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	10.1%	D208Y (GAC→TAC)	thrA →	Bifunctional aspartokinase/homoserine dehydrogenase 1
RA	2,617	G→T	22.0%	E761* (GAA→TAA)	thrA →	Bifunctional aspartokinase/homoserine dehydrogenase 1
RA	5,144	G→A	100%	intergenic (+124/‑90)	thrC → / → yaaX	L‑threonine synthase/DUF2502 family putative periplasmic protein
RA	10,444	G→T	100%	F17L (TTC→TTA)	satP ←	succinate‑acetate transporter
RA	11,971	G→T	5.3%	intergenic (‑185/‑192)	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	17,376	C→A	27.2%	intergenic (+370/‑113)	sokC → / → nhaA	sRNA antisense regulator blocking mokC, and hence hokC, translation/sodium‑proton antiporter
RA	24,601	C→A	27.2%	T737T (ACC→ACA)	ileS →	isoleucyl‑tRNA synthetase
RA	25,546	G→T	100%	D114Y (GAC→TAC)	lspA →	prolipoprotein signal peptidase (signal peptidase II)
RA	29,139	G→T	100%	G256C (GGT→TGT)	dapB →	dihydrodipicolinate reductase
RA	31,153	G→T	7.3%	V113F (GTC→TTC)	carB →	carbamoyl‑phosphate synthase large subunit
RA	31,710	C→A	87.3%	I298I (ATC→ATA)	carB →	carbamoyl‑phosphate synthase large subunit
RA	32,527	C→A	29.5%	R571S (CGT→AGT)	carB →	carbamoyl‑phosphate synthase large subunit
RA	32,659	C→A	86.9%	R615S (CGC→AGC)	carB →	carbamoyl‑phosphate synthase large subunit
RA	32,802	C→A	88.2%	I662I (ATC→ATA)	carB →	carbamoyl‑phosphate synthase large subunit
RA	40,957	C→A	80.2%	V325V (GTG→GTT)	caiT ←	putative transporter
RA	42,079	G→A	7.7%	intergenic (‑148/‑324)	caiT ← / → fixA	putative transporter/anaerobic carnitine reduction putative electron transfer flavoprotein subunit
RA	42,150	G→A	100%	intergenic (‑219/‑253)	caiT ← / → fixA	putative transporter/anaerobic carnitine reduction putative electron transfer flavoprotein subunit
RA	42,415	A→C	7.9%	T5P (ACT→CCT)	fixA →	anaerobic carnitine reduction putative electron transfer flavoprotein subunit
RA	49,840	G→T	100%	A6A (GCG→GCT)	folA →	dihydrofolate reductase
RA	54,242	G→T	5.7%	P154Q (CCG→CAG)	surA ←	peptidyl‑prolyl cis‑trans isomerase (PPIase)
RA	54,392	G→T	90.7%	A104E (GCG→GAG)	surA ←	peptidyl‑prolyl cis‑trans isomerase (PPIase)
RA	55,590	G→T	100%	T507K (ACG→AAG)	lptD ←	LPS assembly OM complex LptDE, beta‑barrel component
RA	56,677	G→T	100%	R145S (CGC→AGC)	lptD ←	LPS assembly OM complex LptDE, beta‑barrel component
RA	66,077	G→T	6.9%	pseudogene (456/678 nt)	araD ←	pseudogene, truncated
RA	69,367	C→A	8.3%	M16I (ATG→ATT)	thiQ ←	thiamine, thiamine pyrophosphate ABC transporter ATPase; ThiBPQ thiamine, thiamine pyrophosphate importer
RA	70,465	G→T	11.1%	H182N (CAT→AAT)	thiP ←	thiamine, thiamine pyrophosphate ABC transporter permease; ThiBPQ thiamine, thiamine pyrophosphate importer
RA	72,743	C→A	7.8%	A348A (GCG→GCT)	sgrR ←	transcriptional DNA‑binding transcriptional activator of sgrS sRNA
RA	76,821	G→T	100%	G177G (GGC→GGA)	leuC ←	3‑isopropylmalate dehydratase large subunit
RA	80,123	C→T	100%	G25S (GGC→AGC)	leuL ←	leu operon leader peptide
RA	81,562	C→A	100%	I236I (ATC→ATA)	leuO →	global transcription factor
RA	82,037	C→T	85.5%	intergenic (+238/‑80)	leuO → / → ilvI	global transcription factor/acetolactate synthase 3 large subunit
RA	90,252	G→T	10.4%	A200A (GCG→GCT)	murE →	UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate:meso‑ diaminopimelate ligase
RA	91,765	C→A	6.6%	P210Q (CCG→CAG)	murF →	UDP‑N‑acetylmuramoyl‑tripeptide:D‑alanyl‑D‑ alanine ligase
RA	93,391	G→T	100%	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	102,736	C→A	86.1%	I315I (ATC→ATA)	ftsZ →	GTP‑binding tubulin‑like cell division protein
RA	102,769	G→T	85.5%	V326V (GTG→GTT)	ftsZ →	GTP‑binding tubulin‑like cell division protein
RA	102,964	T→C	7.6%	intergenic (+21/‑80)	ftsZ → / → lpxC	GTP‑binding tubulin‑like cell division protein/UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase
RA	103,467	G→T	100%	D142Y (GAT→TAT)	lpxC →	UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase
RA	104,561	G→T	100%	A124S (GCG→TCG)	secM →	regulator of secA translation
RA	108,039	C→A	85.7%	intergenic (+119/+97)	mutT → / ← yacG	nucleoside triphosphate pyrophosphohydrolase, marked preference for dGTP/DNA gyrase inhibitor
RA	108,648	Δ1 bp	100%	coding (439/744 nt)	zapD ←	FtsZ stabilizer
RA	112,729	G→T	7.6%	D286E (GAC→GAA)	hofB ←	T2SE secretion family protein; P‑loop ATPase superfamily protein
RA	116,956	C→T	8.2%	L361L (CTG→CTA)	aroP ←	aromatic amino acid transporter
RA	118,873	G→T	100%	D99Y (GAC→TAC)	pdhR →	pyruvate dehydrogenase complex repressor; autorepressor
RA	119,536	G→T	84.6%	P11P (CCG→CCT)	aceE →	pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding
RA	120,313	C→A	9.4%	T270T (ACC→ACA)	aceE →	pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding
RA	122,790	G→T	14.2%	A203A (GCG→GCT)	aceF →	pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2
RA	126,784	C→A	6.0%	D322Y (GAT→TAT)	yacH ←	uncharacterized protein
RA	134,028	G→T	100%	A153A (GCG→GCT)	cueO →	multicopper oxidase (laccase)
RA	135,557	G→T	5.2%	A719E (GCG→GAG)	gcd ←	glucose dehydrogenase
RA	137,071	G→T	88.7%	I214I (ATC→ATA)	gcd ←	glucose dehydrogenase
RA	137,915	G→T	37.2%	intergenic (‑203/‑3)	gcd ← / → hpt	glucose dehydrogenase/hypoxanthine phosphoribosyltransferase
RA	142,460	T→A	100%	F298Y (TTC→TAC)	yadE →	putative polysaccharide deacetylase lipoprotein
RA	144,698	C→A	8.8%	A195A (GCG→GCT)	panC ←	pantothenate synthetase
RA	145,771	G→T	8.6%	A106A (GCC→GCA)	panB ←	3‑methyl‑2‑oxobutanoate hydroxymethyltransferase
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	100%	D78Y (GAC→TAC)	ligT ←	2'‑5' RNA ligase
RA	159,666	G→T	83.8%	G359C (GGT→TGT)	hrpB →	putative ATP‑dependent helicase
RA	162,905	G→T	12.1%	V563V (GTG→GTT)	mrcB →	fused glycosyl transferase and transpeptidase
RA	166,662	C→A	90.1%	S133* (TCG→TAG)	fhuC →	iron‑hydroxamate transporter subunit
RA	173,725	G→T	91.3%	G129G (GGC→GGA)	yadS ←	UPF0126 family inner membrane protein
RA	176,783	G→T	100%	D354Y (GAT→TAT)	dgt →	deoxyguanosine triphosphate triphosphohydrolase
RA	176,797	G→T	18.6%	A358A (GCG→GCT)	dgt →	deoxyguanosine triphosphate triphosphohydrolase
RA	185,393	A→T	88.7%	F201I (TTC→ATC)	map ←	methionine aminopeptidase
RA	186,159	A→G	86.7%	intergenic (‑166/‑40)	map ← / → tff	methionine aminopeptidase/novel sRNA, function unknown
RA	196,832	C→A	46.7%	I806I (ATC→ATA)	bamA →	BamABCDE complex OM biogenesis outer membrane pore‑forming assembly factor
RA	199,229	G→T	83.6%	E61D (GAG→GAT)	lpxA →	UDP‑N‑acetylglucosamine acetyltransferase
RA	201,962	A→T	100%	D117V (GAT→GTT)	dnaE →	DNA polymerase III alpha subunit
RA	204,948	A→T	9.7%	T1112T (ACA→ACT)	dnaE →	DNA polymerase III alpha subunit
RA	209,477	G→T	8.7%	E220D (GAG→GAT)	tilS →	tRNA(Ile)‑lysidine synthetase
RA	214,084	G→T	87.5%	G393G (GGC→GGA)	proS ←	prolyl‑tRNA synthetase
RA	217,887	C→T	86.1%	W74* (TGG→TGA)	metI ←	DL‑methionine transporter subunit
RA	217,932	A→C	100%	I59M (ATT→ATG)	metI ←	DL‑methionine transporter subunit
RA	225,030	C→A	18.5%	noncoding (2785/2904 nt)	rrlH →	23S ribosomal RNA of rrnH operon
RA	227,530	G→T	9.9%	intergenic (‑162/‑79)	yafC ← / → yafD	LysR family putative transcriptional regulator/endo/exonuclease/phosphatase family protein
RA	229,707	G→T	8.9%	R246S (CGT→AGT)	mltD ←	putative membrane‑bound lytic murein transglycosylase D
RA	230,579	C→T	100%	E231K (GAA→AAA)	gloB ←	hydroxyacylglutathione hydrolase
RA	231,378	C→A	89.7%	R26S (CGC→AGC)	yafS →	putative S‑adenosyl‑L‑methionine‑dependent methyltransferase
RA	232,860	G→T	100%	D103Y (GAT→TAT)	dnaQ →	DNA polymerase III epsilon subunit
RA	234,984	G→T	11.0%	I80I (ATC→ATA) ‡	ykfM ←	lethality reduction protein, putative inner membrane protein
RA	234,985	A→T	5.9%	I80N (ATC→AAC) ‡	ykfM ←	lethality reduction protein, putative inner membrane protein
RA	234,990	G→T	10.7%	F78L (TTC→TTA)	ykfM ←	lethality reduction protein, putative inner membrane protein
RA	234,994	G→T	18.7%	S77* (TCA→TAA)	ykfM ←	lethality reduction protein, putative inner membrane protein
RA	235,005	C→A	11.8%	T73T (ACG→ACT) ‡	ykfM ←	lethality reduction protein, putative inner membrane protein
RA	235,006	G→T	8.0%	T73K (ACG→AAG) ‡	ykfM ←	lethality reduction protein, putative inner membrane protein
RA	235,010	G→T	12.6%	L72I (CTT→ATT)	ykfM ←	lethality reduction protein, putative inner membrane protein
RA	235,019	C→A	22.0%	V69L (GTA→TTA)	ykfM ←	lethality reduction protein, putative inner membrane protein
RA	235,022	G→T	16.1%	H68N (CAT→AAT)	ykfM ←	lethality reduction protein, putative inner membrane protein
RA	235,036	G→T	10.9%	S63Y (TCC→TAC)	ykfM ←	lethality reduction protein, putative inner membrane protein
RA	236,234	A→T	100%	V148E (GTG→GAG)	yafV ←	putative NAD(P)‑binding C‑N hydrolase family amidase
RA	238,195	G→T	100%	V532V (GTC→GTA)	fadE ←	acyl coenzyme A dehydrogenase
RA	247,048	G→T	5.2%	pseudogene (490/756 nt)	lafU →	pseudogene, lateral flagellar motor protein fragment
RA	248,447	C→T	86.0%	intergenic (+7/‑45)	dinB → / → yafN	DNA polymerase IV/antitoxin of the YafO‑YafN toxin‑antitoxin system
RA	248,486	C→A	85.3%	intergenic (+46/‑6)	dinB → / → yafN	DNA polymerase IV/antitoxin of the YafO‑YafN toxin‑antitoxin system
RA	250,909	A→T	88.7%	L432Q (CTG→CAG)	pepD ←	aminoacyl‑histidine dipeptidase (peptidase D)
RA	253,855	G→T	83.5%	R281L (CGT→CTT)	frsA →	fermentation‑respiration switch protein; PTS Enzyme IIA(Glc)‑binding protein; pNP‑butyrate esterase activity
RA	255,487	A→T	85.4%	S109T (TCT→ACT)	phoE ←	outer membrane phosphoporin protein E
RA	259,494	G→T	82.6%	C75* (TGC→TGA)	yafW ←	CP4‑6 prophage; antitoxin of the YkfI‑YafW toxin‑antitoxin system
RA	262,114	C→A	100%	D51Y (GAT→TAT)	yafY ←	lipoprotein, inner membrane; overproduction stimulates degP expression; CP4‑6 prophage
RA	263,270	C→A	10.1%	V149V (GTG→GTT)	yafZ ←	CP4‑6 prophage; conserved protein
RA	270,864	G→T	8.6%	intergenic (‑36/‑172)	insH1 ← / → mmuP	IS5 transposase and trans‑activator/CP4‑6 prophage; putative S‑methylmethionine transporter
RA	274,735	A→T	100%	pseudogene (138/348 nt)	afuB ←	pseudogene, CP4‑6 prophage; ABC transporter permease family;Phage or Prophage Related
RA	279,334	C→A	90.2%	I141I (ATC→ATA)	yagF →	CP4‑6 prophage; dehydratase family protein
RA	279,800	G→T	91.3%	E297* (GAA→TAA)	yagF →	CP4‑6 prophage; dehydratase family protein
RA	288,249	T→A	87.2%	T137T (ACA→ACT)	yagK ←	CP4‑6 prophage; conserved protein
RA	290,012	C→T	86.7%	D167N (GAT→AAT)	yagM ←	CP4‑6 prophage; uncharacterized protein
RA	291,348	G→A	94.8%	intergenic (‑58/+59)	yagN ← / ← intF	CP4‑6 prophage; uncharacterized protein/CP4‑6 prophage; putative phage integrase
RA	294,929	C→A	88.0%	E573* (GAA→TAA)	paoC ←	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
RA	300,770	C→A	91.3%	V49V (GTG→GTT)	ecpE ←	ECP production pilus chaperone
RA	301,508	G→A	9.1%	L341F (CTC→TTC)	ecpD ←	polymerized tip adhesin of ECP fibers
RA	302,428	G→T	89.7%	P34Q (CCG→CAG)	ecpD ←	polymerized tip adhesin of ECP fibers
RA	306,357	G→T	5.9%	A9D (GCT→GAT)	ecpA ←	ECP pilin
RA	307,315	A→T	5.3%	intergenic (‑268/‑508)	ecpR ← / → ykgL	putative transcriptional regulator for the ecp operon/uncharacterized protein
RA	307,479	G→A	86.8%	intergenic (‑432/‑344)	ecpR ← / → ykgL	putative transcriptional regulator for the ecp operon/uncharacterized protein
RA	309,541	C→A	5.4%	intergenic (‑25/‑527)	ykgP ← / → eaeH	pseudogene, oxidoreductase family/pseudogene, attaching and effacing protein homology;factor; Not classified
RA	312,532	G→A	100%	pseudogene (349/684 nt)	ykgA ←	pseudogene, AraC family;putative regulator; Not classified; putative ARAC‑type regulatory protein
RA	314,566	C→A	86.1%	D383Y (GAT→TAT)	rclA ←	reactive chlorine stress species (RCS) resistance protein; pyridine nucleotide‑dependent disulfide oxidoreductase family
RA	317,205	G→A	100%	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	319,024	C→A	85.3%	R326S (CGC→AGC)	ykgF →	ferridoxin‑like LutB family protein; putative electron transport chain YkgEFG component
RA	319,381	G→T	86.1%	D445Y (GAC→TAC)	ykgF →	ferridoxin‑like LutB family protein; putative electron transport chain YkgEFG component
RA	319,890	C→A	5.1%	S141* (TCG→TAG)	ykgG →	LutC 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	100%	intergenic (‑148/+65)	ykgH ← / ← betA	putative inner membrane protein/choline dehydrogenase, a flavoprotein
RA	332,599	G→T	83.0%	A37A (GCG→GCT)	yahF →	putative NAD(P)‑binding succinyl‑CoA synthase
RA	335,247	C→A	87.2%	N404K (AAC→AAA)	yahG →	DUF1116 family protein
RA	337,720	G→T	86.4%	E295D (GAG→GAT)	yahJ →	putative metallo‑dependent hydrolase domain deaminase
RA	344,800	G→T	100%	E136D (GAG→GAT)	prpB →	2‑methylisocitrate lyase
RA	345,428	T→C	6.2%	intergenic (+145/‑295)	prpB → / → prpC	2‑methylisocitrate lyase/2‑methylcitrate synthase
RA	353,486	A→T	7.5%	intergenic (+321/+16)	codA → / ← cynR	cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor
RA	360,157	T→G	8.0%	intergenic (‑91/+504)	lacZ ← / ← lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
RA	360,181	G→C	7.7%	intergenic (‑115/+480)	lacZ ← / ← lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
RA	360,752	A→G	100%	V331A (GTG→GCG)	lacI ←	DNA‑binding transcriptional repressor
RA	360,969	C→A	5.7%	E259* (GAG→TAG)	lacI ←	DNA‑binding transcriptional repressor
RA	361,692	G→T	35.9%	Q18K (CAG→AAG)	lacI ←	DNA‑binding transcriptional repressor
RA	361,756	G→T	15.1%	intergenic (‑13/+64)	lacI ← / ← mhpR	DNA‑binding transcriptional repressor/mhp operon transcriptional activator
RA	361,806	G→A	93.7%	intergenic (‑63/+14)	lacI ← / ← mhpR	DNA‑binding transcriptional repressor/mhp operon transcriptional activator
RA	362,159	G→T	100%	I165I (ATC→ATA)	mhpR ←	mhp operon transcriptional activator
RA	362,629	A→T	89.4%	Y9N (TAC→AAC)	mhpR ←	mhp operon transcriptional activator
RA	364,561	G→T	84.5%	D18Y (GAC→TAC)	mhpB →	2,3‑dihydroxyphenylpropionate 1,2‑dioxygenase
RA	372,091	C→A	84.6%	R393R (CGG→AGG)	mhpT →	3‑hydroxyphenylpropionic transporter
RA	372,581	G→T	86.6%	A118A (GCG→GCT)	yaiL →	DUF2058 family protein
RA	375,212	G→T	6.1%	I42I (ATC→ATA)	frmR ←	regulator protein that represses frmRAB operon
RA	378,179	A→T	100%	pseudogene (150/282 nt)	yaiX ←	pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase
RA	380,236	C→A	9.5%	intergenic (‑164/‑452)	yaiS ← / → tauA	putative PIG‑L family deacetylase/taurine transporter subunit
RA	385,485	C→T	7.0%	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	100%	pseudogene (109/1458 nt)	yaiT →	pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein
RA	389,022	C→G	6.4%	pseudogene (597/1449 nt)	yaiT →	pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein
RA	390,551	T→G	90.1%	L197R (CTG→CGG)	yaiV →	putative transcriptional regulator
RA	395,884	G→T	5.4%	R166S (CGT→AGT)	ddlA ←	D‑alanine‑D‑alanine ligase A
RA	396,272	G→T	5.1%	F36L (TTC→TTA)	ddlA ←	D‑alanine‑D‑alanine ligase A
RA	396,883	A→G	100%	Q14Q (CAA→CAG)	iraP →	anti‑RssB factor, RpoS stabilzer during Pi starvation; anti‑adapter protein
RA	397,959	G→A	100%	A253T (GCG→ACG)	phoA →	bacterial alkaline phosphatase
RA	398,902	G→T	7.1%	D56Y (GAT→TAT)	psiF →	PsiF family protein
RA	400,594	G→T	86.8%	V169V (GTC→GTA)	proC ←	pyrroline‑5‑carboxylate reductase, NAD(P)‑binding
RA	402,340	G→T	100%	V160V (GTG→GTT)	aroL →	shikimate kinase II
RA	406,075	C→A	100%	P159Q (CCG→CAG)	mak →	manno(fructo)kinase
RA	409,615	A→G	7.2%	L532S (TTA→TCA)	sbcC ←	exonuclease, dsDNA, ATP‑dependent
RA	411,027	G→T	100%	L61L (CTC→CTA)	sbcC ←	exonuclease, dsDNA, ATP‑dependent
RA	415,122	A→C	8.7%	N26H (AAC→CAC)	brnQ →	branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val
RA	416,199	G→T	14.2%	D385Y (GAC→TAC)	brnQ →	branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val
RA	417,087	G→T	5.0%	E216* (GAA→TAA)	proY →	proline‑specific permease
RA	421,799	C→A	100%	I69I (ATC→ATA)	tgt →	tRNA‑guanine transglycosylase
RA	425,143	G→T	100%	T61T (ACG→ACT)	secF →	SecYEG protein translocase auxillary subunit
RA	432,762	G→T	88.4%	P277Q (CCG→CAG)	yajO ←	2‑carboxybenzaldehyde reductase
RA	433,551	G→T	100%	S14Y (TCC→TAC)	yajO ←	2‑carboxybenzaldehyde reductase
RA	434,663	A→C	100%	I324S (ATC→AGC)	dxs ←	1‑deoxyxylulose‑5‑phosphate synthase, thiamine triphosphate‑binding, FAD‑requiring
RA	435,336	G→T	100%	Q100K (CAG→AAG)	dxs ←	1‑deoxyxylulose‑5‑phosphate synthase, thiamine triphosphate‑binding, FAD‑requiring
RA	435,862	A→T	85.2%	T232T (ACT→ACA)	ispA ←	geranyltranstransferase
RA	437,672	T→A	100%	V223E (GTG→GAG)	thiI →	tRNA s(4)U8 sulfurtransferase
RA	444,489	G→A	100%	R537C (CGT→TGT)	cyoB ←	cytochrome o ubiquinol oxidase subunit I
RA	446,369	T→G	100%	Q233P (CAG→CCG)	cyoA ←	cytochrome o ubiquinol oxidase subunit II
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	450,333	A→T	9.7%	intergenic (+88/‑256)	bolA → / → tig	stationary‑phase morphogene, transcriptional repressor for mreB; also regulator for dacA, dacC, and ampC/peptidyl‑prolyl cis/trans isomerase (trigger factor)
RA	450,766	G→T	84.2%	A60S (GCG→TCG)	tig →	peptidyl‑prolyl cis/trans isomerase (trigger factor)
RA	456,298	T→A	100%	L652Q (CTG→CAG)	lon →	DNA‑binding ATP‑dependent protease La
RA	456,588	G→T	100%	D749Y (GAC→TAC)	lon →	DNA‑binding ATP‑dependent protease La
RA	458,681	C→A	6.8%	I437I (ATC→ATA)	ppiD →	periplasmic folding chaperone, has an inactive PPIase domain
RA	461,499	G→T	87.9%	R424S (CGC→AGC)	ybaE ←	putative ABC superfamily transporter periplasmic‑binding protein
RA	463,131	G→T	5.1%	A88A (GCG→GCT)	cof →	thiamine pyrimidine pyrophosphate hydrolase; HMP‑PP phosphatase
RA	463,179	C→A	91.0%	I104I (ATC→ATA)	cof →	thiamine pyrimidine pyrophosphate hydrolase; HMP‑PP phosphatase
RA	467,995	G→T	24.8%	intergenic (+122/‑59)	mdlB → / → glnK	putative multidrug transporter subunit of ABC superfamily, ATP‑binding component/nitrogen assimilation regulatory protein for GlnL, GlnE, and AmtB
RA	474,138	G→T	100%	intergenic (‑65/+99)	ylaB ← / ← ylaC	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase/DUF1449 family inner membrane protein
RA	475,805	C→A	100%	A120A (GCG→GCT)	tomB ←	Hha toxicity attenuator; conjugation‑related protein
RA	477,267	G→T	87.2%	Q865K (CAG→AAG)	acrB ←	multidrug efflux system protein
RA	479,122	G→T	7.7%	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	100%	D86N (GAC→AAC)	acrA ←	multidrug efflux system
RA	481,667	G→A	100%	A151T (GCG→ACG)	acrR →	transcriptional repressor
