239)	fucA ← / → fucP	L‑fuculose‑1‑phosphate aldolase/L‑fucose transporter
RA	2,929,009	C→A	6.5%	R23S (CGT→AGT)	fucI →	L‑fucose isomerase
RA	2,931,717	C→A	90.6%	N307K (AAC→AAA)	fucK →	L‑fuculokinase
RA	2,932,832	C→A	8.9%	R36S (CGT→AGT)	fucR →	l‑fucose operon activator
RA	2,932,835	C→T	71.8%	R37C (CGC→TGC)	fucR →	l‑fucose operon activator
RA	2,934,843	G→T	87.9%	H50N (CAT→AAT)	ygdD ←	UPF0382 family inner membrane protein
RA	2,936,686	G→T	19.8%	intergenic (‑182/‑10)	ygdI ← / → csdA	DUF903 family verified lipoprotein/cysteine sulfinate desulfinase
RA	2,938,035	G→T	46.9%	P45P (CCG→CCT)	csdE →	CsdA‑binding activator; Fe‑S protein
RA	2,957,480	C→A	13.3%	L19F (TTG→TTT)	ppdA ←	putative prepilin peptidase‑dependent protein
RA	2,959,004	G→A	92.1%	I131I (ATC→ATT)	lgt ←	phosphatidylglycerol‑prolipoprotein diacylglyceryl transferase
RA	2,961,295	G→T	51.2%	R167S (CGC→AGC)	ptsP ←	fused PTS enzyme: PEP‑protein phosphotransferase (enzyme I)/GAF domain containing protein
RA	2,962,962	T→A	66.9%	intergenic (‑626/‑59)	rppH ← / → mutH	RNA pyrophosphohydrolase/methyl‑directed mismatch repair protein
RA	2,965,691	C→A	5.8%	L246I (CTC→ATC)	tas →	putative NADP(H)‑dependent aldo‑keto reductase
RA	2,967,572	A→G	14.2%	F601S (TTT→TCT)	aas ←	fused 2‑acylglycerophospho‑ethanolamine acyl transferase/acyl‑acyl carrier protein synthetase
RA	2,967,724	G→T	5.6%	I550I (ATC→ATA)	aas ←	fused 2‑acylglycerophospho‑ethanolamine acyl transferase/acyl‑acyl carrier protein synthetase
RA	2,970,703	C→A	37.1%	A249E (GCG→GAG)	galR →	galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor
RA	2,977,548	C→A	7.6%	intergenic (‑65/+222)	kduI ← / ← yqeF	hexuronate isomerase; hexuronate utilization in high osmolarity/short chain acyltransferase
RA	2,985,256	G→T	9.4%	intergenic (+138/‑197)	ygeG → / → ygeH	SycD‑like chaperone family TPR‑repeat‑containing protein/putative transcriptional regulator
RA	2,985,884	C→T	69.8%	I144I (ATC→ATT)	ygeH →	putative transcriptional regulator
RA	2,986,911	A→T	5.9%	intergenic (+82/‑86)	ygeH → / → ygeI	putative transcriptional regulator/uncharacterized protein
RA	2,987,787	C→A	8.7%	pseudogene (47/60 nt)	pbl →	pseudogene, peptidoglycan‑binding enzyme family
RA	2,988,554	G→A	62.7%	intergenic (‑103/+119)	ygeK ← / ← ygeN	pseudogene; putative 2‑component transcriptional regulator/pseudogene
RA	2,988,641	T→C	48.1%	intergenic (‑190/+32)	ygeK ← / ← ygeN	pseudogene; putative 2‑component transcriptional regulator/pseudogene
RA	2,988,737	T→G	6.2%	pseudogene (383/447 nt)	ygeN ←	pseudogene
RA	2,989,295	C→A	93.5%	pseudogene (85/261 nt)	ygeN ←	pseudogene
RA	2,993,211	C→A	92.5%	V14L (GTG→TTG)	ygeR ←	LysM domain‑containing M23 family putative peptidase; septation lipoprotein
RA	2,993,699	C→A	92.3%	intergenic (‑449/‑5)	ygeR ← / → xdhA	LysM domain‑containing M23 family putative peptidase; septation lipoprotein/xanthine dehydrogenase, molybdenum binding subunit
RA	2,995,335	C→A	6.7%	V544V (GTC→GTA)	xdhA →	xanthine dehydrogenase, molybdenum binding subunit
RA	3,009,187	G→T	74.0%	intergenic (+90/‑232)	mocA → / → ygfK	CTP:molybdopterin cytidylyltransferase/putative Fe‑S subunit oxidoreductase subunit
RA	3,009,287	G→T	7.4%	intergenic (+190/‑132)	mocA → / → ygfK	CTP:molybdopterin cytidylyltransferase/putative Fe‑S subunit oxidoreductase subunit
RA	3,016,372	C→A	10.5%	F566L (TTC→TTA)	xdhD →	putative hypoxanthine oxidase, molybdopterin‑binding/Fe‑S binding
RA	3,017,285	G→T	100%	D871Y (GAC→TAC)	xdhD →	putative hypoxanthine oxidase, molybdopterin‑binding/Fe‑S binding
RA	3,019,203	G→T	20.7%	E27* (GAG→TAG)	guaD →	guanine deaminase
RA	3,021,141	T→C	10.5%	I221T (ATC→ACC)	ygfQ →	putative purine permease
RA	3,024,081	A→C	71.5%	V70V (GTT→GTG)	ygfT ←	putative oxidoreductase, Fe‑S subunit/nucleotide‑binding subunit
RA	3,024,983	C→G	93.9%	G86G (GGC→GGG)	uacT →	uric acid permease
RA	3,025,678	A→T	8.8%	Q318L (CAA→CTA)	uacT →	uric acid permease
RA	3,028,224	G→T	5.5%	L104I (CTC→ATC)	lysS ←	lysine tRNA synthetase, constitutive
RA	3,028,266	C→A	10.6%	D90Y (GAC→TAC)	lysS ←	lysine tRNA synthetase, constitutive
RA	3,030,181	G→T	70.6%	H429N (CAT→AAT)	recJ ←	ssDNA exonuclease, 5' ‑‑> 3'‑specific
RA	3,041,026	C→A	6.0%	D459Y (GAC→TAC)	gcvP ←	glycine decarboxylase, PLP‑dependent, subunit (protein P) of glycine cleavage complex
RA	3,043,595	C→A	11.9%	M144I (ATG→ATT)	gcvT ←	aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex
RA	3,044,281	G→A	7.6%	intergenic (‑255/+193)	gcvT ← / ← ubiI	aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex/2‑octaprenylphenol hydroxylase, FAD‑dependent
RA	3,044,464	G→A	94.1%	intergenic (‑438/+10)	gcvT ← / ← ubiI	aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex/2‑octaprenylphenol hydroxylase, FAD‑dependent
RA	3,055,069	C→A	15.6%	V287V (GTC→GTA)	scpA →	methylmalonyl‑CoA mutase
RA	3,058,692	C→T	12.0%	P178S (CCT→TCT)	scpC →	propionyl‑CoA:succinate CoA transferase
RA	3,058,769	C→T	71.6%	I203I (ATC→ATT)	scpC →	propionyl‑CoA:succinate CoA transferase
RA	3,059,577	G→T	47.6%	D473Y (GAT→TAT)	scpC →	propionyl‑CoA:succinate CoA transferase
RA	3,064,406	A→T	6.2%	A66A (GCT→GCA)	fbaA ←	fructose‑bisphosphate aldolase, class II
RA	3,064,914	G→T	91.7%	I356I (ATC→ATA)	pgk ←	phosphoglycerate kinase
RA	3,068,135	G→T	11.2%	F140L (TTC→TTA)	yggD ←	MtlR family putative transcriptional repressor
RA	3,068,620	C→A	6.2%	G308C (GGC→TGC)	yggF ←	fructose 1,6 bisphosphatase isozyme
RA	3,072,314	C→A	10.8%	E126* (GAA→TAA)	cmtB ←	putative mannitol‑specific enzyme IIA component of PTS
RA	3,075,114	C→A	100%	intergenic (‑120/‑158)	tktA ← / → loiP	transketolase 1, thiamine triphosphate‑binding/Phe‑Phe periplasmic metalloprotease, OM lipoprotein; low salt‑inducible; heat shock protein that binds Era
RA	3,076,526	C→A	93.4%	D211Y (GAC→TAC)	speB ←	agmatinase
RA	3,080,618	T→A	92.7%	V185E (GTG→GAG)	metK →	S‑adenosylmethionine synthetase
RA	3,081,500	C→A	8.9%	intergenic (+281/‑143)	metK → / → galP	S‑adenosylmethionine synthetase/D‑galactose transporter
RA	3,085,649	C→A	5.4%	T138K (ACG→AAG)	gshB →	glutathione synthetase
RA	3,088,065	C→A	65.3%	V125V (GTG→GTT)	yggR ←	putative PilT family AAA+ ATPase
RA	3,088,235	C→A	5.1%	A69S (GCC→TCC)	yggR ←	putative PilT family AAA+ ATPase
RA	3,091,476	C→A	39.7%	T284K (ACG→AAG)	yggW →	HemN family putative oxidoreductase
RA	3,092,182	C→A	5.9%	C248F (TGT→TTT)	yggM ←	DUF1202 family putative secreted protein
RA	3,096,283	G→T	7.1%	intergenic (‑72/‑89)	trmI ← / → mutY	tRNA m(7)G46 methyltransferase, SAM‑dependent/adenine DNA glycosylase
RA	3,096,445	A→T	6.9%	Q25L (CAA→CTA)	mutY →	adenine DNA glycosylase
RA	3,097,200	C→A	8.2%	R277R (CGG→AGG)	mutY →	adenine DNA glycosylase
RA	3,097,262	C→T	64.6%	F297F (TTC→TTT)	mutY →	adenine DNA glycosylase
RA	3,099,851	C→A	6.9%	S260* (TCG→TAG)	nupG →	nucleoside transporter
RA	3,102,092	G→T	5.4%	F141L (TTC→TTA)	speC ←	ornithine decarboxylase, constitutive
RA	3,102,941	T→A	9.4%	S10R (AGT→AGA)	yqgA →	DUF554 family putative inner membrane protein
RA	3,104,247	C→A	6.7%	R80L (CGA→CTA)	yghD ←	putative membrane‑anchored secretion pathway M‑type protein
RA	3,109,544	C→A	5.8%	T976T (ACG→ACT)	yghJ ←	DUF4092 family putative lipoprotein peptidase
RA	3,110,751	C→A	94.2%	R574L (CGT→CTT)	yghJ ←	DUF4092 family putative lipoprotein peptidase
RA	3,111,434	C→A	93.3%	A346A (GCG→GCT)	yghJ ←	DUF4092 family putative lipoprotein peptidase
