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

Predicted mutations
evidence	position	mutation	annotation	gene	description
RA	4,701	T→A	L323Q (CTG→CAG)	thrC →	L‑threonine synthase
RA	5,144	G→A	intergenic (+124/‑90)	thrC → / → yaaX	L‑threonine synthase/DUF2502 family putative periplasmic protein
RA	7,522	G→T	F146L (TTC→TTA)	yaaJ ←	putative transporter
RA	10,444	G→T	F17L (TTC→TTA)	satP ←	succinate‑acetate transporter
RA	12,901	G→A	D247N (GAT→AAT)	dnaK →	chaperone Hsp70, with co‑chaperone DnaJ
RA	13,962	A→C	E600D (GAA→GAC)	dnaK →	chaperone Hsp70, with co‑chaperone DnaJ
RA	24,783	T→A	L798Q (CTG→CAG)	ileS →	isoleucyl‑tRNA synthetase
RA	25,546	G→T	D114Y (GAC→TAC)	lspA →	prolipoprotein signal peptidase (signal peptidase II)
RA	27,307	C→T	I5I (ATC→ATT)	rihC →	ribonucleoside hydrolase 3
RA	29,139	G→T	G256C (GGT→TGT)	dapB →	dihydrodipicolinate reductase
RA	31,710	C→A	I298I (ATC→ATA)	carB →	carbamoyl‑phosphate synthase large subunit
RA	32,659	C→A	R615S (CGC→AGC)	carB →	carbamoyl‑phosphate synthase large subunit
RA	32,802	C→A	I662I (ATC→ATA)	carB →	carbamoyl‑phosphate synthase large subunit
RA	34,225	A→G	intergenic (+187/‑75)	carB → / → caiF	carbamoyl‑phosphate synthase large subunit/cai operon transcriptional activator
RA	40,957	C→A	V325V (GTG→GTT)	caiT ←	putative transporter
RA	42,150	G→A	intergenic (‑219/‑253)	caiT ← / → fixA	putative transporter/anaerobic carnitine reduction putative electron transfer flavoprotein subunit
RA	48,263	G→T	M165I (ATG→ATT)	kefC →	potassium:proton antiporter
RA	49,840	G→T	A6A (GCG→GCT)	folA →	dihydrofolate reductase
RA	54,392	G→T	A104E (GCG→GAG)	surA ←	peptidyl‑prolyl cis‑trans isomerase (PPIase)
RA	54,429	A→C	S92A (TCC→GCC)	surA ←	peptidyl‑prolyl cis‑trans isomerase (PPIase)
RA	55,590	G→T	T507K (ACG→AAG)	lptD ←	LPS assembly OM complex LptDE, beta‑barrel component
RA	56,677	G→T	R145S (CGC→AGC)	lptD ←	LPS assembly OM complex LptDE, beta‑barrel component
RA	61,967	A→C	L433R (CTG→CGG)	rapA ←	RNA polymerase remodeling/recycling factor ATPase; RNA polymerase‑associated, ATP‑dependent RNA translocase
RA	68,546	C→A	R237S (CGC→AGC)	yabI →	DedA family inner membrane protein
RA	76,821	G→T	G177G (GGC→GGA)	leuC ←	3‑isopropylmalate dehydratase large subunit
RA	77,710	A→T	S246T (TCC→ACC)	leuB ←	3‑isopropylmalate dehydrogenase, NAD(+)‑dependent
RA	78,007	C→A	G147C (GGT→TGT)	leuB ←	3‑isopropylmalate dehydrogenase, NAD(+)‑dependent
RA	80,123	C→T	G25S (GGC→AGC)	leuL ←	leu operon leader peptide
RA	81,562	C→A	I236I (ATC→ATA)	leuO →	global transcription factor
RA	82,037	C→T	intergenic (+238/‑80)	leuO → / → ilvI	global transcription factor/acetolactate synthase 3 large subunit
RA	93,391	G→T	T301T (ACG→ACT)	mraY →	phospho‑N‑acetylmuramoyl‑pentapeptide transferase
RA	94,963	C→A	A25E (GCG→GAG)	ftsW →	lipid II flippase; integral membrane protein involved in stabilizing FstZ ring during cell division
RA	97,521	C→A	A90A (GCC→GCA)	murC →	UDP‑N‑acetylmuramate:L‑alanine ligase
RA	102,736	C→A	I315I (ATC→ATA)	ftsZ →	GTP‑binding tubulin‑like cell division protein
RA	102,769	G→T	V326V (GTG→GTT)	ftsZ →	GTP‑binding tubulin‑like cell division protein
RA	103,467	G→T	D142Y (GAT→TAT)	lpxC →	UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase
RA	104,561	G→T	A124S (GCG→TCG)	secM →	regulator of secA translation
RA	108,039	C→A	intergenic (+119/+97)	mutT → / ← yacG	nucleoside triphosphate pyrophosphohydrolase, marked preference for dGTP/DNA gyrase inhibitor
RA	108,651	Δ1 bp	coding (436/744 nt)	zapD ←	FtsZ stabilizer
RA	118,548	G→A	intergenic (‑510/‑31)	aroP ← / → pdhR	aromatic amino acid transporter/pyruvate dehydrogenase complex repressor; autorepressor
RA	118,873	G→T	D99Y (GAC→TAC)	pdhR →	pyruvate dehydrogenase complex repressor; autorepressor
RA	119,536	G→T	P11P (CCG→CCT)	aceE →	pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding
RA	133,890	A→T	V107V (GTA→GTT)	cueO →	multicopper oxidase (laccase)
RA	134,028	G→T	A153A (GCG→GCT)	cueO →	multicopper oxidase (laccase)
RA	134,297	C→A	S243* (TCG→TAG)	cueO →	multicopper oxidase (laccase)
RA	135,254	G→A	intergenic (+134/+68)	cueO → / ← gcd	multicopper oxidase (laccase)/glucose dehydrogenase
RA	137,071	G→T	I214I (ATC→ATA)	gcd ←	glucose dehydrogenase
RA	137,915	G→T	intergenic (‑203/‑3)	gcd ← / → hpt	glucose dehydrogenase/hypoxanthine phosphoribosyltransferase
RA	142,460	T→A	F298Y (TTC→TAC)	yadE →	putative polysaccharide deacetylase lipoprotein
RA	145,894	G→T	I65I (ATC→ATA)	panB ←	3‑methyl‑2‑oxobutanoate hydroxymethyltransferase
RA	147,501	A→T	Y196N (TAC→AAC)	yadK ←	putative fimbrial‑like adhesin protein
RA	150,452	C→A	E488* (GAA→TAA)	htrE ←	putative outer membrane usher protein
RA	153,472	G→T	intergenic (‑102/+268)	yadN ← / ← folK	putative fimbrial‑like adhesin protein/2‑amino‑4‑hydroxy‑6‑hydroxymethyldihyropteridine pyrophosphokinase
RA	158,287	C→A	D78Y (GAC→TAC)	ligT ←	2'‑5' RNA ligase
RA	159,666	G→T	G359C (GGT→TGT)	hrpB →	putative ATP‑dependent helicase
RA	166,662	C→A	S133* (TCG→TAG)	fhuC →	iron‑hydroxamate transporter subunit
RA	167,932	G→T	A291S (GCC→TCC)	fhuD →	iron‑hydroxamate transporter subunit
RA	173,725	G→T	G129G (GGC→GGA)	yadS ←	UPF0126 family inner membrane protein
RA	176,783	G→T	D354Y (GAT→TAT)	dgt →	deoxyguanosine triphosphate triphosphohydrolase
RA	185,393	A→T	F201I (TTC→ATC)	map ←	methionine aminopeptidase
RA	186,159	A→G	intergenic (‑166/‑40)	map ← / → tff	methionine aminopeptidase/novel sRNA, function unknown
RA	193,157	T→C	I42T (ATA→ACA)	rseP →	inner membrane zinc RIP metalloprotease; RpoE activator, by degrading RseA; cleaved signal peptide endoprotease
RA	196,832	C→A	I806I (ATC→ATA)	bamA →	BamABCDE complex OM biogenesis outer membrane pore‑forming assembly factor
RA	199,229	G→T	E61D (GAG→GAT)	lpxA →	UDP‑N‑acetylglucosamine acetyltransferase
RA	201,962	A→T	D117V (GAT→GTT)	dnaE →	DNA polymerase III alpha subunit
RA	208,013	G→T	M616I (ATG→ATT)	ldcC →	lysine decarboxylase 2, constitutive
RA	214,084	G→T	G393G (GGC→GGA)	proS ←	prolyl‑tRNA synthetase
RA	216,136	G→T	P116Q (CCA→CAA)	rcsF ←	putative outer membrane protein
RA	217,887	C→T	W74* (TGG→TGA)	metI ←	DL‑methionine transporter subunit
RA	217,932	A→C	I59M (ATT→ATG)	metI ←	DL‑methionine transporter subunit
RA	223,096	C→A	noncoding (851/2904 nt)	rrlH →	23S ribosomal RNA of rrnH operon
RA	229,915	C→A	M176I (ATG→ATT)	mltD ←	putative membrane‑bound lytic murein transglycosylase D
RA	230,579	C→T	E231K (GAA→AAA)	gloB ←	hydroxyacylglutathione hydrolase
RA	231,378	C→A	R26S (CGC→AGC)	yafS →	putative S‑adenosyl‑L‑methionine‑dependent methyltransferase
RA	232,860	G→T	D103Y (GAT→TAT)	dnaQ →	DNA polymerase III epsilon subunit
RA	236,234	A→T	V148E (GTG→GAG)	yafV ←	putative NAD(P)‑binding C‑N hydrolase family amidase
RA	238,195	G→T	V532V (GTC→GTA)	fadE ←	acyl coenzyme A dehydrogenase
RA	238,303	A→T	V496V (GTT→GTA)	fadE ←	acyl coenzyme A dehydrogenase
RA	239,583	C→A	A70S (GCG→TCG)	fadE ←	acyl coenzyme A dehydrogenase
RA	245,020	G→T	pseudogene (1538/1713 nt)	lfhA ←	pseudogene, flagellar system protein, promoterless fragment; flagellar biosynthesis
RA	245,058	G→T	pseudogene (1500/1713 nt)	lfhA ←	pseudogene, flagellar system protein, promoterless fragment; flagellar biosynthesis
RA	248,447	C→T	intergenic (+7/‑45)	dinB → / → yafN	DNA polymerase IV/antitoxin of the YafO‑YafN toxin‑antitoxin system
RA	248,486	C→A	intergenic (+46/‑6)	dinB → / → yafN	DNA polymerase IV/antitoxin of the YafO‑YafN toxin‑antitoxin system
RA	248,529	C→T	T13I (ACT→ATT)	yafN →	antitoxin of the YafO‑YafN toxin‑antitoxin system
RA	250,909	A→T	L432Q (CTG→CAG)	pepD ←	aminoacyl‑histidine dipeptidase (peptidase D)
RA	253,855	G→T	R281L (CGT→CTT)	frsA →	fermentation‑respiration switch protein; PTS Enzyme IIA(Glc)‑binding protein; pNP‑butyrate esterase activity
RA	255,487	A→T	S109T (TCT→ACT)	phoE ←	outer membrane phosphoporin protein E
RA	255,899	G→A	intergenic (‑88/‑200)	phoE ← / → proB	outer membrane phosphoporin protein E/gamma‑glutamate kinase
RA	257,734	A→T	Q174L (CAG→CTG)	proA →	gamma‑glutamylphosphate reductase
RA	259,494	G→T	C75* (TGC→TGA)	yafW ←	CP4‑6 prophage; antitoxin of the YkfI‑YafW toxin‑antitoxin system
RA	262,114	C→A	D51Y (GAT→TAT)	yafY ←	lipoprotein, inner membrane; overproduction stimulates degP expression; CP4‑6 prophage
RA	274,735	A→T	pseudogene (138/348 nt)	afuB ←	pseudogene, CP4‑6 prophage; ABC transporter permease family;Phage or Prophage Related
RA	279,098	G→T	E63* (GAG→TAG)	yagF →	CP4‑6 prophage; dehydratase family protein
RA	279,334	C→A	I141I (ATC→ATA)	yagF →	CP4‑6 prophage; dehydratase family protein
RA	279,800	G→T	E297* (GAA→TAA)	yagF →	CP4‑6 prophage; dehydratase family protein
RA	285,966	A→T	P17P (CCT→CCA)	argF ←	ornithine carbamoyltransferase 2, chain F; CP4‑6 prophage
RA	288,249	T→A	T137T (ACA→ACT)	yagK ←	CP4‑6 prophage; conserved protein
RA	290,012	C→T	D167N (GAT→AAT)	yagM ←	CP4‑6 prophage; uncharacterized protein
RA	291,348	G→A	intergenic (‑58/+59)	yagN ← / ← intF	CP4‑6 prophage; uncharacterized protein/CP4‑6 prophage; putative phage integrase
RA	294,795	C→A	L617L (CTG→CTT)	paoC ←	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
RA	294,929	C→A	E573* (GAA→TAA)	paoC ←	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
RA	300,770	C→A	V49V (GTG→GTT)	ecpE ←	ECP production pilus chaperone
RA	302,428	G→T	P34Q (CCG→CAG)	ecpD ←	polymerized tip adhesin of ECP fibers
RA	307,479	G→A	intergenic (‑432/‑344)	ecpR ← / → ykgL	putative transcriptional regulator for the ecp operon/uncharacterized protein
RA	312,532	G→A	pseudogene (349/684 nt)	ykgA ←	pseudogene, AraC family;putative regulator; Not classified; putative ARAC‑type regulatory protein
RA	314,566	C→A	D383Y (GAT→TAT)	rclA ←	reactive chlorine stress species (RCS) resistance protein; pyridine nucleotide‑dependent disulfide oxidoreductase family
RA	317,203	G→A	intergenic (+411/‑116)	rclR → / → ykgE	reactive chlorine species (RCS)‑specific activator of the rcl genes/cysteine‑rich LutA family protein; putative electron transport chain YkgEFG component
RA	317,205	2 bp→AA	intergenic (+413/‑113)	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	R326S (CGC→AGC)	ykgF →	ferridoxin‑like LutB family protein; putative electron transport chain YkgEFG component
RA	319,381	G→T	D445Y (GAC→TAC)	ykgF →	ferridoxin‑like LutB family protein; putative electron transport chain YkgEFG component
RA	320,920	G→A	S52S (AGC→AGT)	ykgH ←	putative inner membrane protein
RA	321,223	C→A	intergenic (‑148/+65)	ykgH ← / ← betA	putative inner membrane protein/choline dehydrogenase, a flavoprotein
RA	327,051	A→T	E626D (GAA→GAT)	betT →	choline transporter of high affinity
RA	329,372	A→T	L258Q (CTG→CAG)	yahB ←	putative DNA‑bindng transcriptional regulator
RA	332,599	G→T	A37A (GCG→GCT)	yahF →	putative NAD(P)‑binding succinyl‑CoA synthase
RA	335,247	C→A	N404K (AAC→AAA)	yahG →	DUF1116 family protein
RA	337,720	G→T	E295D (GAG→GAT)	yahJ →	putative metallo‑dependent hydrolase domain deaminase
RA	339,348	G→T	D252Y (GAC→TAC)	yahK →	aldehyde reductase, NADPH‑dependent, Zn‑containing, broad specificity
RA	344,800	G→T	E136D (GAG→GAT)	prpB →	2‑methylisocitrate lyase
RA	350,062	T→A	L549Q (CTG→CAG)	prpE →	propionate‑‑CoA ligase
RA	350,559	G→T	intergenic (+256/‑74)	prpE → / → codB	propionate‑‑CoA ligase/cytosine transporter
RA	360,752	A→G	V331A (GTG→GCG)	lacI ←	DNA‑binding transcriptional repressor