RA	482,757	G→T	81.9%	A256S (GCG→TCG)	mscK →	mechanosensitive channel protein, intermediate conductance, K+ regulated
RA	486,494	C→A	85.0%	R53S (CGC→AGC)	ybaN →	DUF454 family inner membrane protein
RA	495,020	T→A	86.0%	E137V (GAA→GTA)	aes ←	acetyl esterase
RA	497,531	C→A	5.7%	E388D (GAG→GAT)	ybaL ←	inner membrane putative NAD(P)‑binding transporter
RA	509,737	G→A	100%	E97K (GAG→AAG)	cueR →	copper‑responsive regulon transcriptional regulator
RA	512,167	G→T	5.4%	A43A (GCG→GCT)	fetB →	iron exporter permease subunit, ABC transporter FetAB; peroxide resistance protein
RA	512,872	A→T	5.3%	intergenic (+54/+9)	fetB → / ← ybbN	iron exporter permease subunit, ABC transporter FetAB; peroxide resistance protein/DnaK co‑chaperone, thioredoxin‑like protein
RA	514,572	T→A	5.2%	K12* (AAA→TAA)	ybbO ←	putative oxidoreductase
RA	515,662	A→T	7.9%	A158A (GCA→GCT)	ybbA →	putative ABC superfamily transporter ATP‑binding subunit
RA	517,392	G→T	38.4%	A507A (GCG→GCT)	ybbP →	putative ABC transporter permease
RA	518,321	A→T	7.4%	intergenic (+35/‑396)	ybbP → / → rhsD	putative ABC transporter permease/Rhs family putative polymorphic toxin
RA	518,820	C→A	88.7%	A35E (GCG→GAG)	rhsD →	Rhs family putative polymorphic toxin
RA	519,869	C→A	7.6%	L385I (CTT→ATT)	rhsD →	Rhs family putative polymorphic toxin
RA	521,011	G→T	8.5%	E765D (GAG→GAT)	rhsD →	Rhs family putative polymorphic toxin
RA	524,334:1	+T	100%	pseudogene (239/491 nt)	ybbD →	pseudogene
RA	524,496	T→G	83.0%	pseudogene (401/491 nt)	ybbD →	pseudogene
RA	530,466	C→A	100%	F365L (TTC→TTA)	gcl →	glyoxylate carboligase
RA	531,155	G→A	8.5%	intergenic (+2/‑11)	gcl → / → hyi	glyoxylate carboligase/hydroxypyruvate isomerase
RA	540,762	C→T	12.3%	intergenic (‑14/+8)	allC ← / ← allD	allantoate amidohydrolase/ureidoglycolate dehydrogenase
RA	542,200	Δ1 bp	100%	coding (65/1668 nt)	fdrA →	putative NAD(P)‑binding acyl‑CoA synthetase
RA	546,231	G→T	13.9%	D113Y (GAT→TAT)	ybcF →	putative carbonate kinase
RA	546,491	G→T	100%	V199V (GTG→GTT)	ybcF →	putative carbonate kinase
RA	547,082	G→T	9.0%	S323R (AGC→AGA)	purK ←	N5‑carboxyaminoimidazole ribonucleotide synthase
RA	549,397	G→T	100%	intergenic (‑1/+2)	lpxH ← / ← ppiB	UDP‑2,3‑diacylglucosamine pyrophosphohydrolase/peptidyl‑prolyl cis‑trans isomerase B (rotamase B)
RA	551,499	G→T	86.5%	R171S (CGC→AGC)	ybcI ←	DUF457 family inner membrane protein
RA	557,592	G→T	100%	D814Y (GAC→TAC)	sfmD →	putative outer membrane export usher protein
RA	557,784	G→T	12.0%	intergenic (+28/‑8)	sfmD → / → sfmH	putative outer membrane export usher protein/FimA homolog
RA	560,284	A→C	16.1%	I384R (ATA→AGA)	intD ←	DLP12 prophage; putative phage integrase
RA	565,131	G→A	8.9%	G258G (GGG→GGA)	ybcK →	DLP12 prophage; putative recombinase
RA	569,073	A→T	8.3%	T83S (ACT→TCT)	rusA →	DLP12 prophage; endonuclease RUS
RA	569,775	G→A	7.3%	V122I (GTT→ATT)	quuD →	DLP12 prophage; putative antitermination protein
RA	576,998	G→T	100%	pseudogene (189/309 nt)	aaaD →	pseudogene; DLP12 prophage; tail fiber assembly protein family;Phage or Prophage Related
RA	581,203	A→T	100%	intergenic (‑114/‑310)	ompT ← / → pauD	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)/tRNA‑OTHER
RA	583,341	T→G	100%	S33R (AGT→CGT)	ybcH ←	PRK09936 family protein
RA	591,864	C→A	76.8%	A270E (GCG→GAG)	cusC →	copper/silver efflux system, outer membrane component
RA	592,932	G→T	8.7%	intergenic (+13/‑3)	cusF → / → cusB	periplasmic copper‑ and silver‑binding protein/copper/silver efflux system, membrane fusion protein
RA	601,847	A→T	73.8%	I331I (ATT→ATA)	ybdK ←	weak gamma‑glutamyl:cysteine ligase
RA	603,207	G→T	13.3%	noncoding (18/59 nt)	sokE →	sRNA at remnant mokE/hokE locus
RA	607,931	G→A	100%	S7F (TCC→TTC)	fepA ←	iron‑enterobactin outer membrane transporter
RA	608,104	G→T	19.7%	intergenic (‑154/‑89)	fepA ← / → fes	iron‑enterobactin outer membrane transporter/enterobactin/ferric enterobactin esterase
RA	613,755	G→T	7.5%	D16Y (GAT→TAT)	fepE →	regulator of length of O‑antigen component of lipopolysaccharide chains
RA	619,048	C→A	100%	A307S (GCC→TCC)	fepB ←	iron‑enterobactin transporter subunit
RA	623,284	C→T	8.6%	F45F (TTC→TTT)	entB →	isochorismatase
RA	623,812	G→T	5.3%	V221V (GTG→GTT)	entB →	isochorismatase
RA	624,669	G→T	88.1%	T221T (ACG→ACT)	entA →	2,3‑dihydro‑2,3‑dihydroxybenzoate dehydrogenase
RA	625,174	G→T	86.4%	intergenic (+5/‑176)	entH → / → cstA	enterobactin synthesis proofreading thioesterase/carbon starvation protein involved in peptide utilization; APC peptide transporter family protein
RA	625,364	G→T	100%	G5G (GGG→GGT)	cstA →	carbon starvation protein involved in peptide utilization; APC peptide transporter family protein
RA	627,428	C→A	85.9%	I693I (ATC→ATA)	cstA →	carbon starvation protein involved in peptide utilization; APC peptide transporter family protein
RA	629,276	A→T	11.4%	K79* (AAA→TAA)	ybdL →	methionine aminotransferase, PLP‑dependent
RA	638,123	G→T	9.9%	G194C (GGT→TGT)	ybdR →	putative Zn‑dependent NAD(P)‑binding oxidoreductase
RA	639,231	G→A	100%	L65F (CTT→TTT)	rnk ←	regulator of nucleoside diphosphate kinase
RA	643,406	T→A	8.7%	Q29L (CAA→CTA)	citX ←	apo‑citrate lyase phosphoribosyl‑dephospho‑CoA transferase
RA	643,999	G→T	5.5%	H343Q (CAC→CAA)	citF ←	citrate lyase, citrate‑ACP transferase (alpha) subunit
RA	647,234	C→T	100%	E27K (GAA→AAA)	citC ←	[citrate [pro‑3S]‑lyase] ligase
RA	647,422	G→T	100%	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	100%	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	652,597	C→T	100%	intergenic (+24/‑151)	pagP → / → cspE	phospholipid:lipid A palmitoyltransferase/constitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein
RA	652,865	Δ1 bp	100%	coding (118/210 nt)	cspE →	constitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein
RA	659,689	G→T	89.0%	R320S (CGC→AGC)	rlpA ←	septal ring protein, suppressor of prc, minor lipoprotein
RA	662,108	A→T	100%	V522V (GTT→GTA)	mrdA ←	transpeptidase involved in peptidoglycan synthesis (penicillin‑binding protein 2)
RA	662,631	C→A	100%	R348L (CGC→CTC)	mrdA ←	transpeptidase involved in peptidoglycan synthesis (penicillin‑binding protein 2)
RA	667,348	G→T	100%	Q99K (CAG→AAG)	lptE ←	LPS assembly OM complex LptDE, lipoprotein component
RA	667,899	C→A	86.5%	D781Y (GAT→TAT)	leuS ←	leucyl‑tRNA synthetase
RA	672,142	T→A	100%	intergenic (‑139/‑25)	ybeQ ← / → ybeR	Sel1 family TPR‑like repeat protein/uncharacterized protein
RA	680,846	G→T	88.9%	F180L (TTC→TTA)	gltK ←	glutamate, aspartate ABC transporter permease subunit
RA	683,316	G→T	19.5%	intergenic (‑113/+137)	gltI ← / ← insH1	glutamate, aspartate binding protein, periplasmic; part of GltJKLI ABC transporter/IS5 transposase and trans‑activator
RA	687,786	C→A	9.9%	V4V (GTG→GTT)	ybeY ←	ssRNA‑specific endoribonuclease; co‑endoribonuclease working with RNase R in 16S rRNA 3' end maturation and quality control; rRNA transcription antitermination factor
RA	693,739	G→T	100%	H299N (CAC→AAC)	asnB ←	asparagine synthetase B
RA	699,157	C→T	24.8%	intergenic (‑90/‑243)	nagB ← / → nagE	glucosamine‑6‑phosphate deaminase/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	100%	T2T (ACT→ACG)  *29G (TGA→GGA)	fur ← uof ←	ferric iron uptake regulon transcriptional repressor; autorepressor ryhB‑regulated fur leader peptide
RA	706,479	C→A	10.2%	R148L (CGT→CTT)	fldA ←	flavodoxin 1
RA	710,187	A→T	90.1%	S392C (AGT→TGT)	pgm →	phosphoglucomutase
RA	719,056	C→T	6.8%	R272Q (CGG→CAG)	kdpD ←	fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein
RA	723,859	G→T	89.8%	V110V (GTC→GTA)	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	725,508	C→A	5.1%	A157E (GCA→GAA)	rhsC →	Rhs family putative polymorphic toxin
RA	726,087	G→T	39.4%	R350L (CGT→CTT)	rhsC →	Rhs family putative polymorphic toxin
RA	727,616	A→T	14.3%	N860Y (AAC→TAC)	rhsC →	Rhs family putative polymorphic toxin
RA	729,456	G→A	94.8%	R75R (AGG→AGA)	ybfB →	putative membrane protein
RA	730,891	G→T	31.5%	pseudogene (1303/1521 nt)	rhsO →	pseudogene, Rhs family protein
RA	731,543	A→T	18.5%	S146S (TCA→TCT)	ybfC →	putative periplasmic protein
RA	732,416	G→A	6.3%	pseudogene (136/1137 nt)	ybfL →	pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein
RA	732,494	G→T	100%	pseudogene (214/1137 nt)	ybfL →	pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein
RA	732,655	G→T	31.6%	pseudogene (375/1137 nt)	ybfL →	pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein
RA	737,635	G→T	84.1%	G126G (GGC→GGA)	dtpD ←	dipeptide and tripeptide permease D
RA	743,797	G→T	88.1%	R214R (CGC→CGA)	ybgO ←	putative fimbrial protein
RA	745,420	C→A	14.2%	G736C (GGT→TGT)	ybgQ ←	putative outer membrane protein
RA	746,783	C→A	24.2%	T281T (ACG→ACT)	ybgQ ←	putative outer membrane protein
RA	747,973	C→A	86.0%	P93P (CCG→CCT)	ybgD ←	putative fimbrial‑like adhesin protein
RA	748,707	A→T	89.0%	I406I (ATT→ATA)	gltA ←	citrate synthase
RA	753,549	G→T	88.0%	Q135H (CAG→CAT)	sdhB →	succinate dehydrogenase, FeS subunit
RA	754,572	G→T	100%	E137D (GAG→GAT)	sucA →	2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding
RA	759,000	C→A	100%	F177L (TTC→TTA)	sucC →	succinyl‑CoA synthetase, beta subunit
RA	767,399	A→T	81.1%	E162D (GAA→GAT)	cydA →	cytochrome d terminal oxidase, subunit I
RA	772,664	A→C	9.1%	K289N (AAA→AAC)	tolA →	membrane anchored protein in TolA‑TolQ‑TolR complex
RA	777,823	G→T	14.6%	A95S (GCC→TCC)	nadA →	quinolinate synthase, subunit A
RA	780,417	G→T	15.8%	T119T (ACC→ACA)	ybgS ←	putative periplasmic protein
RA	784,094	G→T	85.0%	A67E (GCG→GAG)	galM ←	aldose 1‑epimerase; type‑1 mutarotase
RA	788,902	G→T	100%	R115S (CGT→AGT)	modF ←	fused molybdate transporter subunits of ABC superfamily: ATP‑binding components
RA	793,225	G→A	7.5%	F221F (TTC→TTT)	ybhA ←	pyridoxal phosphate (PLP) phosphatase
RA	800,488	G→T	100%	V510V (GTG→GTT)	ybhJ →	putative hydratase
RA	800,779	G→T	100%	E607D (GAG→GAT)	ybhJ →	putative hydratase
RA	809,212	G→T	84.8%	M77I (ATG→ATT)	uvrB →	excinulease of nucleotide excision repair, DNA damage recognition component
RA	811,486	G→T	7.9%	I206I (ATC→ATA)	ybhK ←	putative NAD(P)‑binding transferase
RA	811,920	C→A	23.4%	D62Y (GAT→TAT)	ybhK ←	putative NAD(P)‑binding transferase
RA	815,168	C→A	8.1%	R140R (CGG→AGG)	moaE →	molybdopterin synthase, large subunit
RA	816,302	G→T	88.4%	R18S (AGG→AGT)	ybhM →	UPF0005 family inner membrane protein
RA	820,503	C→A	86.7%	T354T (ACG→ACT)	ybhR ←	inner membrane putative ABC superfamily transporter permease
RA	822,967	C→A	26.9%	V491F (GTT→TTT)	ybhF ←	putative transporter subunit of ABC superfamily: ATP‑binding component
RA	824,171	A→C	26.3%	F89L (TTT→TTG)	ybhF ←	putative transporter subunit of ABC superfamily: ATP‑binding component
RA	828,374	G→T	100%	V11V (GTC→GTA)	ybiA ←	DUF1768 family protein
RA	829,009	G→T	85.6%	D162Y (GAT→TAT)	dinG →	ATP‑dependent DNA helicase
RA	832,445	G→T	100%	P213P (CCG→CCT)	ybiC →	putative dehydrogenase
RA	834,612	G→T	6.3%	R18S (CGC→AGC)	ybiX ←	Fe(II)‑dependent oxygenase superfamily protein
RA	837,716	G→T	80.7%	intergenic (‑204/‑72)	mcbA ← / → rlmF	colanic acid mucoidy stimulation protein/23S rRNA m(6)A1618 methyltransferase, SAM‑dependent
RA	842,041	C→A	84.0%	E179* (GAA→TAA)	glnP ←	glutamine transporter subunit
RA	843,299	C→A	100%	W54C (TGG→TGT)	glnH ←	glutamine transporter subunit
RA	850,161	G→T	32.1%	P353P (CCG→CCT)	ybiR →	putative transporter
RA	858,992	C→T	7.0%	intergenic (‑25/‑106)	ybiY ← / → fsaA	putative pyruvate formate lyase activating enzyme/fructose‑6‑phosphate aldolase 1
RA	867,350	G→T	25.5%	R2L (CGA→CTA)	gsiD →	glutathione transporter, permease component, ABC superfamily
RA	868,500	A→T	90.5%	S22S (TCA→TCT)	yliE →	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	876,395	G→T	85.2%	M71I (ATG→ATT)	dacC →	D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 6a)
RA	876,447	G→A	100%	D89N (GAT→AAT)	dacC →	D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 6a)
RA	876,738	G→T	10.4%	D186Y (GAT→TAT)	dacC →	D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 6a)
RA	879,085	G→T	100%	intergenic (‑241/‑44)	ybjG ← / → mdfA	undecaprenyl pyrophosphate phosphatase/multidrug efflux system protein
RA	891,169	G→T	28.6%	P241P (CCG→CCT)	potG →	putrescine transporter subunit: ATP‑binding component of ABC superfamily
RA	892,358	G→T	100%	V257L (GTG→TTG)	potH →	putrescine transporter subunit: membrane component of ABC superfamily
RA	896,095	C→A	6.3%	intergenic (‑64/+227)	artJ ← / ← artM	arginine binding protein, periplasmic/arginine transporter subunit
RA	907,074	A→G	8.4%	I178T (ATC→ACC)	hcr ←	HCP oxidoreductase, NADH‑dependent
RA	918,410	G→T	7.6%	A14A (GCG→GCT)	clpS →	regulatory protein for ClpA substrate specificity
RA	924,054	G→T	8.7%	R200S (CGC→AGC)	cydC ←	fused glutathione, cysteine exporter subunits of ABC superfamily: membrane component/ATP‑binding component
RA	925,160	G→T	100%	S420* (TCA→TAA)	cydD ←	fused glutathione, cysteine exporter subunits of ABC superfamily: membrane component/ATP‑binding component
RA	929,510	G→T	8.2%	E277D (GAG→GAT)	ftsK →	DNA translocase at septal ring sorting daughter chromsomes
RA	943,573	G→T	100%	A297S (GCC→TCC)	ycaM →	putative transporter
RA	955,568	A→T	100%	intergenic (+17/‑152)	aroA → / → ycaL	5‑enolpyruvylshikimate‑3‑phosphate synthetase/putative peptidase‑related chaperone
RA	962,925	G→T	5.3%	T283T (ACG→ACT)	msbA →	fused lipid transporter subunits of ABC superfamily: membrane component/ATP‑binding component
RA	964,173	G→T	6.5%	D118Y (GAT→TAT)	lpxK →	lipid A 4'kinase
RA	964,594	G→T	7.9%	C258F (TGT→TTT)	lpxK →	lipid A 4'kinase
RA	968,415	G→T	100%	S148* (TCG→TAG)	ycbC ←	DUF218 superfamily protein
RA	969,415	A→T	8.0%	P141P (CCA→CCT)	smtA →	putative S‑adenosyl‑L‑methionine‑dependent methyltransferase
RA	970,288	G→T	7.6%	D172Y (GAC→TAC)	mukF →	chromosome condensin MukBEF, kleisin‑like subunit, binds calcium
RA	981,159	C→T	9.1%	E3K (GAG→AAG)	aspC ←	aspartate aminotransferase, PLP‑dependent
RA	987,103	C→T	10.2%	I342I (ATC→ATT)	pepN →	aminopeptidase N
RA	992,767	C→A	84.9%	D68Y (GAT→TAT)	ssuE ←	NAD(P)H‑dependent FMN reductase
RA	994,328	G→T	87.7%	G128V (GGA→GTA)	elfD →	putative periplasmic pilin chaperone
RA	997,673	A→T	85.7%	T137T (ACA→ACT)	elfG →	putative fimbrial‑like adhesin protein
RA	997,965	G→T	100%	D235Y (GAT→TAT)	elfG →	putative fimbrial‑like adhesin protein
RA	998,782	C→A	7.4%	A146A (GCC→GCA)	ycbU →	putative fimbriae protein
RA	1,000,841	G→T	88.6%	A206A (GCG→GCT)	pyrD →	dihydro‑orotate oxidase, FMN‑linked
RA	1,003,597	G→T	88.6%	D100Y (GAC→TAC)	rlmL →	fused 23S rRNA m(2)G2445 and m(7)G2069 methyltransferase, SAM‑dependent
RA	1,011,929	T→A	36.4%	intergenic (‑3/+66)	fabA ← / ← ycbZ	beta‑hydroxydecanoyl thioester dehydrase/putative peptidase
RA	1,015,042	G→T	8.5%	I156I (ATC→ATA)	ompA ←	outer membrane protein A (3a;II*;G;d)
RA	1,020,029	G→T	9.4%	E35* (GAA→TAA)	helD →	DNA helicase IV
RA	1,024,300	G→T	5.3%	H376N (CAT→AAT)	rlmI ←	23S rRNA m(5)C1962 methyltransferase, SAM‑dependent
RA	1,024,703	G→T	100%	G241G (GGC→GGA)	rlmI ←	23S rRNA m(5)C1962 methyltransferase, SAM‑dependent
RA	1,038,316	G→T	85.7%	R451S (CGT→AGT)	etk ←	tyrosine‑protein kinase, role in O‑antigen capsule formation
RA	1,048,928	C→A	100%	E903* (GAA→TAA)	torS ←	hybrid sensory histidine kinase in two‑component regulatory system with TorR
RA	1,049,407	G→T	100%	T743K (ACG→AAG)	torS ←	hybrid sensory histidine kinase in two‑component regulatory system with TorR
RA	1,055,132	G→T	86.7%	E141* (GAA→TAA)	torA →	trimethylamine N‑oxide (TMAO) reductase I, catalytic subunit
RA	1,077,911	A→C	100%	K71N (AAA→AAC)	efeO →	inactive ferrous ion transporter EfeUOB
RA	1,079,951	G→T	6.9%	D374Y (GAT→TAT)	efeB →	deferrrochelatase, periplasmic
RA	1,083,443	G→T	100%	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	100%	L404* (TTA→TAA)	pgaB ←	poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine (PGA) N‑deacetylase outer membrane export lipoprotein
RA	1,088,607	C→A	6.2%	V92V (GTC→GTA)	ycdT →	diguanylate cyclase, membrane‑anchored
RA	1,088,734	G→T	5.3%	V135F (GTT→TTT)	ycdT →	diguanylate cyclase, membrane‑anchored
RA	1,089,009	G→T	8.8%	V226V (GTG→GTT)	ycdT →	diguanylate cyclase, membrane‑anchored
RA	1,099,378	A→C	10.6%	intergenic (‑726/‑29)	csgD ← / → csgB	csgBAC operon transcriptional regulator/curlin nucleator protein, minor subunit in curli complex
RA	1,099,528	C→A	12.8%	S41Y (TCT→TAT)	csgB →	curlin nucleator protein, minor subunit in curli complex
RA	1,103,006	G→T	8.5%	G399V (GGC→GTC)	clsC →	stationary phase cardiolipin synthase 3
RA	1,104,639	C→A	86.0%	intergenic (‑242/‑152)	opgC ← / → opgG	osmoregulated periplasmic glucan succinylation membrane protein/osmoregulated periplasmic glucan (OPG) biosynthesis periplasmic protein
RA	1,106,953	C→A	19.9%	A212E (GCG→GAG)	opgH →	membrane glycosyltransferase; nutrient‑dependent cell size regulator, FtsZ assembly antagonist
RA	1,107,069	T→G	6.6%	C251G (TGT→GGT)	opgH →	membrane glycosyltransferase; nutrient‑dependent cell size regulator, FtsZ assembly antagonist
RA	1,107,180	A→C	21.7%	N288H (AAC→CAC)	opgH →	membrane glycosyltransferase; nutrient‑dependent cell size regulator, FtsZ assembly antagonist
RA	1,113,450	A→T	86.0%	I161I (ATT→ATA)	yceI ←	secreted protein
RA	1,114,329	C→A	100%	L58F (TTG→TTT)	yceJ ←	putative cytochrome b561
RA	1,116,548	T→A	31.7%	intergenic (‑137/+150)	bssS ← / ← dinI	biofilm regulator/DNA damage‑inducible protein I
RA	1,116,874	C→A	27.8%	E24* (GAA→TAA)	dinI ←	DNA damage‑inducible protein I
RA	1,116,964	A→G	100%	intergenic (‑21/+53)	dinI ← / ← pyrC	DNA damage‑inducible protein I/dihydro‑orotase
RA	1,122,994	C→A	36.7%	R245S (CGC→AGC)	yceM →	putative oxidoreductase
RA	1,125,785	C→A	5.4%	A179S (GCC→TCC)	flgA ←	assembly protein for flagellar basal‑body periplasmic P ring
RA	1,131,521	C→A	100%	Q168K (CAG→AAG)	flgH →	flagellar protein of basal‑body outer‑membrane L ring
RA	1,137,384	G→T	89.5%	R814S (CGC→AGC)	rne ←	fused ribonucleaseE: endoribonuclease/RNA‑binding protein/RNA degradosome binding protein
RA	1,139,402	C→A	89.8%	R141L (CGC→CTC)	rne ←	fused ribonucleaseE: endoribonuclease/RNA‑binding protein/RNA degradosome binding protein
RA	1,145,840	C→A	8.4%	I219I (ATC→ATA)	fabD →	malonyl‑CoA‑[acyl‑carrier‑protein] transacylase
RA	1,146,692	A→T	82.4%	T189T (ACA→ACT)	fabG →	3‑oxoacyl‑[acyl‑carrier‑protein] reductase