RA	3,120,216	C→A	92.4%	D389Y (GAT→TAT)	glcD ←	glycolate oxidase subunit, FAD‑linked
RA	3,121,999	G→T	12.1%	V123V (GTG→GTT)	glcC →	glycolate‑inducible glc operon transcriptional repressor; autorepressor
RA	3,132,601	T→G	16.4%	I172M (ATT→ATG)	yghU →	putative S‑transferase
RA	3,132,984	G→A	42.0%	intergenic (+32/+91)	yghU → / ← hybG	putative S‑transferase/hydrogenase 2 accessory protein
RA	3,136,368	G→T	48.4%	R386S (CGT→AGT)	hybB ←	putative hydrogenase 2 cytochrome b type component
RA	3,139,427	G→T	6.3%	S65Y (TCT→TAT)	hybO ←	hydrogenase 2, small subunit
RA	3,142,668	G→T	68.2%	L55I (CTC→ATC)	yqhA ←	UPF0114 family putative inner membrane protein
RA	3,143,342	G→T	5.7%	D108Y (GAT→TAT)	yghA →	putative oxidoreductase
RA	3,144,158	C→A	93.2%	intergenic (+253/+19)	yghA → / ← exbD	putative oxidoreductase/membrane spanning protein in TonB‑ExbB‑ExbD complex
RA	3,164,230	C→A	67.8%	R130S (CGT→AGT)	qseC →	quorum sensing sensory histidine kinase in two‑component regulatory system with QseB
RA	3,173,669	G→T	91.1%	A189A (GCG→GCT)	ygiB →	DUF1190 family protein
RA	3,176,051	C→A	6.3%	S48* (TCA→TAA)	zupT →	zinc transporter
RA	3,176,733	G→T	72.9%	intergenic (+51/+439)	zupT → / ← ribB	zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase
RA	3,208,550	T→A	45.4%	K95* (AAA→TAA)	mug ←	G/U mismatch‑specific DNA glycosylase; xanthine DNA glycosylase
RA	3,211,527	C→A	5.9%	A303A (GCG→GCT)	aer ←	fused signal transducer for aerotaxis sensory component/methyl accepting chemotaxis component
RA	3,215,927	C→A	10.5%	intergenic (+119/‑65)	ebgR → / → ebgA	transcriptional repressor/evolved beta‑D‑galactosidase, alpha subunit
RA	3,217,098	C→A	7.0%	I369I (ATC→ATA)	ebgA →	evolved beta‑D‑galactosidase, alpha subunit
RA	3,217,289	A→T	64.6%	H433L (CAC→CTC)	ebgA →	evolved beta‑D‑galactosidase, alpha subunit
RA	3,224,419	C→A	7.4%	R725S (CGT→AGT)	ygjK →	alpha‑glucosidase
RA	3,224,927	C→A	92.1%	intergenic (+329/‑97)	ygjK → / → fadH	alpha‑glucosidase/2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked
RA	3,226,008	G→T	8.0%	A329S (GCC→TCC)	fadH →	2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked
RA	3,230,012	C→A	8.6%	R38R (CGC→CGA)	ygjQ →	DUF218 superfamily protein
RA	3,230,857	C→G	75.5%	A63G (GCC→GGC)	ygjR →	putative NAD(P)‑dependent dehydrogenase
RA	3,231,349	A→C	67.0%	Q227P (CAG→CCG)	ygjR →	putative NAD(P)‑dependent dehydrogenase
RA	3,233,218	C→A	52.2%	intergenic (+314/‑85)	alx → / → sstT	putative membrane‑bound redox modulator/sodium:serine/threonine symporter
RA	3,237,654	C→A	6.6%	M149I (ATG→ATT)	uxaC ←	uronate isomerase
RA	3,245,848	G→T	94.3%	L62L (CTG→CTT)	yhaH →	DUF805 family inner membrane protein
RA	3,246,634	A→T	15.2%	intergenic (+8/+43)	yhaI → / ← yhaJ	DUF805 family inner membrane protein/LysR family putative transcriptional regulator
RA	3,252,258	C→A	90.3%	D251Y (GAT→TAT)	tdcG ←	L‑serine dehydratase 3, anaerobic
RA	3,257,209	C→A	40.9%	E390* (GAA→TAA)	tdcC ←	L‑threonine/L‑serine transporter
RA	3,257,764	C→A	13.1%	D205Y (GAC→TAC)	tdcC ←	L‑threonine/L‑serine transporter
RA	3,262,394	C→A	5.5%	I207I (ATC→ATA)	yhaC →	pentapetide repeats‑related protein
RA	3,263,460	C→A	7.4%	intergenic (+499/+115)	yhaC → / ← rnpB	pentapetide repeats‑related protein/RNase P, M1 RNA component
RA	3,263,466	G→T	8.1%	intergenic (+505/+109)	yhaC → / ← rnpB	pentapetide repeats‑related protein/RNase P, M1 RNA component
RA	3,263,951	C→A	11.7%	noncoding (1/377 nt)	rnpB ←	RNase P, M1 RNA component
RA	3,266,646	C→A	87.9%	G91C (GGT→TGT)	garL ←	alpha‑dehydro‑beta‑deoxy‑D‑glucarate aldolase
RA	3,267,286	C→A	43.9%	P327P (CCG→CCT)	garP ←	putative (D)‑galactarate transporter
RA	3,285,381	G→T	7.1%	D228Y (GAT→TAT)	yraK →	putative fimbrial‑like adhesin protein
RA	3,285,974	C→A	5.4%	D241Y (GAC→TAC)	rsmI ←	16S rRNA C1402 2'‑O‑ribose methyltransferase, SAM‑dependent
RA	3,292,182	G→T	7.4%	G8G (GGC→GGA)	yraR ←	putative nucleoside‑diphosphate‑sugar epimerase
RA	3,292,914	C→A	52.6%	D121Y (GAT→TAT)	yhbP ←	UPF0306 family protein
RA	3,296,612	G→T	75.2%	A255A (GCG→GCT)	yhbV →	U32 peptidase family protein
RA	3,298,059	C→A	46.4%	R373L (CGC→CTC)	mtr ←	tryptophan transporter of high affinity
RA	3,302,027	G→T	100%	S86* (TCG→TAG)	nlpI ←	lipoprotein involved in osmotic sensitivity and filamentation
RA	3,311,488	G→T	38.7%	intergenic (‑123/+84)	rimP ← / ← metY	ribosome maturation factor for 30S subunits/tRNA‑Met
RA	3,311,950	C→A	8.2%	intergenic (‑302/‑46)	metY ← / → argG	tRNA‑Met/argininosuccinate synthetase
RA	3,312,862	T→A	10.5%	R289R (CGT→CGA)	argG →	argininosuccinate synthetase
RA	3,314,870	C→A	94.6%	A35S (GCG→TCG)	yhbX ←	putative EptAB family phosphoethanolamine transferase, inner membrane protein
RA	3,322,345	C→A	9.8%	I8I (ATC→ATA)	dacB →	D‑alanyl‑D‑alanine carboxypeptidase
RA	3,323,238	C→A	10.8%	S306* (TCG→TAG)	dacB →	D‑alanyl‑D‑alanine carboxypeptidase
RA	3,332,632	G→T	54.1%	L265I (CTT→ATT)	mlaF ←	ABC transporter maintaining OM lipid asymmetry, ATP‑binding protein
RA	3,332,963	C→A	17.9%	A154A (GCG→GCT)	mlaF ←	ABC transporter maintaining OM lipid asymmetry, ATP‑binding protein
RA	3,335,651	C→A	42.8%	S7* (TCG→TAG)	kdsC →	3‑deoxy‑D‑manno‑octulosonate 8‑phosphate phosphatase
RA	3,347,778	G→A	100%	intergenic (‑369/‑306)	yhcC ← / → gltB	putative Fe‑S oxidoreductase, Radical SAM superfamily protein/glutamate synthase, large subunit
RA	3,351,650	G→T	61.8%	E1189D (GAG→GAT)	gltB →	glutamate synthase, large subunit
RA	3,354,405	C→T	92.8%	intergenic (+430/‑130)	gltD → / → gltF	glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
RA	3,356,472	A→T	7.4%	K103* (AAA→TAA)	yhcD →	putative outer membrane fimbrial subunit usher protein
RA	3,357,204	G→T	9.2%	E347* (GAA→TAA)	yhcD →	putative outer membrane fimbrial subunit usher protein
RA	3,357,229	C→A	13.3%	S355* (TCG→TAG)	yhcD →	putative outer membrane fimbrial subunit usher protein
RA	3,365,607	G→T	100%	I109I (ATC→ATA)	nanT ←	sialic acid transporter
RA	3,373,985	C→A	91.9%	intergenic (+37/‑117)	yhcB → / → degQ	DUF1043 family inner membrane‑anchored protein/serine endoprotease, periplasmic
RA	3,374,042	C→A	12.6%	intergenic (+94/‑60)	yhcB → / → degQ	DUF1043 family inner membrane‑anchored protein/serine endoprotease, periplasmic
RA	3,375,260	G→T	100%	D387Y (GAT→TAT)	degQ →	serine endoprotease, periplasmic
RA	3,380,174	C→A	14.4%	S458S (TCG→TCT)	aaeB ←	p‑hydroxybenzoic acid efflux system component
RA	3,381,195	G→T	6.1%	S118* (TCG→TAG)	aaeB ←	p‑hydroxybenzoic acid efflux system component
RA	3,386,672	C→A	12.6%	P982P (CCG→CCT)	yhdP ←	DUF3971‑AsmA2 domains protein
RA	3,387,166	C→A	5.8%	V818F (GTT→TTT)	yhdP ←	DUF3971‑AsmA2 domains protein
RA	3,396,082	G→T	92.4%	R204S (CGT→AGT)	csrD ←	targeting factor for csrBC sRNA degradation
RA	3,397,077	G→T	47.8%	A79S (GCC→TCC)	acuI →	putative acryloyl‑CoA reductase
RA	3,397,642	C→A	6.3%	S267* (TCA→TAA)	acuI →	putative acryloyl‑CoA reductase
RA	3,404,497	C→A	5.8%	L287I (CTC→ATC)	dusB →	tRNA‑dihydrouridine synthase B
RA	3,407,007	G→A	69.4%	intergenic (‑183/‑216)	acrS ← / → acrE	acrAB operon transcriptional repressor/cytoplasmic membrane lipoprotein
RA	3,407,008	G→A	8.8%	intergenic (‑184/‑215)	acrS ← / → acrE	acrAB operon transcriptional repressor/cytoplasmic membrane lipoprotein
RA	3,411,136	G→T	6.0%	A915A (GCG→GCT)	acrF →	multidrug efflux system protein
RA	3,415,551	C→A	10.8%	P290T (CCT→ACT)	yhdY →	putative amino‑acid transporter subunit