RA	361,806	G→A	intergenic (‑63/+14)	lacI ← / ← mhpR	DNA‑binding transcriptional repressor/mhp operon transcriptional activator
RA	362,159	G→T	I165I (ATC→ATA)	mhpR ←	mhp operon transcriptional activator
RA	362,629	A→T	Y9N (TAC→AAC)	mhpR ←	mhp operon transcriptional activator
RA	364,561	G→T	D18Y (GAC→TAC)	mhpB →	2,3‑dihydroxyphenylpropionate 1,2‑dioxygenase
RA	372,091	C→A	R393R (CGG→AGG)	mhpT →	3‑hydroxyphenylpropionic transporter
RA	372,581	G→T	A118A (GCG→GCT)	yaiL →	DUF2058 family protein
RA	375,478	(G)10→11	intergenic (‑141/+47)	frmR ← / ← yaiO	regulator protein that represses frmRAB operon/outer membrane protein
RA	378,179	A→T	pseudogene (150/282 nt)	yaiX ←	pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase
RA	385,815	G→T	pseudogene (109/1458 nt)	yaiT →	pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein
RA	390,551	T→G	L197R (CTG→CGG)	yaiV →	putative transcriptional regulator
RA	396,883	A→G	Q14Q (CAA→CAG)	iraP →	anti‑RssB factor, RpoS stabilzer during Pi starvation; anti‑adapter protein
RA	397,959	G→A	A253T (GCG→ACG)	phoA →	bacterial alkaline phosphatase
RA	400,594	G→T	V169V (GTC→GTA)	proC ←	pyrroline‑5‑carboxylate reductase, NAD(P)‑binding
RA	402,340	G→T	V160V (GTG→GTT)	aroL →	shikimate kinase II
RA	404,712	A→T	F255Y (TTC→TAC)	rdgC ←	nucleoid‑associated ssDNA and dsDNA binding protein; competitive inhibitor of RecA function
RA	406,075	C→A	P159Q (CCG→CAG)	mak →	manno(fructo)kinase
RA	411,027	G→T	L61L (CTC→CTA)	sbcC ←	exonuclease, dsDNA, ATP‑dependent
RA	411,556	C→A	D285Y (GAT→TAT)	sbcD ←	exonuclease, dsDNA, ATP‑dependent
RA	415,049	G→T	M1M (ATG→ATT) †	brnQ →	branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val
RA	421,799	C→A	I69I (ATC→ATA)	tgt →	tRNA‑guanine transglycosylase
RA	425,143	G→T	T61T (ACG→ACT)	secF →	SecYEG protein translocase auxillary subunit
RA	426,157	G→T	E33* (GAG→TAG)	yajD →	HNH nuclease family protein
RA	427,575	A→G	intergenic (‑106/+193)	tsx ← / ← yajI	nucleoside channel, receptor of phage T6 and colicin K/putative lipoprotein
RA	430,523	G→A	A141T (GCA→ACA)	ribE →	riboflavin synthase beta chain
RA	432,762	G→T	P277Q (CCG→CAG)	yajO ←	2‑carboxybenzaldehyde reductase
RA	433,551	G→T	S14Y (TCC→TAC)	yajO ←	2‑carboxybenzaldehyde reductase
RA	434,663	A→C	I324S (ATC→AGC)	dxs ←	1‑deoxyxylulose‑5‑phosphate synthase, thiamine triphosphate‑binding, FAD‑requiring
RA	435,336	G→T	Q100K (CAG→AAG)	dxs ←	1‑deoxyxylulose‑5‑phosphate synthase, thiamine triphosphate‑binding, FAD‑requiring
RA	435,862	A→T	T232T (ACT→ACA)	ispA ←	geranyltranstransferase
RA	437,672	T→A	V223E (GTG→GAG)	thiI →	tRNA s(4)U8 sulfurtransferase
RA	444,489	G→A	R537C (CGT→TGT)	cyoB ←	cytochrome o ubiquinol oxidase subunit I
RA	446,369	T→G	Q233P (CAG→CCG)	cyoA ←	cytochrome o ubiquinol oxidase subunit II
RA	450,290	G→A	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	450,766	G→T	A60S (GCG→TCG)	tig →	peptidyl‑prolyl cis/trans isomerase (trigger factor)
RA	453,868	G→T	P329P (CCG→CCT)	clpX →	ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease
RA	456,298	T→A	L652Q (CTG→CAG)	lon →	DNA‑binding ATP‑dependent protease La
RA	456,588	G→T	D749Y (GAC→TAC)	lon →	DNA‑binding ATP‑dependent protease La
RA	459,325	T→A	intergenic (+83/‑68)	ppiD → / → ybaV	periplasmic folding chaperone, has an inactive PPIase domain/putative competence‑suppressing periplasmic helix‑hairpin‑helix DNA‑binding protein
RA	461,499	G→T	R424S (CGC→AGC)	ybaE ←	putative ABC superfamily transporter periplasmic‑binding protein
RA	463,179	C→A	I104I (ATC→ATA)	cof →	thiamine pyrimidine pyrophosphate hydrolase; HMP‑PP phosphatase
RA	469,232	G→T	E271* (GAA→TAA)	amtB →	ammonium transporter
RA	469,775	C→A	V281V (GTG→GTT)	tesB ←	acyl‑CoA thioesterase 2
RA	474,138	G→T	intergenic (‑65/+99)	ylaB ← / ← ylaC	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase/DUF1449 family inner membrane protein
RA	475,805	C→A	A120A (GCG→GCT)	tomB ←	Hha toxicity attenuator; conjugation‑related protein
RA	477,267	G→T	Q865K (CAG→AAG)	acrB ←	multidrug efflux system protein
RA	479,244	C→A	A206S (GCC→TCC)	acrB ←	multidrug efflux system protein
RA	480,820	C→T	D86N (GAC→AAC)	acrA ←	multidrug efflux system
RA	481,667	G→A	A151T (GCG→ACG)	acrR →	transcriptional repressor
RA	482,757	G→T	A256S (GCG→TCG)	mscK →	mechanosensitive channel protein, intermediate conductance, K+ regulated
RA	486,494	C→A	R53S (CGC→AGC)	ybaN →	DUF454 family inner membrane protein
RA	490,022	C→A	I54I (ATC→ATA)	recR →	gap repair protein
RA	490,089	C→A	R77S (CGT→AGT)	recR →	gap repair protein
RA	495,020	T→A	E137V (GAA→GTA)	aes ←	acetyl esterase
RA	496,210	G→T	M210I (ATG→ATT)	gsk →	inosine/guanosine kinase
RA	503,944	G→T	E91* (GAA→TAA)	ybaQ →	putative DNA‑binding transcriptional regulator
RA	509,737	G→A	E97K (GAG→AAG)	cueR →	copper‑responsive regulon transcriptional regulator
RA	517,392	G→T	A507A (GCG→GCT)	ybbP →	putative ABC transporter permease
RA	517,551	G→T	P560P (CCG→CCT)	ybbP →	putative ABC transporter permease
RA	518,243	G→T	R791L (CGA→CTA)	ybbP →	putative ABC transporter permease
RA	518,820	C→A	A35E (GCG→GAG)	rhsD →	Rhs family putative polymorphic toxin
RA	524,341	(T)7→8	pseudogene (246/491 nt)	ybbD →	pseudogene
RA	524,496	T→G	pseudogene (401/491 nt)	ybbD →	pseudogene
RA	525,079	A→T	pseudogene (38/66 nt)	ylbG ←	pseudogene, DNA‑binding transcriptional regulator homology
RA	525,268	C→A	pseudogene (205/357 nt)	ylbG ←	pseudogene, DNA‑binding transcriptional regulator homology
RA	530,466	C→A	F365L (TTC→TTA)	gcl →	glyoxylate carboligase
RA	535,073	C→A	I157I (ATC→ATA)	allB →	allantoinase
RA	542,200	Δ1 bp	coding (65/1668 nt)	fdrA →	putative NAD(P)‑binding acyl‑CoA synthetase
RA	542,948	T→A	I271I (ATT→ATA)	fdrA →	putative NAD(P)‑binding acyl‑CoA synthetase
RA	546,491	G→T	V199V (GTG→GTT)	ybcF →	putative carbonate kinase
RA	549,397	G→T	intergenic (‑1/+2)	lpxH ← / ← ppiB	UDP‑2,3‑diacylglucosamine pyrophosphohydrolase/peptidyl‑prolyl cis‑trans isomerase B (rotamase B)
RA	551,499	G→T	R171S (CGC→AGC)	ybcI ←	DUF457 family inner membrane protein
RA	554,868	G→T	E147* (GAA→TAA)	sfmC →	putative periplasmic pilus chaperone
RA	555,927	G→T	D259Y (GAT→TAT)	sfmD →	putative outer membrane export usher protein
RA	557,592	G→T	D814Y (GAC→TAC)	sfmD →	putative outer membrane export usher protein
RA	559,245	G→T	G154C (GGT→TGT)	sfmF →	FimA homolog
RA	571,730	G→T	pseudogene (552/1040 nt)	nmpC ←	DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage
RA	576,998	G→T	pseudogene (189/309 nt)	aaaD →	pseudogene; DLP12 prophage; tail fiber assembly protein family;Phage or Prophage Related
RA	579,692	G→A	D186N (GAT→AAT)	appY →	global transcriptional activator; DLP12 prophage
RA	580,366	G→T	R242S (CGC→AGC)	ompT ←	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
RA	581,203	A→T	intergenic (‑114/‑310)	ompT ← / → pauD	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)/tRNA‑OTHER
RA	582,322	C→A	E15* (GAA→TAA)	envY ←	porin thermoregulatory transcriptional activator
RA	583,341	T→G	S33R (AGT→CGT)	ybcH ←	PRK09936 family protein
RA	591,864	C→A	A270E (GCG→GAG)	cusC →	copper/silver efflux system, outer membrane component
RA	601,847	A→T	I331I (ATT→ATA)	ybdK ←	weak gamma‑glutamyl:cysteine ligase
RA	607,931	G→A	S7F (TCC→TTC)	fepA ←	iron‑enterobactin outer membrane transporter
RA	608,104	G→T	intergenic (‑154/‑89)	fepA ← / → fes	iron‑enterobactin outer membrane transporter/enterobactin/ferric enterobactin esterase
RA	608,575	T→A	L128Q (CTG→CAG)	fes →	enterobactin/ferric enterobactin esterase
RA	614,726	G→T	A339A (GCG→GCT)	fepE →	regulator of length of O‑antigen component of lipopolysaccharide chains
RA	619,048	C→A	A307S (GCC→TCC)	fepB ←	iron‑enterobactin transporter subunit
RA	624,669	G→T	T221T (ACG→ACT)	entA →	2,3‑dihydro‑2,3‑dihydroxybenzoate dehydrogenase
RA	625,174	G→T	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	G5G (GGG→GGT)	cstA →	carbon starvation protein involved in peptide utilization; APC peptide transporter family protein
RA	627,428	C→A	I693I (ATC→ATA)	cstA →	carbon starvation protein involved in peptide utilization; APC peptide transporter family protein
RA	631,020	G→T	Q336K (CAG→AAG)	ybdN ←	PAPS reductase‑like domain protein
RA	634,078	T→A	intergenic (‑49/‑323)	dsbG ← / → ahpC	thiol:disulfide interchange protein, periplasmic/alkyl hydroperoxide reductase, C22 subunit
RA	639,231	G→A	L65F (CTT→TTT)	rnk ←	regulator of nucleoside diphosphate kinase
RA	647,234	C→T	E27K (GAA→AAA)	citC ←	[citrate [pro‑3S]‑lyase] ligase
RA	647,422	G→T	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	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	F122L (TTC→TTA)	citA →	sensory histidine kinase in two‑component regulatory system with CitB
RA	652,574	G→T	intergenic (+1/‑174)	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	652,597	C→T	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	652,866	Δ1 bp	coding (119/210 nt)	cspE →	constitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein
RA	656,992	T→A	intergenic (‑158/+101)	ybeF ← / ← lipB	LysR family putative transcriptional regulator/octanoyltransferase; octanoyl‑[ACP]:protein N‑octanoyltransferase
RA	659,689	G→T	R320S (CGC→AGC)	rlpA ←	septal ring protein, suppressor of prc, minor lipoprotein
RA	662,108	A→T	V522V (GTT→GTA)	mrdA ←	transpeptidase involved in peptidoglycan synthesis (penicillin‑binding protein 2)
RA	662,631	C→A	R348L (CGC→CTC)	mrdA ←	transpeptidase involved in peptidoglycan synthesis (penicillin‑binding protein 2)
RA	667,348	G→T	Q99K (CAG→AAG)	lptE ←	LPS assembly OM complex LptDE, lipoprotein component
RA	667,899	C→A	D781Y (GAT→TAT)	leuS ←	leucyl‑tRNA synthetase
RA	672,142	T→A	intergenic (‑139/‑25)	ybeQ ← / → ybeR	Sel1 family TPR‑like repeat protein/uncharacterized protein
RA	680,846	G→T	F180L (TTC→TTA)	gltK ←	glutamate, aspartate ABC transporter permease subunit
RA	693,739	G→T	H299N (CAC→AAC)	asnB ←	asparagine synthetase B
RA	699,167	(T)6→7	intergenic (‑100/‑233)	nagB ← / → nagE	glucosamine‑6‑phosphate deaminase/fused N‑acetyl glucosamine specific PTS enzyme: IIC, IIB, and IIA components
RA	705,588	C→A	intergenic (+16/+68)	chiQ → / ← fur	chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor
RA	706,097	A→C	T2T (ACT→ACG)  *29G (TGA→GGA)	fur ← uof ←	ferric iron uptake regulon transcriptional repressor; autorepressor ryhB‑regulated fur leader peptide
RA	710,187	A→T	S392C (AGT→TGT)	pgm →	phosphoglucomutase
RA	715,686	A→T	R77R (CGT→CGA)	speF ←	ornithine decarboxylase isozyme, inducible
RA	715,924	C→T	intergenic (‑8/‑115)	speF ← / → ybfK	ornithine decarboxylase isozyme, inducible/uncharacterized protein
RA	720,816	G→T	I559I (ATC→ATA)	kdpB ←	potassium translocating ATPase, subunit B
RA	723,859	G→T	V110V (GTC→GTA)	kdpA ←	potassium translocating ATPase, subunit A
RA	724,813	A→T	intergenic (+17/‑226)	ybfA → / → rhsC	DUF2517 family protein/Rhs family putative polymorphic toxin
RA	726,087	G→T	R350L (CGT→CTT)	rhsC →	Rhs family putative polymorphic toxin
RA	729,456	G→A	R75R (AGG→AGA)	ybfB →	putative membrane protein
RA	730,891	G→T	pseudogene (1303/1521 nt)	rhsO →	pseudogene, Rhs family protein
RA	732,494	G→T	pseudogene (214/1137 nt)	ybfL →	pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein
RA	732,655	G→T	pseudogene (375/1137 nt)	ybfL →	pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein
RA	737,635	G→T	G126G (GGC→GGA)	dtpD ←	dipeptide and tripeptide permease D
RA	743,797	G→T	R214R (CGC→CGA)	ybgO ←	putative fimbrial protein
RA	745,893	G→A	S578L (TCG→TTG)	ybgQ ←	putative outer membrane protein
RA	746,916	A→T	F237Y (TTC→TAC)	ybgQ ←	putative outer membrane protein
RA	747,973	C→A	P93P (CCG→CCT)	ybgD ←	putative fimbrial‑like adhesin protein
RA	748,707	A→T	I406I (ATT→ATA)	gltA ←	citrate synthase
RA	753,549	G→T	Q135H (CAG→CAT)	sdhB →	succinate dehydrogenase, FeS subunit
RA	754,572	G→T	E137D (GAG→GAT)	sucA →	2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding
RA	759,000	C→A	F177L (TTC→TTA)	sucC →	succinyl‑CoA synthetase, beta subunit
RA	767,399	A→T	E162D (GAA→GAT)	cydA →	cytochrome d terminal oxidase, subunit I
RA	769,423	C→T	A309V (GCA→GTA)	cydB →	cytochrome d terminal oxidase, subunit II
RA	784,094	G→T	A67E (GCG→GAG)	galM ←	aldose 1‑epimerase; type‑1 mutarotase
RA	788,902	G→T	R115S (CGT→AGT)	modF ←	fused molybdate transporter subunits of ABC superfamily: ATP‑binding components
RA	797,280	T→A	intergenic (+13/‑63)	ybhH → / → ybhI	putative PrpF family isomerase/putative transporter
RA	800,488	G→T	V510V (GTG→GTT)	ybhJ →	putative hydratase
RA	800,779	G→T	E607D (GAG→GAT)	ybhJ →	putative hydratase
RA	809,212	G→T	M77I (ATG→ATT)	uvrB →	excinulease of nucleotide excision repair, DNA damage recognition component
RA	816,302	G→T	R18S (AGG→AGT)	ybhM →	UPF0005 family inner membrane protein
RA	819,200	G→T	H252N (CAT→AAT)	ybhP ←	endo/exonuclease/phosphatase family protein
RA	820,503	C→A	T354T (ACG→ACT)	ybhR ←	inner membrane putative ABC superfamily transporter permease
RA	828,374	G→T	V11V (GTC→GTA)	ybiA ←	DUF1768 family protein
RA	829,009	G→T	D162Y (GAT→TAT)	dinG →	ATP‑dependent DNA helicase
RA	832,445	G→T	P213P (CCG→CCT)	ybiC →	putative dehydrogenase
RA	837,132	C→T	intergenic (‑145/+120)	fiu ← / ← mcbA	catecholate siderophore receptor Fiu/colanic acid mucoidy stimulation protein
RA	837,716	G→T	intergenic (‑204/‑72)	mcbA ← / → rlmF	colanic acid mucoidy stimulation protein/23S rRNA m(6)A1618 methyltransferase, SAM‑dependent
RA	842,041	C→A	E179* (GAA→TAA)	glnP ←	glutamine transporter subunit
RA	843,299	C→A	W54C (TGG→TGT)	glnH ←	glutamine transporter subunit
RA	850,161	G→T	P353P (CCG→CCT)	ybiR →	putative transporter
RA	861,926	C→A	intergenic (‑106/‑98)	moeA ← / → iaaA	molybdopterin molybdenumtransferase; molybdopterin biosynthesis protein/Isoaspartyl peptidase
RA	868,500	A→T	S22S (TCA→TCT)	yliE →	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	872,975	C→A	E173* (GAA→TAA)	rimO ←	ribosomal protein S12 methylthiotransferase; radical SAM superfamily
RA	875,468	C→A	D157Y (GAC→TAC)	gstB ←	glutathione S‑transferase
RA	876,395	G→T	M71I (ATG→ATT)	dacC →	D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 6a)
RA	876,447	G→A	D89N (GAT→AAT)	dacC →	D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 6a)
RA	879,085	G→T	intergenic (‑241/‑44)	ybjG ← / → mdfA	undecaprenyl pyrophosphate phosphatase/multidrug efflux system protein
RA	882,672	G→T	L42I (CTC→ATC)	ybjJ ←	putative transporter
RA	888,964	C→T	intergenic (+75/‑276)	ybjN → / → potF	negative regulator of motility; multicopy suppressor of coaA(Ts)/putrescine transporter subunit: periplasmic‑binding component of ABC superfamily
RA	892,358	G→T	V257L (GTG→TTG)	potH →	putrescine transporter subunit: membrane component of ABC superfamily
RA	899,388	T→G	intergenic (‑198/+20)	artP ← / ← ybjP	arginine transporter subunit/lipoprotein
RA	907,893	C→A	D460Y (GAT→TAT)	hcp ←	hybrid‑cluster [4Fe‑2S‑2O] protein in anaerobic terminal reductases
RA	925,160	G→T	S420* (TCA→TAA)	cydD ←	fused glutathione, cysteine exporter subunits of ABC superfamily: membrane component/ATP‑binding component
RA	942,724	A→T	N14Y (AAC→TAC)	ycaM →	putative transporter
RA	943,573	G→T	A297S (GCC→TCC)	ycaM →	putative transporter
RA	955,568	A→T	intergenic (+17/‑152)	aroA → / → ycaL	5‑enolpyruvylshikimate‑3‑phosphate synthetase/putative peptidase‑related chaperone
RA	968,415	G→T	S148* (TCG→TAG)	ycbC ←	DUF218 superfamily protein
RA	982,574	C→A	intergenic (‑136/+467)	ompF ← / ← asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
RA	992,767	C→A	D68Y (GAT→TAT)	ssuE ←	NAD(P)H‑dependent FMN reductase
RA	994,328	G→T	G128V (GGA→GTA)	elfD →	putative periplasmic pilin chaperone
RA	997,673	A→T	T137T (ACA→ACT)	elfG →	putative fimbrial‑like adhesin protein
RA	997,965	G→T	D235Y (GAT→TAT)	elfG →	putative fimbrial‑like adhesin protein
RA	1,000,841	G→T	A206A (GCG→GCT)	pyrD →	dihydro‑orotate oxidase, FMN‑linked
RA	1,003,597	G→T	D100Y (GAC→TAC)	rlmL →	fused 23S rRNA m(2)G2445 and m(7)G2069 methyltransferase, SAM‑dependent
RA	1,011,929	T→A	intergenic (‑3/+66)	fabA ← / ← ycbZ	beta‑hydroxydecanoyl thioester dehydrase/putative peptidase
RA	1,024,003	C→A	D59Y (GAT→TAT)	hspQ ←	heat shock protein involved in degradation of mutant DnaA; hemimethylated oriC DNA‑binding protein
RA	1,024,703	G→T	G241G (GGC→GGA)	rlmI ←	23S rRNA m(5)C1962 methyltransferase, SAM‑dependent
RA	1,038,316	G→T	R451S (CGT→AGT)	etk ←	tyrosine‑protein kinase, role in O‑antigen capsule formation
RA	1,048,928	C→A	E903* (GAA→TAA)	torS ←	hybrid sensory histidine kinase in two‑component regulatory system with TorR
RA	1,049,407	G→T	T743K (ACG→AAG)	torS ←	hybrid sensory histidine kinase in two‑component regulatory system with TorR
RA	1,052,229	G→T	L171F (TTG→TTT)	torT →	periplasmic sensory protein associated with the TorRS two‑component regulatory system
RA	1,055,132	G→T	E141* (GAA→TAA)	torA →	trimethylamine N‑oxide (TMAO) reductase I, catalytic subunit
RA	1,057,226	G→T	E839* (GAA→TAA)	torA →	trimethylamine N‑oxide (TMAO) reductase I, catalytic subunit
RA	1,063,702	G→T	D56Y (GAC→TAC)	ymdF →	KGG family protein
RA	1,077,911	A→C	K71N (AAA→AAC)	efeO →	inactive ferrous ion transporter EfeUOB
RA	1,083,443	G→T	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	L404* (TTA→TAA)	pgaB ←	poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine (PGA) N‑deacetylase outer membrane export lipoprotein
RA	1,103,665	G→T	R245S (CGT→AGT)	opgC ←	osmoregulated periplasmic glucan succinylation membrane protein
RA	1,103,899	A→T	S167T (TCT→ACT)	opgC ←	osmoregulated periplasmic glucan succinylation membrane protein
RA	1,104,639	C→A	intergenic (‑242/‑152)	opgC ← / → opgG	osmoregulated periplasmic glucan succinylation membrane protein/osmoregulated periplasmic glucan (OPG) biosynthesis periplasmic protein
RA	1,106,503	C→A	S62* (TCA→TAA)	opgH →	membrane glycosyltransferase; nutrient‑dependent cell size regulator, FtsZ assembly antagonist
RA	1,113,450	A→T	I161I (ATT→ATA)	yceI ←	secreted protein
RA	1,114,329	C→A	L58F (TTG→TTT)	yceJ ←	putative cytochrome b561
RA	1,116,548	T→A	intergenic (‑137/+150)	bssS ← / ← dinI	biofilm regulator/DNA damage‑inducible protein I
RA	1,116,964	A→G	intergenic (‑21/+53)	dinI ← / ← pyrC	DNA damage‑inducible protein I/dihydro‑orotase
RA	1,122,994	C→A	R245S (CGC→AGC)	yceM →	putative oxidoreductase
RA	1,128,764	C→A	I245I (ATC→ATA)	flgE →	flagellar hook protein
RA	1,129,972	G→T	D239Y (GAT→TAT)	flgF →	flagellar component of cell‑proximal portion of basal‑body rod
RA	1,131,521	C→A	Q168K (CAG→AAG)	flgH →	flagellar protein of basal‑body outer‑membrane L ring
RA	1,131,601	C→A	T194T (ACC→ACA)	flgH →	flagellar protein of basal‑body outer‑membrane L ring
RA	1,133,311	T→A	L162Q (CTG→CAG)	flgJ →	flagellar rod assembly protein and murein hydrolase; flagellum‑specific muramidase
RA	1,137,384	G→T	R814S (CGC→AGC)	rne ←	fused ribonucleaseE: endoribonuclease/RNA‑binding protein/RNA degradosome binding protein
RA	1,139,402	C→A	R141L (CGC→CTC)	rne ←	fused ribonucleaseE: endoribonuclease/RNA‑binding protein/RNA degradosome binding protein
RA	1,146,692	A→T	T189T (ACA→ACT)	fabG →	3‑oxoacyl‑[acyl‑carrier‑protein] reductase
RA	1,151,750	G→T	R178L (CGC→CTC)	holB →	DNA polymerase III, delta prime subunit
RA	1,152,278	G→T	E16* (GAA→TAA)	ycfH →	putative DNase
RA	1,153,214	T→C	intergenic (+184/‑111)	ycfH → / → ptsG	putative DNase/fused glucose‑specific PTS enzymes: IIB component/IIC component
RA	1,156,310	G→T	S233* (TCA→TAA)	fhuE ←	ferric‑rhodotorulic acid outer membrane transporter
RA	1,181,504	G→T	D69Y (GAT→TAT)	pepT →	peptidase T
RA	1,191,280	G→T	M234I (ATG→ATT)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,207,417	C→A	G15C (GGT→TGT)	iraM ←	RpoS stabilzer during Mg starvation, anti‑RssB factor
RA	1,211,169	C→A	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	1,214,055	T→A	I424I (ATT→ATA)	ycgG →	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	1,218,601	T→A	K7* (AAG→TAG)	ymgI ←	uncharacterized protein
RA	1,219,533	A→G	intergenic (+170/+202)	ycgI → / ← minE	pseudogene/cell division topological specificity factor
RA	1,220,996	G→T	R181R (CGG→AGG)	minC ←	cell division inhibitor
RA	1,224,292	G→A	D8N (GAT→AAT)	ycgN →	UPF0153 family cysteine cluster protein
RA	1,226,292	T→A	C24S (TGT→AGT)	umuD →	DNA polymerase V, subunit D
RA	1,228,591	G→T	intergenic (‑105/+41)	dsbB ← / ← nhaB	oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I/sodium:proton antiporter
RA	1,241,397	T→A	H479L (CAC→CTC)	treA ←	periplasmic trehalase
RA	1,249,227	G→T	R728S (CGT→AGT)	ycgV ←	putative adhesin
RA	1,255,258	A→T	A334A (GCT→GCA)	dauA ←	C4‑dicarboxylic acid transporter
RA	1,257,232	G→T	R34S (CGC→AGC)	prs ←	phosphoribosylpyrophosphate synthase
RA	1,261,810	G→A	A87A (GCG→GCA)	prmC →	N5‑glutamine methyltransferase, modifies release factors RF‑1 and RF‑2
RA	1,264,442	G→T	V274V (GTG→GTT)	kdsA →	3‑deoxy‑D‑manno‑octulosonate 8‑phosphate synthase
RA	1,277,786	G→A	D823N (GAC→AAC)	narG →	nitrate reductase 1, alpha subunit
RA	1,281,042	C→A	R150S (CGT→AGT)	narJ →	molybdenum‑cofactor‑assembly chaperone subunit (delta subunit) of nitrate reductase 1
RA	1,288,669	A→T	intergenic (‑291/‑314)	hns ← / → tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
RA	1,289,975	G→T	pseudogene (474/567 nt)	insZ ←	pseudogene, transposase homolog
RA	1,290,033	G→T	pseudogene (416/567 nt)	insZ ←	pseudogene, transposase homolog
RA	1,293,952	G→A	intergenic (‑375/‑102)	adhE ← / → ychE	fused acetaldehyde‑CoA dehydrogenase/iron‑dependent alcohol dehydrogenase/pyruvate‑formate lyase deactivase/UPF0056 family inner membrane protein
RA	1,296,729	C→A	H431N (CAC→AAC)	oppA →	oligopeptide transporter subunit
RA	1,322,140	T→A	T159S (ACG→TCG)	btuR ←	cob(I)yrinic acid a,c‑diamide adenosyltransferase
RA	1,325,982	G→T	T226T (ACG→ACT)	topA →	DNA topoisomerase I, omega subunit
RA	1,326,726	A→T	P474P (CCA→CCT)	topA →	DNA topoisomerase I, omega subunit
RA	1,330,955	G→T	D290Y (GAT→TAT)	acnA →	aconitate hydratase 1
RA	1,331,654	G→T	D523Y (GAT→TAT)	acnA →	aconitate hydratase 1
RA	1,335,356	A→T	H181L (CAT→CTT)	yciM →	envelope integrity maintenance protein; EnvC‑interacting protein
RA	1,335,922	C→T	H370Y (CAT→TAT)	yciM →	envelope integrity maintenance protein; EnvC‑interacting protein
RA	1,337,533	G→T	A18E (GCA→GAA)	osmB ←	lipoprotein
RA	1,341,886	T→A	A428A (GCA→GCT)	rnb ←	ribonuclease II
RA	1,348,772	G→T	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	S159R (AGC→AGA)	sapA ←	antimicrobial peptide transport ABC transporter periplasmic binding protein
RA	1,351,022	G→T	R116S (CGT→AGT)	sapA ←	antimicrobial peptide transport ABC transporter periplasmic binding protein
RA	1,358,855	G→T	G123C (GGC→TGC)	puuB →	gamma‑glutamylputrescine oxidoreductase