RA	1,147,164	G→A	10.8%	D32N (GAC→AAC)	acpP →	acyl carrier protein (ACP)
RA	1,150,407	G→T	8.8%	P280P (CCG→CCT)	yceG →	septation protein, ampicillin sensitivity
RA	1,151,750	G→T	100%	R178L (CGC→CTC)	holB →	DNA polymerase III, delta prime subunit
RA	1,152,278	G→T	100%	E16* (GAA→TAA)	ycfH →	putative DNase
RA	1,153,110	T→A	7.0%	intergenic (+80/‑215)	ycfH → / → ptsG	putative DNase/fused glucose‑specific PTS enzymes: IIB component/IIC component
RA	1,154,905	G→T	9.3%	F701L (TTC→TTA)	fhuE ←	ferric‑rhodotorulic acid outer membrane transporter
RA	1,156,310	G→T	81.8%	S233* (TCA→TAA)	fhuE ←	ferric‑rhodotorulic acid outer membrane transporter
RA	1,170,814	T→A	5.3%	intergenic (‑193/‑69)	ycfT ← / → lolC	inner membrane protein/lipoprotein‑releasing system transmembrane protein
RA	1,172,212	C→A	15.4%	S46S (TCC→TCA)	lolD →	outer membrane‑specific lipoprotein transporter subunit
RA	1,191,676	C→T	100%	H366H (CAC→CAT)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,207,097	A→T	12.2%	intergenic (+64/+39)	icdC → / ← iraM	pseudogene, isocitrate dehydrogenase C‑terminal gene fragment; idcC' is a 54 codon 3' gene fragment created during e14 prophage insertion/RpoS stabilzer during Mg starvation, anti‑RssB factor
RA	1,208,587	T→A	18.4%	intergenic (‑24/+197)	ycgX ← / ← bluR	DUF1398 family protein/repressor of blue light‑responsive genes
RA	1,209,445	T→A	5.1%	Q24L (CAA→CTA)	bluR ←	repressor of blue light‑responsive genes
RA	1,210,671	A→T	13.5%	F87L (TTT→TTA)	bluF ←	anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; has c‑di‑GMP phosphodiesterase‑like EAL domain, but does not degrade c‑di‑GMP
RA	1,211,169	C→A	100%	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	1,213,332	G→T	30.7%	M183I (ATG→ATT)	ycgG →	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	1,219,533	A→G	100%	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	100%	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	1,228,033	C→A	10.7%	A152S (GCT→TCT)	dsbB ←	oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I
RA	1,228,591	G→T	100%	intergenic (‑105/+41)	dsbB ← / ← nhaB	oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I/sodium:proton antiporter
RA	1,235,606	G→T	6.2%	intergenic (+201/+185)	dadX → / ← cvrA	alanine racemase, catabolic, PLP‑binding/putative cation/proton antiporter
RA	1,236,753	G→T	7.2%	R259S (CGC→AGC)	cvrA ←	putative cation/proton antiporter
RA	1,245,056	A→C	8.5%	L53R (CTC→CGC)	dhaL ←	dihydroxyacetone kinase, C‑terminal domain
RA	1,246,435	T→A	9.9%	intergenic (‑141/‑87)	dhaK ← / → dhaR	dihydroxyacetone kinase, PTS‑dependent, dihydroxyacetone‑binding subunit/dhaKLM operon transcription activator
RA	1,249,227	G→T	85.9%	R728S (CGT→AGT)	ycgV ←	putative adhesin
RA	1,256,431	G→T	15.2%	R301S (CGT→AGT)	prs ←	phosphoribosylpyrophosphate synthase
RA	1,256,770	C→A	8.1%	D188Y (GAT→TAT)	prs ←	phosphoribosylpyrophosphate synthase
RA	1,257,076	T→A	5.6%	T86S (ACC→TCC)	prs ←	phosphoribosylpyrophosphate synthase
RA	1,261,810	G→A	83.5%	A87A (GCG→GCA)	prmC →	N5‑glutamine methyltransferase, modifies release factors RF‑1 and RF‑2
RA	1,264,442	G→T	86.1%	V274V (GTG→GTT)	kdsA →	3‑deoxy‑D‑manno‑octulosonate 8‑phosphate synthase
RA	1,264,654	C→A	30.7%	A26A (GCG→GCT)	ldrA ←	toxic polypeptide, small
RA	1,276,723	C→A	13.1%	T468T (ACC→ACA)	narG →	nitrate reductase 1, alpha subunit
RA	1,277,786	G→A	100%	D823N (GAC→AAC)	narG →	nitrate reductase 1, alpha subunit
RA	1,282,421	A→T	12.7%	intergenic (+439/+101)	narI → / ← rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
RA	1,282,696	G→A	8.5%	intergenic (‑4/+4)	rttR ← / ← tyrV	rtT sRNA, processed from tyrT transcript/tRNA‑Tyr
RA	1,284,124	C→A	8.1%	intergenic (‑44/+6)	purU ← / ← ychJ	formyltetrahydrofolate hydrolase/UPF0225 family protein
RA	1,284,545	A→C	7.8%	L15R (CTA→CGA)	ychJ ←	UPF0225 family protein
RA	1,288,669	A→T	100%	intergenic (‑291/‑314)	hns ← / → tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
RA	1,290,033	G→T	86.2%	pseudogene (416/567 nt)	insZ ←	pseudogene, transposase homolog
RA	1,296,729	C→A	87.5%	H431N (CAC→AAC)	oppA →	oligopeptide transporter subunit
RA	1,299,742	C→A	12.3%	A244A (GCC→GCA)	oppD →	oligopeptide transporter subunit
RA	1,315,886	C→A	28.8%	E440* (GAG→TAG)	trpE ←	component I of anthranilate synthase
RA	1,320,402	C→T	5.1%	P467L (CCA→CTA)	yciQ →	enhancer of membrane protein expression; putative inner membrane protein
RA	1,322,140	T→A	100%	T159S (ACG→TCG)	btuR ←	cob(I)yrinic acid a,c‑diamide adenosyltransferase
RA	1,325,982	G→T	86.6%	T226T (ACG→ACT)	topA →	DNA topoisomerase I, omega subunit
RA	1,330,955	G→T	100%	D290Y (GAT→TAT)	acnA →	aconitate hydratase 1
RA	1,335,356	A→T	86.5%	H181L (CAT→CTT)	yciM →	envelope integrity maintenance protein; EnvC‑interacting protein
RA	1,337,533	G→T	100%	A18E (GCA→GAA)	osmB ←	lipoprotein
RA	1,341,061	C→A	13.0%	Y3* (TAC→TAA)	ymiB →	uncharacterized protein
RA	1,348,772	G→T	91.1%	P2T (CCT→ACT)  A319D (GCC→GAC)	sapC ← sapB ←	antimicrobial peptide transport ABC transporter permease antimicrobial peptide transport ABC transporter permease
RA	1,350,891	G→T	84.2%	S159R (AGC→AGA) ‡	sapA ←	antimicrobial peptide transport ABC transporter periplasmic binding protein
RA	1,350,892	C→A	7.0%	S159I (AGC→ATC) ‡	sapA ←	antimicrobial peptide transport ABC transporter periplasmic binding protein
RA	1,351,022	G→T	91.8%	R116S (CGT→AGT)	sapA ←	antimicrobial peptide transport ABC transporter periplasmic binding protein
RA	1,355,635	G→T	8.1%	D87Y (GAC→TAC)	puuD →	gamma‑glutamyl‑gamma‑aminobutyrate hydrolase
RA	1,356,842	G→T	25.6%	intergenic (+117/‑158)	puuR → / → puuC	repressor for the divergent puu operons, putrescine inducible/gamma‑glutamyl‑gamma‑aminobutyraldehyde dehydrogenase; succinate semialdehyde dehydrogenase
RA	1,356,855	G→T	28.9%	intergenic (+130/‑145)	puuR → / → puuC	repressor for the divergent puu operons, putrescine inducible/gamma‑glutamyl‑gamma‑aminobutyraldehyde dehydrogenase; succinate semialdehyde dehydrogenase
RA	1,358,837	G→T	15.9%	D117Y (GAC→TAC)	puuB →	gamma‑glutamylputrescine oxidoreductase
RA	1,358,855	G→T	86.7%	G123C (GGC→TGC)	puuB →	gamma‑glutamylputrescine oxidoreductase
RA	1,364,452	C→T	8.1%	intergenic (+192/‑21)	pspE → / → ycjM	thiosulfate:cyanide sulfurtransferase (rhodanese)/alpha amylase catalytic domain family protein
RA	1,365,283	G→T	100%	E271* (GAG→TAG)	ycjM →	alpha amylase catalytic domain family protein
RA	1,373,167	C→A	23.9%	H343N (CAT→AAT)	ycjT →	putative family 65 glycosyl hydrolase
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	100%	A275A (GCG→GCA)	ycjW ←	LacI family putative transcriptional repressor
RA	1,377,693	C→A	27.1%	D176Y (GAT→TAT)	ycjW ←	LacI family putative transcriptional repressor
RA	1,384,386	T→A	6.1%	H157L (CAC→CTC)	mpaA ←	murein peptide amidase A
RA	1,386,008	G→T	100%	Q35K (CAG→AAG)	ycjY ←	S9 homolog non‑peptidase family protein
RA	1,388,406	G→T	100%	R308L (CGC→CTC)	mppA →	murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit
RA	1,389,852	G→T	89.3%	R110S (CGC→AGC)	ynaI ←	mechanosensitive channel protein, very small conductance
RA	1,393,781	C→A	7.5%	M1M (ATG→ATT) †	fnr ←	oxygen‑sensing anaerobic growth regulon transcriptional regulator; autorepressor
RA	1,419,219	G→A	10.0%	R394H (CGT→CAT)	trkG →	Rac prophage; potassium transporter subunit
RA	1,424,234	C→A	100%	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	1,429,850	G→T	8.7%	I9I (ATC→ATA)	uspF ←	stress‑induced protein, ATP‑binding protein
RA	1,430,873	G→T	87.8%	S93* (TCA→TAA)	ompN ←	outer membrane pore protein N, non‑specific
RA	1,434,587	G→T	7.7%	S152* (TCG→TAG)	pfo ←	pyruvate‑flavodoxin oxidoreductase
RA	1,439,518	C→A	100%	S737S (TCC→TCA)	ydbH →	putative membrane‑anchored protein, function unknown
RA	1,441,854	C→A	9.6%	R27S (CGT→AGT)	feaB →	phenylacetaldehyde dehydrogenase
RA	1,445,781	G→T	9.0%	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	12.5%	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	8.9%	L79F (CTC→TTC)	paaA →	ring 1,2‑phenylacetyl‑CoA epoxidase subunit
RA	1,449,763	C→A	6.9%	R115S (CGT→AGT)	paaC →	ring 1,2‑phenylacetyl‑CoA epoxidase subunit
RA	1,451,422	A→T	100%	T246S (ACG→TCG)	paaE →	ring 1,2‑phenylacetyl‑CoA epoxidase, NAD(P)H oxidoreductase component
RA	1,454,568	C→A	7.4%	R420S (CGT→AGT)	paaH →	3‑hydroxyadipyl‑CoA dehydrogenase, NAD+‑dependent
RA	1,454,724	G→T	100%	G472C (GGT→TGT)	paaH →	3‑hydroxyadipyl‑CoA dehydrogenase, NAD+‑dependent
RA	1,457,725	G→T	84.5%	intergenic (+30/‑71)	paaK → / → paaX	phenylacetyl‑CoA ligase/transcriptional repressor of phenylacetic acid degradation paa operon, phenylacetyl‑CoA inducer
RA	1,460,593	C→G	5.5%	pseudogene (945/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA	1,460,602	T→C	5.3%	pseudogene (954/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA	1,460,761	A→G	7.8%	pseudogene (1113/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA	1,460,819	G→A	6.2%	pseudogene (1171/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA	1,477,570	G→A	7.4%	D85N (GAC→AAC)	hrpA →	putative ATP‑dependent helicase
RA	1,478,971	G→A	100%	E552K (GAG→AAG)	hrpA →	putative ATP‑dependent helicase
RA	1,479,733	G→T	82.9%	D806Y (GAT→TAT)	hrpA →	putative ATP‑dependent helicase
RA	1,482,005	G→T	87.7%	D172Y (GAT→TAT)	ydcF →	DUF218 superfamily protein, SAM‑binding
RA	1,489,197	C→T	8.2%	K44K (AAG→AAA)	ydcI ←	putative DNA‑binding transcriptional regulator
RA	1,489,938	C→A	20.3%	R132S (CGC→AGC)	ydcJ →	putative metalloenzyme
RA	1,499,759	G→T	7.3%	V193V (GTC→GTA)	ydcO ←	BenE family inner membrane putative transporter
RA	1,503,324	T→A	10.5%	intergenic (‑3/‑219)	yncJ ← / → hicA	uncharacterized protein/mRNA interferase toxin of the HicAB toxin‑antitoxin system
RA	1,508,681	C→A	82.6%	F198L (TTC→TTA)	ydcU →	putative spermidine/putrescine transporter subunit
RA	1,512,325	G→T	31.3%	I88I (ATC→ATA)	ydcZ ←	DUF606 family inner membrane protein
RA	1,514,177	G→T	87.6%	E298D (GAG→GAT)	curA →	curcumin/dihydrocurcumin reductase, NADPH‑dependent
RA	1,514,858	G→A	82.8%	E114K (GAA→AAA)	mcbR →	colanic acid and biofilm gene transcriptional regulator, MqsR‑controlled
RA	1,515,742	A→T	18.7%	I527I (ATT→ATA)	yncD ←	putative iron outer membrane transporter
RA	1,515,792	C→A	7.4%	D511Y (GAT→TAT)	yncD ←	putative iron outer membrane transporter
RA	1,519,349	T→A	100%	K297* (AAA→TAA)	ansP ←	L‑asparagine transporter
RA	1,522,387	C→A	36.8%	pseudogene (229/2037 nt)	rhsE →	pseudogene, Rhs family protein
RA	1,523,317	G→T	82.7%	pseudogene (1159/2037 nt)	rhsE →	pseudogene, Rhs family protein
RA	1,525,685	G→A	7.2%	pseudogene (104/315 nt)	yncI →	pseudogene
RA	1,526,607	G→A	100%	D179N (GAT→AAT)	ydcC →	H repeat‑associated putative transposase
RA	1,531,029	G→T	84.3%	R180S (CGC→AGC)	narW ←	nitrate reductase 2 (NRZ), delta subunit (assembly subunit)
RA	1,534,409	G→T	88.2%	V813V (GTC→GTA)	narZ ←	nitrate reductase 2 (NRZ), alpha subunit
RA	1,535,087	G→T	6.0%	T587T (ACC→ACA)	narZ ←	nitrate reductase 2 (NRZ), alpha subunit
RA	1,536,606	G→A	6.4%	T81I (ACT→ATT)	narZ ←	nitrate reductase 2 (NRZ), alpha subunit
RA	1,537,806	A→T	89.9%	L171* (TTA→TAA)	narU ←	nitrate/nitrite transporter
RA	1,539,827	C→A	85.1%	pseudogene (145/951 nt)	yddK ←	pseudogene, leucine‑rich protein; putative glycoportein
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	1,548,216	A→T	87.3%	intergenic (‑121/+13)	adhP ← / ← maeA	ethanol‑active dehydrogenase/acetaldehyde‑active reductase/malate dehydrogenase, (decarboxylating, NAD‑requiring) (malic enzyme)
RA	1,552,629	C→A	93.9%	D216Y (GAT→TAT)	ddpD ←	D,D‑dipeptide permease system, ATP‑binding component
RA	1,555,076	C→A	5.6%	A37A (GCG→GCT)	ddpB ←	D‑ala‑D‑ala transporter subunit
RA	1,558,685	G→T	84.8%	R436S (CGC→AGC)	dosP ←	oxygen sensor, c‑di‑GMP phosphodiesterase, heme‑regulated; cold‑ and stationary phase‑induced bioflim regulator
RA	1,561,151	C→A	6.8%	D83Y (GAT→TAT)	dosC ←	diguanylate cyclase, cold‑ and stationary phase‑induced oxygen‑dependent biofilm regulator
RA	1,563,276	G→T	100%	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	1,566,423	A→T	20.4%	intergenic (‑121/+241)	gadB ← / ← pqqL	glutamate decarboxylase B, PLP‑dependent/putative periplasmic M16 family zinc metalloendopeptidase
RA	1,569,502	T→G	88.7%	intergenic (‑43/+2)	pqqL ← / ← yddB	putative periplasmic M16 family zinc metalloendopeptidase/putative TonB‑dependent outer membrane receptor
RA	1,570,428	G→T	86.5%	I483I (ATC→ATA)	yddB ←	putative TonB‑dependent outer membrane receptor
RA	1,570,826	C→A	88.5%	D351Y (GAC→TAC)	yddB ←	putative TonB‑dependent outer membrane receptor
RA	1,574,523	T→A	85.7%	L175F (TTA→TTT)	ydeM ←	putative YdeN‑specific sulfatase‑maturating enzyme
RA	1,575,339	G→T	100%	F481L (TTC→TTA)	ydeN ←	putative Ser‑type periplasmic non‑aryl sulfatase
RA	1,576,325	T→A	35.9%	N153Y (AAT→TAT)	ydeN ←	putative Ser‑type periplasmic non‑aryl sulfatase
RA	1,580,852	C→A	36.1%	intergenic (‑109/+225)	ydeP ← / ← ydeQ	putative oxidoreductase/putative fimbrial‑like adhesin protein
RA	1,586,871	G→T	89.7%	intergenic (‑172/+51)	hipB ← / ← yneO	antitoxin of HipAB toxin‑antitoxin system/pseudogene, AidA homolog
RA	1,590,878	A→T	36.2%	pseudogene (1367/5323 nt)	yneO ←	pseudogene, AidA homolog
RA	1,592,700	G→T	6.7%	intergenic (‑456/+174)	yneO ← / ← lsrK	pseudogene, AidA homolog/autoinducer‑2 (AI‑2) kinase
RA	1,603,440	G→A	100%	intergenic (‑161/+46)	yneE ← / ← uxaB	bestrophin family putative inner membrane protein/altronate oxidoreductase, NAD‑dependent
RA	1,604,949	T→C	7.8%	intergenic (‑12/+215)	uxaB ← / ← yneF	altronate oxidoreductase, NAD‑dependent/putative membrane‑bound diguanylate cyclase
RA	1,610,766	C→T	8.4%	S249S (AGC→AGT)	yneK →	uncharacterized protein
RA	1,611,158	G→T	11.0%	intergenic (+23/‑127)	yneK → / → ydeA	uncharacterized protein/arabinose efflux transporter, arabinose‑inducible
RA	1,611,967	C→T	6.7%	A228V (GCA→GTA)	ydeA →	arabinose efflux transporter, arabinose‑inducible
RA	1,614,089	G→T	87.6%	E87* (GAG→TAG)	marA →	multiple antibiotic resistance transcriptional regulator
RA	1,615,508	C→A	6.8%	intergenic (‑114/‑81)	eamA ← / → ydeE	cysteine and O‑acetyl‑L‑serine efflux system/putative transporter
RA	1,617,633	G→T	7.3%	L159I (CTT→ATT)	dgcZ ←	diguanylate cyclase, zinc‑sensing
RA	1,618,960	A→C	6.7%	intergenic (‑206/‑70)	ydeI ← / → ydeJ	hydrogen peroxide resistance OB fold protein; putative periplasmic protein/inactive PncC family protein
RA	1,620,961	T→G	100%	Q226P (CAA→CCA)	dcp ←	dipeptidyl carboxypeptidase II
RA	1,623,532	G→T	9.0%	G21C (GGC→TGC)	ydfZ →	selenoprotein, function unknown
RA	1,628,207	G→A	100%	G110E (GGA→GAA)	pinQ →	Qin prophage; putative site‑specific recombinase
RA	1,642,135	C→T	85.0%	intergenic (‑28/‑56)	dicC ← / → dicA	Qin prophage; DNA‑binding transcriptional regulator for DicB/Qin prophage; putative regulator for DicB
RA	1,646,372	C→A	37.0%	pseudogene (565/1158 nt)	intQ →	pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related
RA	1,646,412	A→T	10.9%	pseudogene (605/1158 nt)	intQ →	pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related
RA	1,649,014	C→A	5.8%	D129Y (GAT→TAT)	rspA ←	bifunctional D‑altronate/D‑mannonate dehydratase
RA	1,656,349	G→T	7.2%	D513Y (GAT→TAT)	ynfF →	S‑ and N‑oxide reductase, A subunit, periplasmic
RA	1,659,309	C→A	11.3%	R183S (CGC→AGC)	dmsD →	twin‑argninine leader‑binding protein for DmsA and TorA
RA	1,661,763	C→A	100%	P353P (CCG→CCT)	mlc ←	glucosamine anaerobic growth regulon transcriptional repressor; autorepressor
RA	1,669,592	G→T	88.7%	F342L (TTC→TTA)	pntB ←	pyridine nucleotide transhydrogenase, beta subunit
RA	1,674,854	C→A	12.2%	L347L (CTC→CTA)	ydgI →	putative arginine/ornithine antiporter transporter
RA	1,680,642	C→A	84.9%	E68D (GAG→GAT)	fumC ←	fumarate hydratase (fumarase C),aerobic Class II
RA	1,684,105	C→A	84.2%	intergenic (+97/‑4)	manA → / → ydgA	mannose‑6‑phosphate isomerase/DUF945 family protein
RA	1,689,180	T→G	100%	E383D (GAA→GAC)	uidA ←	beta‑D‑glucuronidase
RA	1,692,573	C→A	100%	D289Y (GAT→TAT)	malI ←	transcriptional repressor of Mal regulon
RA	1,693,444	G→T	6.3%	intergenic (‑7/‑168)	malI ← / → malX	transcriptional repressor of Mal regulon/fused maltose and glucose‑specific PTS enzymes: IIB component, IIC component
RA	1,696,612	A→T	100%	E41D (GAA→GAT)	add →	adenosine deaminase
RA	1,699,862	T→A	100%	L119* (TTG→TAG)	ydgK →	DUF2569 family inner membrane protein
RA	1,701,260	T→A	5.4%	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	11.5%	R597R (CGT→CGA)	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,703,062	T→A	12.4%	R629R (CGT→CGA)	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,703,071	A→T	10.4%	A632A (GCA→GCT)	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,711,397	C→T	100%	R28Q (CGA→CAA)	tyrS ←	tyrosyl‑tRNA synthetase
RA	1,723,809	G→T	100%	E156* (GAA→TAA)	lhr →	putative ATP‑dependent helicase
RA	1,724,141	C→A	6.6%	G266G (GGC→GGA)	lhr →	putative ATP‑dependent helicase
RA	1,726,169	C→A	9.8%	F942L (TTC→TTA)	lhr →	putative ATP‑dependent helicase
RA	1,727,929	C→A	6.7%	S1529* (TCA→TAA)	lhr →	putative ATP‑dependent helicase
RA	1,728,910	C→A	12.5%	T73T (ACC→ACA)	mepH →	murein DD‑endopeptidase, space‑maker hydrolase
RA	1,732,093	G→T	8.7%	intergenic (‑291/‑8)	ynhF ← / → purR	stress response membrane/transcriptional repressor, hypoxanthine‑binding
RA	1,734,355	C→A	6.6%	P63Q (CCG→CAG)	ydhC →	putative arabinose efflux transporter
RA	1,738,967	A→C	23.4%	P418P (CCA→CCC)	mdtK →	multidrug efflux system transporter
RA	1,751,430	C→A	6.2%	intergenic (+63/‑248)	pykF → / → lpp	pyruvate kinase I/murein lipoprotein
RA	1,753,173	C→A	24.9%	A125A (GCG→GCT)	sufE ←	sulfur acceptor protein
RA	1,754,004	G→T	6.5%	V259V (GTC→GTA)	sufS ←	cysteine desulfurase, stimulated by SufE; selenocysteine lyase, PLP‑dependent
RA	1,754,950	T→A	100%	I367F (ATT→TTT)	sufD ←	component of SufBCD Fe‑S cluster assembly scaffold
RA	1,764,150	G→T	100%	D274Y (GAT→TAT)	ydiK →	UPF0118 family inner membrane protein
RA	1,766,772	T→A	10.2%	S2T (TCT→ACT)	ydiN →	MFS transporter superfamily protein
RA	1,768,689	C→A	85.2%	S215* (TCA→TAA)	ydiB →	quinate/shikimate 5‑dehydrogenase, NAD(P)‑binding
RA	1,769,763	T→A	46.3%	intergenic (+62/‑81)	aroD → / → ydiF	3‑dehydroquinate dehydratase/putative acetyl‑CoA:acetoacetyl‑CoA transferase: alpha subunit/beta subunit