RA	3,416,276	C→A	6.7%	S161* (TCG→TAG)	yhdZ →	putative amino‑acid transporter subunit
RA	3,416,890	T→G	9.1%	noncoding (12/120 nt)	rrfF ←	5S ribosomal RNA of rrnD operon
RA	3,416,899	A→G	5.4%	noncoding (3/120 nt)	rrfF ←	5S ribosomal RNA of rrnD operon
RA	3,417,999	C→A	6.7%	noncoding (2144/2904 nt)	rrlD ←	23S ribosomal RNA of rrnD operon
RA	3,422,304	G→T	9.5%	intergenic (‑183/‑291)	rrsD ← / → yrdA	16S ribosomal RNA of rrnD operon/bacterial transferase hexapeptide domain protein
RA	3,422,575	C→A	9.2%	intergenic (‑454/‑20)	rrsD ← / → yrdA	16S ribosomal RNA of rrnD operon/bacterial transferase hexapeptide domain protein
RA	3,433,018	T→G	42.1%	E114A (GAG→GCG)	rplQ ←	50S ribosomal subunit protein L17
RA	3,433,737	G→T	9.9%	R218S (CGT→AGT)	rpoA ←	RNA polymerase, alpha subunit
RA	3,437,010	C→A	12.1%	V149V (GTG→GTT)	secY ←	preprotein translocase membrane subunit
RA	3,440,151	G→T	93.7%	I31I (ATC→ATA)	rpsN ←	30S ribosomal subunit protein S14
RA	3,440,444	G→T	100%	S118S (TCC→TCA)	rplE ←	50S ribosomal subunit protein L5
RA	3,440,832	T→C	87.0%	N99D (AAC→GAC)	rplX ←	50S ribosomal subunit protein L24
RA	3,444,570	G→T	7.6%	R52S (CGT→AGT)	rplB ←	50S ribosomal subunit protein L2
RA	3,447,853	A→T	10.6%	V302E (GTA→GAA)	gspA ←	general secretory pathway component, cryptic
RA	3,455,867	C→A	93.2%	I55I (ATC→ATA)	gspJ →	putative general secretory pathway component, cryptic
RA	3,456,739	G→T	6.0%	D153Y (GAT→TAT)	gspK →	general secretory pathway component, cryptic
RA	3,457,607	G→T	47.8%	V109V (GTG→GTT)	gspL →	general secretory pathway component, cryptic
RA	3,457,896	C→A	42.3%	P206T (CCT→ACT)	gspL →	general secretory pathway component, cryptic
RA	3,462,472	G→T	7.2%	G247G (GGC→GGA)	chiA ←	periplasmic endochitinase
RA	3,467,941	C→T	11.6%	intergenic (‑30/+96)	rpsL ← / ← tusB	30S ribosomal subunit protein S12/mnm(5)‑s(2)U34‑tRNA synthesis 2‑thiolation protein
RA	3,473,139	G→T	100%	I276I (ATC→ATA)	kefB ←	potassium:proton antiporter
RA	3,474,382	C→A	7.1%	D47Y (GAT→TAT)	kefG ←	potassium‑efflux system ancillary protein for KefB, glutathione‑regulated
RA	3,477,607	G→T	7.5%	E11* (GAA→TAA)	yheU →	UPF0270 family protein
RA	3,479,769	A→T	93.8%	E97D (GAA→GAT)	crp →	cAMP‑activated global transcription factor, mediator of catabolite repression
RA	3,483,095	C→A	9.0%	V149F (GTT→TTT)	argD ←	bifunctional acetylornithine aminotransferase/ succinyldiaminopimelate aminotransferase
RA	3,485,823	C→T	5.5%	intergenic (‑167/‑104)	ppiA ← / → tsgA	peptidyl‑prolyl cis‑trans isomerase A (rotamase A)/putative transporter
RA	3,487,320	G→A	44.7%	intergenic (+212/‑50)	tsgA → / → nirB	putative transporter/nitrite reductase, large subunit, NAD(P)H‑binding
RA	3,488,966	G→C	90.5%	A533P (GCC→CCC)	nirB →	nitrite reductase, large subunit, NAD(P)H‑binding
RA	3,489,397	C→A	91.4%	F676L (TTC→TTA)	nirB →	nitrite reductase, large subunit, NAD(P)H‑binding
RA	3,490,359	C→T	5.4%	intergenic (+123/‑3)	nirD → / → nirC	nitrite reductase, NAD(P)H‑binding, small subunit/nitrite transporter
RA	3,495,516	C→A	50.9%	S297* (TCG→TAG)	frlB →	fructoselysine‑6‑P‑deglycase
RA	3,500,138	G→T	35.8%	I186I (ATC→ATA)	yhfT ←	inner membrane protein
RA	3,501,571	C→A	92.5%	G127C (GGC→TGC)	php ←	phosphotriesterase homology protein
RA	3,504,143	G→T	65.2%	R65S (CGT→AGT)	yhfX ←	putative pyridoxal 5'‑phosphate binding protein
RA	3,504,943	C→A	9.9%	R254L (CGA→CTA)	yhfZ ←	putative DNA‑binding transcriptional regulator
RA	3,505,704	A→C	6.9%	intergenic (‑1/+289)	yhfZ ← / ← trpS	putative DNA‑binding transcriptional regulator/tryptophanyl‑tRNA synthetase
RA	3,507,749	G→T	88.0%	H224N (CAT→AAT)	rpe ←	D‑ribulose‑5‑phosphate 3‑epimerase
RA	3,508,588	C→A	6.4%	D229Y (GAT→TAT)	dam ←	DNA adenine methyltransferase
RA	3,508,852	G→T	5.8%	P141T (CCC→ACC)	dam ←	DNA adenine methyltransferase
RA	3,510,311	C→A	14.6%	G119C (GGT→TGT)	damX ←	cell division protein that binds to the septal ring
RA	3,513,424	A→T	67.7%	V213V (GTT→GTA)	hofQ ←	DNA catabolic putative fimbrial transporter
RA	3,519,657	G→T	100%	intergenic (‑149/‑171)	nudE ← / → yrfF	adenosine nucleotide hydrolase; substrates include Ap3A, Ap2A, ADP‑ribose, NADH/inner membrane protein
RA	3,523,740	T→A	6.1%	L203* (TTA→TAA)	hslO →	heat shock protein Hsp33
RA	3,525,007	T→A	7.3%	L264F (TTA→TTT)	yhgE ←	DUF4153 family putative inner membrane protein
RA	3,525,950	C→T	7.3%	intergenic (‑152/‑227)	yhgE ← / → pck	DUF4153 family putative inner membrane protein/phosphoenolpyruvate carboxykinase
RA	3,541,951	C→A	7.5%	V493V (GTG→GTT)	malQ ←	4‑alpha‑glucanotransferase (amylomaltase)
RA	3,543,959	G→T	100%	A625E (GCG→GAG)	malP ←	maltodextrin phosphorylase
RA	3,544,369	T→A	10.3%	E488D (GAA→GAT)	malP ←	maltodextrin phosphorylase
RA	3,550,177	T→A	5.5%	Q11L (CAG→CTG)	rtcA ←	RNA 3'‑terminal phosphate cyclase
RA	3,554,204	C→A	6.1%	V203V (GTG→GTT)	glpG ←	rhomboid intramembrane serine protease
RA	3,555,984	C→A	6.9%	N204K (AAC→AAA)	glpD →	sn‑glycerol‑3‑phosphate dehydrogenase, aerobic, FAD/NAD(P)‑binding
RA	3,557,815	T→A	44.8%	K709N (AAA→AAT)	glgP ←	glycogen phosphorylase
RA	3,561,258	C→A	5.1%	D46Y (GAT→TAT)	glgA ←	glycogen synthase
RA	3,561,574	C→A	100%	W372L (TGG→TTG)	glgC ←	glucose‑1‑phosphate adenylyltransferase
RA	3,562,409	C→A	16.3%	E94* (GAA→TAA)	glgC ←	glucose‑1‑phosphate adenylyltransferase
RA	3,563,911	C→A	47.8%	E257* (GAA→TAA)	glgX ←	glycogen debranching enzyme
RA	3,568,708	C→A	5.8%	S93* (TCA→TAA)	yhgN →	UPF0056 family inner membrane protein
RA	3,571,118	G→T	42.2%	F323L (TTC→TTA)	gntR ←	d‑gluconate inducible gluconate regulon transcriptional repressor
RA	3,571,950	T→A	39.1%	E46V (GAA→GTA) ‡	gntR ←	d‑gluconate inducible gluconate regulon transcriptional repressor
RA	3,571,951	C→A	7.1%	E46* (GAA→TAA) ‡	gntR ←	d‑gluconate inducible gluconate regulon transcriptional repressor
RA	3,574,500	G→T	9.4%	M1M (ATG→ATT) †	yhhY →	putative acetyltransferase
RA	3,575,640	C→A	6.5%	L140I (CTT→ATT)	yhhZ →	putative Hcp1 family polymorphic toxin protein; putative colicin‑like DNase/tRNase activity
RA	3,576,895	T→A	8.4%	V18E (GTG→GAG)	insA →	IS1 repressor TnpA
RA	3,585,079	C→A	17.1%	A203S (GCC→TCC)	ugpB ←	glycerol‑3‑phosphate transporter subunit
RA	3,588,904	A→T	11.1%	L287Q (CTG→CAG)	livH ←	leucine/isoleucine/valine transporter subunit
RA	3,590,930	T→A	41.3%	intergenic (‑10/‑414)	livK ← / → panM	leucine transporter subunit/PanD autocleavage accelerator, panothenate synthesis
RA	3,603,619	G→T	10.2%	R102L (CGT→CTT)	dcrB →	putative lipoprotein
RA	3,623,258	T→A	8.2%	A235A (GCA→GCT)	yhiI ←	putative membrane fusion protein (MFP) of efflux pump
RA	3,626,167	A→T	5.4%	intergenic (‑217/+45)	yhiJ ← / ← yhiL	DUF4049 family protein/pseudogene, DUF4049 family protein
RA	3,632,600	T→G	18.3%	intergenic (+99/+145)	pitA → / ← uspB	phosphate transporter, low‑affinity; tellurite importer/universal stress (ethanol tolerance) protein B
RA	3,639,127	G→T	6.2%	R128L (CGT→CTT)	rlmJ →	23S rRNA m(6)A2030 methyltransferase, SAM‑dependent
RA	3,639,551	C→A	11.4%	T269T (ACC→ACA)	rlmJ →	23S rRNA m(6)A2030 methyltransferase, SAM‑dependent
RA	3,641,650	G→A	13.4%	intergenic (+144/‑4)	agrA → / → agrB	Inactive antisense sRNA/Antisense sRNA antitoxin for the DinQ toxin
RA	3,643,207	C→A	7.4%	L305I (CTT→ATT)	arsB →	arsenite/antimonite transporter
RA	3,647,164	C→A	8.5%	intergenic (+91/‑157)	yhiS → / → slp	pseudogene/outer membrane lipoprotein