RA	1,365,283	G→T	E271* (GAG→TAG)	ycjM →	alpha amylase catalytic domain family protein
RA	1,367,252	G→T	E363* (GAA→TAA)	ycjN →	putative ABC superfamily sugar transporter periplasmic‑binding protein
JC JC	1,376,043	IS5 (–) +4 bp	pseudogene (10‑13/126 nt)	ycjV →	pseudogene; putative ATP‑binding component of a transport system
RA	1,377,394	C→T	A275A (GCG→GCA)	ycjW ←	LacI family putative transcriptional repressor
RA	1,378,237	G→T	intergenic (‑19/‑137)	ycjW ← / → ycjX	LacI family putative transcriptional repressor/DUF463 family protein, putative P‑loop NTPase
RA	1,381,373	A→C	N133H (AAT→CAT)	tyrR →	aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase
RA	1,386,008	G→T	Q35K (CAG→AAG)	ycjY ←	S9 homolog non‑peptidase family protein
RA	1,388,406	G→T	R308L (CGC→CTC)	mppA →	murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit
RA	1,389,852	G→T	R110S (CGC→AGC)	ynaI ←	mechanosensitive channel protein, very small conductance
RA	1,394,355	G→T	R47S (CGC→AGC)	ogt ←	O‑6‑alkylguanine‑DNA:cysteine‑protein methyltransferase
RA	1,397,366	A→T	S49S (TCT→TCA)	abgB ←	p‑aminobenzoyl‑glutamate hydrolase, B subunit
RA	1,407,139	A→T	C118* (TGT→TGA)	intR ←	Rac prophage; integrase
RA	1,412,385	G→T	N34K (AAC→AAA)	kilR ←	Rac prophage; inhibitor of ftsZ, killing protein
RA	1,421,685	T→A	pseudogene (40/210 nt)	lomR →	pseudogene, Rac prophage lom homolog;Phage or Prophage Related; interrupted by IS5 and N‑ter deletion
RA	1,424,234	C→A	S310* (TCA→TAA)	stfR →	Rac prophage; putative tail fiber protein
JC JC	1,428,894	IS2 (–) +5 bp	intergenic (‑413/+317)	ynaE ← / ← ttcC	cold shock protein, Rac prophage/pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related
RA	1,430,873	G→T	S93* (TCA→TAA)	ompN ←	outer membrane pore protein N, non‑specific
RA	1,437,184	G→T	intergenic (‑84/‑124)	ldhA ← / → ydbH	fermentative D‑lactate dehydrogenase, NAD‑dependent/putative membrane‑anchored protein, function unknown
RA	1,439,518	C→A	S737S (TCC→TCA)	ydbH →	putative membrane‑anchored protein, function unknown
RA	1,442,008	G→T	R78L (CGA→CTA)	feaB →	phenylacetaldehyde dehydrogenase
RA	1,451,422	A→T	T246S (ACG→TCG)	paaE →	ring 1,2‑phenylacetyl‑CoA epoxidase, NAD(P)H oxidoreductase component
RA	1,454,724	G→T	G472C (GGT→TGT)	paaH →	3‑hydroxyadipyl‑CoA dehydrogenase, NAD+‑dependent
RA	1,457,725	G→T	intergenic (+30/‑71)	paaK → / → paaX	phenylacetyl‑CoA ligase/transcriptional repressor of phenylacetic acid degradation paa operon, phenylacetyl‑CoA inducer
RA	1,461,041	A→T	pseudogene (1393/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA	1,470,453	C→A	V351V (GTC→GTA)	ydbD →	PF10971 family putative periplasmic methylglyoxal resistance protein
RA	1,478,971	G→A	E552K (GAG→AAG)	hrpA →	putative ATP‑dependent helicase
RA	1,479,733	G→T	D806Y (GAT→TAT)	hrpA →	putative ATP‑dependent helicase
RA	1,482,005	G→T	D172Y (GAT→TAT)	ydcF →	DUF218 superfamily protein, SAM‑binding
RA	1,483,460	G→T	A324A (GCG→GCT)	aldA →	aldehyde dehydrogenase A, NAD‑linked
RA	1,502,848	T→A	V604E (GTA→GAA)	ydcP →	putative peptidase
RA	1,503,262	G→T	L20L (CTC→CTA)	yncJ ←	uncharacterized protein
RA	1,507,433	G→T	E120D (GAG→GAT)	ydcT →	putative spermidine/putrescine transporter subunit
RA	1,508,681	C→A	F198L (TTC→TTA)	ydcU →	putative spermidine/putrescine transporter subunit
RA	1,510,923	G→T	T363T (ACG→ACT)	patD →	gamma‑aminobutyraldehyde dehydrogenase
RA	1,514,177	G→T	E298D (GAG→GAT)	curA →	curcumin/dihydrocurcumin reductase, NADPH‑dependent
RA	1,514,858	G→A	E114K (GAA→AAA)	mcbR →	colanic acid and biofilm gene transcriptional regulator, MqsR‑controlled
RA	1,519,349	T→A	K297* (AAA→TAA)	ansP ←	L‑asparagine transporter
RA	1,522,007	C→A	intergenic (+598/‑152)	yncH → / → rhsE	IPR020099 family protein/pseudogene, Rhs family protein
RA	1,522,387	C→A	pseudogene (229/2037 nt)	rhsE →	pseudogene, Rhs family protein
RA	1,523,317	G→T	pseudogene (1159/2037 nt)	rhsE →	pseudogene, Rhs family protein
RA	1,526,607	G→A	D179N (GAT→AAT)	ydcC →	H repeat‑associated putative transposase
RA	1,531,029	G→T	R180S (CGC→AGC)	narW ←	nitrate reductase 2 (NRZ), delta subunit (assembly subunit)
RA	1,534,409	G→T	V813V (GTC→GTA)	narZ ←	nitrate reductase 2 (NRZ), alpha subunit
RA	1,537,806	A→T	L171* (TTA→TAA)	narU ←	nitrate/nitrite transporter
RA	1,539,827	C→A	pseudogene (145/951 nt)	yddK ←	pseudogene, leucine‑rich protein; putative glycoportein
RA	1,542,503	G→T	T282T (ACG→ACT)	fdnG →	formate dehydrogenase‑N, alpha subunit, nitrate‑inducible
RA	1,544,432	G→T	T925T (ACG→ACT)	fdnG →	formate dehydrogenase‑N, alpha subunit, nitrate‑inducible
RA	1,548,144	G→T	intergenic (‑49/+85)	adhP ← / ← maeA	ethanol‑active dehydrogenase/acetaldehyde‑active reductase/malate dehydrogenase, (decarboxylating, NAD‑requiring) (malic enzyme)
RA	1,548,216	A→T	intergenic (‑121/+13)	adhP ← / ← maeA	ethanol‑active dehydrogenase/acetaldehyde‑active reductase/malate dehydrogenase, (decarboxylating, NAD‑requiring) (malic enzyme)
RA	1,551,828	T→A	A156A (GCA→GCT)	ddpF ←	D,D‑dipeptide permease system, ATP‑binding component
RA	1,552,629	C→A	D216Y (GAT→TAT)	ddpD ←	D,D‑dipeptide permease system, ATP‑binding component
RA	1,552,648	C→A	A209A (GCG→GCT)	ddpD ←	D,D‑dipeptide permease system, ATP‑binding component
RA	1,557,390	G→T	intergenic (‑57/+201)	ddpX ← / ← dosP	D‑ala‑D‑ala dipeptidase, Zn‑dependent/oxygen sensor, c‑di‑GMP phosphodiesterase, heme‑regulated; cold‑ and stationary phase‑induced bioflim regulator
RA	1,558,685	G→T	R436S (CGC→AGC)	dosP ←	oxygen sensor, c‑di‑GMP phosphodiesterase, heme‑regulated; cold‑ and stationary phase‑induced bioflim regulator
RA	1,563,276	G→T	H491N (CAC→AAC)	gadC ←	glutamate:gamma‑aminobutyric acid antiporter
RA	1,565,497	G→A	S269L (TCG→TTG)	gadB ←	glutamate decarboxylase B, PLP‑dependent
RA	1,569,502	T→G	intergenic (‑43/+2)	pqqL ← / ← yddB	putative periplasmic M16 family zinc metalloendopeptidase/putative TonB‑dependent outer membrane receptor
RA	1,570,428	G→T	I483I (ATC→ATA)	yddB ←	putative TonB‑dependent outer membrane receptor
RA	1,570,826	C→A	D351Y (GAC→TAC)	yddB ←	putative TonB‑dependent outer membrane receptor
RA	1,571,658	C→A	A73A (GCG→GCT)	yddB ←	putative TonB‑dependent outer membrane receptor
RA	1,572,026	A→T	L525* (TTA→TAA)	yddA ←	putative multidrug transporter subunit of ABC superfamily, membrane component/ATP‑binding component
RA	1,574,523	T→A	L175F (TTA→TTT)	ydeM ←	putative YdeN‑specific sulfatase‑maturating enzyme
RA	1,575,339	G→T	F481L (TTC→TTA)	ydeN ←	putative Ser‑type periplasmic non‑aryl sulfatase
RA	1,576,325	T→A	N153Y (AAT→TAT)	ydeN ←	putative Ser‑type periplasmic non‑aryl sulfatase
RA	1,580,852	C→A	intergenic (‑109/+225)	ydeP ← / ← ydeQ	putative oxidoreductase/putative fimbrial‑like adhesin protein
RA	1,586,871	G→T	intergenic (‑172/+51)	hipB ← / ← yneO	antitoxin of HipAB toxin‑antitoxin system/pseudogene, AidA homolog
RA	1,590,878	A→T	pseudogene (1367/5323 nt)	yneO ←	pseudogene, AidA homolog
RA	1,601,871	C→A	P90Q (CCG→CAG)	tam →	trans‑aconitate methyltransferase
RA	1,602,054	A→T	Y151F (TAC→TTC)	tam →	trans‑aconitate methyltransferase
RA	1,603,440	G→A	intergenic (‑161/+46)	yneE ← / ← uxaB	bestrophin family putative inner membrane protein/altronate oxidoreductase, NAD‑dependent
RA	1,604,988	G→A	intergenic (‑51/+176)	uxaB ← / ← yneF	altronate oxidoreductase, NAD‑dependent/putative membrane‑bound diguanylate cyclase
RA	1,613,895	T→A	L22Q (CTG→CAG)	marA →	multiple antibiotic resistance transcriptional regulator
RA	1,614,089	G→T	E87* (GAG→TAG)	marA →	multiple antibiotic resistance transcriptional regulator
RA	1,614,245	C→A	intergenic (+31/‑1)	marA → / → marB	multiple antibiotic resistance transcriptional regulator/mar operon regulator, periplasmic
RA	1,615,694	C→A	R36S (CGC→AGC)	ydeE →	putative transporter
RA	1,620,961	T→G	Q226P (CAA→CCA)	dcp ←	dipeptidyl carboxypeptidase II
RA	1,621,733	T→A	intergenic (‑96/‑41)	dcp ← / → ydfG	dipeptidyl carboxypeptidase II/NADP‑dependent 3‑hydroxy acid dehydrogenase; malonic semialdehyde reductase
RA	1,626,780	A→T	intergenic (‑238/‑549)	ydfJ ← / → ydfK	pseudogene, MFS transporter family; interrupted by Qin prophage;Phage or Prophage Related; putative transport protein/cold shock protein, function unknown, Qin prophage
RA	1,628,207	G→A	G110E (GGA→GAA)	pinQ →	Qin prophage; putative site‑specific recombinase
RA	1,631,894	C→T	S49N (AGC→AAC)	gnsB ←	Qin prophage; multicopy suppressor of secG(Cs) and fabA6(Ts)
RA	1,642,051	T→G	A19A (GCA→GCC)	dicC ←	Qin prophage; DNA‑binding transcriptional regulator for DicB
RA	1,642,135	C→T	intergenic (‑28/‑56)	dicC ← / → dicA	Qin prophage; DNA‑binding transcriptional regulator for DicB/Qin prophage; putative regulator for DicB
RA	1,642,639	G→T	intergenic (+41/‑126)	dicA → / → ydfA	Qin prophage; putative regulator for DicB/Qin prophage; uncharacterized protein
RA	1,646,372	C→A	pseudogene (565/1158 nt)	intQ →	pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related
RA	1,655,286	A→T	V158V (GTA→GTT)	ynfF →	S‑ and N‑oxide reductase, A subunit, periplasmic
RA	1,661,763	C→A	P353P (CCG→CCT)	mlc ←	glucosamine anaerobic growth regulon transcriptional repressor; autorepressor
RA	1,669,592	G→T	F342L (TTC→TTA)	pntB ←	pyridine nucleotide transhydrogenase, beta subunit
RA	1,671,963	T→A	S66S (TCA→TCT)	pntA ←	pyridine nucleotide transhydrogenase, alpha subunit
RA	1,680,642	C→A	E68D (GAG→GAT)	fumC ←	fumarate hydratase (fumarase C),aerobic Class II
RA	1,683,582	C→A	F250L (TTC→TTA)	manA →	mannose‑6‑phosphate isomerase
RA	1,684,105	C→A	intergenic (+97/‑4)	manA → / → ydgA	mannose‑6‑phosphate isomerase/DUF945 family protein
RA	1,687,003	T→A	R36* (AGA→TGA)	uidC ←	putative outer membrane porin for beta‑glucuronides porin protein
RA	1,688,819	C→A	E504* (GAA→TAA)	uidA ←	beta‑D‑glucuronidase
RA	1,689,180	T→G	E383D (GAA→GAC)	uidA ←	beta‑D‑glucuronidase
RA	1,692,573	C→A	D289Y (GAT→TAT)	malI ←	transcriptional repressor of Mal regulon
RA	1,696,612	A→T	E41D (GAA→GAT)	add →	adenosine deaminase
RA	1,699,862	T→A	L119* (TTG→TAG)	ydgK →	DUF2569 family inner membrane protein
RA	1,700,008	T→A	intergenic (+61/‑16)	ydgK → / → rsxA	DUF2569 family inner membrane protein/SoxR iron‑sulfur cluster reduction factor component; inner membrane protein of electron transport complex
RA	1,711,397	C→T	R28Q (CGA→CAA)	tyrS ←	tyrosyl‑tRNA synthetase
RA	1,715,383	C→A	F34L (TTC→TTA)	ydhI →	DUF1656 family putative inner membrane efflux pump associated protein
RA	1,720,180	C→A	intergenic (‑3/‑100)	ydhL ← / → nemR	DUF1289 family protein/transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated
RA	1,723,809	G→T	E156* (GAA→TAA)	lhr →	putative ATP‑dependent helicase
RA	1,731,596	C→A	intergenic (‑49/+117)	ydhP ← / ← ynhF	putative transporter/stress response membrane
RA	1,754,950	T→A	I367F (ATT→TTT)	sufD ←	component of SufBCD Fe‑S cluster assembly scaffold
RA	1,760,702	G→T	I747I (ATC→ATA)	ydiJ ←	putative FAD‑linked oxidoreductase
RA	1,764,150	G→T	D274Y (GAT→TAT)	ydiK →	UPF0118 family inner membrane protein
RA	1,767,220	T→A	F151Y (TTC→TAC)	ydiN →	MFS transporter superfamily protein
RA	1,768,689	C→A	S215* (TCA→TAA)	ydiB →	quinate/shikimate 5‑dehydrogenase, NAD(P)‑binding
RA	1,769,763	T→A	intergenic (+62/‑81)	aroD → / → ydiF	3‑dehydroquinate dehydratase/putative acetyl‑CoA:acetoacetyl‑CoA transferase: alpha subunit/beta subunit