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	9.9%	V31V (GTC→GTA)	ydiS →	putative oxidoreductase
RA	1,777,451	C→A	100%	A55E (GCG→GAG)	fadK →	short chain acyl‑CoA synthetase, anaerobic
RA	1,779,717	C→A	20.4%	P551P (CCG→CCT)	ppsA ←	phosphoenolpyruvate synthase
RA	1,783,091	G→T	86.4%	E134* (GAG→TAG)	aroH →	3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tryptophan repressible
RA	1,796,101	C→A	30.5%	D243Y (GAC→TAC)	thrS ←	threonyl‑tRNA synthetase
RA	1,800,129	C→T	38.5%	W71* (TGG→TAG)	ydiY ←	acid‑inducible putative outer membrane protein
RA	1,800,416	C→T	9.3%	intergenic (‑76/‑211)	ydiY ← / → pfkB	acid‑inducible putative outer membrane protein/6‑phosphofructokinase II
RA	1,802,047	G→A	100%	intergenic (+100/‑6)	ydiZ → / → yniA	uncharacterized protein/fructosamine kinase family protein
RA	1,802,229	C→A	30.1%	A59A (GCC→GCA)	yniA →	fructosamine kinase family protein
RA	1,803,109	C→T	100%	A128T (GCC→ACC)	yniB ←	putative inner membrane protein
RA	1,804,587	G→T	6.6%	L40L (CTG→CTT)	ydjM →	inner membrane protein regulated by LexA
RA	1,811,368	C→A	30.4%	A9S (GCC→TCC)	chbG ←	chito‑oligosaccharide deacetylase
RA	1,812,514	C→A	84.6%	D82Y (GAT→TAT)	chbF ←	phospho‑chitobiase; general 6‑phospho‑beta‑glucosidase activity
RA	1,818,886	C→A	35.7%	S103S (TCG→TCT)	ves ←	cold‑ and stress‑inducible protein
RA	1,820,888	C→A	90.8%	C98F (TGC→TTC)	astE ←	succinylglutamate desuccinylase
RA	1,821,696	A→T	100%	L274Q (CTG→CAG)	astB ←	succinylarginine dihydrolase
RA	1,823,835	A→C	7.3%	W53G (TGG→GGG)	astD ←	succinylglutamic semialdehyde dehydrogenase
RA	1,825,763	C→A	100%	A159A (GCG→GCT)	astC ←	succinylornithine transaminase, PLP‑dependent
RA	1,826,476	A→G	7.0%	intergenic (‑237/‑209)	astC ← / → xthA	succinylornithine transaminase, PLP‑dependent/exonuclease III
RA	1,832,413	C→A	100%	L315L (CTC→CTA)	ynjC →	inner membrane putative ABC superfamily transporter permease
RA	1,833,730	C→A	100%	R3S (CGT→AGT)	ynjE →	molybdopterin synthase sulfurtransferase
RA	1,836,192	T→A	44.3%	I67I (ATA→ATT)	ynjH ←	DUF1496 family protein
RA	1,850,880	C→A	13.5%	V102V (GTG→GTT)	ydjH ←	putative kinase
RA	1,852,274	C→A	83.9%	D273Y (GAT→TAT)	ydjJ ←	putative Zn‑dependent NAD(P)‑binding oxidoreductase
RA	1,860,183	G→T	83.7%	R183S (CGC→AGC)	mipA ←	scaffolding protein for murein synthesizing machinery
RA	1,865,000	C→A	88.8%	P120Q (CCA→CAA)	yeaI →	putative membrane‑anchored diguanylate cyclase
RA	1,865,422	C→A	100%	R261R (CGA→AGA)	yeaI →	putative membrane‑anchored diguanylate cyclase
RA	1,870,743	C→A	84.0%	H272N (CAT→AAT)	yeaN →	putative transporter
RA	1,872,054	A→T	88.8%	E28V (GAG→GTG)	yeaP →	diguanylate cyclase
RA	1,872,520	G→T	100%	P183P (CCG→CCT)	yeaP →	diguanylate cyclase
RA	1,875,096	G→T	86.2%	intergenic (‑80/+47)	leuE ← / ← dmlR	leucine efflux protein/transcriptional activator of dmlA
RA	1,881,645	C→A	24.9%	D202Y (GAT→TAT)	rnd ←	ribonuclease D
RA	1,885,611	G→T	80.0%	R628S (CGT→AGT)	yoaA ←	putative ATP‑dependent helicase, DinG family
RA	1,886,725	G→T	86.9%	I256I (ATC→ATA)	yoaA ←	putative ATP‑dependent helicase, DinG family
RA	1,892,659	G→T	9.0%	intergenic (+106/‑25)	sdaA → / → yoaD	L‑serine dehydratase 1/putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase, regulator of cellulose production
RA	1,895,069	C→T	5.4%	G258G (GGG→GGA)	yoaE ←	putative membrane protein/conserved protein
RA	1,908,989	C→T	6.9%	A29T (GCT→ACT)	prc ←	carboxy‑terminal protease for penicillin‑binding protein 3
RA	1,909,342	T→A	100%	E150D (GAA→GAT)	proQ ←	RNA chaperone, putative ProP translation regulator
RA	1,913,162	G→T	9.9%	V466F (GTT→TTT)	yebT →	MCE domain protein
RA	1,935,501	C→A	23.8%	R131L (CGT→CTT)	mepM ←	murein DD‑endopeptidase, space‑maker hydrolase, septation protein
RA	1,940,498	G→T	87.9%	intergenic (‑61/‑10)	yobI ← / → yebB	uncharacterized protein/DUF830 family protein
RA	1,942,706	T→A	8.8%	T62S (ACC→TCC)	nudB ←	dihydroneopterin triphosphate pyrophosphatase
RA	1,944,177	C→A	100%	L201L (CTG→CTT)	aspS ←	aspartyl‑tRNA synthetase
RA	1,946,583	G→A	24.4%	V21I (GTC→ATC)	yecN →	MAPEG family inner membrane protein
RA	1,948,352	T→C	5.5%	N218N (AAT→AAC)	cmoB →	tRNA (cmo5U34)‑carboxymethyltransferase, carboxy‑SAM‑dependent
RA	1,951,334	C→A	28.7%	T352T (ACG→ACT)	torY ←	TMAO reductase III (TorYZ), cytochrome c‑type subunit
RA	1,952,575	T→C	21.0%	intergenic (‑186/+202)	torY ← / ← cutC	TMAO reductase III (TorYZ), cytochrome c‑type subunit/copper homeostasis protein
RA	1,953,371	C→A	14.6%	T51T (ACG→ACT)	cutC ←	copper homeostasis protein
RA	1,953,876	C→A	90.5%	P76P (CCG→CCT)	yecM ←	putative metal‑binding enzyme
RA	1,959,915	C→A	100%	P178P (CCG→CCT)	flhB ←	flagellin export apparatus, substrate specificity protein
RA	1,962,923	C→A	88.6%	M233I (ATG→ATT)	cheR ←	chemotaxis regulator, protein‑glutamate methyltransferase
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	1,984,987	C→A	100%	T38T (ACG→ACT)	yecA ←	UPF0149 family protein
RA	1,985,007	C→T	8.0%	E32K (GAG→AAG)	yecA ←	UPF0149 family protein
RA	1,986,289	T→A	100%	N4Y (AAT→TAT)	pgsA ←	phosphatidylglycerophosphate synthetase
RA	1,993,530	C→A	84.0%	E113* (GAG→TAG)	fliY ←	cystine transporter subunit
RA	1,994,623	G→T	5.2%	V216V (GTC→GTA)	fliA ←	RNA polymerase, sigma 28 (sigma F) factor
RA	1,997,314	G→T	100%	intergenic (‑227/‑39)	fliC ← / → fliD	flagellar filament structural protein (flagellin)/flagellar filament capping protein
RA	1,999,632	G→T	100%	intergenic (+73/‑5)	fliT → / → amyA	putative flagellar synthesis and assembly chaperone/cytoplasmic alpha‑amylase
RA	2,004,533	G→T	89.3%	T151T (ACG→ACT)	yedL →	putative acyl transferase
RA	2,007,090	G→T	20.0%	V127V (GTG→GTT)	fliF →	flagellar basal‑body MS‑ring and collar protein
RA	2,020,166	C→A	100%	D445Y (GAC→TAC)	yedQ ←	putative membrane‑anchored diguanylate cyclase
RA	2,027,150	G→T	7.8%	noncoding (21/91 nt)	rseX →	sRNA antisense regulator of ompA and ompC translation, Hfq‑dependent
RA	2,035,090	C→A	100%	Q79K (CAG→AAG)	zinT →	zinc and cadmium binding protein, periplasmic
RA	2,036,546	C→A	5.1%	intergenic (+167/+403)	yodB → / ← serU	cytochrome b561 homolog/tRNA‑Ser
RA	2,039,694	C→T	7.8%	R426C (CGC→TGC)	yeeJ →	putative adhesin
RA	2,041,346	C→A	36.0%	I976I (ATC→ATA)	yeeJ →	putative adhesin
RA	2,046,600	G→T	87.1%	pseudogene (210/1053 nt)	yeeL ←	pseudogene, glycosyltransferase homology
RA	2,049,111	C→A	30.8%	T190T (ACC→ACA)	amn →	AMP nucleosidase
RA	2,066,165	A→T	10.1%	G382G (GGA→GGT)	flu →	CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
RA	2,070,265	A→T	5.9%	intergenic (+30/‑33)	yeeS → / → yeeT	CP4‑44 prophage; putative DNA repair protein/CP4‑44 prophage; uncharacterized protein
RA	2,074,680	A→T	100%	W22R (TGG→AGG)	sbmC ←	DNA gyrase inhibitor
RA	2,076,300	C→T	29.0%	H22Y (CAC→TAC)	sbcB →	exodeoxyribonuclease I; exonuclease I
RA	2,077,212	A→T	100%	N326Y (AAT→TAT)	sbcB →	exodeoxyribonuclease I; exonuclease I
JC JC	2,080,274	IS2 (–) +5 bp	36.0%	coding (266‑270/1359 nt)	plaP ←	putrescine importer, low affinity
RA	2,080,679	A→T	7.2%	intergenic (‑84/+131)	yoeI ← / ← yeeY	uncharacterized protein/LysR family putative transcriptional regulator
RA	2,082,792	A→T	9.1%	L52* (TTG→TAG)	yoeB ←	toxin of the YoeB‑YefM toxin‑antitoxin system
RA	2,086,004	C→A	86.7%	A42A (GCC→GCA)	hisC →	histidinol‑phosphate aminotransferase
RA	2,098,995	C→A	100%	G182* (GGA→TGA)	wbbI ←	d‑Galf:alpha‑d‑Glc beta‑1,6‑galactofuranosyltransferase
RA	2,101,912	T→G	87.8%	E385A (GAG→GCG)	wzxB ←	putative polisoprenol‑linked O‑antigen transporter
RA	2,108,219:1	+A	100%	coding (1159/1395 nt)	wcaM ←	colanic acid biosynthesis protein
RA	2,108,459	T→A	9.2%	N307Y (AAT→TAT)	wcaM ←	colanic acid biosynthesis protein
RA	2,110,346	G→A	100%	T88I (ACC→ATC)	wcaL ←	putative glycosyl transferase
RA	2,114,911	A→T	100%	L42Q (CTG→CAG)	wcaJ ←	colanic biosynthesis UDP‑glucose lipid carrier transferase
RA	2,122,013	G→T	34.4%	T119T (ACC→ACA)	wcaF ←	putative acyl transferase
RA	2,122,266	G→T	86.1%	S35* (TCG→TAG)	wcaF ←	putative acyl transferase
RA	2,122,453	C→T	84.2%	A227T (GCT→ACT)	wcaE ←	putative glycosyl transferase
RA	2,122,653	C→T	85.3%	W160* (TGG→TAG)	wcaE ←	putative glycosyl transferase
RA	2,126,819	C→A	6.4%	A20A (GCG→GCT)	wcaA ←	putative glycosyl transferase
RA	2,128,128	T→A	32.6%	K336* (AAA→TAA)	wzc ←	colanic acid production tyrosine‑protein kinase; autokinase; Ugd phosphorylase
RA	2,128,696	C→A	7.0%	E146D (GAG→GAT)	wzc ←	colanic acid production tyrosine‑protein kinase; autokinase; Ugd phosphorylase
RA	2,129,228	G→A	8.9%	R118C (CGC→TGC)	wzb ←	colanic acid production protein‑tyrosine‑phosphatase; Wzc‑P dephosphorylase
RA	2,139,910	G→T	100%	R1055L (CGA→CTA)	yegE →	putative diguanylate cyclase
RA	2,144,474	C→A	100%	intergenic (‑8/‑192)	yegI ← / → yegJ	protein kinase‑related putative non‑specific DNA‑binding protein/uncharacterized protein
RA	2,146,030	T→A	9.1%	S194C (AGT→TGT)	yegL ←	VMA domain protein
RA	2,149,603	A→T	100%	E287V (GAA→GTA)	mdtB →	multidrug efflux system, subunit B
RA	2,150,955	G→T	9.0%	D738Y (GAT→TAT)	mdtB →	multidrug efflux system, subunit B
RA	2,152,444	C→A	90.5%	A193E (GCG→GAG)	mdtC →	multidrug efflux system, subunit C
RA	2,168,795	C→A	100%	D336Y (GAT→TAT)	gatZ ←	D‑tagatose 1,6‑bisphosphate aldolase 2, subunit
RA	2,170,707	C→A	20.7%	intergenic (‑24/+284)	gatY ← / ← fbaB	D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA	2,170,713	C→A	26.0%	intergenic (‑30/+278)	gatY ← / ← fbaB	D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA	2,170,724	G→T	21.7%	intergenic (‑41/+267)	gatY ← / ← fbaB	D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA	2,170,757	T→A	6.6%	intergenic (‑74/+234)	gatY ← / ← fbaB	D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA	2,179,205	G→T	100%	A24E (GCG→GAG)	rcnR ←	transcriptional repressor of rcnA
RA	2,181,645	A→G	100%	N83N (AAT→AAC)	yehA ←	putative fimbrial‑like adhesin protein
RA	2,194,695	T→A	100%	L313Q (CTA→CAA)	yehI →	DUF4132 domain‑containing protein
RA	2,195,449	A→T	100%	E564D (GAA→GAT)	yehI →	DUF4132 domain‑containing protein
RA	2,204,432	G→T	10.6%	pseudogene (1854/2001 nt)	yehQ →	pseudogene
RA	2,209,162	C→A	100%	I9I (ATC→ATA)	yohO →	putative membrane protein
RA	2,214,191	C→A	6.1%	V426V (GTG→GTT)	bglX ←	beta‑D‑glucoside glucohydrolase, periplasmic
RA	2,214,896	C→A	5.3%	A191A (GCG→GCT)	bglX ←	beta‑D‑glucoside glucohydrolase, periplasmic
RA	2,216,296	C→A	100%	I211I (ATC→ATA)	dld →	D‑lactate dehydrogenase, FAD‑binding, NADH independent
RA	2,218,022	C→A	31.7%	E110* (GAA→TAA)	pbpG ←	D‑alanyl‑D‑alanine endopeptidase
RA	2,222,970	T→A	80.1%	N299Y (AAT→TAT)	dusC ←	tRNA‑dihydrouridine synthase C
RA	2,223,247	C→T	100%	W206* (TGG→TGA)	dusC ←	tRNA‑dihydrouridine synthase C
RA	2,225,190	C→T	100%	G231G (GGC→GGT)	yohK →	LrgB family inner membrane protein
RA	2,234,532	C→A	83.6%	D206Y (GAT→TAT)	galS ←	galactose‑ and fucose‑inducible galactose regulon transcriptional isorepressor; mgl operon transcriptional repressor; autorepressor
RA	2,237,098	G→T	100%	H12N (CAT→AAT)	folE ←	GTP cyclohydrolase I
RA	2,241,222	T→G	88.1%	I264L (ATT→CTT)	lysP ←	lysine transporter
RA	2,248,657	C→A	87.7%	K3N (AAG→AAT)	rihB ←	ribonucleoside hydrolase 2
RA	2,262,060	C→A	31.4%	F251L (TTC→TTA)	yeiR →	Zn‑stimulated GTPase involved in zinc homeostasis; mutants are cadmium and EDTA sensitive; Zn(2+) binding protein
RA	2,263,137	C→A	100%	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	2,264,143	G→A	100%	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	2,267,932	G→T	7.9%	R92L (CGC→CTC)	yejB →	microcin C transporter YejABEF, permease subunit; ABC family
RA	2,275,993	G→T	30.6%	intergenic (+122/‑3)	yejH → / → rplY	putative ATP‑dependent DNA or RNA helicase/50S ribosomal subunit protein L25
RA	2,287,028	C→A	5.8%	T452T (ACG→ACT)	ccmF ←	heme lyase, CcmF subunit
RA	2,287,829	C→A	100%	S185S (TCG→TCT)	ccmF ←	heme lyase, CcmF subunit
RA	2,289,043	C→A	100%	W8L (TGG→TTG)	ccmD ←	cytochrome c biogenesis protein
RA	2,289,374	C→A	100%	V142V (GTG→GTT)	ccmC ←	heme exporter subunit
RA	2,295,603	C→A	6.6%	V210V (GTG→GTT)	napA ←	nitrate reductase, periplasmic, large subunit
RA	2,298,128	C→T	11.4%	intergenic (+256/+459)	eco → / ← mqo	ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA	2,298,159	T→C	6.8%	intergenic (+287/+428)	eco → / ← mqo	ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA	2,298,467	T→C	6.0%	intergenic (+595/+120)	eco → / ← mqo	ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA	2,303,070	T→G	100%	Q272P (CAG→CCG)	ada ←	fused DNA‑binding transcriptional dual regulator/O6‑methylguanine‑DNA methyltransferase
RA	2,305,116	C→A	100%	intergenic (‑103/+9)	apbE ← / ← ompC	putative thiamine‑synthetic flavin transferase lipoprotein/outer membrane porin protein C
RA	2,305,135	T→C	100%	Y365C (TAC→TGC)	ompC ←	outer membrane porin protein C
RA	2,307,391	C→A	7.9%	P142Q (CCG→CAG)	rcsD →	phosphotransfer intermediate protein in two‑component regulatory system with RcsBC
RA	2,310,604	C→A	6.1%	G918C (GGT→TGT)	rcsC ←	hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA	2,318,772	G→T	32.9%	D180Y (GAT→TAT)	atoE →	short chain fatty acid transporter
RA	2,318,825	G→T	86.1%	V197V (GTG→GTT)	atoE →	short chain fatty acid transporter
RA	2,321,041	G→T	11.8%	F194L (TTC→TTA)	yfaP ←	DUF2135 family protein, putative host defense protein
RA	2,322,609	C→A	81.7%	W223L (TGG→TTG)	yfaQ ←	tandem DUF2300 domain protein, putative host defense protein
RA	2,329,729	G→T	14.1%	A132E (GCG→GAG)	yfaA ←	DUF2138 family protein, putative host defense protein
RA	2,330,502	C→A	100%	D800Y (GAT→TAT)	gyrA ←	DNA gyrase (type II topoisomerase), subunit A
RA	2,335,383	T→A	14.7%	N756Y (AAC→TAC)	yfaL ←	adhesin
RA	2,339,930	A→T	7.6%	K529N (AAA→AAT)	nrdA →	ribonucleoside‑diphosphate reductase 1, alpha subunit
RA	2,342,897	C→A	83.8%	D19Y (GAC→TAC)	inaA ←	acid‑inducible Kdo/WaaP family putative kinase
RA	2,348,894	T→A	100%	V384E (GTG→GAG)	glpB →	sn‑glycerol‑3‑phosphate dehydrogenase (anaerobic), membrane anchor subunit
RA	2,349,191	C→A	24.0%	V64V (GTC→GTA)	glpC →	anaerobic sn‑glycerol‑3‑phosphate dehydrogenase, C subunit, 4Fe‑4S iron‑sulfur cluster
RA	2,352,082	C→A	6.7%	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	2,358,641	G→T	36.3%	I153I (ATC→ATA)	ais ←	putative LPS core heptose(II)‑phosphate phosphatase
RA	2,359,673	G→T	100%	M89I (ATG→ATT)	arnB →	uridine 5'‑(beta‑1‑threo‑pentapyranosyl‑4‑ulose diphosphate) aminotransferase, PLP‑dependent
RA	2,362,338	T→A	100%	L274Q (CTG→CAG)	arnA →	fused UDP‑L‑Ara4N formyltransferase/UDP‑GlcA C‑4'‑decarboxylase
RA	2,363,066	C→A	25.0%	L517I (CTC→ATC)	arnA →	fused UDP‑L‑Ara4N formyltransferase/UDP‑GlcA C‑4'‑decarboxylase
RA	2,365,571	C→T	8.9%	F395F (TTC→TTT)	arnT →	4‑amino‑4‑deoxy‑L‑arabinose transferase
RA	2,370,361:1	+G	100%	coding (711/759 nt)	menH ←	2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
RA	2,370,987	C→A	100%	E29* (GAA→TAA)	menH ←	2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
RA	2,376,688	T→A	28.3%	L166* (TTA→TAA)	elaD →	protease, capable of cleaving an AMC‑ubiquitin model substrate
RA	2,376,959	C→T	89.2%	N256N (AAC→AAT)	elaD →	protease, capable of cleaving an AMC‑ubiquitin model substrate
RA	2,380,078	C→T	100%	S247F (TCT→TTT)	yfbL →	putative peptidase
RA	2,383,897	C→A	100%	R363L (CGC→CTC)	nuoN ←	NADH:ubiquinone oxidoreductase, membrane subunit N
RA	2,399,210	G→T	100%	S304* (TCA→TAA)	lrhA ←	transcriptional repressor of flagellar, motility and chemotaxis genes
RA	2,400,847	A→G	19.4%	intergenic (‑727/‑193)	lrhA ← / → alaA	transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2
RA	2,400,858	C→A	86.4%	intergenic (‑738/‑182)	lrhA ← / → alaA	transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2
RA	2,403,485	C→A	6.9%	L449L (CTG→CTT)	yfbS ←	putative transporter
RA	2,404,772	C→A	32.3%	A20A (GCG→GCT)	yfbS ←	putative transporter
RA	2,405,946	T→G	100%	Q43P (CAG→CCG)	yfbU ←	UPF0304 family protein
RA	2,412,205	C→A	100%	D151Y (GAT→TAT)	yfcD ←	putative NUDIX hydrolase
RA	2,413,769	C→A	7.1%	D66Y (GAT→TAT)	yfcF ←	glutathione S‑transferase
RA	2,416,101	C→A	100%	intergenic (+21/+27)	yfcH → / ← yfcI	putative NAD‑dependent nucleotide‑sugar epimerase/transposase_31 family protein
RA	2,417,358	C→A	8.6%	E211* (GAA→TAA)	hisP ←	histidine/lysine/arginine/ornithine transporter subunit
RA	2,422,841	C→A	100%	D293Y (GAT→TAT)	purF ←	amidophosphoribosyltransferase
RA	2,423,202	C→A	19.7%	A172A (GCG→GCT)	purF ←	amidophosphoribosyltransferase
RA	2,424,074	C→T	100%	D57N (GAC→AAC)	cvpA ←	colicin V production membrane protein
RA	2,425,061	G→T	20.7%	Q35K (CAG→AAG)	dedD ←	membrane‑anchored periplasmic protein involved in septation
RA	2,437,510	C→A	8.0%	D47Y (GAC→TAC)	yfcL ←	uncharacterized protein
RA	2,438,529	A→C	11.0%	F171V (TTC→GTC)	yfcA ←	UPF0721 family inner membrane protein
RA	2,442,971	C→A	12.6%	E186D (GAG→GAT)	yfcO ←	DUF2544 family putative outer membrane protein
RA	2,443,918	T→G	6.0%	Y51S (TAT→TCT)	yfcP ←	putative fimbrial‑like adhesin protein
RA	2,450,335	C→T	100%	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	100%	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	100%	E39D (GAA→GAC)	yfcZ ←	UPF0381 family protein
RA	2,456,705	C→A	86.5%	S72Y (TCC→TAC)	yfdF →	uncharacterized protein
RA	2,459,976	G→T	85.7%	intergenic (+114/‑48)	argW → / → intS	tRNA‑Arg/CPS‑53 (KpLE1) prophage; putative prophage CPS‑53 integrase
RA	2,463,906	C→A	27.6%	Q433K (CAA→AAA)	gtrS →	serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
RA	2,463,915	C→A	16.4%	Q436K (CAA→AAA)	gtrS →	serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
RA	2,463,920	C→A	10.3%	D437E (GAC→GAA)	gtrS →	serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
RA	2,467,219	C→A	5.2%	S46* (TCA→TAA)	yfdP →	CPS‑53 (KpLE1) prophage; uncharacterized protein
RA	2,468,161	A→T	8.8%	E217D (GAA→GAT)	yfdQ →	CPS‑53 (KpLE1) prophage; uncharacterized protein
RA	2,474,353	G→T	88.7%	Q435K (CAG→AAG)	emrY ←	putative multidrug efflux system
RA	2,474,418	G→T	100%	S413* (TCA→TAA)	emrY ←	putative multidrug efflux system
RA	2,479,579	C→A	32.8%	S576* (TCA→TAA)	evgS →	hybrid sensory histidine kinase in two‑component regulatory system with EvgA
RA	2,481,974	G→T	86.8%	S225* (TCA→TAA)	yfdE ←	acetyl‑CoA:oxalate CoA‑transferase
RA	2,491,279	G→T	11.6%	R166S (CGT→AGT)	alaC ←	valine‑pyruvate aminotransferase 3