RA	3,651,969	G→A	8.0%	A82T (GCT→ACT)	gadE →	gad regulon transcriptional activator
RA	3,652,308	G→T	6.3%	intergenic (+55/‑284)	gadE → / → mdtE	gad regulon transcriptional activator/anaerobic multidrug efflux transporter, ArcA‑regulated
RA	3,652,326	G→T	9.1%	intergenic (+73/‑266)	gadE → / → mdtE	gad regulon transcriptional activator/anaerobic multidrug efflux transporter, ArcA‑regulated
RA	3,662,660	T→C	89.1%	intergenic (‑112/‑292)	yhjA ← / → treF	putative cytochrome C peroxidase/cytoplasmic trehalase
RA	3,667,977	C→T	6.2%	intergenic (+242/‑169)	yhjD → / → yhjE	inner membrane putative BrbK family alternate lipid exporter/MFS superfamily sugar transport 1 family protein
RA	3,670,214	C→A	6.6%	T499T (ACG→ACT)	yhjG ←	putative inner membrane‑anchored periplasmic AsmA family protein
RA	3,676,466	C→A	7.4%	A114A (GCG→GCT)	dctA ←	C4‑dicarboxylic acid, orotate and citrate transporter
RA	3,676,827	C→T	5.9%	intergenic (‑20/+163)	dctA ← / ← yhjK	C4‑dicarboxylic acid, orotate and citrate transporter/cyclic‑di‑GMP phosphodiesterase
RA	3,679,301	T→G	100%	Q1078P (CAG→CCG)	bcsC ←	cellulose synthase subunit
RA	3,679,324	C→A	100%	M1070I (ATG→ATT)	bcsC ←	cellulose synthase subunit
RA	3,680,910	G→T	90.5%	H542N (CAT→AAT)	bcsC ←	cellulose synthase subunit
RA	3,681,080	C→A	6.7%	R485L (CGG→CTG)	bcsC ←	cellulose synthase subunit
RA	3,688,591	A→C	5.7%	S2R (AGT→AGG)	bcsA ←	cellulose synthase, catalytic subunit
RA	3,689,369	C→A	5.8%	A59A (GCG→GCT)	yhjR ←	DUF2629 family protein
RA	3,698,875	G→T	59.8%	F92L (TTC→TTA)	dppB ←	dipeptide/heme transporter
RA	3,701,561	G→A	13.6%	intergenic (‑496/+415)	dppA ← / ← proK	dipeptide transporter/tRNA‑Pro
RA	3,702,965	C→A	10.8%	D291Y (GAT→TAT)	eptB ←	KDO phosphoethanolamine transferase, Ca(2+)‑inducible
RA	3,703,272	C→A	14.5%	A188A (GCG→GCT)	eptB ←	KDO phosphoethanolamine transferase, Ca(2+)‑inducible
RA	3,708,861	C→A	6.0%	E298D (GAG→GAT)	bisC ←	biotin sulfoxide reductase
RA	3,717,788	C→A	94.8%	P297P (CCG→CCT)	glyQ ←	glycine tRNA synthetase, alpha subunit
RA	3,718,959	C→A	15.7%	L38F (TTG→TTT)	ysaB ←	uncharacterized protein
RA	3,721,485	T→G	6.7%	Y416S (TAC→TCC)	xylB ←	xylulokinase
RA	3,730,615	C→A	9.5%	intergenic (‑78/‑242)	bax ← / → malS	putative glucosaminidase/alpha‑amylase
RA	3,732,978	C→T	6.1%	intergenic (+91/‑87)	malS → / → avtA	alpha‑amylase/valine‑pyruvate aminotransferase 1
RA	3,738,431	C→A	91.6%	P90T (CCA→ACA)	yiaN →	2,3‑diketo‑L‑gulonate TRAP transporter large permease protein
RA	3,740,731	G→T	43.5%	G96G (GGG→GGT)	lyxK →	L‑xylulose kinase
RA	3,744,809	C→A	46.4%	E140D (GAG→GAT)	yiaT ←	putative outer membrane protein
RA	3,759,388	C→A	9.6%	N1282K (AAC→AAA)	rhsA →	Rhs family protein, putative polymorphic toxin; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor
RA	3,767,000	G→T	65.7%	D454Y (GAC→TAC)	mtlA →	fused mannitol‑specific PTS enzymes: IIA components/IIB components/IIC components
RA	3,767,143	C→A	11.7%	I501I (ATC→ATA)	mtlA →	fused mannitol‑specific PTS enzymes: IIA components/IIB components/IIC components
RA	3,774,466	G→C	7.8%	intergenic (+89/‑109)	lldD → / → trmL	L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent
RA	3,774,518	A→C	10.8%	intergenic (+141/‑57)	lldD → / → trmL	L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent
RA	3,777,924	C→A	53.8%	intergenic (‑122/+20)	grxC ← / ← yibN	glutaredoxin 3/putative rhodanese‑related sulfurtransferase
RA	3,785,915	G→T	87.6%	intergenic (‑4/+271)	kbl ← / ← yibB	glycine C‑acetyltransferase/YibB family protein, function unknown
RA	3,791,588	T→A	8.0%	intergenic (+21/+11)	waaL → / ← waaU	O‑antigen ligase/lipopolysaccharide core biosynthesis
RA	3,793,319	C→A	5.2%	D80Y (GAT→TAT)	waaZ ←	lipopolysaccharide core biosynthesis protein
JC JC	3,795,902	IS5 (+) +4 bp	7.0%	coding (514‑517/1020 nt)	waaR ←	UDP‑D‑galactose:(glucosyl)lipopolysaccharide‑ alpha‑1,3‑D‑galactosyltransferase
RA	3,802,238	A→T	10.7%	A113A (GCA→GCT)	waaA →	3‑deoxy‑D‑manno‑octulosonic‑acid transferase (KDO transferase)
RA	3,809,236	G→T	40.3%	pseudogene (6/48 nt)	rph ←	ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
RA	3,810,195	C→A	93.1%	R54S (CGT→AGT)	yicC →	UPF0701 family protein
RA	3,814,302	T→A	11.7%	S77C (AGC→TGC)	ligB ←	DNA ligase, NAD(+)‑dependent
RA	3,815,043	C→A	7.5%	R86S (CGT→AGT)	gmk →	guanylate kinase
RA	3,816,601	A→T	90.4%	H281L (CAC→CTC)	spoT →	bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
RA	3,816,686	G→T	47.3%	S309S (TCG→TCT)	spoT →	bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
RA	3,818,010	C→A	94.1%	H46N (CAT→AAT)	trmH →	tRNA mG18‑2'‑O‑methyltransferase, SAM‑dependent
RA	3,825,702	C→A	94.6%	K732N (AAG→AAT)	yicI ←	putative alpha‑glucosidase
RA	3,829,020	G→T	45.0%	F90L (TTC→TTA)	yicJ ←	putative transporter
RA	3,829,416	C→A	8.0%	intergenic (‑127/‑166)	yicJ ← / → selC	putative transporter/tRNA‑Sec
RA	3,829,715	T→G	10.7%	intergenic (+39/‑70)	selC → / → yicT	tRNA‑Sec/pseudogene
RA	3,830,197	C→A	91.7%	intergenic (+281/‑116)	yicT → / → setC	pseudogene/putative arabinose efflux transporter
RA	3,830,311	G→T	90.9%	intergenic (+395/‑2)	yicT → / → setC	pseudogene/putative arabinose efflux transporter
RA	3,834,958	G→T	43.3%	Q48K (CAG→AAG)	nepI ←	putative transporter
RA	3,835,154	G→A	9.4%	intergenic (‑55/+156)	nepI ← / ← yicN	putative transporter/DUF1198 family protein
RA	3,837,177	C→T	5.6%	intergenic (‑28/‑147)	yicO ← / → ade	putative adenine permease/cryptic adenine deaminase
RA	3,839,034	C→A	49.7%	Q571K (CAG→AAG)	ade →	cryptic adenine deaminase
RA	3,846,307	C→A	8.0%	A14A (GCG→GCT)	ivbL ←	ilvB operon leader peptide
RA	3,846,427	G→T	6.1%	intergenic (‑79/+51)	ivbL ← / ← istR	ilvB operon leader peptide/sRNA antisense regulators IstR‑1 and IstR‑2, affectr tisB, Hfq‑dependent
RA	3,853,869	T→A	6.0%	L76* (TTA→TAA)	yidL →	AraC family putative transcriptional regulator
RA	3,858,963	A→T	48.7%	V224E (GTA→GAA)	yidE ←	putative transporter
RA	3,860,159	C→A	92.7%	P33P (CCG→CCT)	ibpB ←	heat shock chaperone
RA	3,860,327	C→A	67.0%	intergenic (‑70/+42)	ibpB ← / ← ibpA	heat shock chaperone/heat shock chaperone
RA	3,860,653	C→A	65.6%	E44* (GAA→TAA)	ibpA ←	heat shock chaperone
RA	3,865,120	C→A	70.9%	intergenic (‑30/+90)	dgoT ← / ← dgoD	D‑galactonate transporter/galactonate dehydratase
RA	3,866,350	G→T	7.6%	I3I (ATC→ATA)	dgoD ←	galactonate dehydratase
RA	3,876,274	C→A	6.7%	P272P (CCG→CCT)	dnaA ←	chromosomal replication initiator protein DnaA, DNA‑binding transcriptional dual regulator
RA	3,882,020	G→T	52.0%	intergenic (+151/‑70)	tnaC → / → tnaA	tryptophanase leader peptide/tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent
RA	3,883,535	T→A	7.5%	intergenic (+30/‑61)	tnaA → / → tnaB	tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent/tryptophan transporter of low affinity
RA	3,888,563	G→T	36.9%	Q184H (CAG→CAT)	chrR →	chromate reductase, Class I, flavoprotein
RA	3,891,652	G→T	12.3%	E91* (GAA→TAA)	cbrC →	UPF0167 family protein
RA	3,893,385	C→A	10.7%	D185Y (GAT→TAT)	yieL ←	putative xylanase
RA	3,895,052	G→T	5.2%	R177R (CGG→AGG)	bglH ←	carbohydrate‑specific outer membrane porin, cryptic
RA	3,896,189	G→T	8.5%	T291T (ACC→ACA)	bglB ←	cryptic phospho‑beta‑glucosidase B
RA	3,897,754	T→G	8.6%	T402P (ACG→CCG)	bglF ←	fused beta‑glucoside‑specific PTS enzymes: IIA component/IIB component/IIC component