RA	1,770,281	T→A	D146E (GAT→GAA)	ydiF →	putative acetyl‑CoA:acetoacetyl‑CoA transferase: alpha subunit/beta subunit
RA	1,770,878	C→A	I345I (ATC→ATA)	ydiF →	putative acetyl‑CoA:acetoacetyl‑CoA transferase: alpha subunit/beta subunit
RA	1,777,451	C→A	A55E (GCG→GAG)	fadK →	short chain acyl‑CoA synthetase, anaerobic
RA	1,781,790	A→T	Q30L (CAA→CTA)	ppsR →	bifunctional regulatory protein: PEP synthase kinase and PEP synthase pyrophosphorylase
RA	1,783,091	G→T	E134* (GAG→TAG)	aroH →	3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tryptophan repressible
RA	1,787,242	C→A	D192Y (GAT→TAT)	btuD ←	vitamin B12 transporter subunit : ATP‑binding component of ABC superfamily
RA	1,788,346	C→A	T7T (ACG→ACT)	btuE ←	glutathione peroxidase
RA	1,796,101	C→A	D243Y (GAC→TAC)	thrS ←	threonyl‑tRNA synthetase
RA	1,800,129	C→T	W71* (TGG→TAG)	ydiY ←	acid‑inducible putative outer membrane protein
RA	1,802,047	G→A	intergenic (+100/‑6)	ydiZ → / → yniA	uncharacterized protein/fructosamine kinase family protein
RA	1,803,109	C→T	A128T (GCC→ACC)	yniB ←	putative inner membrane protein
RA	1,812,514	C→A	D82Y (GAT→TAT)	chbF ←	phospho‑chitobiase; general 6‑phospho‑beta‑glucosidase activity
RA	1,820,888	C→A	C98F (TGC→TTC)	astE ←	succinylglutamate desuccinylase
RA	1,821,696	A→T	L274Q (CTG→CAG)	astB ←	succinylarginine dihydrolase
RA	1,823,802	C→A	V64F (GTT→TTT)	astD ←	succinylglutamic semialdehyde dehydrogenase
RA	1,825,763	C→A	A159A (GCG→GCT)	astC ←	succinylornithine transaminase, PLP‑dependent
RA	1,827,137	T→A	D151E (GAT→GAA)	xthA →	exonuclease III
RA	1,829,319	C→A	I85I (ATC→ATA)	ydjZ →	TVP38/TMEM64 family inner membrane protein
RA	1,832,413	C→A	L315L (CTC→CTA)	ynjC →	inner membrane putative ABC superfamily transporter permease
RA	1,833,730	C→A	R3S (CGT→AGT)	ynjE →	molybdopterin synthase sulfurtransferase
RA	1,836,179	G→A	Q72* (CAG→TAG)	ynjH ←	DUF1496 family protein
RA	1,836,192	T→A	I67I (ATA→ATT)	ynjH ←	DUF1496 family protein
RA	1,842,276	T→A	intergenic (‑11/+106)	selD ← / ← ydjA	selenophosphate synthase/putative oxidoreductase
RA	1,852,274	C→A	D273Y (GAT→TAT)	ydjJ ←	putative Zn‑dependent NAD(P)‑binding oxidoreductase
RA	1,858,693	T→A	L196Q (CTG→CAG)	yeaD →	D‑hexose‑6‑phosphate epimerase‑like protein
RA	1,859,132	A→C	A254A (GCT→GCG)	yeaE ←	aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent
RA	1,860,183	G→T	R183S (CGC→AGC)	mipA ←	scaffolding protein for murein synthesizing machinery
RA	1,865,000	C→A	P120Q (CCA→CAA)	yeaI →	putative membrane‑anchored diguanylate cyclase
RA	1,865,422	C→A	R261R (CGA→AGA)	yeaI →	putative membrane‑anchored diguanylate cyclase
RA	1,865,836	G→T	D399Y (GAT→TAT)	yeaI →	putative membrane‑anchored diguanylate cyclase
RA	1,870,743	C→A	H272N (CAT→AAT)	yeaN →	putative transporter
RA	1,872,054	A→T	E28V (GAG→GTG)	yeaP →	diguanylate cyclase
RA	1,872,520	G→T	P183P (CCG→CCT)	yeaP →	diguanylate cyclase
RA	1,872,783	C→A	S271* (TCG→TAG)	yeaP →	diguanylate cyclase
RA	1,873,059	A→T	V10V (GTA→GTT)	yoaK →	inner membrane‑associated protein
RA	1,874,924	T→A	V31V (GTA→GTT)	leuE ←	leucine efflux protein
RA	1,875,096	G→T	intergenic (‑80/+47)	leuE ← / ← dmlR	leucine efflux protein/transcriptional activator of dmlA
RA	1,881,557	C→A	R231L (CGC→CTC)	rnd ←	ribonuclease D
RA	1,881,645	C→A	D202Y (GAT→TAT)	rnd ←	ribonuclease D
RA	1,885,611	G→T	R628S (CGT→AGT)	yoaA ←	putative ATP‑dependent helicase, DinG family
RA	1,886,725	G→T	I256I (ATC→ATA)	yoaA ←	putative ATP‑dependent helicase, DinG family
RA	1,899,504	T→C	V149V (GTT→GTC)	yobD →	UPF0266 family inner membrane protein
RA	1,909,342	T→A	E150D (GAA→GAT)	proQ ←	RNA chaperone, putative ProP translation regulator
RA	1,916,375	G→T	intergenic (+102/‑3)	yebV → / → yebW	uncharacterized protein/uncharacterized protein
RA	1,932,701	C→A	Q266K (CAG→AAG)	pykA →	pyruvate kinase II
RA	1,940,498	G→T	intergenic (‑61/‑10)	yobI ← / → yebB	uncharacterized protein/DUF830 family protein
RA	1,944,177	C→A	L201L (CTG→CTT)	aspS ←	aspartyl‑tRNA synthetase
RA	1,951,334	C→A	T352T (ACG→ACT)	torY ←	TMAO reductase III (TorYZ), cytochrome c‑type subunit
RA	1,953,658	G→T	S149* (TCG→TAG)	yecM ←	putative metal‑binding enzyme
RA	1,953,876	C→A	P76P (CCG→CCT)	yecM ←	putative metal‑binding enzyme
RA	1,959,915	C→A	P178P (CCG→CCT)	flhB ←	flagellin export apparatus, substrate specificity protein
RA	1,962,923	C→A	M233I (ATG→ATT)	cheR ←	chemotaxis regulator, protein‑glutamate methyltransferase
RA	1,963,622	A→T	intergenic (‑1/+18)	cheR ← / ← tap	chemotaxis regulator, protein‑glutamate methyltransferase/methyl‑accepting protein IV
RA	1,969,291	G→T	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	T38T (ACG→ACT)	yecA ←	UPF0149 family protein
RA	1,986,289	T→A	N4Y (AAT→TAT)	pgsA ←	phosphatidylglycerophosphate synthetase
RA	1,993,530	C→A	E113* (GAG→TAG)	fliY ←	cystine transporter subunit
RA	1,997,314	G→T	intergenic (‑227/‑39)	fliC ← / → fliD	flagellar filament structural protein (flagellin)/flagellar filament capping protein
RA	1,999,632	G→T	intergenic (+73/‑5)	fliT → / → amyA	putative flagellar synthesis and assembly chaperone/cytoplasmic alpha‑amylase
RA	2,002,354	C→A	L199L (CTC→CTA)	yedE →	UPF0394 family sulfur transport domain‑containing inner membrane protein
RA	2,003,722	G→T	E141* (GAA→TAA)	yedK →	DUF159 family protein
RA	2,004,533	G→T	T151T (ACG→ACT)	yedL →	putative acyl transferase
RA	2,008,669	C→A	T103T (ACC→ACA)	fliG →	flagellar motor switching and energizing component
RA	2,011,048	G→T	P338P (CCG→CCT)	fliI →	flagellum‑specific ATP synthase
RA	2,015,913	G→T	T188T (ACG→ACT)	fliP →	flagellar biosynthesis protein
RA	2,020,166	C→A	D445Y (GAC→TAC)	yedQ ←	putative membrane‑anchored diguanylate cyclase
RA	2,035,090	C→A	Q79K (CAG→AAG)	zinT →	zinc and cadmium binding protein, periplasmic
RA	2,036,102	C→A	S85* (TCG→TAG)	yodB →	cytochrome b561 homolog
RA	2,040,890	C→A	G824G (GGC→GGA)	yeeJ →	putative adhesin
RA	2,041,346	C→A	I976I (ATC→ATA)	yeeJ →	putative adhesin
RA	2,043,643	T→A	L1742Q (CTG→CAG)	yeeJ →	putative adhesin
RA	2,046,600	G→T	pseudogene (210/1053 nt)	yeeL ←	pseudogene, glycosyltransferase homology
RA	2,049,111	C→A	T190T (ACC→ACA)	amn →	AMP nucleosidase
RA	2,064,466	C→A	pseudogene (326/552 nt)	yeeP →	pseudogene, CP4‑44 prophage; 50S ribosome‑binding GTPase family;Phage or Prophage Related; putative histone
RA	2,074,680	A→T	W22R (TGG→AGG)	sbmC ←	DNA gyrase inhibitor
RA	2,076,118	C→T	intergenic (‑90/‑119)	dacD ← / → sbcB	D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 6b)/exodeoxyribonuclease I; exonuclease I
RA	2,077,212	A→T	N326Y (AAT→TAT)	sbcB →	exodeoxyribonuclease I; exonuclease I
JC JC	2,080,274	IS2 (–) +5 bp	coding (266‑270/1359 nt)	plaP ←	putrescine importer, low affinity
RA	2,086,004	C→A	A42A (GCC→GCA)	hisC →	histidinol‑phosphate aminotransferase
RA	2,093,906	C→A	E282* (GAG→TAG)	gnd ←	6‑phosphogluconate dehydrogenase, decarboxylating
RA	2,098,995	C→A	G182* (GGA→TGA)	wbbI ←	d‑Galf:alpha‑d‑Glc beta‑1,6‑galactofuranosyltransferase
RA	2,099,341	T→G	L66F (TTA→TTC)	wbbI ←	d‑Galf:alpha‑d‑Glc beta‑1,6‑galactofuranosyltransferase
RA	2,101,912	T→G	E385A (GAG→GCG)	wzxB ←	putative polisoprenol‑linked O‑antigen transporter
RA	2,102,391	A→C	S225S (TCT→TCG)	wzxB ←	putative polisoprenol‑linked O‑antigen transporter
RA	2,107,728	C→A	E27D (GAG→GAT)	wcaN ←	putative regulatory subunit for GalU
RA	2,108,226	(A)7→8	coding (1152/1395 nt)	wcaM ←	colanic acid biosynthesis protein
RA	2,110,346	G→A	T88I (ACC→ATC)	wcaL ←	putative glycosyl transferase
RA	2,114,911	A→T	L42Q (CTG→CAG)	wcaJ ←	colanic biosynthesis UDP‑glucose lipid carrier transferase
RA	2,122,013	G→T	T119T (ACC→ACA)	wcaF ←	putative acyl transferase
RA	2,122,266	G→T	S35* (TCG→TAG)	wcaF ←	putative acyl transferase
RA	2,122,453	C→T	A227T (GCT→ACT)	wcaE ←	putative glycosyl transferase
RA	2,122,653	C→T	W160* (TGG→TAG)	wcaE ←	putative glycosyl transferase
RA	2,128,128	T→A	K336* (AAA→TAA)	wzc ←	colanic acid production tyrosine‑protein kinase; autokinase; Ugd phosphorylase
RA	2,138,702	T→A	S652R (AGT→AGA)	yegE →	putative diguanylate cyclase
RA	2,139,910	G→T	R1055L (CGA→CTA)	yegE →	putative diguanylate cyclase
RA	2,144,474	C→A	intergenic (‑8/‑192)	yegI ← / → yegJ	protein kinase‑related putative non‑specific DNA‑binding protein/uncharacterized protein
RA	2,146,333	C→A	D93Y (GAT→TAT)	yegL ←	VMA domain protein
RA	2,149,603	A→T	E287V (GAA→GTA)	mdtB →	multidrug efflux system, subunit B
RA	2,152,444	C→A	A193E (GCG→GAG)	mdtC →	multidrug efflux system, subunit C
RA	2,167,068	C→A	V230V (GTG→GTT)	gatC ←	galactitol PTS permease ‑ GatC subunit
RA	2,168,795	C→A	D336Y (GAT→TAT)	gatZ ←	D‑tagatose 1,6‑bisphosphate aldolase 2, subunit
RA	2,170,534	C→A	T50T (ACG→ACT)	gatY ←	D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit
RA	2,179,205	G→T	A24E (GCG→GAG)	rcnR ←	transcriptional repressor of rcnA
RA	2,179,279	A→T	intergenic (‑4/‑117)	rcnR ← / → rcnA	transcriptional repressor of rcnA/membrane protein conferring nickel and cobalt resistance
RA	2,181,645	A→G	N83N (AAT→AAC)	yehA ←	putative fimbrial‑like adhesin protein
RA	2,183,642	C→A	D250Y (GAT→TAT)	yehB ←	putative outer membrane protein
RA	2,194,695	T→A	L313Q (CTA→CAA)	yehI →	DUF4132 domain‑containing protein
RA	2,195,449	A→T	E564D (GAA→GAT)	yehI →	DUF4132 domain‑containing protein
RA	2,198,343	C→A	S90Y (TCT→TAT)	yehL →	putative ABC superfamily transporter ATP‑binding subunit
RA	2,201,014	C→A	A614E (GCG→GAG)	yehM →	uncharacterized protein
RA	2,209,162	C→A	I9I (ATC→ATA)	yohO →	putative membrane protein
RA	2,211,664	C→A	D125Y (GAT→TAT)	yehY ←	inner membrane putative ABC superfamily transporter permease
RA	2,216,296	C→A	I211I (ATC→ATA)	dld →	D‑lactate dehydrogenase, FAD‑binding, NADH independent
RA	2,218,022	C→A	E110* (GAA→TAA)	pbpG ←	D‑alanyl‑D‑alanine endopeptidase
RA	2,222,970	T→A	N299Y (AAT→TAT)	dusC ←	tRNA‑dihydrouridine synthase C
RA	2,223,247	C→T	W206* (TGG→TGA)	dusC ←	tRNA‑dihydrouridine synthase C
RA	2,225,190	C→T	G231G (GGC→GGT)	yohK →	LrgB family inner membrane protein
RA	2,226,594	G→T	G80C (GGT→TGT)	sanA →	vancomycin high temperature exclusion protein, DUF218 superfamily protein
RA	2,234,532	C→A	D206Y (GAT→TAT)	galS ←	galactose‑ and fucose‑inducible galactose regulon transcriptional isorepressor; mgl operon transcriptional repressor; autorepressor
RA	2,237,098	G→T	H12N (CAT→AAT)	folE ←	GTP cyclohydrolase I
RA	2,240,676	C→A	D446Y (GAC→TAC)	lysP ←	lysine transporter
RA	2,241,222	T→G	I264L (ATT→CTT)	lysP ←	lysine transporter
RA	2,241,793	A→T	A73A (GCT→GCA)	lysP ←	lysine transporter
RA	2,248,657	C→A	K3N (AAG→AAT)	rihB ←	ribonucleoside hydrolase 2
RA	2,263,137	C→A	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	intergenic (+119/‑62)	mepS → / → rtn	murein DD‑endopeptidase, space‑maker hydrolase, mutational suppressor of prc thermosensitivity, outer membrane lipoprotein/resistance protein for phages lambda and N4, putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	2,270,918	C→A	N380K (AAC→AAA)	yejF →	microcin C transporter, ATP‑binding subunit; ABC family
RA	2,287,829	C→A	S185S (TCG→TCT)	ccmF ←	heme lyase, CcmF subunit
RA	2,289,043	C→A	W8L (TGG→TTG)	ccmD ←	cytochrome c biogenesis protein
RA	2,289,374	C→A	V142V (GTG→GTT)	ccmC ←	heme exporter subunit
RA	2,294,862	G→T	I457I (ATC→ATA)	napA ←	nitrate reductase, periplasmic, large subunit
RA	2,303,070	T→G	Q272P (CAG→CCG)	ada ←	fused DNA‑binding transcriptional dual regulator/O6‑methylguanine‑DNA methyltransferase