RA	2,497,946	G→T	87.3%	L7I (CTC→ATC)	fryA ←	putative PTS enzyme, Hpr component/enzyme I component/enzyme IIA component
RA	2,499,568	C→A	88.4%	D182Y (GAC→TAC)	ypdF ←	Xaa‑Pro aminopeptidase
RA	2,501,358	G→T	5.4%	R6S (CGC→AGC)	fryC ←	putative enzyme IIC component of PTS
RA	2,504,320	G→T	26.7%	M404I (ATG→ATT)	yfeO →	putative ion channel protein
RA	2,511,317	C→A	8.4%	intergenic (‑6/+203)	yfeA ← / ← alaX	putative diguanylate cyclase/tRNA‑Ala
RA	2,520,652	C→A	100%	I116I (ATC→ATA)	yfeH →	putative inorganic ion transporter
RA	2,524,056	C→A	86.8%	A179A (GCG→GCT)	zipA ←	FtsZ stabilizer
RA	2,526,794	C→T	88.9%	intergenic (+55/‑329)	cysK → / → ptsH	cysteine synthase A, O‑acetylserine sulfhydrolase A subunit/phosphohistidinoprotein‑hexose phosphotransferase component of PTS system (Hpr)
RA	2,526,851	A→T	9.0%	intergenic (+112/‑272)	cysK → / → ptsH	cysteine synthase A, O‑acetylserine sulfhydrolase A subunit/phosphohistidinoprotein‑hexose phosphotransferase component of PTS system (Hpr)
RA	2,532,553	C→A	9.9%	A130A (GCG→GCT)	cysM ←	cysteine synthase B (O‑acetylserine sulfhydrolase B)
RA	2,533,192	C→A	11.1%	D328Y (GAT→TAT)	cysA ←	sulfate/thiosulfate transporter subunit
RA	2,542,627	T→G	100%	I389M (ATT→ATG)	yfeW →	penicillin binding protein PBP4B; weak DD‑carboxypeptidase activity
RA	2,545,934	G→T	6.8%	R75L (CGC→CTC)	amiA →	N‑acetylmuramoyl‑l‑alanine amidase I
RA	2,549,676	C→A	100%	L28L (CTG→CTT)	eutL ←	putative ethanol utilization carboxysome structural protein
RA	2,553,462	A→G	7.1%	intergenic (+37/‑154)	intZ → / → yffL	CPZ‑55 prophage; putative phage integrase/CPZ‑55 prophage; uncharacterized protein
RA	2,553,580	G→A	5.9%	intergenic (+155/‑36)	intZ → / → yffL	CPZ‑55 prophage; putative phage integrase/CPZ‑55 prophage; uncharacterized protein
RA	2,556,786	G→T	88.5%	intergenic (+310/‑165)	yffP → / → yffQ	CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
RA	2,557,859	C→T	5.4%	intergenic (+128/‑23)	yffR → / → yffS	CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
RA	2,567,211	C→A	88.1%	D152Y (GAT→TAT)	eutT ←	cobalamin adenosyltransferase involved in ethanolamine utilization
RA	2,568,720	C→T	100%	A33T (GCC→ACC)	eutP ←	putative P‑loop NTPase ethanolamine utilization protein
RA	2,574,820	C→A	87.8%	A609E (GCG→GAG)	tktB →	transketolase 2, thiamine triphosphate‑binding
RA	2,576,325	C→A	100%	E171D (GAG→GAT)	nudK ←	GDP‑mannose pyrophosphatase
RA	2,576,567	C→A	5.5%	D91Y (GAC→TAC)	nudK ←	GDP‑mannose pyrophosphatase
RA	2,577,402	C→A	7.9%	V495F (GTC→TTC)	aegA ←	putative oxidoreductase, FeS binding subunit/NAD/FAD‑binding subunit
RA	2,578,959	C→A	6.8%	intergenic (‑75/‑131)	aegA ← / → narQ	putative oxidoreductase, FeS binding subunit/NAD/FAD‑binding subunit/sensory histidine kinase in two‑component regulatory system with NarP (NarL)
RA	2,587,029:1	+G	100%	coding (101/699 nt)	ypfH ←	palmitoyl‑CoA esterase activity, uncertain physiological substrate
RA	2,587,434	T→A	5.4%	L595F (TTA→TTT)	tmcA ←	elongator methionine tRNA (ac4C34) acetyltransferase
RA	2,589,808	G→T	11.7%	Q97K (CAG→AAG)	ypfJ ←	putative neutral zinc metallopeptidase
RA	2,589,933	G→A	100%	T55I (ACC→ATC)	ypfJ ←	putative neutral zinc metallopeptidase
RA	2,590,672	C→A	24.5%	V102V (GTG→GTT)	purC ←	phosphoribosylaminoimidazole‑succinocarboxamide synthetase
RA	2,591,795	C→A	5.1%	D144Y (GAT→TAT)	bamC ←	BamABCDE complex OM biogenesis lipoprotein
RA	2,595,418	C→A	5.1%	S81* (TCG→TAG)	hyfB →	hydrogenase 4, membrane subunit
RA	2,597,028	G→A	6.4%	A618T (GCT→ACT)	hyfB →	hydrogenase 4, membrane subunit
RA	2,597,173	T→G	100%	L666R (CTG→CGG)	hyfB →	hydrogenase 4, membrane subunit
RA	2,598,122	T→G	8.1%	L306R (CTT→CGT)	hyfC →	hydrogenase 4, membrane subunit
RA	2,601,404	C→T	8.5%	L377F (CTC→TTC)	hyfF →	hydrogenase 4, membrane subunit
RA	2,606,516	G→T	100%	D420Y (GAC→TAC)	hyfR →	hydrogenase‑4 transcriptional activator
RA	2,610,919	C→A	100%	intergenic (+3/‑18)	bepA → / → yfgD	periplasmic metalloprotease and chaperone for OM protein maintenance and assembly/putative oxidoreductase
RA	2,614,168	C→A	100%	D22Y (GAT→TAT)	upp ←	uracil phosphoribosyltransferase
RA	2,618,693	G→T	100%	E74* (GAA→TAA)	ppx →	exopolyphosphatase
RA	2,626,858	T→A	5.5%	H191L (CAC→CTC)	guaB ←	IMP dehydrogenase
RA	2,632,012	C→A	100%	intergenic (‑1/+10)	bamB ← / ← yfgM	BamABCDE complex OM biogenesis lipoprotein/putative anti‑RcsB factor
RA	2,633,402	C→A	87.6%	R178L (CGC→CTC)	hisS ←	histidyl tRNA synthetase
RA	2,639,116	C→A	89.3%	A523A (GCG→GCT)	pbpC ←	penicillin‑insensitive murein repair transglycosylase; inactive transpeptidase domain
RA	2,643,336	C→A	86.8%	D771Y (GAC→TAC)	yfhM ←	bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein
RA	2,645,592	C→A	84.9%	D19Y (GAC→TAC)	yfhM ←	bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein
RA	2,650,869	C→A	9.2%	D476Y (GAT→TAT)	hscA ←	DnaK‑like molecular chaperone specific for IscU
RA	2,651,665	G→T	100%	G210G (GGC→GGA)	hscA ←	DnaK‑like molecular chaperone specific for IscU
RA	2,659,594	C→A	88.0%	L267L (CTC→CTA)	csiE →	stationary phase inducible protein
RA	2,665,772	G→T	86.0%	E123* (GAA→TAA)	hcaD →	phenylpropionate dioxygenase, ferredoxin reductase subunit
RA	2,669,978	C→A	100%	A69A (GCG→GCT)	yphD ←	inner membrane putative ABC superfamily sugar transporter permease
RA	2,671,274	C→A	100%	T149T (ACG→ACT)	yphE ←	putative sugar transporter subunit of ABC superfamily, ATP‑binding component
RA	2,671,824	C→A	19.0%	V301V (GTG→GTT)	yphF ←	putative ABC superfamily sugar transporter periplasmic‑binding protein
RA	2,675,000	C→A	12.5%	E369* (GAG→TAG)	yphG ←	DUF4380 domain‑containing TPR repeat protein
RA	2,680,109	G→T	5.3%	D306Y (GAT→TAT)	hmp →	fused nitric oxide dioxygenase/dihydropteridine reductase 2
RA	2,681,873	T→A	100%	Q97L (CAG→CTG)	glrR ←	response regulator regulating glmY sRNA in two‑component system with sensor protein GlrK
RA	2,683,829	C→A	100%	R210L (CGT→CTT)	glrK ←	sensor protein kinase regulating glmY sRNA in two‑component system with response regulator GlrR
RA	2,688,006	C→A	85.4%	P299P (CCG→CCT)	purL ←	phosphoribosylformyl‑glycineamide synthetase
RA	2,689,267	C→A	86.2%	I36I (ATC→ATA)	mltF →	membrane‑bound lytic transglycosylase F, murein hydrolase
RA	2,690,643	C→A	9.5%	S495* (TCG→TAG)	mltF →	membrane‑bound lytic transglycosylase F, murein hydrolase
RA	2,692,793	C→A	100%	H226N (CAT→AAT)	yfhH →	putative DNA‑binding transcriptional regulator
RA	2,693,536	C→A	8.0%	L7L (CTG→CTT)	shoB ←	toxic membrane protein
RA	2,694,843	G→T	100%	I82I (ATC→ATA)	pdxJ ←	pyridoxine 5'‑phosphate synthase
RA	2,697,617	C→A	8.6%	intergenic (‑195/+77)	rnc ← / ← lepB	RNase III/leader peptidase (signal peptidase I)
RA	2,699,380	C→A	100%	P368P (CCG→CCT)	lepA ←	back‑translocating elongation factor EF4, GTPase
RA	2,699,880	T→A	89.8%	N202Y (AAC→TAC)	lepA ←	back‑translocating elongation factor EF4, GTPase
RA	2,706,124	G→T	7.9%	intergenic (‑1/‑131)	trmN ← / → srmB	tRNA1(Val) (adenine(37)‑N6)‑methyltransferase/ATP‑dependent RNA helicase
RA	2,711,673	A→C	8.9%	V72G (GTT→GGT)	yfiF ←	putative methyltransferase
RA	2,711,755	C→A	82.4%	D45Y (GAC→TAC)	yfiF ←	putative methyltransferase
RA	2,715,643	G→T	100%	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	2,725,747	G→T	82.8%	R596S (CGC→AGC)	clpB ←	protein disaggregation chaperone
RA	2,726,786	C→A	100%	A249A (GCG→GCT)	clpB ←	protein disaggregation chaperone
RA	2,727,416	C→A	87.3%	L39L (CTG→CTT)	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	2,751,558	G→T	86.2%	T134T (ACC→ACA)	yfjH ←	CP4‑57 prophage; uncharacterized protein
RA	2,753,424	G→T	12.3%	G361* (GGA→TGA)	yfjI →	CP4‑57 prophage; uncharacterized protein
RA	2,753,629	C→A	9.4%	P429Q (CCA→CAA)	yfjI →	CP4‑57 prophage; uncharacterized protein
RA	2,763,008	T→A	9.4%	intergenic (+163/‑54)	yfjQ → / → yfjR	CP4‑57 prophage; uncharacterized protein/CP4‑57 prophage; putative DNA‑binding transcriptional regulator
RA	2,763,057	C→A	85.8%	intergenic (+212/‑5)	yfjQ → / → yfjR	CP4‑57 prophage; uncharacterized protein/CP4‑57 prophage; putative DNA‑binding transcriptional regulator
RA	2,771,358	G→A	100%	intergenic (+217/+147)	ypjF → / ← ypjA	CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter
RA	2,776,219	C→A	14.0%	intergenic (‑134/+205)	ypjA ← / ← pinH	adhesin‑like autotransporter/pseudogene, invertase resolvase family
RA	2,778,820	G→A	88.0%	intergenic (‑450/+301)	ypjC ← / ← ileY	pseudogene/tRNA‑Ile
RA	2,779,067	C→A	100%	intergenic (‑697/+54)	ypjC ← / ← ileY	pseudogene/tRNA‑Ile
RA	2,780,652	A→T	6.7%	pseudogene (897/2253 nt)	ygaQ →	uncharacterized protein; putative enzyme
RA	2,790,370	G→T	6.9%	I6I (ATC→ATA)	yqaE ←	cyaR sRNA‑regulated protein
RA	2,795,947	C→A	5.3%	S414Y (TCC→TAC)	nrdE →	ribonucleoside‑diphosphate reductase 2, alpha subunit
RA	2,798,195	A→T	80.1%	K8* (AAA→TAA)	proV →	glycine betaine transporter subunit
RA	2,801,706	C→A	83.7%	pseudogene (32/1178 nt)	ygaY →	pseudogene, major facilitator transporter superfamily;putative transport; Not classified; putative transport protein
RA	2,805,420	C→A	12.7%	A212E (GCG→GAG)	emrA →	multidrug efflux system
RA	2,808,907	C→A	87.2%	E298* (GAA→TAA)	gshA ←	glutamate‑cysteine ligase
RA	2,808,987	G→T	6.0%	S271* (TCG→TAG)	gshA ←	glutamate‑cysteine ligase
RA	2,825,783	C→T	100%	intergenic (‑135/‑52)	norR ← / → norV	anaerobic nitric oxide reductase DNA‑binding transcriptional activator/anaerobic nitric oxide reductase flavorubredoxin
RA	2,828,952	C→A	100%	T611T (ACG→ACT)	hypF ←	carbamoyl phosphate phosphatase and maturation protein for [NiFe] hydrogenases
RA	2,831,086	C→A	100%	E127* (GAA→TAA)	hydN ←	formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit
RA	2,831,929	T→A	37.9%	E232V (GAA→GTA)	ascG ←	asc operon transcriptional repressor; prpBC operon repressor
RA	2,833,263	C→A	7.5%	V127V (GTC→GTA)	ascF →	fused cellobiose/arbutin/salicin‑specific PTS enzymes: IIB component/IC component
RA	2,835,094	C→A	100%	P249Q (CCG→CAG)	ascB →	cryptic 6‑phospho‑beta‑glucosidase
RA	2,836,079	C→A	30.4%	V108V (GTG→GTT)	hycI ←	protease involved in processing C‑terminal end of HycE
RA	2,836,554	G→T	35.4%	I84I (ATC→ATA)	hycH ←	hydrogenase 3 maturation protein
RA	2,837,298	G→A	7.8%	A91V (GCA→GTA)	hycG ←	hydrogenase 3 and formate hydrogenase complex, HycG subunit
RA	2,837,721	C→A	86.3%	D131Y (GAC→TAC)	hycF ←	formate hydrogenlyase complex iron‑sulfur protein
RA	2,840,562	C→A	7.6%	V70V (GTG→GTT)	hycD ←	hydrogenase 3, membrane subunit
RA	2,841,044	C→A	100%	A519A (GCG→GCT)	hycC ←	hydrogenase 3, membrane subunit
RA	2,846,112	C→A	100%	I206I (ATC→ATA)	hypD →	hydrogenase maturation protein
RA	2,846,721	G→T	8.3%	D37Y (GAT→TAT)	hypE →	carbamoyl dehydratase, hydrogenases 1,2,3 maturation protein
RA	2,848,002	T→A	81.0%	C102* (TGT→TGA)	fhlA →	formate hydrogenlyase transcriptional activator
RA	2,850,790	C→A	100%	I113I (ATC→ATA)	mutS →	methyl‑directed mismatch repair protein
RA	2,852,854	G→T	90.5%	P801P (CCG→CCT)	mutS →	methyl‑directed mismatch repair protein
RA	2,857,901	C→A	40.7%	H103N (CAT→AAT)	ygbM →	putative hydroxypyruvate isomerase
RA	2,869,780	G→A	87.4%	intergenic (‑92/‑160)	cysD ← / → iap	sulfate adenylyltransferase, subunit 2/aminopeptidase in alkaline phosphatase isozyme conversion
RA	2,870,278	C→A	29.3%	I113I (ATC→ATA)	iap →	aminopeptidase in alkaline phosphatase isozyme conversion
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	100%	G246G (GGG→GGA)	casA ←	CRISP RNA (crRNA) containing Cascade antiviral complex protein
RA	2,878,668	G→T	100%	V637V (GTC→GTA)	ygcB ←	R‑loop helicase‑annealase Cas3 needed for Cascade anti‑viral activity
RA	2,879,222	C→A	6.6%	E453* (GAA→TAA)	ygcB ←	R‑loop helicase‑annealase Cas3 needed for Cascade anti‑viral activity
RA	2,879,449	G→T	100%	S377* (TCA→TAA)	ygcB ←	R‑loop helicase‑annealase Cas3 needed for Cascade anti‑viral activity
RA	2,884,185	G→T	13.4%	T358K (ACG→AAG)	cysJ ←	sulfite reductase, alpha subunit, flavoprotein
RA	2,884,385	G→T	84.9%	V291V (GTC→GTA)	cysJ ←	sulfite reductase, alpha subunit, flavoprotein
RA	2,888,584	G→T	100%	I185I (ATC→ATA)	ygcQ ←	putative flavoprotein
RA	2,889,129	C→A	88.4%	A4S (GCA→TCA)	ygcQ ←	putative flavoprotein
RA	2,893,446	T→A	100%	K63* (AAA→TAA)	ygcW ←	putative dehydrogenase
RA	2,908,287	C→A	37.9%	D25Y (GAC→TAC)	rlmD ←	23S rRNA m(5)U1939 methyltransferase, SAM‑dependent
RA	2,915,998	C→A	29.3%	A116S (GCT→TCT)	yqcA ←	short‑chain flavodoxin, FMN‑binding
RA	2,917,972	C→T	10.6%	intergenic (‑89/+122)	csrB ← / ← syd	CsrA‑binding sRNA, antagonizing CsrA regulation/SecY‑interacting protein
RA	2,918,415	G→A	84.7%	P75P (CCC→CCT)	syd ←	SecY‑interacting protein
RA	2,919,922	G→T	83.2%	D86Y (GAT→TAT)	ygdH →	UPF0717 family protein
RA	2,920,050	C→A	87.3%	I128I (ATC→ATA)	ygdH →	UPF0717 family protein
RA	2,921,101	C→A	85.9%	intergenic (+70/‑487)	ygdH → / → sdaC	UPF0717 family protein/putative serine transporter
RA	2,921,245	G→T	86.0%	intergenic (+214/‑343)	ygdH → / → sdaC	UPF0717 family protein/putative serine transporter
RA	2,931,717	C→A	100%	N307K (AAC→AAA)	fucK →	L‑fuculokinase
RA	2,932,835	C→T	100%	R37C (CGC→TGC)	fucR →	l‑fucose operon activator
RA	2,934,843	G→T	100%	H50N (CAT→AAT)	ygdD ←	UPF0382 family inner membrane protein
RA	2,936,836	C→A	88.2%	A47A (GCC→GCA)	csdA →	cysteine sulfinate desulfinase
RA	2,937,895	Δ1 bp	6.8%	coding (1200/1206 nt)	csdA →	cysteine sulfinate desulfinase
RA	2,938,035	G→T	9.6%	P45P (CCG→CCT)	csdE →	CsdA‑binding activator; Fe‑S protein
RA	2,945,306	C→G	84.3%	G172A (GGC→GCC)	recD ←	exonuclease V (RecBCD complex), alpha chain
RA	2,950,594	G→T	5.7%	V550V (GTC→GTA)	ptrA ←	protease III
RA	2,956,284	C→A	5.1%	D78Y (GAT→TAT)	ygdB ←	DUF2509 family protein
RA	2,959,004	G→A	100%	I131I (ATC→ATT)	lgt ←	phosphatidylglycerol‑prolipoprotein diacylglyceryl transferase
RA	2,961,295	G→T	8.2%	R167S (CGC→AGC)	ptsP ←	fused PTS enzyme: PEP‑protein phosphotransferase (enzyme I)/GAF domain containing protein
RA	2,962,962	T→A	100%	intergenic (‑626/‑59)	rppH ← / → mutH	RNA pyrophosphohydrolase/methyl‑directed mismatch repair protein
RA	2,966,846	C→A	7.4%	E126* (GAA→TAA)	lplT ←	lysophospholipid transporter
RA	2,970,168	G→T	9.9%	D71Y (GAT→TAT)	galR →	galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor
RA	2,970,703	C→A	6.0%	A249E (GCG→GAG)	galR →	galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor
RA	2,974,073	C→T	83.8%	intergenic (‑79/+50)	ygeA ← / ← araE	Asp/Glu_racemase family protein/arabinose transporter
RA	2,980,488	C→A	86.7%	intergenic (+53/‑407)	yqeG → / → yqeH	putative transporter/putative LuxR family transcriptional regulator
RA	2,983,183	C→A	16.1%	D26Y (GAT→TAT)	yqeL ←	uncharacterized protein
RA	2,984,747	G→T	89.0%	D41Y (GAT→TAT)	ygeG →	SycD‑like chaperone family TPR‑repeat‑containing protein
RA	2,985,256	G→T	83.8%	intergenic (+138/‑197)	ygeG → / → ygeH	SycD‑like chaperone family TPR‑repeat‑containing protein/putative transcriptional regulator
RA	2,985,884	C→T	100%	I144I (ATC→ATT)	ygeH →	putative transcriptional regulator
RA	2,986,052	G→T	88.9%	L200F (TTG→TTT)	ygeH →	putative transcriptional regulator
RA	2,988,355	C→A	100%	pseudogene (97/633 nt)	ygeK ←	pseudogene; putative 2‑component transcriptional regulator
RA	2,988,554	G→A	100%	intergenic (‑103/+119)	ygeK ← / ← ygeN	pseudogene; putative 2‑component transcriptional regulator/pseudogene
RA	2,988,641	T→C	10.4%	intergenic (‑190/+32)	ygeK ← / ← ygeN	pseudogene; putative 2‑component transcriptional regulator/pseudogene
RA	2,989,295	C→A	100%	pseudogene (85/261 nt)	ygeN ←	pseudogene
RA	2,993,211	C→A	100%	V14L (GTG→TTG)	ygeR ←	LysM domain‑containing M23 family putative peptidase; septation lipoprotein
RA	2,993,612	C→T	5.7%	intergenic (‑362/‑92)	ygeR ← / → xdhA	LysM domain‑containing M23 family putative peptidase; septation lipoprotein/xanthine dehydrogenase, molybdenum binding subunit
RA	2,993,699	C→A	100%	intergenic (‑449/‑5)	ygeR ← / → xdhA	LysM domain‑containing M23 family putative peptidase; septation lipoprotein/xanthine dehydrogenase, molybdenum binding subunit
RA	2,999,827	C→A	85.0%	D69E (GAC→GAA)	ygeW →	putative carbamoyltransferase
RA	3,006,444	G→T	35.2%	I385I (ATC→ATA)	yqeB ←	XdhC‑CoxI family protein with NAD(P)‑binding Rossman fold
RA	3,007,908	T→G	14.6%	Q170P (CAG→CCG)	yqeC ←	putative selenium‑dependent hydroxylase accessory protein
RA	3,009,187	G→T	100%	intergenic (+90/‑232)	mocA → / → ygfK	CTP:molybdopterin cytidylyltransferase/putative Fe‑S subunit oxidoreductase subunit
RA	3,014,888	C→A	22.7%	R72S (CGT→AGT)	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	3,018,544	G→T	87.2%	A279S (GCC→TCC)	xanQ →	xanthine permease
RA	3,018,952	G→T	7.8%	E415* (GAA→TAA)	xanQ →	xanthine permease
RA	3,022,562	C→T	86.5%	G577R (GGA→AGA)	ygfT ←	putative oxidoreductase, Fe‑S subunit/nucleotide‑binding subunit
RA	3,024,081	A→C	100%	V70V (GTT→GTG)	ygfT ←	putative oxidoreductase, Fe‑S subunit/nucleotide‑binding subunit
RA	3,024,983	C→G	100%	G86G (GGC→GGG)	uacT →	uric acid permease
RA	3,030,181	G→T	100%	H429N (CAT→AAT)	recJ ←	ssDNA exonuclease, 5' ‑‑> 3'‑specific
RA	3,030,978	A→T	5.3%	L163* (TTG→TAG)	recJ ←	ssDNA exonuclease, 5' ‑‑> 3'‑specific
RA	3,034,367	A→T	20.4%	D21E (GAT→GAA)	sdhE ←	flavinator of succinate dehydrogenase; antitoxin of CptAB toxin‑antitoxin pair
RA	3,038,798	C→A	6.1%	D155Y (GAT→TAT)	ygfF ←	putative NAD(P)‑dependent oxidoreductase with NAD(P)‑binding Rossmann‑fold domain
RA	3,039,409	T→G	14.9%	intergenic (‑149/+118)	ygfF ← / ← gcvP	putative NAD(P)‑dependent oxidoreductase with NAD(P)‑binding Rossmann‑fold domain/glycine decarboxylase, PLP‑dependent, subunit (protein P) of glycine cleavage complex
RA	3,039,703	C→A	86.0%	A900S (GCG→TCG)	gcvP ←	glycine decarboxylase, PLP‑dependent, subunit (protein P) of glycine cleavage complex
RA	3,041,321	G→T	89.8%	I360I (ATC→ATA)	gcvP ←	glycine decarboxylase, PLP‑dependent, subunit (protein P) of glycine cleavage complex
RA	3,042,913	C→A	6.9%	intergenic (‑5/+19)	gcvH ← / ← gcvT	glycine cleavage complex lipoylprotein/aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex
RA	3,044,432	G→T	5.5%	intergenic (‑406/+42)	gcvT ← / ← ubiI	aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex/2‑octaprenylphenol hydroxylase, FAD‑dependent
RA	3,044,449	C→A	19.9%	intergenic (‑423/+25)	gcvT ← / ← ubiI	aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex/2‑octaprenylphenol hydroxylase, FAD‑dependent