RA	3,906,261	C→A	6.7%	E256D (GAG→GAT)	glmS ←	L‑glutamine:D‑fructose‑6‑phosphate aminotransferase
RA	3,907,508	T→A	5.3%	K351N (AAA→AAT)	glmU ←	fused N‑acetyl glucosamine‑1‑phosphate uridyltransferase/glucosamine‑1‑phosphate acetyl transferase
RA	3,910,487	C→A	6.6%	A83A (GCG→GCT)	atpD ←	F1 sector of membrane‑bound ATP synthase, beta subunit
RA	3,910,894	C→A	92.8%	M244I (ATG→ATT)	atpG ←	F1 sector of membrane‑bound ATP synthase, gamma subunit
RA	3,916,052	C→A	17.1%	intergenic (‑252/+365)	atpI ← / ← rsmG	ATP synthase, membrane‑bound accessory factor/16S rRNA m(7)G527 methyltransferase, SAM‑dependent; glucose‑inhibited cell‑division protein
RA	3,916,830	C→A	89.9%	D71Y (GAT→TAT)	rsmG ←	16S rRNA m(7)G527 methyltransferase, SAM‑dependent; glucose‑inhibited cell‑division protein
RA	3,917,548	C→A	9.5%	S482S (TCG→TCT)	mnmG ←	5‑methylaminomethyl‑2‑thiouridine modification at tRNA U34
RA	3,920,013	G→T	8.4%	D117E (GAC→GAA)	asnC ←	transcriptional activator of asnA; autorepressor
RA	3,923,028	C→A	64.9%	D476Y (GAC→TAC)	ravA ←	hexameric AAA+ MoxR family ATPase, putative molecular chaperone
RA	3,923,775	G→T	5.6%	H227N (CAT→AAT)	ravA ←	hexameric AAA+ MoxR family ATPase, putative molecular chaperone
RA	3,926,774	G→T	5.1%	D22Y (GAT→TAT)	rbsD →	putative cytoplasmic sugar‑binding protein
RA	3,926,831	G→T	92.0%	D41Y (GAT→TAT)	rbsD →	putative cytoplasmic sugar‑binding protein
RA	3,927,972	G→T	71.5%	E279* (GAA→TAA)	rbsA →	fused D‑ribose transporter subunits of ABC superfamily: ATP‑binding components
RA	3,930,411	C→A	5.8%	I258I (ATC→ATA)	rbsB →	D‑ribose transporter subunit
RA	3,933,525	A→T	9.7%	L150I (TTA→ATA)	hsrA ←	putative multidrug or homocysteine efflux system
RA	3,935,100	G→T	60.3%	intergenic (‑413/‑68)	yieP ← / → rrsC	putative transcriptional regulator/16S ribosomal RNA of rrnC operon
RA	3,950,395	C→A	11.2%	E262D (GAG→GAT)	ilvY ←	transcriptional activator of ilvC; autorepressor
RA	3,952,658	C→T	15.0%	D443D (GAC→GAT)	ilvC →	ketol‑acid reductoisomerase, NAD(P)‑binding
RA	3,952,852	A→T	12.1%	intergenic (+47/+40)	ilvC → / ← ppiC	ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C)
RA	3,959,243	G→T	5.7%	P41P (CCG→CCT)	trxA →	thioredoxin 1
RA	3,960,036	G→A	100%	R87H (CGC→CAC)	rho →	transcription termination factor
RA	3,966,854	C→A	89.9%	R325S (CGT→AGT)	rffG →	dTDP‑glucose 4,6‑dehydratase
RA	3,967,474	G→T	69.0%	A169A (GCG→GCT)	rffH →	glucose‑1‑phosphate thymidylyltransferase
RA	3,969,710	G→T	100%	G25C (GGT→TGT)	wzxE →	O‑antigen translocase
RA	3,971,078	C→A	5.8%	A65E (GCG→GAG)	wecF →	TDP‑Fuc4NAc:lipidIIFuc4NAc transferase
RA	3,984,342	G→T	45.6%	intergenic (‑216/‑171)	hemC ← / → cyaA	hydroxymethylbilane synthase/adenylate cyclase
RA	3,988,075	T→A	90.3%	V65E (GTG→GAG)	yifL →	putative lipoprotein
RA	3,994,076	A→T	92.9%	L114* (TTA→TAA)	yigE ←	DUF2233 family protein
RA	3,994,247	A→T	92.9%	V57E (GTG→GAG)	yigE ←	DUF2233 family protein
RA	3,994,758	G→T	51.5%	intergenic (‑342/‑28)	yigE ← / → corA	DUF2233 family protein/magnesium/nickel/cobalt transporter
RA	3,997,144	G→T	11.4%	A132E (GCG→GAG)	rarD ←	putative chloramphenical resistance permease
RA	3,998,903	C→A	6.9%	L228I (CTC→ATC)	pldA →	outer membrane phospholipase A
RA	4,001,030	G→T	32.1%	V603F (GTT→TTT)	recQ →	ATP‑dependent DNA helicase
RA	4,002,799	C→A	6.3%	R90R (CGC→CGA)	pldB →	lysophospholipase L2
RA	4,002,848	G→T	8.1%	V107F (GTT→TTT)	pldB →	lysophospholipase L2
RA	4,008,236	G→T	13.7%	P608P (CCG→CCT)	metE →	5‑methyltetrahydropteroyltriglutamate‑ homocysteine S‑methyltransferase
RA	4,009,389	G→T	8.7%	A47A (GCC→GCA)	ysgA ←	putative carboxymethylenebutenolidase
RA	4,009,705	G→A	93.7%	intergenic (‑176/‑86)	ysgA ← / → udp	putative carboxymethylenebutenolidase/uridine phosphorylase
RA	4,011,961	G→T	6.6%	A423A (GCG→GCT)	rmuC →	DNA recombination protein
RA	4,023,757	T→A	42.9%	K192I (AAA→ATA)	fadB ←	fused 3‑hydroxybutyryl‑CoA epimerase/delta(3)‑cis‑delta(2)‑trans‑enoyl‑CoA isomerase/enoyl‑CoA hydratase/3‑hydroxyacyl‑CoA dehydrogenase
RA	4,024,233	A→C	41.9%	T33T (ACT→ACG)	fadB ←	fused 3‑hydroxybutyryl‑CoA epimerase/delta(3)‑cis‑delta(2)‑trans‑enoyl‑CoA isomerase/enoyl‑CoA hydratase/3‑hydroxyacyl‑CoA dehydrogenase
RA	4,024,827	G→T	69.6%	D103Y (GAT→TAT)	pepQ →	proline dipeptidase
RA	4,035,421	G→T	68.1%	intergenic (‑62/‑8)	mobA ← / → yihD	molybdopterin‑guanine dinucleotide synthase/DUF1040 protein YihD
RA	4,039,399	G→T	11.0%	F188L (TTC→TTA)	yihG ←	inner membrane protein, inner membrane acyltransferase
RA	4,040,649	G→T	12.9%	A108A (GCG→GCT)	polA →	fused DNA polymerase I 5'‑>3' polymerase/3'‑>5' exonuclease/5'‑>3' exonuclease
RA	4,046,172	A→T	67.7%	K256N (AAA→AAT)	hemN →	coproporphyrinogen III oxidase, SAM and NAD(P)H dependent, oxygen‑independent
RA	4,047,387	G→T	6.1%	H418N (CAT→AAT)	glnG ←	fused DNA‑binding response regulator in two‑component regulatory system with GlnL: response regulator/sigma54 interaction protein
RA	4,049,845	G→T	6.2%	intergenic (‑146/+140)	glnL ← / ← glnA	sensory histidine kinase in two‑component regulatory system with GlnG/glutamine synthetase
RA	4,052,201	C→A	7.8%	F145L (TTC→TTA)	typA →	GTP‑binding protein
RA	4,054,222	T→A	51.6%	V139D (GTT→GAT)	yihL →	putative DNA‑binding transcriptional regulator
RA	4,056,018	T→A	90.5%	F138I (TTC→ATC)	yihN →	MFS transporter family protein
RA	4,062,424	G→T	93.2%	I71I (ATC→ATA)	yihQ ←	alpha‑glucosidase
RA	4,066,133	T→G	92.8%	S267R (AGC→CGC)	yihU ←	gamma‑hydroxybutyrate dehydrogenase, NADH‑dependent
RA	4,068,208	C→A	92.4%	G60G (GGC→GGA)	yihW →	DeoR family putative transcriptional regulator
RA	4,078,761	C→A	47.9%	R141L (CGC→CTC)	fdoG ←	formate dehydrogenase‑O, large subunit
RA	4,089,371	A→T	38.6%	E266D (GAA→GAT)	rhaR →	transcriptional activator of rhaSR
RA	4,094,362	C→A	93.0%	W181L (TGG→TTG)	cpxA ←	sensory histidine kinase in two‑component regulatory system with CpxR
RA	4,096,555	G→T	6.1%	S53S (TCG→TCT)	fieF →	ferrous iron and zinc transporter
RA	4,097,822	G→T	94.2%	E115* (GAA→TAA)	pfkA →	6‑phosphofructokinase I
RA	4,105,186	C→A	8.0%	D108Y (GAT→TAT)	glpX ←	fructose 1,6‑bisphosphatase II
RA	4,122,248	A→T	68.1%	intergenic (+53/‑296)	metL → / → metF	Bifunctional aspartokinase/homoserine dehydrogenase 2/5,10‑methylenetetrahydrofolate reductase
RA	4,127,022	T→G	100%	E188D (GAA→GAC)	yijF ←	DUF1287 family protein
RA	4,128,613	G→T	8.7%	I117I (ATC→ATA)	gldA ←	glycerol dehydrogenase, NAD+ dependent; 1,2‑propanediol:NAD+ oxidoreductase
RA	4,143,375	A→G	5.6%	intergenic (‑349/+249)	ppc ← / ← argE	phosphoenolpyruvate carboxylase/acetylornithine deacetylase
RA	4,143,544	C→T	5.1%	intergenic (‑518/+80)	ppc ← / ← argE	phosphoenolpyruvate carboxylase/acetylornithine deacetylase
RA	4,143,605	G→T	13.3%	intergenic (‑579/+19)	ppc ← / ← argE	phosphoenolpyruvate carboxylase/acetylornithine deacetylase
RA	4,144,606	C→T	8.3%	G57E (GGA→GAA)	argE ←	acetylornithine deacetylase
RA	4,144,697	C→A	7.3%	A27S (GCA→TCA)	argE ←	acetylornithine deacetylase
RA	4,144,818	G→A	6.8%	intergenic (‑43/‑111)	argE ← / → argC	acetylornithine deacetylase/N‑acetyl‑gamma‑glutamylphosphate reductase, NAD(P)‑binding
RA	4,150,043	G→T	13.9%	H226N (CAC→AAC)	sthA ←	pyridine nucleotide transhydrogenase, soluble
RA	4,158,047	G→T	10.7%	noncoding (1461/1542 nt)	rrsB →	16S ribosomal RNA of rrnB operon
RA	4,163,151	G→T	5.8%	V48F (GTT→TTT)	birA →	bifunctional biotin‑[acetylCoA carboxylase] holoenzyme synthetase/ DNA‑binding transcriptional repressor, bio‑5'‑AMP‑binding