RA	2,305,116	C→A	intergenic (‑103/+9)	apbE ← / ← ompC	putative thiamine‑synthetic flavin transferase lipoprotein/outer membrane porin protein C
RA	2,305,135	T→C	Y365C (TAC→TGC)	ompC ←	outer membrane porin protein C
RA	2,310,875	A→T	I827I (ATT→ATA)	rcsC ←	hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA	2,311,982	C→A	E458D (GAG→GAT)	rcsC ←	hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA	2,318,825	G→T	V197V (GTG→GTT)	atoE →	short chain fatty acid transporter
RA	2,319,752	C→A	N55K (AAC→AAA)	atoB →	acetyl‑CoA acetyltransferase
RA	2,322,609	C→A	W223L (TGG→TTG)	yfaQ ←	tandem DUF2300 domain protein, putative host defense protein
RA	2,330,502	C→A	D800Y (GAT→TAT)	gyrA ←	DNA gyrase (type II topoisomerase), subunit A
RA	2,342,897	C→A	D19Y (GAC→TAC)	inaA ←	acid‑inducible Kdo/WaaP family putative kinase
RA	2,348,894	T→A	V384E (GTG→GAG)	glpB →	sn‑glycerol‑3‑phosphate dehydrogenase (anaerobic), membrane anchor subunit
RA	2,352,573	C→A	P353P (CCG→CCT)	rhmT ←	putative L‑rhamnonate transporter
RA	2,358,641	G→T	I153I (ATC→ATA)	ais ←	putative LPS core heptose(II)‑phosphate phosphatase
RA	2,359,673	G→T	M89I (ATG→ATT)	arnB →	uridine 5'‑(beta‑1‑threo‑pentapyranosyl‑4‑ulose diphosphate) aminotransferase, PLP‑dependent
RA	2,362,338	T→A	L274Q (CTG→CAG)	arnA →	fused UDP‑L‑Ara4N formyltransferase/UDP‑GlcA C‑4'‑decarboxylase
RA	2,364,394	C→A	S3* (TCG→TAG)	arnT →	4‑amino‑4‑deoxy‑L‑arabinose transferase
RA	2,370,361	+G	coding (711/759 nt)	menH ←	2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
RA	2,370,987	C→A	E29* (GAA→TAA)	menH ←	2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
RA	2,376,959	C→T	N256N (AAC→AAT)	elaD →	protease, capable of cleaving an AMC‑ubiquitin model substrate
RA	2,380,078	C→T	S247F (TCT→TTT)	yfbL →	putative peptidase
RA	2,383,897	C→A	R363L (CGC→CTC)	nuoN ←	NADH:ubiquinone oxidoreductase, membrane subunit N
RA	2,399,210	G→T	S304* (TCA→TAA)	lrhA ←	transcriptional repressor of flagellar, motility and chemotaxis genes
RA	2,400,858	C→A	intergenic (‑738/‑182)	lrhA ← / → alaA	transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2
RA	2,400,876	C→T	intergenic (‑756/‑164)	lrhA ← / → alaA	transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2
RA	2,404,772	C→A	A20A (GCG→GCT)	yfbS ←	putative transporter
RA	2,405,946	T→G	Q43P (CAG→CCG)	yfbU ←	UPF0304 family protein
RA	2,411,263	T→A	V235E (GTG→GAG)	yfcC →	putative inner membrane transporter, C4‑dicarboxylate anaerobic carrier family
RA	2,411,273	C→A	I238I (ATC→ATA)	yfcC →	putative inner membrane transporter, C4‑dicarboxylate anaerobic carrier family
RA	2,411,701	T→A	L381* (TTA→TAA)	yfcC →	putative inner membrane transporter, C4‑dicarboxylate anaerobic carrier family
RA	2,412,205	C→A	D151Y (GAT→TAT)	yfcD ←	putative NUDIX hydrolase
RA	2,416,101	C→A	intergenic (+21/+27)	yfcH → / ← yfcI	putative NAD‑dependent nucleotide‑sugar epimerase/transposase_31 family protein
RA	2,419,993	G→T	S92* (TCG→TAG)	hisJ ←	histidine/lysine/arginine/ornithine transporter subunit
RA	2,422,841	C→A	D293Y (GAT→TAT)	purF ←	amidophosphoribosyltransferase
RA	2,424,074	C→T	D57N (GAC→AAC)	cvpA ←	colicin V production membrane protein
RA	2,424,448	A→C	intergenic (‑206/+53)	cvpA ← / ← dedD	colicin V production membrane protein/membrane‑anchored periplasmic protein involved in septation
RA	2,427,265	C→A	P47P (CCG→CCT)	accD ←	acetyl‑CoA carboxylase, beta (carboxyltransferase) subunit
RA	2,428,546	C→A	V190V (GTG→GTT)	truA ←	tRNA pseudouridine(38‑40) synthase
RA	2,450,335	C→T	intergenic (‑44/+159)	sixA ← / ← fadJ	phosphohistidine phosphatase/fused enoyl‑CoA hydratase and epimerase and isomerase/3‑hydroxyacyl‑CoA dehydrogenase
RA	2,450,339	A→T	intergenic (‑48/+155)	sixA ← / ← fadJ	phosphohistidine phosphatase/fused enoyl‑CoA hydratase and epimerase and isomerase/3‑hydroxyacyl‑CoA dehydrogenase
RA	2,450,346	G→T	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	P62Q (CCG→CAG)	fadJ ←	fused enoyl‑CoA hydratase and epimerase and isomerase/3‑hydroxyacyl‑CoA dehydrogenase
RA	2,454,297	T→G	E39D (GAA→GAC)	yfcZ ←	UPF0381 family protein
RA	2,456,705	C→A	S72Y (TCC→TAC)	yfdF →	uncharacterized protein
RA	2,459,976	G→T	intergenic (+114/‑48)	argW → / → intS	tRNA‑Arg/CPS‑53 (KpLE1) prophage; putative prophage CPS‑53 integrase
RA	2,474,255	T→A	E467D (GAA→GAT)	emrY ←	putative multidrug efflux system
RA	2,474,353	G→T	Q435K (CAG→AAG)	emrY ←	putative multidrug efflux system
RA	2,474,418	G→T	S413* (TCA→TAA)	emrY ←	putative multidrug efflux system
RA	2,476,524	T→A	N99Y (AAT→TAT)	emrK ←	EmrKY‑TolC multidrug resistance efflux pump, membrane fusion protein component
RA	2,478,201	G→T	E117* (GAA→TAA)	evgS →	hybrid sensory histidine kinase in two‑component regulatory system with EvgA
RA	2,481,488	A→T	intergenic (+42/+14)	evgS → / ← yfdE	hybrid sensory histidine kinase in two‑component regulatory system with EvgA/acetyl‑CoA:oxalate CoA‑transferase
RA	2,481,974	G→T	S225* (TCA→TAA)	yfdE ←	acetyl‑CoA:oxalate CoA‑transferase
RA	2,488,416	G→T	P80P (CCG→CCT)	ypdI →	putative lipoprotein involved in colanic acid biosynthesis
RA	2,488,443	T→A	P89P (CCT→CCA)	ypdI →	putative lipoprotein involved in colanic acid biosynthesis
RA	2,497,946	G→T	L7I (CTC→ATC)	fryA ←	putative PTS enzyme, Hpr component/enzyme I component/enzyme IIA component
RA	2,499,180	G→T	T311K (ACG→AAG)	ypdF ←	Xaa‑Pro aminopeptidase
RA	2,499,568	C→A	D182Y (GAC→TAC)	ypdF ←	Xaa‑Pro aminopeptidase
RA	2,512,031	C→A	S29* (TCA→TAA)	yfeC →	DUF1323 family putative DNA‑binding protein
RA	2,520,652	C→A	I116I (ATC→ATA)	yfeH →	putative inorganic ion transporter
RA	2,524,056	C→A	A179A (GCG→GCT)	zipA ←	FtsZ stabilizer
RA	2,526,794	C→T	intergenic (+55/‑329)	cysK → / → ptsH	cysteine synthase A, O‑acetylserine sulfhydrolase A subunit/phosphohistidinoprotein‑hexose phosphotransferase component of PTS system (Hpr)
RA	2,542,627	T→G	I389M (ATT→ATG)	yfeW →	penicillin binding protein PBP4B; weak DD‑carboxypeptidase activity
RA	2,544,294	C→A	A94A (GCG→GCT)	yfeY ←	RpoE‑regulated lipoprotein
RA	2,546,198	T→G	L163R (CTG→CGG)	amiA →	N‑acetylmuramoyl‑l‑alanine amidase I
RA	2,549,144	C→A	D206Y (GAT→TAT)	eutL ←	putative ethanol utilization carboxysome structural protein
RA	2,549,676	C→A	L28L (CTG→CTT)	eutL ←	putative ethanol utilization carboxysome structural protein
RA	2,556,786	G→T	intergenic (+310/‑165)	yffP → / → yffQ	CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
RA	2,567,211	C→A	D152Y (GAT→TAT)	eutT ←	cobalamin adenosyltransferase involved in ethanolamine utilization
RA	2,567,775	G→T	I196I (ATC→ATA)	eutQ ←	RmlC‑like cupin domain protein
RA	2,568,720	C→T	A33T (GCC→ACC)	eutP ←	putative P‑loop NTPase ethanolamine utilization protein
RA	2,574,820	C→A	A609E (GCG→GAG)	tktB →	transketolase 2, thiamine triphosphate‑binding
RA	2,576,325	C→A	E171D (GAG→GAT)	nudK ←	GDP‑mannose pyrophosphatase
RA	2,579,561	G→T	G158C (GGC→TGC)	narQ →	sensory histidine kinase in two‑component regulatory system with NarP (NarL)
RA	2,587,029	+G	coding (101/699 nt)	ypfH ←	palmitoyl‑CoA esterase activity, uncertain physiological substrate
RA	2,589,933	G→A	T55I (ACC→ATC)	ypfJ ←	putative neutral zinc metallopeptidase
RA	2,596,168	C→A	P331Q (CCG→CAG)	hyfB →	hydrogenase 4, membrane subunit
RA	2,597,173	T→G	L666R (CTG→CGG)	hyfB →	hydrogenase 4, membrane subunit
RA	2,601,496	T→A	F407L (TTT→TTA)	hyfF →	hydrogenase 4, membrane subunit
RA	2,606,516	G→T	D420Y (GAC→TAC)	hyfR →	hydrogenase‑4 transcriptional activator
RA	2,610,919	C→A	intergenic (+3/‑18)	bepA → / → yfgD	periplasmic metalloprotease and chaperone for OM protein maintenance and assembly/putative oxidoreductase
RA	2,614,168	C→A	D22Y (GAT→TAT)	upp ←	uracil phosphoribosyltransferase
RA	2,618,693	G→T	E74* (GAA→TAA)	ppx →	exopolyphosphatase
RA	2,626,389	G→T	I347I (ATC→ATA)	guaB ←	IMP dehydrogenase
RA	2,632,012	C→A	intergenic (‑1/+10)	bamB ← / ← yfgM	BamABCDE complex OM biogenesis lipoprotein/putative anti‑RcsB factor
RA	2,633,402	C→A	R178L (CGC→CTC)	hisS ←	histidyl tRNA synthetase
RA	2,634,417	T→G	K249N (AAA→AAC)	ispG ←	1‑hydroxy‑2‑methyl‑2‑(E)‑butenyl 4‑diphosphate synthase
RA	2,639,116	C→A	A523A (GCG→GCT)	pbpC ←	penicillin‑insensitive murein repair transglycosylase; inactive transpeptidase domain
RA	2,643,336	C→A	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	D19Y (GAC→TAC)	yfhM ←	bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein
RA	2,651,665	G→T	G210G (GGC→GGA)	hscA ←	DnaK‑like molecular chaperone specific for IscU
RA	2,659,594	C→A	L267L (CTC→CTA)	csiE →	stationary phase inducible protein
RA	2,664,138	A→C	E130D (GAA→GAC)	hcaF →	3‑phenylpropionate dioxygenase, small (beta) subunit
RA	2,665,772	G→T	E123* (GAA→TAA)	hcaD →	phenylpropionate dioxygenase, ferredoxin reductase subunit
RA	2,669,978	C→A	A69A (GCG→GCT)	yphD ←	inner membrane putative ABC superfamily sugar transporter permease
RA	2,671,274	C→A	T149T (ACG→ACT)	yphE ←	putative sugar transporter subunit of ABC superfamily, ATP‑binding component
RA	2,681,873	T→A	Q97L (CAG→CTG)	glrR ←	response regulator regulating glmY sRNA in two‑component system with sensor protein GlrK
RA	2,683,829	C→A	R210L (CGT→CTT)	glrK ←	sensor protein kinase regulating glmY sRNA in two‑component system with response regulator GlrR
RA	2,688,006	C→A	P299P (CCG→CCT)	purL ←	phosphoribosylformyl‑glycineamide synthetase
RA	2,689,267	C→A	I36I (ATC→ATA)	mltF →	membrane‑bound lytic transglycosylase F, murein hydrolase
RA	2,691,904	T→A	A2A (GCA→GCT)	pgpC ←	phosphatidylglycerophosphatase C, membrane bound
RA	2,692,793	C→A	H226N (CAT→AAT)	yfhH →	putative DNA‑binding transcriptional regulator
RA	2,694,843	G→T	I82I (ATC→ATA)	pdxJ ←	pyridoxine 5'‑phosphate synthase
RA	2,696,277	C→A	E157* (GAA→TAA)	era ←	membrane‑associated, 16S rRNA‑binding GTPase
RA	2,699,380	C→A	P368P (CCG→CCT)	lepA ←	back‑translocating elongation factor EF4, GTPase
RA	2,699,880	T→A	N202Y (AAC→TAC)	lepA ←	back‑translocating elongation factor EF4, GTPase
JC JC	2,709,656	IS2 (–) +5 bp	coding (149‑153/384 nt)	grcA ←	autonomous glycyl radical cofactor
RA	2,711,755	C→A	D45Y (GAC→TAC)	yfiF ←	putative methyltransferase
RA	2,715,643	G→T	E778* (GAA→TAA)	pka →	protein lysine acetyltransferase
RA	2,718,618	G→T	S163* (TCA→TAA)	kgtP ←	alpha‑ketoglutarate transporter
RA	2,719,426	T→C	intergenic (‑321/+2)	kgtP ← / ← rrfG	alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon
RA	2,725,747	G→T	R596S (CGC→AGC)	clpB ←	protein disaggregation chaperone
RA	2,726,786	C→A	A249A (GCG→GCT)	clpB ←	protein disaggregation chaperone
RA	2,727,416	C→A	L39L (CTG→CTT)	clpB ←	protein disaggregation chaperone
RA	2,733,753	C→T	E253K (GAG→AAG)	aroF ←	3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tyrosine‑repressible
RA	2,736,714	C→A	R325S (CGC→AGC)	yfiN →	putative membrane‑anchored diguanylate cyclase with an N‑terminal periplasmic domain
RA	2,743,438	C→A	intergenic (+19/+36)	yfjD → / ← grpE	UPF0053 family inner membrane protein/heat shock protein
RA	2,751,558	G→T	T134T (ACC→ACA)	yfjH ←	CP4‑57 prophage; uncharacterized protein
RA	2,763,057	C→A	intergenic (+212/‑5)	yfjQ → / → yfjR	CP4‑57 prophage; uncharacterized protein/CP4‑57 prophage; putative DNA‑binding transcriptional regulator
RA	2,771,358	G→A	intergenic (+217/+147)	ypjF → / ← ypjA	CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter
RA	2,778,820	G→A	intergenic (‑450/+301)	ypjC ← / ← ileY	pseudogene/tRNA‑Ile
RA	2,779,067	C→A	intergenic (‑697/+54)	ypjC ← / ← ileY	pseudogene/tRNA‑Ile
RA	2,792,318	C→A	intergenic (‑464/‑205)	stpA ← / → alaE	DNA binding protein, nucleoid‑associated/alanine exporter, alanine‑inducible, stress‑responsive
RA	2,798,195	A→T	K8* (AAA→TAA)	proV →	glycine betaine transporter subunit
RA	2,801,706	C→A	pseudogene (32/1178 nt)	ygaY →	pseudogene, major facilitator transporter superfamily;putative transport; Not classified; putative transport protein
RA	2,807,730	C→A	P121P (CCG→CCT)	luxS ←	S‑ribosylhomocysteine lyase
RA	2,808,907	C→A	E298* (GAA→TAA)	gshA ←	glutamate‑cysteine ligase
RA	2,825,783	C→T	intergenic (‑135/‑52)	norR ← / → norV	anaerobic nitric oxide reductase DNA‑binding transcriptional activator/anaerobic nitric oxide reductase flavorubredoxin
RA	2,828,952	C→A	T611T (ACG→ACT)	hypF ←	carbamoyl phosphate phosphatase and maturation protein for [NiFe] hydrogenases
RA	2,831,086	C→A	E127* (GAA→TAA)	hydN ←	formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit
RA	2,831,929	T→A	E232V (GAA→GTA)	ascG ←	asc operon transcriptional repressor; prpBC operon repressor
RA	2,832,734	A→G	intergenic (‑111/‑149)	ascG ← / → ascF	asc operon transcriptional repressor; prpBC operon repressor/fused cellobiose/arbutin/salicin‑specific PTS enzymes: IIB component/IC component
RA	2,834,052	C→A	I390I (ATC→ATA)	ascF →	fused cellobiose/arbutin/salicin‑specific PTS enzymes: IIB component/IC component
RA	2,835,094	C→A	P249Q (CCG→CAG)	ascB →	cryptic 6‑phospho‑beta‑glucosidase
RA	2,836,145	C→A	M86I (ATG→ATT)	hycI ←	protease involved in processing C‑terminal end of HycE
RA	2,836,554	G→T	I84I (ATC→ATA)	hycH ←	hydrogenase 3 maturation protein
RA	2,837,721	C→A	D131Y (GAC→TAC)	hycF ←	formate hydrogenlyase complex iron‑sulfur protein
RA	2,841,044	C→A	A519A (GCG→GCT)	hycC ←	hydrogenase 3, membrane subunit
RA	2,846,112	C→A	I206I (ATC→ATA)	hypD →	hydrogenase maturation protein
RA	2,848,002	T→A	C102* (TGT→TGA)	fhlA →	formate hydrogenlyase transcriptional activator
RA	2,850,790	C→A	I113I (ATC→ATA)	mutS →	methyl‑directed mismatch repair protein
RA	2,852,854	G→T	P801P (CCG→CCT)	mutS →	methyl‑directed mismatch repair protein
RA	2,855,673	C→A	I295I (ATC→ATA)	ygbJ →	putative dehydrogenase
RA	2,863,542	A→T	V31E (GTG→GAG)	umpG ←	broad specificity 5'(3')‑nucleotidase and polyphosphatase
RA	2,869,780	G→A	intergenic (‑92/‑160)	cysD ← / → iap	sulfate adenylyltransferase, subunit 2/aminopeptidase in alkaline phosphatase isozyme conversion
RA	2,870,278	C→A	I113I (ATC→ATA)	iap →	aminopeptidase in alkaline phosphatase isozyme conversion
RA	2,871,577	C→A	intergenic (+600/+351)	iap → / ← ygbF	aminopeptidase in alkaline phosphatase isozyme conversion/CRISPR adaptation ssRNA endonuclease
RA	2,873,087	G→T	V15V (GTC→GTA)	ygbT ←	multifunctional endonuclease Cas1, CRISPR adaptation protein; DNA repair enzyme
RA	2,876,760	C→T	G246G (GGG→GGA)	casA ←	CRISP RNA (crRNA) containing Cascade antiviral complex protein
RA	2,878,668	G→T	V637V (GTC→GTA)	ygcB ←	R‑loop helicase‑annealase Cas3 needed for Cascade anti‑viral activity
RA	2,879,449	G→T	S377* (TCA→TAA)	ygcB ←	R‑loop helicase‑annealase Cas3 needed for Cascade anti‑viral activity
RA	2,880,751	C→A	noncoding (39/56 nt)	sokX →	sok‑related sRNA, function unknown
RA	2,881,660	G→T	L4L (CTC→CTA)	cysH ←	phosphoadenosine phosphosulfate reductase; PAPS reductase, thioredoxin dependent
RA	2,884,385	G→T	V291V (GTC→GTA)	cysJ ←	sulfite reductase, alpha subunit, flavoprotein
RA	2,888,584	G→T	I185I (ATC→ATA)	ygcQ ←	putative flavoprotein
RA	2,889,129	C→A	A4S (GCA→TCA)	ygcQ ←	putative flavoprotein
RA	2,893,446	T→A	K63* (AAA→TAA)	ygcW ←	putative dehydrogenase
RA	2,913,019	C→A	A363S (GCT→TCT)	gudX ←	glucarate dehydratase‑related protein, substrate unknown
RA	2,915,998	C→A	A116S (GCT→TCT)	yqcA ←	short‑chain flavodoxin, FMN‑binding
RA	2,918,415	G→A	P75P (CCC→CCT)	syd ←	SecY‑interacting protein
RA	2,919,922	G→T	D86Y (GAT→TAT)	ygdH →	UPF0717 family protein
RA	2,920,050	C→A	I128I (ATC→ATA)	ygdH →	UPF0717 family protein
RA	2,921,101	C→A	intergenic (+70/‑487)	ygdH → / → sdaC	UPF0717 family protein/putative serine transporter
RA	2,921,245	G→T	intergenic (+214/‑343)	ygdH → / → sdaC	UPF0717 family protein/putative serine transporter
RA	2,931,717	C→A	N307K (AAC→AAA)	fucK →	L‑fuculokinase
RA	2,932,835	C→T	R37C (CGC→TGC)	fucR →	l‑fucose operon activator
RA	2,934,843	G→T	H50N (CAT→AAT)	ygdD ←	UPF0382 family inner membrane protein
RA	2,936,836	C→A	A47A (GCC→GCA)	csdA →	cysteine sulfinate desulfinase
RA	2,939,832	C→A	E236* (GAA→TAA)	mltA ←	membrane‑bound lytic murein transglycosylase A
RA	2,941,341	G→A	L343L (CTC→CTT)	amiC ←	N‑acetylmuramoyl‑L‑alanine amidase
RA	2,945,306	C→G	G172A (GGC→GCC)	recD ←	exonuclease V (RecBCD complex), alpha chain
RA	2,950,431	T→A	N605Y (AAT→TAT)	ptrA ←	protease III
RA	2,959,004	G→A	I131I (ATC→ATT)	lgt ←	phosphatidylglycerol‑prolipoprotein diacylglyceryl transferase
RA	2,962,962	T→A	intergenic (‑626/‑59)	rppH ← / → mutH	RNA pyrophosphohydrolase/methyl‑directed mismatch repair protein
RA	2,974,073	C→T	intergenic (‑79/+50)	ygeA ← / ← araE	Asp/Glu_racemase family protein/arabinose transporter
RA	2,980,488	C→A	intergenic (+53/‑407)	yqeG → / → yqeH	putative transporter/putative LuxR family transcriptional regulator
RA	2,983,568	C→A	R51I (AGA→ATA)	yqeK ←	uncharacterized protein
RA	2,984,747	G→T	D41Y (GAT→TAT)	ygeG →	SycD‑like chaperone family TPR‑repeat‑containing protein
RA	2,985,256	G→T	intergenic (+138/‑197)	ygeG → / → ygeH	SycD‑like chaperone family TPR‑repeat‑containing protein/putative transcriptional regulator
RA	2,985,472	T→A	F7Y (TTC→TAC)	ygeH →	putative transcriptional regulator
RA	2,985,884	C→T	I144I (ATC→ATT)	ygeH →	putative transcriptional regulator
RA	2,986,052	G→T	L200F (TTG→TTT)	ygeH →	putative transcriptional regulator
RA	2,988,355	C→A	pseudogene (97/633 nt)	ygeK ←	pseudogene; putative 2‑component transcriptional regulator
RA	2,988,554	G→A	intergenic (‑103/+119)	ygeK ← / ← ygeN	pseudogene; putative 2‑component transcriptional regulator/pseudogene
RA	2,988,934	G→T	pseudogene (186/447 nt)	ygeN ←	pseudogene
RA	2,989,295	C→A	pseudogene (85/261 nt)	ygeN ←	pseudogene
RA	2,993,211	C→A	V14L (GTG→TTG)	ygeR ←	LysM domain‑containing M23 family putative peptidase; septation lipoprotein
RA	2,993,699	C→A	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	D69E (GAC→GAA)	ygeW →	putative carbamoyltransferase
RA	3,009,187	G→T	intergenic (+90/‑232)	mocA → / → ygfK	CTP:molybdopterin cytidylyltransferase/putative Fe‑S subunit oxidoreductase subunit
RA	3,010,667	G→T	D417Y (GAC→TAC)	ygfK →	putative Fe‑S subunit oxidoreductase subunit
RA	3,017,285	G→T	D871Y (GAC→TAC)	xdhD →	putative hypoxanthine oxidase, molybdopterin‑binding/Fe‑S binding
RA	3,018,544	G→T	A279S (GCC→TCC)	xanQ →	xanthine permease
RA	3,022,562	C→T	G577R (GGA→AGA)	ygfT ←	putative oxidoreductase, Fe‑S subunit/nucleotide‑binding subunit
RA	3,024,081	A→C	V70V (GTT→GTG)	ygfT ←	putative oxidoreductase, Fe‑S subunit/nucleotide‑binding subunit
RA	3,024,983	C→G	G86G (GGC→GGG)	uacT →	uric acid permease
RA	3,030,181	G→T	H429N (CAT→AAT)	recJ ←	ssDNA exonuclease, 5' ‑‑> 3'‑specific
RA	3,039,703	C→A	A900S (GCG→TCG)	gcvP ←	glycine decarboxylase, PLP‑dependent, subunit (protein P) of glycine cleavage complex
RA	3,040,479	T→G	Q641P (CAG→CCG)	gcvP ←	glycine decarboxylase, PLP‑dependent, subunit (protein P) of glycine cleavage complex
RA	3,041,321	G→T	I360I (ATC→ATA)	gcvP ←	glycine decarboxylase, PLP‑dependent, subunit (protein P) of glycine cleavage complex
RA	3,044,464	G→A	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	R84R (CGG→AGG)	zapA →	FtsZ stabilizer
RA	3,049,740	C→A	L47L (CTC→CTA)	fau →	5‑formyltetrahydrofolate cyclo‑ligase family protein
RA	3,058,769	C→T	I203I (ATC→ATT)	scpC →	propionyl‑CoA:succinate CoA transferase
RA	3,064,914	G→T	I356I (ATC→ATA)	pgk ←	phosphoglycerate kinase
RA	3,065,123	C→T	G287S (GGT→AGT)	pgk ←	phosphoglycerate kinase
RA	3,068,690	C→A	V284V (GTG→GTT)	yggF ←	fructose 1,6 bisphosphatase isozyme
RA	3,074,591	G→T	A135E (GCG→GAG)	tktA ←	transketolase 1, thiamine triphosphate‑binding
RA	3,074,995	T→A	intergenic (‑1/‑277)	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	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	D211Y (GAC→TAC)	speB ←	agmatinase
RA	3,077,302	C→A	D657Y (GAT→TAT)	speA ←	biosynthetic arginine decarboxylase, PLP‑binding
RA	3,080,618	T→A	V185E (GTG→GAG)	metK →	S‑adenosylmethionine synthetase
RA	3,084,798	C→A	L102L (CTC→CTA)	rsmE →	16S rRNA m(3)U1498 methyltransferase, SAM‑dependent
RA	3,088,065	C→A	V125V (GTG→GTT)	yggR ←	putative PilT family AAA+ ATPase
RA	3,097,262	C→T	F297F (TTC→TTT)	mutY →	adenine DNA glycosylase
RA	3,106,685	G→T	S51Y (TCT→TAT)	yghG ←	secretin (GspDbeta) OM localization lipoprotein pilotin
RA	3,107,261	C→A	D151Y (GAT→TAT)	pppA ←	bifunctional prepilin leader peptidase/ methylase
RA	3,110,213	T→A	A753A (GCA→GCT)	yghJ ←	DUF4092 family putative lipoprotein peptidase
RA	3,110,751	C→A	R574L (CGT→CTT)	yghJ ←	DUF4092 family putative lipoprotein peptidase
RA	3,111,434	C→A	A346A (GCG→GCT)	yghJ ←	DUF4092 family putative lipoprotein peptidase
RA	3,116,446	A→C	L240R (CTG→CGG)	glcB ←	malate synthase G
RA	3,120,216	C→A	D389Y (GAT→TAT)	glcD ←	glycolate oxidase subunit, FAD‑linked
RA	3,122,356	G→T	L242F (TTG→TTT)	glcC →	glycolate‑inducible glc operon transcriptional repressor; autorepressor
RA	3,122,778	A→C	pseudogene (725/1101 nt)	yghO ←	pseudogene, DNA‑binding transcriptional regulator homology
RA	3,134,528	C→A	D40Y (GAT→TAT)	hybD ←	maturation protease for hydrogenase 2
RA	3,138,648	T→A	N325Y (AAC→TAC)	hybO ←	hydrogenase 2, small subunit
RA	3,138,777	C→A	G282C (GGT→TGT)	hybO ←	hydrogenase 2, small subunit
RA	3,142,668	G→T	L55I (CTC→ATC)	yqhA ←	UPF0114 family putative inner membrane protein
RA	3,143,969	G→T	intergenic (+64/+208)	yghA → / ← exbD	putative oxidoreductase/membrane spanning protein in TonB‑ExbB‑ExbD complex
RA	3,144,158	C→A	intergenic (+253/+19)	yghA → / ← exbD	putative oxidoreductase/membrane spanning protein in TonB‑ExbB‑ExbD complex
RA	3,164,230	C→A	R130S (CGT→AGT)	qseC →	quorum sensing sensory histidine kinase in two‑component regulatory system with QseB
RA	3,169,196	T→A	E57V (GAA→GTA)	yqiA ←	acyl CoA esterase
RA	3,172,251	C→A	R260S (CGC→AGC)	tolC →	transport channel
RA	3,173,669	G→T	A189A (GCG→GCT)	ygiB →	DUF1190 family protein
RA	3,176,733	G→T	intergenic (+51/+439)	zupT → / ← ribB	zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase
RA	3,176,820	G→T	intergenic (+138/+352)	zupT → / ← ribB	zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase
RA	3,182,647	G→T	pseudogene (1868/2445 nt)	yqiG →	pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein
RA	3,184,211	C→A	S74Y (TCT→TAT)	yqiI →	fimbrial protein
RA	3,199,743	C→A	intergenic (‑128/‑79)	ttdR ← / → ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
RA	3,201,209	C→A	F160L (TTC→TTA)	ttdB →	L‑tartrate dehydratase, beta subunit
RA	3,217,289	A→T	H433L (CAC→CTC)	ebgA →	evolved beta‑D‑galactosidase, alpha subunit
RA	3,224,927	C→A	intergenic (+329/‑97)	ygjK → / → fadH	alpha‑glucosidase/2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked
RA	3,230,857	C→G	A63G (GCC→GGC)	ygjR →	putative NAD(P)‑dependent dehydrogenase