RA	3,044,464	G→A	100%	intergenic (‑438/+10)	gcvT ← / ← ubiI	aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex/2‑octaprenylphenol hydroxylase, FAD‑dependent
RA	3,049,220	C→A	88.1%	R84R (CGG→AGG)	zapA →	FtsZ stabilizer
RA	3,049,740	C→A	31.4%	L47L (CTC→CTA)	fau →	5‑formyltetrahydrofolate cyclo‑ligase family protein
RA	3,052,315	C→A	7.5%	D124Y (GAT→TAT)	rpiA ←	ribose 5‑phosphate isomerase, constitutive
RA	3,053,567	G→T	5.1%	P152P (CCG→CCT)	argP →	transcriptional regulator for arginine transport and DNA replication genes; replication initiation inhibitor
RA	3,058,769	C→T	100%	I203I (ATC→ATT)	scpC →	propionyl‑CoA:succinate CoA transferase
RA	3,059,577	G→T	12.0%	D473Y (GAT→TAT)	scpC →	propionyl‑CoA:succinate CoA transferase
RA	3,064,914	G→T	100%	I356I (ATC→ATA)	pgk ←	phosphoglycerate kinase
RA	3,065,123	C→T	84.9%	G287S (GGT→AGT)	pgk ←	phosphoglycerate kinase
RA	3,074,591	G→T	86.5%	A135E (GCG→GAG)	tktA ←	transketolase 1, thiamine triphosphate‑binding
RA	3,075,034	G→T	8.6%	intergenic (‑40/‑238)	tktA ← / → loiP	transketolase 1, thiamine triphosphate‑binding/Phe‑Phe periplasmic metalloprotease, OM lipoprotein; low salt‑inducible; heat shock protein that binds Era
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	100%	D211Y (GAC→TAC)	speB ←	agmatinase
RA	3,077,302	C→A	34.0%	D657Y (GAT→TAT)	speA ←	biosynthetic arginine decarboxylase, PLP‑binding
RA	3,080,618	T→A	100%	V185E (GTG→GAG)	metK →	S‑adenosylmethionine synthetase
RA	3,080,755	T→G	20.5%	F231V (TTC→GTC)	metK →	S‑adenosylmethionine synthetase
RA	3,082,252	T→A	5.5%	F204I (TTT→ATT)	galP →	D‑galactose transporter
RA	3,084,798	C→A	90.0%	L102L (CTC→CTA)	rsmE →	16S rRNA m(3)U1498 methyltransferase, SAM‑dependent
RA	3,088,065	C→A	100%	V125V (GTG→GTT)	yggR ←	putative PilT family AAA+ ATPase
RA	3,093,860	C→A	28.5%	V76V (GTG→GTT)	ansB ←	periplasmic L‑asparaginase 2
RA	3,097,262	C→T	100%	F297F (TTC→TTT)	mutY →	adenine DNA glycosylase
RA	3,106,685	G→T	88.7%	S51Y (TCT→TAT)	yghG ←	secretin (GspDbeta) OM localization lipoprotein pilotin
RA	3,110,213	T→A	85.5%	A753A (GCA→GCT)	yghJ ←	DUF4092 family putative lipoprotein peptidase
RA	3,110,751	C→A	100%	R574L (CGT→CTT)	yghJ ←	DUF4092 family putative lipoprotein peptidase
RA	3,111,434	C→A	100%	A346A (GCG→GCT)	yghJ ←	DUF4092 family putative lipoprotein peptidase
RA	3,120,216	C→A	100%	D389Y (GAT→TAT)	glcD ←	glycolate oxidase subunit, FAD‑linked
RA	3,122,356	G→T	35.8%	L242F (TTG→TTT)	glcC →	glycolate‑inducible glc operon transcriptional repressor; autorepressor
RA	3,122,778	A→C	69.5%	pseudogene (725/1101 nt)	yghO ←	pseudogene, DNA‑binding transcriptional regulator homology
RA	3,130,516	C→A	6.8%	D456Y (GAC→TAC)	gss ←	fused glutathionylspermidine amidase/glutathionylspermidine synthetase
RA	3,131,612	C→T	7.0%	L90L (CTG→CTA)	gss ←	fused glutathionylspermidine amidase/glutathionylspermidine synthetase
RA	3,132,984	G→A	11.6%	intergenic (+32/+91)	yghU → / ← hybG	putative S‑transferase/hydrogenase 2 accessory protein
RA	3,134,528	C→A	88.1%	D40Y (GAT→TAT)	hybD ←	maturation protease for hydrogenase 2
RA	3,136,368	G→T	14.0%	R386S (CGT→AGT)	hybB ←	putative hydrogenase 2 cytochrome b type component
RA	3,142,668	G→T	100%	L55I (CTC→ATC)	yqhA ←	UPF0114 family putative inner membrane protein
RA	3,144,158	C→A	100%	intergenic (+253/+19)	yghA → / ← exbD	putative oxidoreductase/membrane spanning protein in TonB‑ExbB‑ExbD complex
RA	3,151,225	A→T	9.4%	N73Y (AAT→TAT)	yqhG →	DUF3828 family putative periplasmic protein
RA	3,157,088	C→A	5.4%	D749Y (GAT→TAT)	parC ←	DNA topoisomerase IV, subunit A
RA	3,158,085	C→A	7.3%	A416A (GCG→GCT)	parC ←	DNA topoisomerase IV, subunit A
RA	3,164,230	C→A	100%	R130S (CGT→AGT)	qseC →	quorum sensing sensory histidine kinase in two‑component regulatory system with QseB
RA	3,170,831	C→A	5.4%	E147* (GAA→TAA)	nudF ←	ADP‑ribose pyrophosphatase
RA	3,172,719	C→T	10.8%	L416L (CTG→TTG)	tolC →	transport channel
RA	3,173,669	G→T	100%	A189A (GCG→GCT)	ygiB →	DUF1190 family protein
RA	3,176,733	G→T	100%	intergenic (+51/+439)	zupT → / ← ribB	zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase
RA	3,184,211	C→A	39.1%	S74Y (TCT→TAT)	yqiI →	fimbrial protein
RA	3,191,153	C→A	10.4%	A616A (GCG→GCT)	glnE ←	fused deadenylyltransferase/adenylyltransferase for glutamine synthetase
RA	3,201,209	C→A	30.9%	F160L (TTC→TTA)	ttdB →	L‑tartrate dehydratase, beta subunit
RA	3,208,550	T→A	5.3%	K95* (AAA→TAA)	mug ←	G/U mismatch‑specific DNA glycosylase; xanthine DNA glycosylase
RA	3,217,289	A→T	100%	H433L (CAC→CTC)	ebgA →	evolved beta‑D‑galactosidase, alpha subunit
RA	3,220,448	C→A	7.7%	R286S (CGC→AGC)	ygjI →	putative transporter
RA	3,224,927	C→A	100%	intergenic (+329/‑97)	ygjK → / → fadH	alpha‑glucosidase/2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked
RA	3,230,857	C→G	100%	A63G (GCC→GGC)	ygjR →	putative NAD(P)‑dependent dehydrogenase
RA	3,231,349	A→C	100%	Q227P (CAG→CCG)	ygjR →	putative NAD(P)‑dependent dehydrogenase
RA	3,233,218	C→A	11.4%	intergenic (+314/‑85)	alx → / → sstT	putative membrane‑bound redox modulator/sodium:serine/threonine symporter
RA	3,233,271	G→T	7.8%	intergenic (+367/‑32)	alx → / → sstT	putative membrane‑bound redox modulator/sodium:serine/threonine symporter
RA	3,239,833	G→T	9.5%	A457A (GCG→GCT)	exuT →	hexuronate transporter
RA	3,240,534	A→T	5.1%	Y175F (TAC→TTC)	exuR →	hexuronate regulon transcriptional repressor; autorepressor
RA	3,243,768	C→T	86.2%	intergenic (+33/‑153)	yqjK → / → yqjF	uncharacterized protein/putative quinol oxidase subunit
RA	3,245,848	G→T	100%	L62L (CTG→CTT)	yhaH →	DUF805 family inner membrane protein
RA	3,248,241	G→A	5.5%	G188G (GGG→GGA)	yhaK →	redox‑sensitive bicupin
RA	3,252,258	C→A	100%	D251Y (GAT→TAT)	tdcG ←	L‑serine dehydratase 3, anaerobic
RA	3,254,752	C→A	82.5%	V342V (GTG→GTT)	tdcE ←	pyruvate formate‑lyase 4/2‑ketobutyrate formate‑lyase
RA	3,255,775	C→A	11.0%	M1M (ATG→ATT) †	tdcE ←	pyruvate formate‑lyase 4/2‑ketobutyrate formate‑lyase
RA	3,257,209	C→A	9.2%	E390* (GAA→TAA)	tdcC ←	L‑threonine/L‑serine transporter
RA	3,258,871	G→T	85.1%	L173I (CTC→ATC)	tdcB ←	L‑threonine dehydratase, catabolic
RA	3,261,001	G→A	42.6%	intergenic (+44/‑212)	tdcR → / → yhaB	L‑threonine dehydratase operon activator protein/uncharacterized protein
RA	3,263,315	T→C	6.8%	intergenic (+354/+260)	yhaC → / ← rnpB	pentapetide repeats‑related protein/RNase P, M1 RNA component
RA	3,263,409	C→T	100%	intergenic (+448/+166)	yhaC → / ← rnpB	pentapetide repeats‑related protein/RNase P, M1 RNA component
RA	3,263,460	C→A	7.9%	intergenic (+499/+115)	yhaC → / ← rnpB	pentapetide repeats‑related protein/RNase P, M1 RNA component
RA	3,266,646	C→A	100%	G91C (GGT→TGT)	garL ←	alpha‑dehydro‑beta‑deoxy‑D‑glucarate aldolase
RA	3,267,286	C→A	12.9%	P327P (CCG→CCT)	garP ←	putative (D)‑galactarate transporter
RA	3,268,357	C→A	91.5%	intergenic (‑91/‑284)	garP ← / → garD	putative (D)‑galactarate transporter/(D)‑galactarate dehydrogenase
RA	3,269,983	C→A	9.1%	A448E (GCG→GAG)	garD →	(D)‑galactarate dehydrogenase
RA	3,271,128	A→C	86.8%	T145P (ACC→CCC)	yhaV →	toxin of the SohB(PrlF)‑YhaV toxin‑antitoxin system
RA	3,290,970	A→T	87.2%	R176R (CGT→CGA)	yraQ ←	putative inner membrane permease
RA	3,292,914	C→A	8.2%	D121Y (GAT→TAT)	yhbP ←	UPF0306 family protein
RA	3,295,911	C→A	32.6%	Q22K (CAG→AAG)	yhbV →	U32 peptidase family protein
RA	3,296,612	G→T	100%	A255A (GCG→GCT)	yhbV →	U32 peptidase family protein
RA	3,298,059	C→A	12.7%	R373L (CGC→CTC)	mtr ←	tryptophan transporter of high affinity
RA	3,299,240	A→C	31.9%	intergenic (‑64/+90)	mtr ← / ← deaD	tryptophan transporter of high affinity/ATP‑dependent RNA helicase
RA	3,302,027	G→T	100%	S86* (TCG→TAG)	nlpI ←	lipoprotein involved in osmotic sensitivity and filamentation
RA	3,311,447	C→T	7.4%	intergenic (‑82/+125)	rimP ← / ← metY	ribosome maturation factor for 30S subunits/tRNA‑Met
RA	3,312,055	C→A	31.6%	G20G (GGC→GGA)	argG →	argininosuccinate synthetase
RA	3,314,870	C→A	100%	A35S (GCG→TCG)	yhbX ←	putative EptAB family phosphoethanolamine transferase, inner membrane protein
RA	3,328,038	T→G	10.6%	*324E (TAA→GAA)	ispB →	octaprenyl diphosphate synthase
RA	3,329,692	C→A	6.2%	M54I (ATG→ATT)	murA ←	UDP‑N‑acetylglucosamine 1‑carboxyvinyltransferase
RA	3,332,632	G→T	10.8%	L265I (CTT→ATT)	mlaF ←	ABC transporter maintaining OM lipid asymmetry, ATP‑binding protein
RA	3,332,963	C→A	35.0%	A154A (GCG→GCT)	mlaF ←	ABC transporter maintaining OM lipid asymmetry, ATP‑binding protein
RA	3,334,464	C→A	90.4%	S277R (AGC→AGA)	yrbG →	putative calcium/sodium:proton antiporter
RA	3,334,687	G→T	37.1%	A21A (GCG→GCT)	kdsD →	D‑arabinose 5‑phosphate isomerase
RA	3,347,740	C→A	8.0%	intergenic (‑331/‑344)	yhcC ← / → gltB	putative Fe‑S oxidoreductase, Radical SAM superfamily protein/glutamate synthase, large subunit
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	100%	E1189D (GAG→GAT)	gltB →	glutamate synthase, large subunit
RA	3,354,405	C→T	100%	intergenic (+430/‑130)	gltD → / → gltF	glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
RA	3,365,189	C→A	7.7%	A249S (GCG→TCG)	nanT ←	sialic acid transporter
RA	3,365,253	G→T	5.8%	I227I (ATC→ATA)	nanT ←	sialic acid transporter
RA	3,365,607	G→T	100%	I109I (ATC→ATA)	nanT ←	sialic acid transporter
RA	3,373,457	C→A	34.7%	intergenic (‑101/‑93)	yhcM ← / → yhcB	putative AFG1‑like family P‑loop ATPase/DUF1043 family inner membrane‑anchored protein
RA	3,373,528	C→T	11.4%	intergenic (‑172/‑22)	yhcM ← / → yhcB	putative AFG1‑like family P‑loop ATPase/DUF1043 family inner membrane‑anchored protein
RA	3,373,985	C→A	100%	intergenic (+37/‑117)	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	3,385,505	A→C	11.8%	intergenic (‑118/+312)	tldD ← / ← yhdP	putative peptidase/DUF3971‑AsmA2 domains protein
RA	3,385,516	A→T	7.8%	intergenic (‑129/+301)	tldD ← / ← yhdP	putative peptidase/DUF3971‑AsmA2 domains protein
RA	3,396,082	G→T	100%	R204S (CGT→AGT)	csrD ←	targeting factor for csrBC sRNA degradation
RA	3,403,534	C→T	100%	intergenic (+224/‑105)	prmA → / → dusB	methyltransferase for 50S ribosomal subunit protein L11/tRNA‑dihydrouridine synthase B
RA	3,404,059	C→A	86.4%	R141S (CGC→AGC)	dusB →	tRNA‑dihydrouridine synthase B
RA	3,407,007	G→A	100%	intergenic (‑183/‑216)	acrS ← / → acrE	acrAB operon transcriptional repressor/cytoplasmic membrane lipoprotein
RA	3,407,969	C→A	79.7%	N249K (AAC→AAA)	acrE →	cytoplasmic membrane lipoprotein
RA	3,411,250	G→T	84.2%	E953D (GAG→GAT)	acrF →	multidrug efflux system protein
RA	3,412,595	C→A	6.7%	pseudogene (130/960 nt)	yhdW →	pseudogene, amino‑acid transporter homology;putative transport; Not classified; putative periplasmic binding transport protein; periplasmic‑binding component of ABC superfamily
RA	3,414,519	G→T	24.2%	D343Y (GAT→TAT)	yhdX →	putative amino‑acid transporter subunit
RA	3,416,890	T→G	7.9%	noncoding (12/120 nt)	rrfF ←	5S ribosomal RNA of rrnD operon
RA	3,416,899	A→G	5.7%	noncoding (3/120 nt)	rrfF ←	5S ribosomal RNA of rrnD operon
RA	3,422,726	G→T	40.1%	V44V (GTG→GTT)	yrdA →	bacterial transferase hexapeptide domain protein
RA	3,424,363	T→A	84.3%	T138S (ACC→TCC)	tsaC ←	tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein, threonine‑dependent ADP‑forming ATPase
RA	3,432,444	C→A	6.9%	D16Y (GAC→TAC)	zntR ←	zntA gene transcriptional activator
RA	3,433,018	T→G	8.4%	E114A (GAG→GCG)	rplQ ←	50S ribosomal subunit protein L17
RA	3,439,422	G→T	7.1%	I26I (ATC→ATA)	rplF ←	50S ribosomal subunit protein L6
RA	3,439,800	T→A	19.2%	A35A (GCA→GCT)	rpsH ←	30S ribosomal subunit protein S8
RA	3,440,151	G→T	100%	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	100%	N99D (AAC→GAC)	rplX ←	50S ribosomal subunit protein L24
RA	3,442,244	C→A	7.2%	L95F (TTG→TTT)	rplP ←	50S ribosomal subunit protein L16
RA	3,445,410	C→A	85.6%	R79L (CGT→CTT)	rplD ←	50S ribosomal subunit protein L4
RA	3,448,742	C→A	87.8%	E6* (GAA→TAA)	gspA ←	general secretory pathway component, cryptic
RA	3,455,789	G→T	9.1%	M29I (ATG→ATT)	gspJ →	putative general secretory pathway component, cryptic
RA	3,455,867	C→A	100%	I55I (ATC→ATA)	gspJ →	putative general secretory pathway component, cryptic
RA	3,455,930	C→A	31.0%	I76I (ATC→ATA)	gspJ →	putative general secretory pathway component, cryptic
RA	3,457,607	G→T	11.6%	V109V (GTG→GTT)	gspL →	general secretory pathway component, cryptic
RA	3,457,896	C→A	7.4%	P206T (CCT→ACT)	gspL →	general secretory pathway component, cryptic
RA	3,464,409	T→A	9.1%	T94S (ACC→TCC)	tufA ←	translation elongation factor EF‑Tu 1
RA	3,470,272	C→A	92.9%	V169V (GTG→GTT)	fkpA ←	FKBP‑type peptidyl‑prolyl cis‑trans isomerase (rotamase)
RA	3,471,705	C→T	28.8%	G51D (GGT→GAT)	slyD ←	FKBP‑type peptidyl prolyl cis‑trans isomerase (rotamase)
RA	3,473,139	G→T	100%	I276I (ATC→ATA)	kefB ←	potassium:proton antiporter
RA	3,475,255	C→A	28.4%	S203Y (TCT→TAT)	yheS →	putative transporter subunit of ABC superfamily: ATP‑binding component
RA	3,479,769	A→T	100%	E97D (GAA→GAT)	crp →	cAMP‑activated global transcription factor, mediator of catabolite repression
RA	3,483,772	C→A	7.7%	A139A (GCG→GCT)	pabA ←	aminodeoxychorismate synthase, subunit II
RA	3,484,469	C→A	7.0%	A118A (GCG→GCT)	fic ←	stationary‑phase adenosine monophosphate‑protein transferase domain protein
RA	3,485,872	C→A	11.9%	intergenic (‑216/‑55)	ppiA ← / → tsgA	peptidyl‑prolyl cis‑trans isomerase A (rotamase A)/putative transporter
RA	3,487,320	G→A	10.0%	intergenic (+212/‑50)	tsgA → / → nirB	putative transporter/nitrite reductase, large subunit, NAD(P)H‑binding
RA	3,488,966	G→C	100%	A533P (GCC→CCC)	nirB →	nitrite reductase, large subunit, NAD(P)H‑binding
RA	3,489,397	C→A	100%	F676L (TTC→TTA)	nirB →	nitrite reductase, large subunit, NAD(P)H‑binding
RA	3,493,166	C→T	5.9%	intergenic (+192/‑103)	yhfL → / → frlA	small lipoprotein/putative fructoselysine transporter
RA	3,493,179	G→A	6.4%	intergenic (+205/‑90)	yhfL → / → frlA	small lipoprotein/putative fructoselysine transporter
RA	3,495,516	C→A	9.0%	S297* (TCG→TAG)	frlB →	fructoselysine‑6‑P‑deglycase
RA	3,498,214	T→G	8.6%	intergenic (+72/+80)	frlR → / ← yhfS	putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein
RA	3,501,571	C→A	100%	G127C (GGC→TGC)	php ←	phosphotriesterase homology protein
RA	3,502,584	C→A	8.7%	D197Y (GAT→TAT)	yhfW ←	phosphopentomutase‑related metalloenzyme superfamily protein
RA	3,504,143	G→T	100%	R65S (CGT→AGT)	yhfX ←	putative pyridoxal 5'‑phosphate binding protein
RA	3,507,749	G→T	100%	H224N (CAT→AAT)	rpe ←	D‑ribulose‑5‑phosphate 3‑epimerase
RA	3,509,102	G→T	89.5%	S57R (AGC→AGA)	dam ←	DNA adenine methyltransferase
RA	3,513,424	A→T	100%	V213V (GTT→GTA)	hofQ ←	DNA catabolic putative fimbrial transporter
RA	3,519,188	C→A	40.8%	L107L (CTG→CTT)	nudE ←	adenosine nucleotide hydrolase; substrates include Ap3A, Ap2A, ADP‑ribose, NADH
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	3,522,018	G→T	9.9%	intergenic (+55/‑10)	yrfF → / → yrfG	inner membrane protein/GMP/IMP nucleotidase
RA	3,528,406	G→T	80.5%	I274I (ATC→ATA)	envZ ←	sensory histidine kinase in two‑component regulatory system with OmpR
RA	3,532,054	C→A	5.9%	D437E (GAC→GAA)	yhgF →	putative transcriptional accessory protein
RA	3,535,370	C→A	84.8%	S535R (AGC→AGA)	feoB →	fused ferrous iron transporter, protein B: GTP‑binding protein/membrane protein
RA	3,541,622	C→A	12.7%	R603L (CGT→CTT)	malQ ←	4‑alpha‑glucanotransferase (amylomaltase)
RA	3,542,876	T→G	5.4%	N185T (AAC→ACC)	malQ ←	4‑alpha‑glucanotransferase (amylomaltase)
RA	3,543,959	G→T	100%	A625E (GCG→GAG)	malP ←	maltodextrin phosphorylase
RA	3,551,133	C→A	6.2%	A102A (GCG→GCT)	rtcB ←	RNA‑splicing ligase
RA	3,557,815	T→A	5.8%	K709N (AAA→AAT)	glgP ←	glycogen phosphorylase
RA	3,561,258	C→A	6.0%	D46Y (GAT→TAT)	glgA ←	glycogen synthase
RA	3,561,574	C→A	100%	W372L (TGG→TTG)	glgC ←	glucose‑1‑phosphate adenylyltransferase
RA	3,563,911	C→A	5.7%	E257* (GAA→TAA)	glgX ←	glycogen debranching enzyme
RA	3,564,984	C→A	7.0%	E627* (GAA→TAA)	glgB ←	1,4‑alpha‑glucan branching enzyme
RA	3,567,059	C→A	87.1%	intergenic (‑197/+76)	glgB ← / ← asd	1,4‑alpha‑glucan branching enzyme/aspartate‑semialdehyde dehydrogenase, NAD(P)‑binding
RA	3,571,153	C→A	86.7%	E312* (GAA→TAA)	gntR ←	d‑gluconate inducible gluconate regulon transcriptional repressor
RA	3,571,950	T→A	5.8%	E46V (GAA→GTA)	gntR ←	d‑gluconate inducible gluconate regulon transcriptional repressor
RA	3,574,500	G→T	5.3%	M1M (ATG→ATT) †	yhhY →	putative acetyltransferase
RA	3,582,484	G→T	5.3%	V19V (GTC→GTA)	ugpC ←	glycerol‑3‑phosphate transporter subunit
RA	3,582,807	G→T	85.8%	P194Q (CCG→CAG)	ugpE ←	glycerol‑3‑phosphate transporter subunit
RA	3,587,949	C→A	8.0%	E298* (GAA→TAA)	livM ←	leucine/isoleucine/valine transporter subunit
RA	3,590,906	C→A	30.5%	A5A (GCG→GCT)	livK ←	leucine transporter subunit
RA	3,590,930	T→A	8.9%	intergenic (‑10/‑414)	livK ← / → panM	leucine transporter subunit/PanD autocleavage accelerator, panothenate synthesis
RA	3,593,067	T→C	21.0%	intergenic (‑49/+222)	livJ ← / ← rpoH	leucine/isoleucine/valine transporter subunit/RNA polymerase, sigma 32 (sigma H) factor
RA	3,594,268	C→T	85.2%	intergenic (‑125/+120)	rpoH ← / ← ftsX	RNA polymerase, sigma 32 (sigma H) factor/inner membrane putative ABC superfamily transporter permease
RA	3,596,266	C→A	86.5%	T446T (ACG→ACT)	ftsY ←	Signal Recognition Particle (SRP) receptor
RA	3,597,160	T→G	20.0%	E148D (GAA→GAC)	ftsY ←	Signal Recognition Particle (SRP) receptor
RA	3,598,440	C→A	88.6%	N34K (AAC→AAA)	yhhL →	DUF1145 family protein
RA	3,600,454	G→T	8.0%	R215L (CGA→CTA)	zntA →	zinc, cobalt and lead efflux system
RA	3,602,081	A→C	14.0%	intergenic (+72/+30)	zntA → / ← tusA	zinc, cobalt and lead efflux system/mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase
RA	3,607,110	C→A	87.9%	I28I (ATC→ATA)	nikA →	nickel‑binding, heme‑binding periplasmic protein
RA	3,611,392	C→A	16.3%	A86E (GCG→GAG)	nikE →	nickel transporter subunit
RA	3,612,284	G→T	87.1%	D113Y (GAT→TAT)	nikR →	transcriptional repressor, Ni‑binding
RA	3,616,731	G→T	10.8%	E1394* (GAA→TAA)	rhsB →	Rhs family putative polymorphic toxin, putative neighboring cell growth inhibitor
RA	3,622,058	C→A	85.2%	D281Y (GAT→TAT)	rbbA ←	ribosome‑associated ATPase: ATP‑binding protein/ATP‑binding membrane protein