RA	4,163,570	T→A	15.2%	I187I (ATT→ATA)	birA →	bifunctional biotin‑[acetylCoA carboxylase] holoenzyme synthetase/ DNA‑binding transcriptional repressor, bio‑5'‑AMP‑binding
RA	4,167,908	T→A	7.5%	W80R (TGG→AGG)	nusG →	transcription termination factor
RA	4,168,956	C→A	8.6%	I50I (ATC→ATA)	rplA →	50S ribosomal subunit protein L1
RA	4,172,414	C→A	29.8%	I414I (ATC→ATA)	rpoB →	RNA polymerase, beta subunit
RA	4,173,145	A→T	63.0%	Q658L (CAG→CTG)	rpoB →	RNA polymerase, beta subunit
RA	4,176,339	A→T	10.3%	V354V (GTA→GTT)	rpoC →	RNA polymerase, beta prime subunit
RA	4,176,823	G→T	92.6%	D516Y (GAC→TAC)	rpoC →	RNA polymerase, beta prime subunit
RA	4,178,758	G→T	13.1%	G1161C (GGT→TGT)	rpoC →	RNA polymerase, beta prime subunit
RA	4,179,520	C→A	41.6%	intergenic (+19/‑194)	rpoC → / → yjaZ	RNA polymerase, beta prime subunit/stationary phase growth adaptation protein
RA	4,189,766	C→A	46.4%	T112K (ACG→AAG)	yjaG →	DUF416 domain protein
RA	4,194,337	G→T	14.0%	A364S (GCG→TCG)	zraR →	fused DNA‑binding response regulator in two‑component regulatory system with ZraS: response regulator/sigma54 interaction protein
RA	4,206,153	G→T	7.8%	E250* (GAA→TAA)	aceB →	malate synthase A
RA	4,207,552	G→T	68.0%	M172I (ATG→ATT)	aceA →	isocitrate lyase
RA	4,207,558	G→T	13.4%	A174A (GCG→GCT)	aceA →	isocitrate lyase
RA	4,208,942	C→A	48.9%	A140E (GCG→GAG)	aceK →	isocitrate dehydrogenase kinase/phosphatase
RA	4,208,975	C→A	7.1%	S151Y (TCT→TAT)	aceK →	isocitrate dehydrogenase kinase/phosphatase
RA	4,211,576	G→T	93.0%	S280R (AGC→AGA)	arpA ←	ankyrin repeat protein
RA	4,211,803	G→A	100%	P205S (CCT→TCT)	arpA ←	ankyrin repeat protein
RA	4,214,563	A→T	75.3%	T270S (ACC→TCC)	metH →	homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent
RA	4,217,818	G→T	47.5%	V54F (GTT→TTT)	yjbB →	putative Na+/Pi‑cotransporter
RA	4,218,928	G→A	12.1%	E424K (GAA→AAA)	yjbB →	putative Na+/Pi‑cotransporter
RA	4,219,081	C→A	16.2%	R475S (CGC→AGC)	yjbB →	putative Na+/Pi‑cotransporter
RA	4,219,550	C→A	8.1%	R174L (CGT→CTT)	pepE ←	(alpha)‑aspartyl dipeptidase
RA	4,220,948	G→T	7.2%	D223Y (GAT→TAT)	rluF →	23S rRNA pseudouridine(2604) synthase
RA	4,222,149	G→T	10.9%	S338* (TCG→TAG)	lysC ←	lysine‑sensitive aspartokinase 3
RA	4,230,913	A→T	90.4%	W424R (TGG→AGG)	xylE ←	D‑xylose transporter
RA	4,235,869	G→T	64.7%	A160E (GCG→GAG)	malE ←	maltose transporter subunit
RA	4,237,140	G→T	5.2%	A143A (GCG→GCT)	malK →	fused maltose transport subunit, ATP‑binding component of ABC superfamily/regulatory protein
RA	4,237,418	C→A	5.5%	S236* (TCG→TAG)	malK →	fused maltose transport subunit, ATP‑binding component of ABC superfamily/regulatory protein
RA	4,241,633	C→T	10.5%	pseudogene (745/1323 nt)	yjbI →	pseudogene, SopA‑related, pentapeptide repeats‑containing
RA	4,242,509	C→T	63.0%	L26F (CTC→TTC)	ubiC →	chorismate‑‑pyruvate lyase
RA	4,245,789	A→T	6.8%	R202R (CGT→CGA)	plsB ←	glycerol‑3‑phosphate O‑acyltransferase
RA	4,247,030	C→T	8.9%	intergenic (+97/‑13)	dgkA → / → lexA	diacylglycerol kinase/transcriptional repressor of SOS regulon
RA	4,250,664	A→C	9.8%	A46A (GCA→GCC)	yjbM →	uncharacterized protein
RA	4,256,589	G→T	42.7%	E294* (GAA→TAA)	alr →	alanine racemase, biosynthetic, PLP‑binding
RA	4,256,930	G→T	6.7%	intergenic (+141/‑112)	alr → / → tyrB	alanine racemase, biosynthetic, PLP‑binding/tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent
RA	4,258,418	G→A	48.8%	intergenic (+183/+319)	tyrB → / ← yjbS	tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent/uncharacterized protein
RA	4,259,065	C→A	50.0%	intergenic (‑125/‑277)	yjbS ← / → aphA	uncharacterized protein/acid phosphatase/phosphotransferase, class B, non‑specific
RA	4,259,874	C→A	8.1%	S178* (TCG→TAG)	aphA →	acid phosphatase/phosphotransferase, class B, non‑specific
RA	4,260,920	G→T	5.8%	R112L (CGT→CTT)	yjbR →	DUF419 family protein
RA	4,265,064	C→A	91.9%	intergenic (‑95/‑335)	yjcB ← / → yjcC	putative inner membrane protein/putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	4,268,967	A→T	11.7%	S187S (TCA→TCT)	yjcD →	inner membrane putative guanine permease
RA	4,270,316	G→T	57.7%	E137* (GAA→TAA)	yjcE →	putative cation/proton antiporter
RA	4,271,906	C→T	14.0%	E366E (GAG→GAA)	yjcF ←	pentapeptide repeats protein
RA	4,273,297	A→T	14.0%	W512R (TGG→AGG)	actP ←	acetate transporter
RA	4,274,748	C→A	49.6%	R28L (CGC→CTC)	actP ←	acetate transporter
RA	4,274,926	A→C	91.7%	I72M (ATT→ATG)	yjcH ←	DUF485 family inner membrane protein
RA	4,275,142	C→A	93.3%	intergenic (‑1/+199)	yjcH ← / ← acs	DUF485 family inner membrane protein/acetyl‑CoA synthetase
RA	4,276,940	G→T	49.5%	F120L (TTC→TTA)	acs ←	acetyl‑CoA synthetase
RA	4,277,386	G→T	7.2%	intergenic (‑87/‑306)	acs ← / → nrfA	acetyl‑CoA synthetase/nitrite reductase, formate‑dependent, cytochrome
RA	4,278,325	T→A	6.5%	C212S (TGC→AGC)	nrfA →	nitrite reductase, formate‑dependent, cytochrome
RA	4,281,581	G→T	43.0%	D48Y (GAT→TAT)	nrfE →	heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfE
RA	4,286,118	A→G	6.6%	intergenic (+396/+135)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA	4,290,080	G→T	94.2%	I256I (ATC→ATA)	mdtP ←	outer membrane factor of efflux pump
RA	4,295,218	C→A	12.2%	M399I (ATG→ATT)	yjcS ←	metallo‑beta‑lactamase superfamily protein
RA	4,297,485	G→C	63.1%	G44G (GGC→GGG)	alsK ←	D‑allose kinase
RA	4,297,846	C→A	94.4%	M150I (ATG→ATT)	alsE ←	allulose‑6‑phosphate 3‑epimerase
RA	4,300,333	T→A	14.0%	E155D (GAA→GAT)	alsA ←	fused D‑allose transporter subunits of ABC superfamily: ATP‑binding components
RA	4,303,614	T→A	94.6%	*150R (TGA→AGA)	rpiB →	ribose 5‑phosphate isomerase B/allose 6‑phosphate isomerase
RA	4,304,132	G→T	9.0%	intergenic (+118/+29)	yjdP → / ← phnP	putative periplasmic protein/5‑phospho‑alpha‑D‑ribosyl 1,2‑cyclic phosphate phosphodiesterase
RA	4,305,623	C→A	9.3%	V93L (GTG→TTG)	phnN ←	ribose 1,5‑bisphosphokinase
RA	4,308,395	G→T	13.5%	H63N (CAC→AAC)	phnK ←	carbon‑phosphorus lyase complex subunit, putative ATP transporter ATP‑binding protein
RA	4,317,243	C→A	46.0%	R98S (CGT→AGT)	crfC →	clamp‑binding sister replication fork colocalization protein, dynamin‑related
RA	4,317,249	C→A	5.5%	R100S (CGC→AGC)	crfC →	clamp‑binding sister replication fork colocalization protein, dynamin‑related
RA	4,317,974	G→T	7.5%	A341A (GCG→GCT)	crfC →	clamp‑binding sister replication fork colocalization protein, dynamin‑related
RA	4,322,724	G→T	6.0%	I122I (ATC→ATA)	basS ←	sensory histidine kinase in two‑component regulatory system with BasR
RA	4,330,426	Δ1 bp	100%	intergenic (‑88/+111)	adiA ← / ← melR	arginine decarboxylase/melibiose operon transcriptional regulator; autoregulator
RA	4,335,003	A→T	6.9%	Y125N (TAC→AAC)	yjdF ←	DUF2238 family inner membrane protein
RA	4,335,195	G→T	8.1%	L61I (CTC→ATC)	yjdF ←	DUF2238 family inner membrane protein
RA	4,335,262	C→A	6.5%	V38V (GTG→GTT)	yjdF ←	DUF2238 family inner membrane protein
RA	4,336,424	G→T	8.3%	T240T (ACC→ACA)	fumB ←	anaerobic class I fumarate hydratase (fumarase B)
RA	4,336,681	A→T	8.3%	Y155N (TAC→AAC)	fumB ←	anaerobic class I fumarate hydratase (fumarase B)
RA	4,336,835	C→A	5.8%	P103P (CCG→CCT)	fumB ←	anaerobic class I fumarate hydratase (fumarase B)
RA	4,338,712	T→A	5.4%	intergenic (‑151/+420)	dcuB ← / ← dcuR	C4‑dicarboxylate transporter, anaerobic; DcuS co‑sensor/response regulator in two‑component regulatory system with DcuS