RA	3,622,885	T→A	7.7%	E5V (GAA→GTA)	rbbA ←	ribosome‑associated ATPase: ATP‑binding protein/ATP‑binding membrane protein
RA	3,623,234	G→T	7.0%	V243V (GTC→GTA)	yhiI ←	putative membrane fusion protein (MFP) of efflux pump
RA	3,629,424	T→A	91.3%	intergenic (+171/+144)	yhiM → / ← yhiN	acid resistance protein, inner membrane/putative oxidoreductase
RA	3,634,076	G→A	5.5%	intergenic (+171/‑146)	uspA → / → dtpB	universal stress global response regulator/dipeptide and tripeptide permease B
RA	3,638,926	A→T	8.6%	Y61F (TAT→TTT)	rlmJ →	23S rRNA m(6)A2030 methyltransferase, SAM‑dependent
RA	3,639,239	G→T	85.9%	P165P (CCG→CCT)	rlmJ →	23S rRNA m(6)A2030 methyltransferase, SAM‑dependent
RA	3,644,531	G→A	84.0%	intergenic (+509/‑120)	arsC → / → yhiS	arsenate reductase/pseudogene
RA	3,645,215	C→A	5.5%	pseudogene (565/741 nt)	yhiS →	pseudogene
RA	3,646,984	G→T	85.5%	pseudogene (394/483 nt)	yhiS →	pseudogene
RA	3,649,797	C→A	88.1%	E102* (GAA→TAA)	hdeA ←	stress response protein acid‑resistance protein
RA	3,652,308	G→T	10.4%	intergenic (+55/‑284)	gadE → / → mdtE	gad regulon transcriptional activator/anaerobic multidrug efflux transporter, ArcA‑regulated
RA	3,653,905	C→A	5.4%	T44T (ACC→ACA)	mdtF →	anaerobic multidrug efflux transporter, ArcA‑regulated
RA	3,656,225	A→T	31.9%	N818Y (AAC→TAC)	mdtF →	anaerobic multidrug efflux transporter, ArcA‑regulated
RA	3,657,375	G→A	33.2%	P202S (CCT→TCT)	gadW ←	transcriptional activator of gadA and gadBC; repressor of gadX
RA	3,661,610	A→T	88.5%	F313L (TTT→TTA)	yhjA ←	putative cytochrome C peroxidase
RA	3,662,660	T→C	100%	intergenic (‑112/‑292)	yhjA ← / → treF	putative cytochrome C peroxidase/cytoplasmic trehalase
RA	3,667,784	C→A	22.9%	intergenic (+49/‑362)	yhjD → / → yhjE	inner membrane putative BrbK family alternate lipid exporter/MFS superfamily sugar transport 1 family protein
RA	3,667,959	C→A	88.1%	intergenic (+224/‑187)	yhjD → / → yhjE	inner membrane putative BrbK family alternate lipid exporter/MFS superfamily sugar transport 1 family protein
RA	3,671,686	C→A	8.3%	A9S (GCT→TCT)	yhjG ←	putative inner membrane‑anchored periplasmic AsmA family protein
RA	3,676,886	C→A	5.8%	intergenic (‑79/+104)	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	3,679,824	T→A	8.9%	I904F (ATC→TTC)	bcsC ←	cellulose synthase subunit
RA	3,680,910	G→T	100%	H542N (CAT→AAT)	bcsC ←	cellulose synthase subunit
RA	3,698,119	C→A	85.2%	M1M (ATG→ATT) †	dppC ←	dipeptide/heme transporter
RA	3,698,875	G→T	100%	F92L (TTC→TTA)	dppB ←	dipeptide/heme transporter
RA	3,717,788	C→A	100%	P297P (CCG→CCT)	glyQ ←	glycine tRNA synthetase, alpha subunit
RA	3,721,469	A→C	6.9%	D421E (GAT→GAG)	xylB ←	xylulokinase
RA	3,721,480	T→G	7.4%	T418P (ACG→CCG)	xylB ←	xylulokinase
RA	3,721,485	T→G	8.5%	Y416S (TAC→TCC)	xylB ←	xylulokinase
RA	3,727,580	C→A	87.8%	A167A (GCC→GCA)	xylH →	D‑xylose ABC transporter permease subunit
RA	3,736,722	C→A	28.5%	G210G (GGC→GGA)	yiaK →	2,3‑diketo‑L‑gulonate reductase, NADH‑dependent
RA	3,738,431	C→A	100%	P90T (CCA→ACA)	yiaN →	2,3‑diketo‑L‑gulonate TRAP transporter large permease protein
RA	3,740,731	G→T	5.6%	G96G (GGG→GGT)	lyxK →	L‑xylulose kinase
RA	3,744,809	C→A	8.5%	E140D (GAG→GAT)	yiaT ←	putative outer membrane protein
RA	3,747,595	C→A	6.4%	W65L (TGG→TTG)	yiaW ←	DUF3302 family inner membrane protein
RA	3,747,927	A→T	7.0%	intergenic (‑139/+406)	yiaW ← / ← aldB	DUF3302 family inner membrane protein/aldehyde dehydrogenase B
RA	3,751,135	G→T	47.4%	S18* (TCA→TAA)	yiaY ←	putative Fe‑containing alcohol dehydrogenase, Pfam00465 family
RA	3,765,425	T→C	5.1%	intergenic (‑321/‑216)	yibI ← / → mtlA	DUF3302 family inner membrane protein/fused mannitol‑specific PTS enzymes: IIA components/IIB components/IIC components
RA	3,767,000	G→T	100%	D454Y (GAC→TAC)	mtlA →	fused mannitol‑specific PTS enzymes: IIA components/IIB components/IIC components
RA	3,767,410	G→T	69.4%	V590V (GTG→GTT)	mtlA →	fused mannitol‑specific PTS enzymes: IIA components/IIB components/IIC components
RA	3,769,241	C→A	11.8%	R104S (CGC→AGC)	mtlR →	mannitol operon repressor
RA	3,777,924	C→A	9.2%	intergenic (‑122/+20)	grxC ← / ← yibN	glutaredoxin 3/putative rhodanese‑related sulfurtransferase
RA	3,783,763	G→T	19.1%	R315S (CGT→AGT)	tdh ←	L‑threonine 3‑dehydrogenase, NAD(P)‑binding
RA	3,785,915	G→T	100%	intergenic (‑4/+271)	kbl ← / ← yibB	glycine C‑acetyltransferase/YibB family protein, function unknown
RA	3,786,682	C→A	5.3%	C121F (TGT→TTT)	yibB ←	YibB family protein, function unknown
RA	3,787,487	C→A	13.8%	I47I (ATC→ATA)	hldD →	ADP‑L‑glycero‑D‑mannoheptose‑6‑epimerase, NAD(P)‑binding
RA	3,789,381	C→A	75.0%	L15I (CTC→ATC)	waaC →	ADP‑heptose:LPS heptosyl transferase I
RA	3,791,032	C→T	7.6%	S242F (TCC→TTC)	waaL →	O‑antigen ligase
RA	3,792,145	C→A	5.5%	L176L (CTG→CTT)	waaU ←	lipopolysaccharide core biosynthesis
RA	3,792,673	T→A	5.7%	intergenic (‑1/+32)	waaU ← / ← waaZ	lipopolysaccharide core biosynthesis/lipopolysaccharide core biosynthesis protein
RA	3,796,691	T→A	8.6%	P269P (CCA→CCT)	waaB ←	UDP‑D‑galactose:(glucosyl)lipopolysaccharide‑1, 6‑D‑galactosyltransferase
RA	3,806,714	C→A	5.9%	I208I (ATC→ATA)	dfp →	fused 4'‑phosphopantothenoylcysteine decarboxylase/phosphopantothenoylcysteine synthetase, FMN‑binding
RA	3,809,115	T→A	21.3%	Q5L (CAG→CTG)	pyrE ←	orotate phosphoribosyltransferase
RA	3,809,236	G→T	7.5%	pseudogene (6/48 nt)	rph ←	ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
RA	3,810,195	C→A	100%	R54S (CGT→AGT)	yicC →	UPF0701 family protein
RA	3,813,962	T→A	10.1%	Q190L (CAA→CTA)	ligB ←	DNA ligase, NAD(+)‑dependent
RA	3,816,601	A→T	100%	H281L (CAC→CTC)	spoT →	bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
RA	3,816,686	G→T	8.4%	S309S (TCG→TCT)	spoT →	bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
RA	3,818,010	C→A	100%	H46N (CAT→AAT)	trmH →	tRNA mG18‑2'‑O‑methyltransferase, SAM‑dependent
RA	3,822,340	A→C	11.3%	Q12H (CAA→CAC)	xanP →	xanthine permease
RA	3,824,552	C→A	29.0%	R246S (CGC→AGC)	yicH →	putative inner membrane‑anchored periplasmic AsmA family protein
RA	3,825,702	C→A	100%	K732N (AAG→AAT)	yicI ←	putative alpha‑glucosidase
RA	3,828,206	T→A	85.7%	S362C (AGT→TGT)	yicJ ←	putative transporter
RA	3,829,020	G→T	9.5%	F90L (TTC→TTA)	yicJ ←	putative transporter
RA	3,830,197	C→A	100%	intergenic (+281/‑116)	yicT → / → setC	pseudogene/putative arabinose efflux transporter
RA	3,830,311	G→T	100%	intergenic (+395/‑2)	yicT → / → setC	pseudogene/putative arabinose efflux transporter
RA	3,830,819	T→G	86.7%	F169L (TTT→TTG)	setC →	putative arabinose efflux transporter
RA	3,834,958	G→T	6.1%	Q48K (CAG→AAG)	nepI ←	putative transporter
RA	3,839,034	C→A	8.1%	Q571K (CAG→AAG)	ade →	cryptic adenine deaminase
JC	3,841,409	+CAACCAG	93.4%	coding (576/1320 nt)	uhpC ←	membrane protein regulates uhpT expression
RA	3,858,963	A→T	12.2%	V224E (GTA→GAA)	yidE ←	putative transporter
RA	3,859,661	A→T	5.6%	intergenic (‑28/+168)	yidE ← / ← ibpB	putative transporter/heat shock chaperone
RA	3,860,159	C→A	100%	P33P (CCG→CCT)	ibpB ←	heat shock chaperone
RA	3,860,327	C→A	100%	intergenic (‑70/+42)	ibpB ← / ← ibpA	heat shock chaperone/heat shock chaperone
RA	3,860,653	C→A	100%	E44* (GAA→TAA)	ibpA ←	heat shock chaperone
RA	3,860,676	G→T	7.8%	P36Q (CCG→CAG)	ibpA ←	heat shock chaperone
RA	3,861,553	C→A	42.5%	G373C (GGC→TGC)	yidR ←	DUF3748 family protein
RA	3,863,438	G→T	84.6%	M234I (ATG→ATT)	cbrA →	colicin M resistance protein; FAD‑binding protein, putative oxidoreductase
RA	3,865,120	C→A	100%	intergenic (‑30/+90)	dgoT ← / ← dgoD	D‑galactonate transporter/galactonate dehydratase
RA	3,865,863	T→A	85.0%	T166S (ACC→TCC)	dgoD ←	galactonate dehydratase
RA	3,872,006	T→A	79.4%	S492C (AGC→TGC)	gyrB ←	DNA gyrase, subunit B
RA	3,877,642	C→A	5.3%	intergenic (‑553/‑54)	dnaA ← / → rpmH	chromosomal replication initiator protein DnaA, DNA‑binding transcriptional dual regulator/50S ribosomal subunit protein L34
RA	3,879,461	A→T	7.7%	K342N (AAA→AAT)	yidC →	membrane protein insertase
RA	3,879,935	C→A	5.9%	V500V (GTC→GTA)	yidC →	membrane protein insertase
RA	3,880,731	G→T	34.7%	D182Y (GAT→TAT)	mnmE →	tRNA U34 5‑methylaminomethyl‑2‑thiouridine modification GTPase
RA	3,882,020	G→T	5.5%	intergenic (+151/‑70)	tnaC → / → tnaA	tryptophanase leader peptide/tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent
RA	3,885,201	C→A	28.5%	A76E (GCG→GAG)	mdtL →	multidrug efflux system protein
RA	3,888,563	G→T	7.4%	Q184H (CAG→CAT)	chrR →	chromate reductase, Class I, flavoprotein
RA	3,890,960	T→A	89.9%	F32Y (TTC→TAC)	cbrB →	PRK09823 family inner membrane protein, creBC regulon
RA	3,892,304	C→A	90.6%	P150P (CCG→CCT)	yieK ←	putative 6‑phosphogluconolactonase
RA	3,893,713	C→A	7.7%	P75P (CCG→CCT)	yieL ←	putative xylanase
RA	3,901,867	T→G	5.7%	intergenic (‑141/+42)	pstB ← / ← pstA	phosphate transporter subunit/phosphate transporter subunit
RA	3,904,553	T→A	39.5%	P111P (CCA→CCT)	pstS ←	periplasmic phosphate binding protein, high‑affinity
RA	3,906,384	G→T	84.2%	I215I (ATC→ATA)	glmS ←	L‑glutamine:D‑fructose‑6‑phosphate aminotransferase
RA	3,910,416	C→A	87.8%	R107L (CGT→CTT)	atpD ←	F1 sector of membrane‑bound ATP synthase, beta subunit
RA	3,910,448	G→T	88.5%	V96V (GTC→GTA)	atpD ←	F1 sector of membrane‑bound ATP synthase, beta subunit
RA	3,910,894	C→A	100%	M244I (ATG→ATT)	atpG ←	F1 sector of membrane‑bound ATP synthase, gamma subunit
RA	3,913,979	C→A	7.4%	A90A (GCG→GCT)	atpF ←	F0 sector of membrane‑bound ATP synthase, subunit b
RA	3,916,830	C→A	100%	D71Y (GAT→TAT)	rsmG ←	16S rRNA m(7)G527 methyltransferase, SAM‑dependent; glucose‑inhibited cell‑division protein
RA	3,917,554	C→A	87.7%	L480L (CTG→CTT)	mnmG ←	5‑methylaminomethyl‑2‑thiouridine modification at tRNA U34
RA	3,923,028	C→A	100%	D476Y (GAC→TAC)	ravA ←	hexameric AAA+ MoxR family ATPase, putative molecular chaperone
RA	3,926,618	G→T	5.8%	intergenic (+74/‑93)	kup → / → rbsD	potassium transporter/putative cytoplasmic sugar‑binding protein
RA	3,926,831	G→T	100%	D41Y (GAT→TAT)	rbsD →	putative cytoplasmic sugar‑binding protein
RA	3,927,097	G→T	10.6%	A129A (GCG→GCT)	rbsD →	putative cytoplasmic sugar‑binding protein
RA	3,927,972	G→T	100%	E279* (GAA→TAA)	rbsA →	fused D‑ribose transporter subunits of ABC superfamily: ATP‑binding components
RA	3,931,021	C→A	84.3%	A123E (GCG→GAG)	rbsK →	ribokinase
RA	3,932,671	G→T	5.1%	I434I (ATC→ATA)	hsrA ←	putative multidrug or homocysteine efflux system
RA	3,934,278	A→T	6.4%	L137* (TTA→TAA)	yieP ←	putative transcriptional regulator
RA	3,935,100	G→T	100%	intergenic (‑413/‑68)	yieP ← / → rrsC	putative transcriptional regulator/16S ribosomal RNA of rrnC operon
RA	3,945,181	G→T	27.2%	pseudogene (280/663 nt)	ilvG →	pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive; acetolactate synthase II, large subunit, cryptic, interrupted
RA	3,946,035	C→A	10.2%	S64S (TCC→TCA)	ilvE →	branched‑chain amino‑acid aminotransferase
RA	3,946,395	C→A	6.3%	I184I (ATC→ATA)	ilvE →	branched‑chain amino‑acid aminotransferase
RA	3,958,323	G→T	7.8%	P223Q (CCG→CAG)	rhlB ←	ATP‑dependent RNA helicase
RA	3,958,599	A→T	29.8%	L131Q (CTG→CAG)	rhlB ←	ATP‑dependent RNA helicase
RA	3,958,820	G→T	21.2%	T57T (ACC→ACA)	rhlB ←	ATP‑dependent RNA helicase
RA	3,959,351	G→T	90.3%	P77P (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	100%	R325S (CGT→AGT)	rffG →	dTDP‑glucose 4,6‑dehydratase
RA	3,967,474	G→T	100%	A169A (GCG→GCT)	rffH →	glucose‑1‑phosphate thymidylyltransferase
RA	3,969,710	G→T	100%	G25C (GGT→TGT)	wzxE →	O‑antigen translocase
RA	3,972,296	G→T	82.4%	E112D (GAG→GAT)	wzyE →	putative ECA polysaccharide chain elongation protein
RA	3,972,942	C→A	7.5%	H328N (CAC→AAC)	wzyE →	putative ECA polysaccharide chain elongation protein
RA	3,980,852	G→T	11.8%	R131S (CGT→AGT)	hemY ←	putative protoheme IX synthesis protein
RA	3,984,342	G→T	9.0%	intergenic (‑216/‑171)	hemC ← / → cyaA	hydroxymethylbilane synthase/adenylate cyclase
RA	3,988,075	T→A	100%	V65E (GTG→GAG)	yifL →	putative lipoprotein
RA	3,991,844	C→A	5.2%	Q168K (CAG→AAG)	uvrD →	DNA‑dependent ATPase I and helicase II
RA	3,994,076	A→T	100%	L114* (TTA→TAA)	yigE ←	DUF2233 family protein
RA	3,994,247	A→T	100%	V57E (GTG→GAG)	yigE ←	DUF2233 family protein
RA	3,994,758	G→T	7.4%	intergenic (‑342/‑28)	yigE ← / → corA	DUF2233 family protein/magnesium/nickel/cobalt transporter
RA	3,996,346	T→A	86.7%	I70F (ATC→TTC)	yigG ←	PRK11371 family inner membrane protein
RA	4,000,498	T→A	6.9%	R425R (CGT→CGA)	recQ →	ATP‑dependent DNA helicase
RA	4,009,705	G→A	100%	intergenic (‑176/‑86)	ysgA ← / → udp	putative carboxymethylenebutenolidase/uridine phosphorylase
RA	4,023,757	T→A	9.3%	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	10.3%	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	100%	D103Y (GAT→TAT)	pepQ →	proline dipeptidase
RA	4,035,421	G→T	100%	intergenic (‑62/‑8)	mobA ← / → yihD	molybdopterin‑guanine dinucleotide synthase/DUF1040 protein YihD
RA	4,035,769	G→T	7.5%	intergenic (+71/‑6)	yihD → / → srkA	DUF1040 protein YihD/stress response kinase A; MazF antagonist; Thr/Ser kinase involved in Cpx stress response
RA	4,036,569	G→T	9.8%	L265L (CTG→CTT)	srkA →	stress response kinase A; MazF antagonist; Thr/Ser kinase involved in Cpx stress response
RA	4,037,484	T→A	85.8%	intergenic (+80/‑75)	dsbA → / → yihF	periplasmic protein disulfide isomerase I/DUF945 family protein
RA	4,039,399	G→T	6.5%	F188L (TTC→TTA)	yihG ←	inner membrane protein, inner membrane acyltransferase
RA	4,045,302	G→T	90.8%	intergenic (+86/‑103)	yihI → / → hemN	activator of Der GTPase/coproporphyrinogen III oxidase, SAM and NAD(P)H dependent, oxygen‑independent
RA	4,046,172	A→T	100%	K256N (AAA→AAT)	hemN →	coproporphyrinogen III oxidase, SAM and NAD(P)H dependent, oxygen‑independent
RA	4,054,222	T→A	11.6%	V139D (GTT→GAT)	yihL →	putative DNA‑binding transcriptional regulator
RA	4,056,018	T→A	100%	F138I (TTC→ATC)	yihN →	MFS transporter family protein
RA	4,058,809	G→T	86.9%	I106I (ATC→ATA)	yihO ←	putative transporter
RA	4,062,424	G→T	100%	I71I (ATC→ATA)	yihQ ←	alpha‑glucosidase
RA	4,066,133	T→G	100%	S267R (AGC→CGC)	yihU ←	gamma‑hydroxybutyrate dehydrogenase, NADH‑dependent
RA	4,068,208	C→A	100%	G60G (GGC→GGA)	yihW →	DeoR family putative transcriptional regulator
RA	4,074,579	G→T	34.0%	R4S (CGC→AGC)	fdhE ←	formate dehydrogenase formation protein
RA	4,075,234	C→A	89.3%	D296Y (GAC→TAC)	fdoH ←	formate dehydrogenase‑O, Fe‑S subunit
RA	4,078,536	T→A	6.4%	H216L (CAC→CTC)	fdoG ←	formate dehydrogenase‑O, large subunit
RA	4,078,761	C→A	10.6%	R141L (CGC→CTC)	fdoG ←	formate dehydrogenase‑O, large subunit
RA	4,081,173	C→A	9.9%	T271K (ACG→AAG)	yiiG →	DUF3829 family lipoprotein
RA	4,086,311	A→T	5.4%	intergenic (‑128/+173)	frvA ← / ← rhaM	putative enzyme IIA component of PTS/L‑rhamnose mutarotase
RA	4,087,391	G→T	21.2%	intergenic (‑41/‑273)	rhaD ← / → rhaS	pseudogene, truncated, rhamnulose‑phosphate aldolase/transcriptional activator of rhaBAD and rhaT
RA	4,088,850	C→A	88.8%	R93S (CGT→AGT)	rhaR →	transcriptional activator of rhaSR
RA	4,089,371	A→T	6.2%	E266D (GAA→GAT)	rhaR →	transcriptional activator of rhaSR
RA	4,094,362	C→A	100%	W181L (TGG→TTG)	cpxA ←	sensory histidine kinase in two‑component regulatory system with CpxR
RA	4,097,822	G→T	100%	E115* (GAA→TAA)	pfkA →	6‑phosphofructokinase I
RA	4,104,078	G→T	11.4%	T108K (ACG→AAG)	fpr ←	ferredoxin‑NADP reductase
RA	4,106,085	A→T	24.0%	Y356N (TAC→AAC)	glpK ←	glycerol kinase
RA	4,122,248	A→T	100%	intergenic (+53/‑296)	metL → / → metF	Bifunctional aspartokinase/homoserine dehydrogenase 2/5,10‑methylenetetrahydrofolate reductase
RA	4,125,407	C→A	87.7%	H549N (CAT→AAT)	katG →	catalase‑peroxidase HPI, heme b‑containing
RA	4,127,022	T→G	100%	E188D (GAA→GAC)	yijF ←	DUF1287 family protein
RA	4,129,331	C→T	12.3%	E102E (GAG→GAA)	fsaB ←	fructose‑6‑phosphate aldolase 2
RA	4,135,021	A→T	24.6%	N367Y (AAC→TAC)	pflD →	putative glycine radical domain‑containing pyruvate formate‑lyase
RA	4,135,168	G→T	86.6%	V416L (GTA→TTA)	pflD →	putative glycine radical domain‑containing pyruvate formate‑lyase
RA	4,142,213	G→T	20.6%	R272S (CGC→AGC)	ppc ←	phosphoenolpyruvate carboxylase
RA	4,143,544	C→T	6.0%	intergenic (‑518/+80)	ppc ← / ← argE	phosphoenolpyruvate carboxylase/acetylornithine deacetylase
RA	4,144,896	T→G	8.9%	intergenic (‑121/‑33)	argE ← / → argC	acetylornithine deacetylase/N‑acetyl‑gamma‑glutamylphosphate reductase, NAD(P)‑binding
RA	4,150,054	G→T	87.4%	S222Y (TCT→TAT)	sthA ←	pyridine nucleotide transhydrogenase, soluble
RA	4,152,843	A→T	18.2%	V119E (GTG→GAG)	trmA ←	tRNA m(5)U54 methyltransferase, SAM‑dependent; tmRNA m(5)U341 methyltransferase
RA	4,156,059	C→T	8.7%	T235M (ACG→ATG)	murI →	glutamate racemase
RA	4,158,143	A→T	33.3%	intergenic (+15/‑157)	rrsB → / → gltT	16S ribosomal RNA of rrnB operon/tRNA‑Glu
RA	4,158,149	T→C	35.0%	intergenic (+21/‑151)	rrsB → / → gltT	16S ribosomal RNA of rrnB operon/tRNA‑Glu
RA	4,158,400	G→A	18.9%	intergenic (+25/‑169)	gltT → / → rrlB	tRNA‑Glu/23S ribosomal RNA of rrnB operon
RA	4,158,403	G→T	18.7%	intergenic (+28/‑166)	gltT → / → rrlB	tRNA‑Glu/23S ribosomal RNA of rrnB operon
RA	4,158,404	A→G	18.6%	intergenic (+29/‑165)	gltT → / → rrlB	tRNA‑Glu/23S ribosomal RNA of rrnB operon
RA	4,162,618	C→A	5.6%	H212N (CAT→AAT)	murB →	UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding
RA	4,162,956	T→A	12.8%	P324P (CCT→CCA)	murB →	UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding
RA	4,167,962	G→T	17.4%	D98Y (GAT→TAT)	nusG →	transcription termination factor
RA	4,167,995	G→T	6.0%	D109Y (GAT→TAT)	nusG →	transcription termination factor
RA	4,172,507	C→A	25.9%	I445I (ATC→ATA)	rpoB →	RNA polymerase, beta subunit
RA	4,173,145	A→T	100%	Q658L (CAG→CTG)	rpoB →	RNA polymerase, beta subunit
RA	4,173,179	G→T	87.3%	P669P (CCG→CCT)	rpoB →	RNA polymerase, beta subunit
RA	4,176,417	C→A	8.2%	F380L (TTC→TTA)	rpoC →	RNA polymerase, beta prime subunit
RA	4,176,823	G→T	100%	D516Y (GAC→TAC)	rpoC →	RNA polymerase, beta prime subunit
RA	4,178,969	G→T	85.5%	R1231L (CGT→CTT)	rpoC →	RNA polymerase, beta prime subunit
RA	4,179,520	C→A	6.5%	intergenic (+19/‑194)	rpoC → / → yjaZ	RNA polymerase, beta prime subunit/stationary phase growth adaptation protein
RA	4,182,646	G→T	7.9%	I40I (ATC→ATA)	thiS ←	immediate sulfur donor in thiazole formation
RA	4,189,766	C→A	12.7%	T112K (ACG→AAG)	yjaG →	DUF416 domain protein
RA	4,193,578	G→T	87.3%	D111Y (GAT→TAT)	zraR →	fused DNA‑binding response regulator in two‑component regulatory system with ZraS: response regulator/sigma54 interaction protein
RA	4,207,552	G→T	100%	M172I (ATG→ATT)	aceA →	isocitrate lyase
RA	4,208,942	C→A	9.1%	A140E (GCG→GAG)	aceK →	isocitrate dehydrogenase kinase/phosphatase
RA	4,210,753	C→A	53.2%	E555* (GAA→TAA)	arpA ←	ankyrin repeat protein
RA	4,211,576	G→T	100%	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	100%	T270S (ACC→TCC)	metH →	homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent
RA	4,214,809	G→T	88.8%	E352* (GAA→TAA)	metH →	homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent
RA	4,217,818	G→T	6.5%	V54F (GTT→TTT)	yjbB →	putative Na+/Pi‑cotransporter
RA	4,222,636	C→A	12.3%	E176* (GAA→TAA)	lysC ←	lysine‑sensitive aspartokinase 3
RA	4,225,841	A→C	86.0%	K3T (AAA→ACA)	yjbE →	extracellular polysaccharide production threonine‑rich protein
RA	4,230,913	A→T	100%	W424R (TGG→AGG)	xylE ←	D‑xylose transporter
RA	4,235,869	G→T	100%	A160E (GCG→GAG)	malE ←	maltose transporter subunit
RA	4,235,916	G→T	100%	N144K (AAC→AAA)	malE ←	maltose transporter subunit
RA	4,236,666	C→A	86.4%	intergenic (‑319/‑46)	malE ← / → malK	maltose transporter subunit/fused maltose transport subunit, ATP‑binding component of ABC superfamily/regulatory protein
RA	4,242,509	C→T	100%	L26F (CTC→TTC)	ubiC →	chorismate‑‑pyruvate lyase
RA	4,245,537	G→T	87.5%	N286K (AAC→AAA)	plsB ←	glycerol‑3‑phosphate O‑acyltransferase
RA	4,249,117	G→T	74.3%	intergenic (+68/‑48)	dinF → / → yjbJ	oxidative stress resistance protein; putative MATE family efflux pump; UV and mitomycin C inducible protein/stress‑induced protein, UPF0337 family
RA	4,255,009	A→T	85.9%	V256V (GTA→GTT)	dnaB →	replicative DNA helicase
RA	4,256,589	G→T	9.7%	E294* (GAA→TAA)	alr →	alanine racemase, biosynthetic, PLP‑binding
RA	4,258,418	G→A	5.5%	intergenic (+183/+319)	tyrB → / ← yjbS	tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent/uncharacterized protein
RA	4,259,875	G→T	8.5%	S178S (TCG→TCT)	aphA →	acid phosphatase/phosphotransferase, class B, non‑specific
RA	4,261,049	G→T	6.1%	V917V (GTC→GTA)	uvrA ←	ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC
RA	4,263,834	T→A	9.9%	intergenic (‑35/‑219)	uvrA ← / → ssb	ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC/single‑stranded DNA‑binding protein
RA	4,265,064	C→A	100%	intergenic (‑95/‑335)	yjcB ← / → yjcC	putative inner membrane protein/putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	4,266,318	G→T	27.7%	R307L (CGT→CTT)	yjcC →	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	4,270,316	G→T	8.2%	E137* (GAA→TAA)	yjcE →	putative cation/proton antiporter
RA	4,270,764	T→A	6.3%	V286E (GTG→GAG)	yjcE →	putative cation/proton antiporter
RA	4,272,274	G→A	19.2%	L244F (CTT→TTT)	yjcF ←	pentapeptide repeats protein
RA	4,274,748	C→A	10.8%	R28L (CGC→CTC)	actP ←	acetate transporter
RA	4,274,926	A→C	100%	I72M (ATT→ATG)	yjcH ←	DUF485 family inner membrane protein
RA	4,275,142	C→A	100%	intergenic (‑1/+199)	yjcH ← / ← acs	DUF485 family inner membrane protein/acetyl‑CoA synthetase
RA	4,275,862	C→A	82.4%	D480Y (GAT→TAT)	acs ←	acetyl‑CoA synthetase
RA	4,276,940	G→T	8.8%	F120L (TTC→TTA)	acs ←	acetyl‑CoA synthetase
RA	4,281,581	G→T	11.1%	D48Y (GAT→TAT)	nrfE →	heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfE
RA	4,285,857	T→C	6.5%	intergenic (+135/+396)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA	4,286,083	T→C	11.0%	intergenic (+361/+170)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA	4,288,086	G→T	80.9%	F366L (TTC→TTA)	fdhF ←	formate dehydrogenase‑H, selenopolypeptide subunit
RA	4,290,080	G→T	100%	I256I (ATC→ATA)	mdtP ←	outer membrane factor of efflux pump
RA	4,291,272	G→T	5.0%	R542S (CGT→AGT)	mdtO ←	membrane translocase (MDR) of MdtNOP efflux pump, PET family
RA	4,292,310	C→A	25.3%	D196Y (GAT→TAT)	mdtO ←	membrane translocase (MDR) of MdtNOP efflux pump, PET family
RA	4,297,485	G→C	100%	G44G (GGC→GGG)	alsK ←	D‑allose kinase
RA	4,297,846	C→A	100%	M150I (ATG→ATT)	alsE ←	allulose‑6‑phosphate 3‑epimerase
RA	4,298,238	C→A	15.3%	E20* (GAA→TAA)	alsE ←	allulose‑6‑phosphate 3‑epimerase
RA	4,303,614	T→A	100%	*150R (TGA→AGA)	rpiB →	ribose 5‑phosphate isomerase B/allose 6‑phosphate isomerase
RA	4,317,243	C→A	5.8%	R98S (CGT→AGT)	crfC →	clamp‑binding sister replication fork colocalization protein, dynamin‑related
RA	4,317,823	C→A	8.8%	P291Q (CCG→CAG)	crfC →	clamp‑binding sister replication fork colocalization protein, dynamin‑related
RA	4,318,517	A→T	90.2%	T522T (ACA→ACT)	crfC →	clamp‑binding sister replication fork colocalization protein, dynamin‑related
RA	4,318,645	T→A	29.6%	L565* (TTG→TAG)	crfC →	clamp‑binding sister replication fork colocalization protein, dynamin‑related
RA	4,329,774	C→A	86.6%	D189Y (GAC→TAC)	adiA ←	arginine decarboxylase
RA	4,330,426	Δ1 bp	100%	intergenic (‑88/+111)	adiA ← / ← melR	arginine decarboxylase/melibiose operon transcriptional regulator; autoregulator
RA	4,341,023	A→T	100%	Y153N (TAC→AAC)	dcuS ←	sensory histidine kinase in two‑component regulatory system with DcuR, regulator of anaerobic fumarate respiration
RA	4,342,293	C→A	8.9%	intergenic (+119/‑108)	yjdJ → / → yjdK	putative acyl‑CoA transferase/uncharacterized protein
RA	4,350,223	G→A	84.3%	A510V (GCT→GTT)	cadC ←	cadBA operon transcriptional activator
RA	4,358,390	A→C	89.5%	intergenic (‑246/‑91)	aspA ← / → fxsA	aspartate ammonia‑lyase/suppressor of F exclusion of phage T7
RA	4,358,920	G→T	100%	R147L (CGC→CTC)	fxsA →	suppressor of F exclusion of phage T7
RA	4,358,943	G→T	5.6%	D155Y (GAT→TAT)	fxsA →	suppressor of F exclusion of phage T7
RA	4,371,101	A→T	5.1%	V345V (GTT→GTA)	frdA ←	fumarate reductase (anaerobic) catalytic and NAD/flavoprotein subunit
RA	4,373,522	C→T	10.8%	intergenic (+85/‑134)	epmA → / → yjeM	Elongation Factor P Lys34 lysyltransferase/putative transporter
RA	4,376,178	C→A	100%	E1004* (GAA→TAA)	mscM ←	mechanosensitive channel protein, miniconductance
RA	4,378,778	G→T	100%	S137* (TCG→TAG)	mscM ←	mechanosensitive channel protein, miniconductance
RA	4,381,504	T→A	35.6%	I28I (ATT→ATA)	orn →	oligoribonuclease
RA	4,382,218	C→A	81.8%	noncoding (42/76 nt)	glyV →	tRNA‑Gly
RA	4,388,902	G→T	100%	A558A (GCG→GCT)	mutL →	methyl‑directed mismatch repair protein
RA	4,394,875	G→T	100%	A124A (GCG→GCT)	purA →	adenylosuccinate synthetase
RA	4,396,598	A→T	100%	E43V (GAA→GTA)	rnr →	exoribonuclease R, RNase R
RA	4,396,945	G→T	5.1%	E159* (GAA→TAA)	rnr →	exoribonuclease R, RNase R
RA	4,401,343	A→T	10.4%	S75S (TCA→TCT)	yjfK →	DUF2491 family protein
RA	4,402,850	G→T	100%	L2L (CTG→CTT)	yjfC →	ATP‑Grasp family ATPase
RA	4,404,169	G→T	86.9%	A26A (GCG→GCT)	aidB →	DNA alkylation damage repair protein; flavin‑containing DNA binding protein, weak isovaleryl CoA dehydrogenase
RA	4,405,730	G→T	87.8%	intergenic (+13/+104)	aidB → / ← yjfN	DNA alkylation damage repair protein; flavin‑containing DNA binding protein, weak isovaleryl CoA dehydrogenase/DUF1471 family periplasmic protein
RA	4,406,553	C→A	35.4%	R12L (CGG→CTG)	bsmA ←	bioflm peroxide resistance protein
RA	4,407,017	C→T	6.7%	I83I (ATC→ATT)	yjfP →	acyl CoA esterase
RA	4,407,959	G→T	5.4%	T104T (ACC→ACA)	ulaR ←	transcriptional repressor for the L‑ascorbate utilization (ula) divergent operon
RA	4,410,964	A→C	67.5%	I390L (ATC→CTC)	ulaA →	L‑ascorbate‑specific enzyme IIC permease component of PTS
RA	4,411,145	T→G	9.2%	L450R (CTG→CGG)	ulaA →	L‑ascorbate‑specific enzyme IIC permease component of PTS
RA	4,412,786	G→T	83.9%	E42* (GAA→TAA)	ulaE →	L‑xylulose 5‑phosphate 3‑epimerase
RA	4,413,724	C→A	5.5%	R70S (CGC→AGC)	ulaF →	L‑ribulose 5‑phosphate 4‑epimerase
RA	4,417,122	G→T	86.7%	R40S (CGT→AGT)	yjfZ ←	uncharacterized protein
RA	4,417,551	A→C	100%	pseudogene (41/402 nt)	ytfA →	pseudogene, related to transcriptional regulators
RA	4,427,647	G→A	100%	D42N (GAT→AAT)	ytfI →	uncharacterized protein
RA	4,428,092	G→T	100%	G190V (GGA→GTA)	ytfI →	uncharacterized protein
RA	4,432,031	G→A	85.6%	intergenic (‑38/‑168)	msrA ← / → tamA	methionine sulfoxide reductase A/translocation and assembly module for autotransporter export, outer membrane subunit
RA	4,434,260	C→A	86.8%	P111H (CCT→CAT)	tamB →	translocation and assembly module for autotransporter export, inner membrane subunit
RA	4,445,719	A→T	39.1%	T40S (ACC→TCC)	mpl →	UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase
RA	4,455,810	T→A	28.9%	Q63L (CAA→CTA)	treB ←	fused trehalose(maltose)‑specific PTS enzyme: IIB component/IIC component
RA	4,456,233	G→T	88.0%	I277I (ATC→ATA)	treR ←	trehalose 6‑phosphate‑inducible trehalose regulon transcriptional repressor
RA	4,457,499	C→A	90.3%	R20S (CGT→AGT)	mgtA →	magnesium transporter
RA	4,458,254	T→A	100%	V271V (GTT→GTA)	mgtA →	magnesium transporter
RA	4,458,609	G→T	100%	D390Y (GAT→TAT)	mgtA →	magnesium transporter
RA	4,458,948	G→T	88.5%	D503Y (GAT→TAT)	mgtA →	magnesium transporter
RA	4,461,317	G→T	6.4%	A299E (GCG→GAG)	pyrB ←	aspartate carbamoyltransferase, catalytic subunit
RA	4,465,936	T→A	87.7%	L228* (TTA→TAA)	yjgL →	uncharacterized protein
RA	4,466,436	G→T	31.9%	D395Y (GAT→TAT)	yjgL →	uncharacterized protein
RA	4,466,947	A→T	7.9%	Q565L (CAA→CTA)	yjgL →	uncharacterized protein
RA	4,468,165	A→G	100%	intergenic (‑37/‑125)	argI ← / → rraB	ornithine carbamoyltransferase 1/protein inhibitor of RNase E
RA	4,469,550	G→A	100%	A2T (GCT→ACT)	yjgN →	DUF898 family inner membrane protein
RA	4,470,017	G→A	100%	M157I (ATG→ATA)	yjgN →	DUF898 family inner membrane protein
RA	4,470,873	G→T	100%	R928S (CGT→AGT)	valS ←	valyl‑tRNA synthetase
RA	4,471,930	T→A	87.7%	P575P (CCA→CCT)	valS ←	valyl‑tRNA synthetase
RA	4,476,885	T→A	6.3%	V284E (GTA→GAA)	lptF →	lipopolysaccharide export ABC permease of the LptBFGC export complex
RA	4,480,139	G→T	86.7%	A273E (GCG→GAG)	idnR ←	transcriptional repressor, 5‑gluconate‑binding
RA	4,493,435	T→C	33.3%	intergenic (‑187/‑440)	insG ← / → yjhB	IS4 transposase/putative transporter
RA	4,494,721	G→A	100%	A283T (GCC→ACC)	yjhB →	putative transporter
RA	4,495,859	T→G	82.0%	D252E (GAT→GAG)	yjhC →	putative oxidoreductase
RA	4,505,141	G→T	84.4%	R452S (CGT→AGT)	fecA ←	ferric citrate outer membrane transporter
RA	4,505,600	C→A	10.8%	G299C (GGC→TGC)	fecA ←	ferric citrate outer membrane transporter
RA	4,510,281	G→T	5.7%	intergenic (‑140/+207)	yjhU ← / ← yjhF	putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter
RA	4,511,163	C→A	6.3%	M225I (ATG→ATT)	yjhF ←	putative transporter
RA	4,512,693	T→A	100%	K407* (AAG→TAG)	yjhG ←	putative dehydratase
RA	4,515,432	T→A	7.3%	S63S (TCA→TCT)	yjhI ←	putative DNA‑binding transcriptional regulator
RA	4,519,217	A→T	9.6%	F282I (TTC→ATC)	sgcC ←	putative PTS system EIIC permease component
RA	4,520,701	G→T	86.6%	G256G (GGC→GGA)	sgcX ←	putative endoglucanase with Zn‑dependent exopeptidase domain
RA	4,523,001	T→A	100%	intergenic (‑1/+55)	yjhP ← / ← yjhQ	putative methyltransferase/putative acetyltransferase
RA	4,524,337	G→T	6.2%	pseudogene (156/246 nt)	yjhZ ←	pseudogene, rimK paralog, C‑terminal fragment
RA	4,525,234	G→A	100%	pseudogene (415/1029 nt)	yjhR →	pseudogene, helicase family; putative frameshift suppressor
RA	4,527,044	G→T	5.6%	S123* (TCG→TAG)	nanS ←	9‑O‑acetyl N‑acetylneuraminic acid esterase
RA	4,528,263	A→T	7.0%	V107E (GTA→GAA)	nanM ←	N‑acetylneuraminic acid mutarotase
RA	4,531,143	A→T	100%	I124F (ATT→TTT)	fimB →	tyrosine recombinase/inversion of on/off regulator of fimA
RA	4,541,449	A→T	100%	intergenic (‑336/‑4)	gntP ← / → uxuA	fructuronate transporter/mannonate hydrolase
RA	4,546,426	G→T	5.4%	intergenic (‑289/‑384)	yjiC ← / → iraD	uncharacterized protein/RpoS stabilzer after DNA damage, anti‑RssB factor
RA	4,547,687	G→T	6.0%	V140V (GTC→GTA)	hypT ←	hypochlorite‑responsive transcription factor
RA	4,547,818	C→A	87.7%	D97Y (GAT→TAT)	hypT ←	hypochlorite‑responsive transcription factor
RA	4,554,122	A→C	6.2%	F129V (TTC→GTC)	yjiL ←	putative ATPase, activator of (R)‑hydroxyglutaryl‑CoA dehydratase
RA	4,555,156	G→T	100%	A171E (GCG→GAG)	yjiM ←	putative 2‑hydroxyglutaryl‑CoA dehydratase
RA	4,557,269	C→A	5.8%	V356V (GTG→GTT)	mdtM ←	multidrug efflux system protein
RA	4,561,066	A→T	12.0%	L109* (TTA→TAA)	yjiR ←	putative DNA‑binding transcriptional regulator/putative aminotransferase
RA	4,561,616	C→T	6.2%	Q17* (CAA→TAA)	yjiS →	DUF1127 family protein
RA	4,562,043	C→A	100%	intergenic (+311/‑188)	yjiS → / → yjiT	DUF1127 family protein/pseudogene
RA	4,567,278	G→T	88.2%	I166I (ATC→ATA)	mcrC ←	5‑methylcytosine‑specific restriction enzyme McrBC, subunit McrC
RA	4,570,897	G→T	10.5%	S128Y (TCT→TAT)	hsdS ←	specificity determinant for hsdM and hsdR
RA	4,571,233	G→A	100%	S16F (TCT→TTT)	hsdS ←	specificity determinant for hsdM and hsdR
RA	4,572,227	G→T	9.8%	I213I (ATC→ATA)	hsdM ←	DNA methyltransferase M
RA	4,572,520	A→T	86.0%	Y116N (TAC→AAC)	hsdM ←	DNA methyltransferase M
RA	4,575,173	A→T	6.3%	pseudogene (1460/3567 nt)	hsdR ←	pseudogene, premature stop codon, host restriction; endonuclease R
RA	4,577,193	G→T	7.3%	R143L (CGG→CTG)	mrr →	methylated adenine and cytosine restriction protein
RA	4,584,255	A→C	83.0%	L95L (CTT→CTG)	yjjL ←	L‑galactonate transporter
RA	4,584,381	G→T	100%	I53I (ATC→ATA)	yjjL ←	L‑galactonate transporter
RA	4,584,756	A→T	100%	*305K (TAA→AAA)	yjjM ←	yjjMN operon transcriptional activator
RA	4,584,775	C→A	74.1%	E298D (GAG→GAT)	yjjM ←	yjjMN operon transcriptional activator
RA	4,585,338	A→T	100%	S111T (TCT→ACT)	yjjM ←	yjjMN operon transcriptional activator
RA	4,586,074	G→T	5.1%	V90F (GTT→TTT)	yjjN →	L‑galactonate oxidoreductase
RA	4,586,861	G→T	11.6%	intergenic (+32/+106)	yjjN → / ← opgB	L‑galactonate oxidoreductase/phosphoglycerol transferases I and II
RA	4,586,896	C→A	7.9%	intergenic (+67/+71)	yjjN → / ← opgB	L‑galactonate oxidoreductase/phosphoglycerol transferases I and II
RA	4,588,180	G→T	85.9%	S360* (TCA→TAA)	opgB ←	phosphoglycerol transferases I and II
RA	4,589,130	G→T	88.1%	I43I (ATC→ATA)	opgB ←	phosphoglycerol transferases I and II
RA	4,591,139	C→A	100%	D66Y (GAT→TAT)	dnaT ←	DNA biosynthesis protein (primosomal protein I)
RA	4,596,243	T→A	100%	intergenic (‑25/+243)	leuQ ← / ← rsmC	tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase, SAM‑dependent
RA	4,600,972	G→T	87.2%	intergenic (+152/‑241)	prfC → / → osmY	peptide chain release factor RF‑3/periplasmic protein
RA	4,609,484	G→T	30.6%	R22L (CGC→CTC)	deoB →	phosphopentomutase
RA	4,615,947	G→T	88.4%	E73D (GAG→GAT)	radA →	DNA repair protein
RA	4,617,330	G→T	23.6%	G67C (GGT→TGT)	nadR →	trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor
RA	4,617,341	C→A	87.5%	F70L (TTC→TTA)	nadR →	trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor
RA	4,622,401	G→T	14.0%	V618L (GTG→TTG)	slt →	lytic murein transglycosylase, soluble
RA	4,625,288	T→C	100%	intergenic (‑161/‑50)	rob ← / → creA	right oriC‑binding transcriptional activator, AraC family/putative periplasmic protein
RA	4,630,770	G→T	27.1%	T4T (ACG→ACT)	yjtD →	putative methyltransferase

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	CP009273	373837	375130	1294	193 [190]	[190] 194	frmA–[frmR]	frmA,[frmR]
*	*	÷	CP009273	1191688	1206962	15275	193 [187]	[191] 193	[icd]–[icdC]	[icd],ymfD,ymfE,lit,intE,xisE,ymfI,ymfJ,cohE,croE,ymfL,ymfM,oweE,aaaE,ymfR,beeE,jayE,ymfQ,stfP,tfaP,tfaE,stfE,pinE,mcrA,[icdC]
*	*	÷	CP009273	4100617	4101516	900	193 [191]	[191] 194	tpiA	tpiA

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	360104 =	191 (0.690)	151 (0.540)	78/276	NT	44.2%	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)	3219 (12.260) +TTAATTAA	193/260	NT	93.2%	intergenic (‑212/+383)	lacZ/lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
	?	CP009273	= 361823	251 (0.900)					coding (831/834 nt)	mhpR	mhp operon transcriptional activator
*	?	CP009273	360652 =	335 (1.200)	3038 (16.410) +46 bp	183/184	NT	93.6%	intergenic (‑586/+9)	lacZ/lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
	?	CP009273	= 1317577	287 (1.030)					coding (101/882 nt)	yciV	PHP domain protein
*	?	CP009273	376716 =	NA (NA)	266 (0.950)	143/276	NT	99.3%	intergenic (‑1/‑91)	yaiX/insC1	pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase/IS2 repressor TnpA
	?	CP009273	566411 =	2 (0.010)					coding (63/552 nt)	ybcL	inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
*	?	CP009273	= 378046	NA (NA)	257 (0.920)	137/276	NT	99.2%	intergenic (+11/+1)	insD1/yaiX	IS2 transposase TnpB/pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase
	?	CP009273	= 566415	2 (0.010)					coding (67/552 nt)	ybcL	inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
*	?	CP009273	777033 =	219 (0.790)	68 (0.250) +G	7/274	NT	25.0%	noncoding (1/76 nt)	lysQ	tRNA‑Lys
	?	CP009273	= 2514488	191 (0.690)					noncoding (216/1345 nt)	IS186	repeat region
*	?	CP009273	1486399 =	286 (1.030)	27 (0.100)	18/276	NT	9.2%	noncoding (24/56 nt)	sokB	sRNA antisense regulator blocking mokB, and hence hokB, translation
	?	CP009273	3713993 =	246 (0.880)					intergenic (‑1/‑47)	mokA/insJ	pseudogene, overlapping regulatory peptide, enables hokB; completely contained in another CDS/IS150 transposase A
*	?	CP009273	= 1486401	285 (1.020)	25 (0.090)	18/270	NT	8.3%	noncoding (26/56 nt)	sokB	sRNA antisense regulator blocking mokB, and hence hokB, translation
	?	CP009273	= 3715435	277 (1.020)					intergenic (+26/‑1)	insK/sokA	IS150 transposase B/pseudogene, sRNA antisense regulator blocking mokA/hokA translation
*	?	CP009273	1635219 =	3 (0.010)	293 (1.070)	145/272	NT	99.0%	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	2 (0.010)	287 (1.030)	143/276	NT	99.3%	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	= 3180783	NA (NA)	296 (1.080)	148/272	NT	94.3%	pseudogene (4/2445 nt)	yqiG	pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein
	?	CP009273	= 3833569	18 (0.060)					intergenic (‑216/‑6)	nlpA/yicS	cytoplasmic membrane lipoprotein‑28/putative periplasmic protein
*	?	CP009273	3744959 =	269 (0.970)	192 (0.690)	106/276	NT	40.6%	coding (270/741 nt)	yiaT	putative outer membrane protein
	?	CP009273	= 3752673	292 (1.050)					coding (549/1845 nt)	selB	selenocysteinyl‑tRNA‑specific translation factor
*	?	CP009273	3833562 =	10 (0.040)	270 (0.980)	135/274	NT	96.5%	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