RA	4,341,023	A→T	92.4%	Y153N (TAC→AAC)	dcuS ←	sensory histidine kinase in two‑component regulatory system with DcuR, regulator of anaerobic fumarate respiration
RA	4,345,995	C→A	17.2%	V78V (GTG→GTT)	dtpC ←	dipeptide and tripeptide permease
RA	4,349,694	G→A	10.6%	S52L (TCG→TTG)	cadB ←	putative lysine/cadaverine transporter
RA	4,353,069	A→T	6.4%	I19I (ATT→ATA)	yjdC ←	putative transcriptional regulator
RA	4,354,610	A→T	13.1%	W84R (TGG→AGG)	dsbD ←	fused thiol:disulfide interchange protein: activator of DsbC/conserved protein
RA	4,355,606	G→T	9.3%	H329N (CAT→AAT)	dcuA ←	C4‑dicarboxylate antiporter
RA	4,358,920	G→T	62.5%	R147L (CGC→CTC)	fxsA →	suppressor of F exclusion of phage T7
RA	4,358,943	G→T	38.5%	D155Y (GAT→TAT)	fxsA →	suppressor of F exclusion of phage T7
RA	4,366,263	T→G	5.4%	intergenic (+4/‑107)	ecnA → / → ecnB	entericidin A membrane lipoprotein, antidote entericidin B/entericidin B membrane lipoprotein
RA	4,368,389	G→T	11.9%	L125I (CTC→ATC)	ampC ←	penicillin‑binding protein; beta‑lactamase, intrinsically weak
RA	4,371,380	G→T	10.7%	G252G (GGC→GGA)	frdA ←	fumarate reductase (anaerobic) catalytic and NAD/flavoprotein subunit
RA	4,372,891	A→T	21.1%	A144A (GCA→GCT)	epmA →	Elongation Factor P Lys34 lysyltransferase
RA	4,373,522	C→T	45.3%	intergenic (+85/‑134)	epmA → / → yjeM	Elongation Factor P Lys34 lysyltransferase/putative transporter
RA	4,375,157	A→C	10.0%	*501S (TAA→TCA)	yjeM →	putative transporter
RA	4,376,178	C→A	75.2%	E1004* (GAA→TAA)	mscM ←	mechanosensitive channel protein, miniconductance
RA	4,378,778	G→T	68.4%	S137* (TCG→TAG)	mscM ←	mechanosensitive channel protein, miniconductance
RA	4,381,462	G→A	13.7%	E14E (GAG→GAA)	orn →	oligoribonuclease
RA	4,386,747	G→T	7.4%	R289L (CGT→CTT)	amiB →	N‑acetylmuramoyl‑l‑alanine amidase II
RA	4,388,902	G→T	90.8%	A558A (GCG→GCT)	mutL →	methyl‑directed mismatch repair protein
RA	4,390,034	G→T	13.8%	intergenic (+15/‑71)	miaA → / → hfq	delta(2)‑isopentenylpyrophosphate tRNA‑adenosine transferase/global sRNA chaperone; HF‑I, host factor for RNA phage Q beta replication
RA	4,394,391	G→T	7.0%	T63T (ACG→ACT)	yjeT →	DUF2065 family protein
RA	4,394,875	G→T	56.1%	A124A (GCG→GCT)	purA →	adenylosuccinate synthetase
RA	4,396,598	A→T	100%	E43V (GAA→GTA)	rnr →	exoribonuclease R, RNase R
RA	4,401,343	A→T	45.6%	S75S (TCA→TCT)	yjfK →	DUF2491 family protein
RA	4,402,850	G→T	67.6%	L2L (CTG→CTT)	yjfC →	ATP‑Grasp family ATPase
RA	4,405,735	G→T	10.8%	intergenic (+18/+99)	aidB → / ← yjfN	DNA alkylation damage repair protein; flavin‑containing DNA binding protein, weak isovaleryl CoA dehydrogenase/DUF1471 family periplasmic protein
RA	4,407,017	C→T	45.4%	I83I (ATC→ATT)	yjfP →	acyl CoA esterase
RA	4,413,286	C→A	5.7%	V208V (GTC→GTA)	ulaE →	L‑xylulose 5‑phosphate 3‑epimerase
RA	4,414,219	A→T	8.1%	intergenic (+16/+114)	ulaF → / ← yjfY	L‑ribulose 5‑phosphate 4‑epimerase/YhcN family protein, periplasmic
RA	4,417,551	A→C	93.1%	pseudogene (41/402 nt)	ytfA →	pseudogene, related to transcriptional regulators
RA	4,425,271	T→G	7.5%	Q371P (CAG→CCG)	cpdB ←	2':3'‑cyclic‑nucleotide 2'‑phosphodiesterase
RA	4,425,324	G→A	6.8%	S353S (AGC→AGT)	cpdB ←	2':3'‑cyclic‑nucleotide 2'‑phosphodiesterase
RA	4,428,092	G→T	72.3%	G190V (GGA→GTA)	ytfI →	uncharacterized protein
RA	4,429,851	C→A	5.4%	P394P (CCG→CCT)	ytfL ←	UPF0053 family inner membrane protein
RA	4,431,420	G→T	6.6%	H192N (CAT→AAT)	msrA ←	methionine sulfoxide reductase A
RA	4,433,219	G→T	7.9%	D341Y (GAT→TAT)	tamA →	translocation and assembly module for autotransporter export, outer membrane subunit
RA	4,435,607	C→A	8.4%	A560E (GCG→GAG)	tamB →	translocation and assembly module for autotransporter export, inner membrane subunit
RA	4,440,321	C→A	10.2%	I181I (ATC→ATA)	ytfQ →	galactofuranose binding proteint: periplasmic‑binding component of ABC superfamily
RA	4,444,527	G→T	10.3%	I300I (ATC→ATA)	fbp ←	fructose‑1,6‑bisphosphatase I
RA	4,458,254	T→A	100%	V271V (GTT→GTA)	mgtA →	magnesium transporter
RA	4,458,609	G→T	93.7%	D390Y (GAT→TAT)	mgtA →	magnesium transporter
RA	4,460,919	T→A	5.3%	S116C (AGC→TGC)	pyrI ←	aspartate carbamoyltransferase, regulatory subunit
RA	4,461,317	G→T	45.2%	A299E (GCG→GAG)	pyrB ←	aspartate carbamoyltransferase, catalytic subunit
RA	4,462,966	A→T	8.5%	Y21N (TAT→AAT)	yjgH ←	UPF0131 family protein
RA	4,465,086	G→T	5.8%	A136A (GCG→GCT)	tabA →	biofilm modulator regulated by toxins; DUF386 family protein, cupin superfamily
RA	4,465,624	C→T	10.6%	S124F (TCC→TTC)	yjgL →	uncharacterized protein
RA	4,465,818	A→C	6.4%	N189H (AAT→CAT)	yjgL →	uncharacterized protein
RA	4,468,165	A→G	87.8%	intergenic (‑37/‑125)	argI ← / → rraB	ornithine carbamoyltransferase 1/protein inhibitor of RNase E
RA	4,469,550	G→A	88.2%	A2T (GCT→ACT)	yjgN →	DUF898 family inner membrane protein
RA	4,469,639	T→G	8.5%	N31K (AAT→AAG)	yjgN →	DUF898 family inner membrane protein
RA	4,470,017	G→A	91.5%	M157I (ATG→ATA)	yjgN →	DUF898 family inner membrane protein
RA	4,470,873	G→T	64.9%	R928S (CGT→AGT)	valS ←	valyl‑tRNA synthetase
RA	4,474,354	G→A	5.8%	A472V (GCC→GTC)	pepA ←	multifunctional aminopeptidase A: a cyteinylglycinase, transcription regulator and site‑specific recombination factor
RA	4,474,571	T→A	5.2%	N400Y (AAT→TAT)	pepA ←	multifunctional aminopeptidase A: a cyteinylglycinase, transcription regulator and site‑specific recombination factor
RA	4,481,249	A→T	8.4%	V365E (GTG→GAG)	idnT ←	L‑idonate and D‑gluconate transporter
RA	4,494,150	C→A	5.4%	V92V (GTC→GTA)	yjhB →	putative transporter
RA	4,494,721	G→A	70.8%	A283T (GCC→ACC)	yjhB →	putative transporter
RA	4,495,063	A→G	8.6%	K397E (AAA→GAA)	yjhB →	putative transporter
RA	4,495,560	A→T	14.7%	N153Y (AAC→TAC)	yjhC →	putative oxidoreductase
RA	4,497,253	G→T	7.2%	pseudogene (240/255 nt)	insO →	pseudogene, IS911 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related
RA	4,512,693	T→A	92.4%	K407* (AAG→TAG)	yjhG ←	putative dehydratase
RA	4,514,591	G→T	7.2%	V79V (GTC→GTA)	yjhH ←	putative lyase/synthase
RA	4,519,217	A→T	51.7%	F282I (TTC→ATC)	sgcC ←	putative PTS system EIIC permease component
RA	4,523,001	T→A	60.5%	intergenic (‑1/+55)	yjhP ← / ← yjhQ	putative methyltransferase/putative acetyltransferase
RA	4,523,345	G→T	7.7%	A86E (GCG→GAG)	yjhQ ←	putative acetyltransferase
RA	4,525,234	G→A	92.0%	pseudogene (415/1029 nt)	yjhR →	pseudogene, helicase family; putative frameshift suppressor
RA	4,530,002	C→A	7.7%	intergenic (‑684/‑772)	nanC ← / → fimB	N‑acetylnuraminic acid outer membrane channel protein/tyrosine recombinase/inversion of on/off regulator of fimA
RA	4,530,011	C→T	5.2%	intergenic (‑693/‑763)	nanC ← / → fimB	N‑acetylnuraminic acid outer membrane channel protein/tyrosine recombinase/inversion of on/off regulator of fimA
RA	4,531,143	A→T	100%	I124F (ATT→TTT)	fimB →	tyrosine recombinase/inversion of on/off regulator of fimA
RA	4,531,451	A→G	5.0%	intergenic (+75/‑403)	fimB → / → fimE	tyrosine recombinase/inversion of on/off regulator of fimA/tyrosine recombinase/inversion of on/off regulator of fimA
RA	4,531,503	G→A	9.0%	intergenic (+127/‑351)	fimB → / → fimE	tyrosine recombinase/inversion of on/off regulator of fimA/tyrosine recombinase/inversion of on/off regulator of fimA
RA	4,532,449	G→T	7.2%	*199L (TGA→TTA)	fimE →	tyrosine recombinase/inversion of on/off regulator of fimA
RA	4,534,466	G→A	7.9%	E116K (GAA→AAA)	fimC →	periplasmic chaperone
RA	4,541,449	A→T	64.6%	intergenic (‑336/‑4)	gntP ← / → uxuA	fructuronate transporter/mannonate hydrolase
RA	4,552,902	A→T	6.0%	N173K (AAT→AAA)	yjiK ←	SdiA‑regulated family putative membrane‑anchored protein; putative phytase‑like esterase
RA	4,555,156	G→T	92.9%	A171E (GCG→GAG)	yjiM ←	putative 2‑hydroxyglutaryl‑CoA dehydratase
RA	4,562,043	C→A	93.8%	intergenic (+311/‑188)	yjiS → / → yjiT	DUF1127 family protein/pseudogene
RA	4,564,939	G→T	7.4%	pseudogene (1204/2937 nt)	yjiV →	pseudogene; conserved hypothetical protein
RA	4,565,742	C→A	8.8%	pseudogene (2007/2937 nt)	yjiV →	pseudogene; conserved hypothetical protein
RA	4,566,347	C→A	9.3%	pseudogene (2612/2937 nt)	yjiV →	pseudogene; conserved hypothetical protein
RA	4,568,419	G→T	13.3%	R246S (CGT→AGT)	mcrB ←	5‑methylcytosine‑specific restriction enzyme McrBC, subunit McrB
RA	4,569,668	C→A	6.3%	noncoding (17/77 nt)	symR →	sRNA antisense regulator destabilizing divergent and overlapping symE mRNA
RA	4,571,233	G→A	66.1%	S16F (TCT→TTT)	hsdS ←	specificity determinant for hsdM and hsdR
RA	4,572,227	G→T	43.0%	I213I (ATC→ATA)	hsdM ←	DNA methyltransferase M
RA	4,572,581	G→T	6.0%	T95T (ACC→ACA)	hsdM ←	DNA methyltransferase M
RA	4,573,623	C→A	5.9%	pseudogene (3010/3567 nt)	hsdR ←	pseudogene, premature stop codon, host restriction; endonuclease R
RA	4,577,836	C→A	9.8%	D283Y (GAC→TAC)	yjiA ←	GTP‑binding protein, putative GTPase
RA	4,584,381	G→T	93.8%	I53I (ATC→ATA)	yjjL ←	L‑galactonate transporter
RA	4,584,756	A→T	74.2%	*305K (TAA→AAA)	yjjM ←	yjjMN operon transcriptional activator
RA	4,585,338	A→T	94.1%	S111T (TCT→ACT)	yjjM ←	yjjMN operon transcriptional activator
RA	4,586,861	G→T	47.6%	intergenic (+32/+106)	yjjN → / ← opgB	L‑galactonate oxidoreductase/phosphoglycerol transferases I and II
RA	4,588,264	G→T	10.6%	T332K (ACA→AAA)	opgB ←	phosphoglycerol transferases I and II
RA	4,590,074	A→C	13.2%	V240G (GTA→GGA)	dnaC ←	DNA biosynthesis protein
RA	4,591,139	C→A	66.0%	D66Y (GAT→TAT)	dnaT ←	DNA biosynthesis protein (primosomal protein I)
RA	4,596,243	T→A	72.3%	intergenic (‑25/+243)	leuQ ← / ← rsmC	tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase, SAM‑dependent
RA	4,609,367	A→T	13.3%	*441L (TAA→TTA)	deoA →	thymidine phosphorylase
RA	4,612,781	C→A	5.6%	A399E (GCG→GAG)	yjjJ →	putative protein kinase
RA	4,620,700	G→T	8.6%	V51L (GTG→TTG)	slt →	lytic murein transglycosylase, soluble
RA	4,624,581	C→A	5.6%	E183* (GAA→TAA)	rob ←	right oriC‑binding transcriptional activator, AraC family
RA	4,624,764	C→A	9.7%	E122* (GAA→TAA)	rob ←	right oriC‑binding transcriptional activator, AraC family
RA	4,625,288	T→C	92.9%	intergenic (‑161/‑50)	rob ← / → creA	right oriC‑binding transcriptional activator, AraC family/putative periplasmic protein
RA	4,629,324	G→T	12.1%	D444Y (GAT→TAT)	creD →	inner membrane protein
RA	4,629,649	A→T	15.8%	Y159N (TAC→AAC)	arcA ←	response regulator in two‑component regulatory system with ArcB or CpxA

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	CP009273	373843	375109	1267	170 [168]	[167] 170	frmA–[frmR]	frmA,[frmR]
*	*	÷	CP009273	4100625	4101523	899	174 [169]	[165] 171	tpiA	tpiA

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	360104 =	200 (0.770)	234 (0.900)	113/278	NT	53.9%	intergenic (‑38/+557)	lacZ/lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
	?	CP009273	= 360286	NA (NA)					intergenic (‑220/+375)	lacZ/lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
*	?	CP009273	= 360278	NA (NA)	7460 (30.560) +TTAATTAA	197/262	NT	97.1%	intergenic (‑212/+383)	lacZ/lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
	?	CP009273	= 361823	240 (0.930)					coding (831/834 nt)	mhpR	mhp operon transcriptional activator
*	?	CP009273	360652 =	301 (1.160)	7145 (41.360) +46 bp	186/186	NT	97.5%	intergenic (‑586/+9)	lacZ/lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
	?	CP009273	= 1317577	256 (0.990)					coding (101/882 nt)	yciV	PHP domain protein
*	?	CP009273	376716 =	NA (NA)	212 (0.820)	114/278	NT	91.0%	intergenic (‑1/‑91)	yaiX/insC1	pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase/IS2 repressor TnpA
	?	CP009273	566411 =	21 (0.080)					coding (63/552 nt)	ybcL	inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
*	?	CP009273	= 378046	NA (NA)	225 (0.870)	115/278	NT	91.1%	intergenic (+11/+1)	insD1/yaiX	IS2 transposase TnpB/pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase
	?	CP009273	= 566415	22 (0.080)					coding (67/552 nt)	ybcL	inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
*	?	CP009273	1203246 =	12 (0.050)	33 (0.140)	24/246	NT	73.7%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	CP009273	1205075 =	13 (0.060)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	CP009273	= 1203261	11 (0.040)	46 (0.200)	31/246	NT	80.2%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	CP009273	= 1205058	13 (0.060)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	CP009273	1462167 =	NA (NA)	3 (0.010)	3/278	NT	NA	noncoding (1331/1331 nt)	IS2	repeat region
	?	CP009273	= 1463498	NA (NA)					pseudogene (1/53 nt)	ydbA	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
*	?	CP009273	1635219 =	20 (0.080)	219 (0.860)	126/274	NT	91.6%	intergenic (‑377/+377)	essQ/cspB	Qin prophage; putative S lysis protein/Qin prophage; cold shock protein
	?	CP009273	= 2063752	NA (NA)					noncoding (1/1331 nt)	IS2	repeat region
*	?	CP009273	= 1635223	20 (0.080)	284 (1.100)	134/278	NT	93.4%	intergenic (‑381/+373)	essQ/cspB	Qin prophage; putative S lysis protein/Qin prophage; cold shock protein
	?	CP009273	= 1645805	NA (NA)					intergenic (+11/‑3)	insD1/intQ	IS2 transposase TnpB;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related
*	?	CP009273	= 1645805	NA (NA)	16 (0.060)	13/278	NT	6.4%	intergenic (+11/‑3)	insD1/intQ	IS2 transposase TnpB;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related
	?	CP009273	2310157 =	234 (0.900)					coding (502/651 nt)	rcsB	response regulator in two‑component regulatory system with RcsC and YojN
*	?	CP009273	= 2310161	233 (0.900)	20 (0.080)	13/278	NT	7.9%	coding (506/651 nt)	rcsB	response regulator in two‑component regulatory system with RcsC and YojN
	?	CP009273	= 2991050	NA (NA)					noncoding (1/1331 nt)	IS2	repeat region
*	?	CP009273	= 3180783	NA (NA)	193 (0.760)	106/274	NT	70.7%	pseudogene (4/2445 nt)	yqiG	pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein
	?	CP009273	= 3833569	81 (0.310)					intergenic (‑216/‑6)	nlpA/yicS	cytoplasmic membrane lipoprotein‑28/putative periplasmic protein
*	?	CP009273	= 3180784	NA (NA)	14 (0.050)	10/276	NT	5.1%	pseudogene (5/2445 nt)	yqiG	pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein
	?	CP009273	3829186 =	262 (1.010)					coding (104/1383 nt)	yicJ	putative transporter
*	?	CP009273	3744959 =	241 (0.930)	221 (0.850)	108/278	NT	46.4%	coding (270/741 nt)	yiaT	putative outer membrane protein
	?	CP009273	= 3752673	270 (1.040)					coding (549/1845 nt)	selB	selenocysteinyl‑tRNA‑specific translation factor
*	?	CP009273	3833562 =	88 (0.340)	196 (0.760)	98/276	NT	69.2%	intergenic (‑209/‑13)	nlpA/yicS	cytoplasmic membrane lipoprotein‑28/putative periplasmic protein
	?	CP009273	4487999 =	NA (NA)					intergenic (+242/‑90)	intB/insC1	pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase/IS2 repressor TnpA