RA	3,231,349	A→C	Q227P (CAG→CCG)	ygjR →	putative NAD(P)‑dependent dehydrogenase
RA	3,238,283	C→A	intergenic (‑183/‑180)	uxaC ← / → exuT	uronate isomerase/hexuronate transporter
RA	3,243,768	C→T	intergenic (+33/‑153)	yqjK → / → yqjF	uncharacterized protein/putative quinol oxidase subunit
RA	3,245,848	G→T	L62L (CTG→CTT)	yhaH →	DUF805 family inner membrane protein
RA	3,252,258	C→A	D251Y (GAT→TAT)	tdcG ←	L‑serine dehydratase 3, anaerobic
RA	3,254,752	C→A	V342V (GTG→GTT)	tdcE ←	pyruvate formate‑lyase 4/2‑ketobutyrate formate‑lyase
RA	3,258,871	G→T	L173I (CTC→ATC)	tdcB ←	L‑threonine dehydratase, catabolic
RA	3,261,001	G→A	intergenic (+44/‑212)	tdcR → / → yhaB	L‑threonine dehydratase operon activator protein/uncharacterized protein
RA	3,263,409	C→T	intergenic (+448/+166)	yhaC → / ← rnpB	pentapetide repeats‑related protein/RNase P, M1 RNA component
RA	3,266,646	C→A	G91C (GGT→TGT)	garL ←	alpha‑dehydro‑beta‑deoxy‑D‑glucarate aldolase
RA	3,268,357	C→A	intergenic (‑91/‑284)	garP ← / → garD	putative (D)‑galactarate transporter/(D)‑galactarate dehydrogenase
RA	3,271,128	A→C	T145P (ACC→CCC)	yhaV →	toxin of the SohB(PrlF)‑YhaV toxin‑antitoxin system
RA	3,275,210	A→G	intergenic (+226/‑125)	agaA → / → agaS	pseudogene, N‑acetylgalactosamine‑6‑phosphate deacetylase fragment; putative N‑acetylgalactosamine‑6‑phosphate deacetylase/tagatose‑6‑phosphate ketose/aldose isomerase
RA	3,290,970	A→T	R176R (CGT→CGA)	yraQ ←	putative inner membrane permease
RA	3,295,911	C→A	Q22K (CAG→AAG)	yhbV →	U32 peptidase family protein
RA	3,296,612	G→T	A255A (GCG→GCT)	yhbV →	U32 peptidase family protein
RA	3,299,240	A→C	intergenic (‑64/+90)	mtr ← / ← deaD	tryptophan transporter of high affinity/ATP‑dependent RNA helicase
RA	3,302,027	G→T	S86* (TCG→TAG)	nlpI ←	lipoprotein involved in osmotic sensitivity and filamentation
RA	3,307,024	C→A	G784C (GGT→TGT)	infB ←	translation initiation factor IF‑2
RA	3,312,055	C→A	G20G (GGC→GGA)	argG →	argininosuccinate synthetase
RA	3,314,870	C→A	A35S (GCG→TCG)	yhbX ←	putative EptAB family phosphoethanolamine transferase, inner membrane protein
RA	3,332,963	C→A	A154A (GCG→GCT)	mlaF ←	ABC transporter maintaining OM lipid asymmetry, ATP‑binding protein
RA	3,334,464	C→A	S277R (AGC→AGA)	yrbG →	putative calcium/sodium:proton antiporter
RA	3,334,687	G→T	A21A (GCG→GCT)	kdsD →	D‑arabinose 5‑phosphate isomerase
RA	3,340,038	C→A	I34I (ATC→ATA)	ptsN →	sugar‑specific enzyme IIA component of PTS
RA	3,343,975	C→A	noncoding (40/121 nt)	arcZ →	sRNA positive antisense regulator of rpoS; binds Hfq
RA	3,347,778	G→A	intergenic (‑369/‑306)	yhcC ← / → gltB	putative Fe‑S oxidoreductase, Radical SAM superfamily protein/glutamate synthase, large subunit
RA	3,350,663	C→A	T860T (ACC→ACA)	gltB →	glutamate synthase, large subunit
RA	3,351,650	G→T	E1189D (GAG→GAT)	gltB →	glutamate synthase, large subunit
RA	3,354,405	C→T	intergenic (+430/‑130)	gltD → / → gltF	glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
RA	3,365,607	G→T	I109I (ATC→ATA)	nanT ←	sialic acid transporter
RA	3,373,457	C→A	intergenic (‑101/‑93)	yhcM ← / → yhcB	putative AFG1‑like family P‑loop ATPase/DUF1043 family inner membrane‑anchored protein
RA	3,373,985	C→A	intergenic (+37/‑117)	yhcB → / → degQ	DUF1043 family inner membrane‑anchored protein/serine endoprotease, periplasmic
RA	3,375,260	G→T	D387Y (GAT→TAT)	degQ →	serine endoprotease, periplasmic
RA	3,381,943	C→A	T181T (ACG→ACT)	aaeA ←	p‑hydroxybenzoic acid efflux system component
RA	3,396,082	G→T	R204S (CGT→AGT)	csrD ←	targeting factor for csrBC sRNA degradation
RA	3,403,534	C→T	intergenic (+224/‑105)	prmA → / → dusB	methyltransferase for 50S ribosomal subunit protein L11/tRNA‑dihydrouridine synthase B
RA	3,404,059	C→A	R141S (CGC→AGC)	dusB →	tRNA‑dihydrouridine synthase B
RA	3,407,007	G→A	intergenic (‑183/‑216)	acrS ← / → acrE	acrAB operon transcriptional repressor/cytoplasmic membrane lipoprotein
RA	3,407,969	C→A	N249K (AAC→AAA)	acrE →	cytoplasmic membrane lipoprotein
RA	3,409,856	A→C	T489P (ACC→CCC)	acrF →	multidrug efflux system protein
RA	3,411,250	G→T	E953D (GAG→GAT)	acrF →	multidrug efflux system protein
RA	3,415,702	T→A	L340Q (CTG→CAG)	yhdY →	putative amino‑acid transporter subunit
RA	3,422,726	G→T	V44V (GTG→GTT)	yrdA →	bacterial transferase hexapeptide domain protein
RA	3,424,363	T→A	T138S (ACC→TCC)	tsaC ←	tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein, threonine‑dependent ADP‑forming ATPase
RA	3,433,098	G→T	F87L (TTC→TTA)	rplQ ←	50S ribosomal subunit protein L17
RA	3,440,151	G→T	I31I (ATC→ATA)	rpsN ←	30S ribosomal subunit protein S14
RA	3,440,444	G→T	S118S (TCC→TCA)	rplE ←	50S ribosomal subunit protein L5
RA	3,440,832	T→C	N99D (AAC→GAC)	rplX ←	50S ribosomal subunit protein L24
RA	3,445,410	C→A	R79L (CGT→CTT)	rplD ←	50S ribosomal subunit protein L4
RA	3,448,742	C→A	E6* (GAA→TAA)	gspA ←	general secretory pathway component, cryptic
RA	3,455,867	C→A	I55I (ATC→ATA)	gspJ →	putative general secretory pathway component, cryptic
RA	3,455,930	C→A	I76I (ATC→ATA)	gspJ →	putative general secretory pathway component, cryptic
RA	3,470,272	C→A	V169V (GTG→GTT)	fkpA ←	FKBP‑type peptidyl‑prolyl cis‑trans isomerase (rotamase)
RA	3,471,705	C→T	G51D (GGT→GAT)	slyD ←	FKBP‑type peptidyl prolyl cis‑trans isomerase (rotamase)
RA	3,473,139	G→T	I276I (ATC→ATA)	kefB ←	potassium:proton antiporter
RA	3,475,255	C→A	S203Y (TCT→TAT)	yheS →	putative transporter subunit of ABC superfamily: ATP‑binding component
RA	3,475,763	G→T	A372A (GCG→GCT)	yheS →	putative transporter subunit of ABC superfamily: ATP‑binding component
RA	3,479,769	A→T	E97D (GAA→GAT)	crp →	cAMP‑activated global transcription factor, mediator of catabolite repression
RA	3,487,342	C→T	intergenic (+234/‑28)	tsgA → / → nirB	putative transporter/nitrite reductase, large subunit, NAD(P)H‑binding
RA	3,488,966	G→C	A533P (GCC→CCC)	nirB →	nitrite reductase, large subunit, NAD(P)H‑binding
RA	3,489,397	C→A	F676L (TTC→TTA)	nirB →	nitrite reductase, large subunit, NAD(P)H‑binding
RA	3,493,210	C→T	intergenic (+236/‑59)	yhfL → / → frlA	small lipoprotein/putative fructoselysine transporter
RA	3,501,571	C→A	G127C (GGC→TGC)	php ←	phosphotriesterase homology protein
RA	3,504,143	G→T	R65S (CGT→AGT)	yhfX ←	putative pyridoxal 5'‑phosphate binding protein
RA	3,507,749	G→T	H224N (CAT→AAT)	rpe ←	D‑ribulose‑5‑phosphate 3‑epimerase
RA	3,509,102	G→T	S57R (AGC→AGA)	dam ←	DNA adenine methyltransferase
RA	3,513,424	A→T	V213V (GTT→GTA)	hofQ ←	DNA catabolic putative fimbrial transporter
RA	3,518,052	C→A	P608Q (CCG→CAG)	mrcA →	fused penicillin‑binding protein 1a: murein transglycosylase/murein transpeptidase
RA	3,519,188	C→A	L107L (CTG→CTT)	nudE ←	adenosine nucleotide hydrolase; substrates include Ap3A, Ap2A, ADP‑ribose, NADH
RA	3,519,657	G→T	intergenic (‑149/‑171)	nudE ← / → yrfF	adenosine nucleotide hydrolase; substrates include Ap3A, Ap2A, ADP‑ribose, NADH/inner membrane protein
RA	3,528,406	G→T	I274I (ATC→ATA)	envZ ←	sensory histidine kinase in two‑component regulatory system with OmpR
RA	3,535,370	C→A	S535R (AGC→AGA)	feoB →	fused ferrous iron transporter, protein B: GTP‑binding protein/membrane protein
RA	3,538,583	C→A	R115S (CGC→AGC)	gntX →	DNA catabolic protein
RA	3,543,959	G→T	A625E (GCG→GAG)	malP ←	maltodextrin phosphorylase
RA	3,545,077	C→A	L252L (CTG→CTT)	malP ←	maltodextrin phosphorylase
RA	3,561,574	C→A	W372L (TGG→TTG)	glgC ←	glucose‑1‑phosphate adenylyltransferase
RA	3,566,100	G→T	R255S (CGC→AGC)	glgB ←	1,4‑alpha‑glucan branching enzyme
RA	3,567,059	C→A	intergenic (‑197/+76)	glgB ← / ← asd	1,4‑alpha‑glucan branching enzyme/aspartate‑semialdehyde dehydrogenase, NAD(P)‑binding
RA	3,571,015	C→T	intergenic (‑63/+76)	gntK ← / ← gntR	gluconate kinase 2/d‑gluconate inducible gluconate regulon transcriptional repressor
RA	3,571,153	C→A	E312* (GAA→TAA)	gntR ←	d‑gluconate inducible gluconate regulon transcriptional repressor
RA	3,575,032	C→A	intergenic (+46/‑191)	yhhY → / → yhhZ	putative acetyltransferase/putative Hcp1 family polymorphic toxin protein; putative colicin‑like DNase/tRNase activity
RA	3,576,745	G→T	pseudogene (348/381 nt)	yrhA →	pseudogene, interrupted by IS1E
RA	3,577,827	A→G	intergenic (+158/‑292)	yrhA → / → yrhB	pseudogene, interrupted by IS1E/stable heat shock chaperone
RA	3,582,807	G→T	P194Q (CCG→CAG)	ugpE ←	glycerol‑3‑phosphate transporter subunit
RA	3,590,636	G→T	Y95* (TAC→TAA)	livK ←	leucine transporter subunit
RA	3,590,906	C→A	A5A (GCG→GCT)	livK ←	leucine transporter subunit
RA	3,591,957	T→G	V354V (GTA→GTC)	livJ ←	leucine/isoleucine/valine transporter subunit
RA	3,594,268	C→T	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	T446T (ACG→ACT)	ftsY ←	Signal Recognition Particle (SRP) receptor
RA	3,598,440	C→A	N34K (AAC→AAA)	yhhL →	DUF1145 family protein
RA	3,604,608	C→A	A162A (GCG→GCT)	yhhS ←	putative arabinose efflux transporter
RA	3,607,110	C→A	I28I (ATC→ATA)	nikA →	nickel‑binding, heme‑binding periplasmic protein
RA	3,612,284	G→T	D113Y (GAT→TAT)	nikR →	transcriptional repressor, Ni‑binding
RA	3,618,536	C→A	R267R (CGG→AGG)	yhhI →	putative transposase
RA	3,622,058	C→A	D281Y (GAT→TAT)	rbbA ←	ribosome‑associated ATPase: ATP‑binding protein/ATP‑binding membrane protein
RA	3,629,424	T→A	intergenic (+171/+144)	yhiM → / ← yhiN	acid resistance protein, inner membrane/putative oxidoreductase
RA	3,633,710	A→T	P80P (CCA→CCT)	uspA →	universal stress global response regulator
RA	3,638,641	C→A	intergenic (‑99/‑104)	prlC ← / → rlmJ	oligopeptidase A/23S rRNA m(6)A2030 methyltransferase, SAM‑dependent
RA	3,639,239	G→T	P165P (CCG→CCT)	rlmJ →	23S rRNA m(6)A2030 methyltransferase, SAM‑dependent
RA	3,644,531	G→A	intergenic (+509/‑120)	arsC → / → yhiS	arsenate reductase/pseudogene
RA	3,646,984	G→T	pseudogene (394/483 nt)	yhiS →	pseudogene
RA	3,649,797	C→A	E102* (GAA→TAA)	hdeA ←	stress response protein acid‑resistance protein
RA	3,657,375	G→A	P202S (CCT→TCT)	gadW ←	transcriptional activator of gadA and gadBC; repressor of gadX
RA	3,661,610	A→T	F313L (TTT→TTA)	yhjA ←	putative cytochrome C peroxidase
RA	3,662,660	T→C	intergenic (‑112/‑292)	yhjA ← / → treF	putative cytochrome C peroxidase/cytoplasmic trehalase
RA	3,665,383	G→T	intergenic (‑129/‑391)	yhjB ← / → yhjC	putative DNA‑binding transcriptional response regulator/LysR family putative transcriptional regulator
RA	3,667,959	C→A	intergenic (+224/‑187)	yhjD → / → yhjE	inner membrane putative BrbK family alternate lipid exporter/MFS superfamily sugar transport 1 family protein
RA	3,674,442	G→T	R287S (CGT→AGT)	yhjJ ←	putative periplasmic M16 family chaperone
RA	3,674,730	C→A	D191Y (GAT→TAT)	yhjJ ←	putative periplasmic M16 family chaperone
RA	3,679,301	T→G	Q1078P (CAG→CCG)	bcsC ←	cellulose synthase subunit
RA	3,679,324	C→A	M1070I (ATG→ATT)	bcsC ←	cellulose synthase subunit
RA	3,680,910	G→T	H542N (CAT→AAT)	bcsC ←	cellulose synthase subunit
RA	3,686,345	C→A	R751L (CGC→CTC)	bcsA ←	cellulose synthase, catalytic subunit
RA	3,691,787	C→T	L72L (CTG→TTG)	bcsG →	DUF3260 family inner membrane protein associated with cellulose production
RA	3,692,994	T→A	F474Y (TTC→TAC)	bcsG →	DUF3260 family inner membrane protein associated with cellulose production
RA	3,698,119	C→A	M1M (ATG→ATT) †	dppC ←	dipeptide/heme transporter
RA	3,698,875	G→T	F92L (TTC→TTA)	dppB ←	dipeptide/heme transporter
RA	3,717,788	C→A	P297P (CCG→CCT)	glyQ ←	glycine tRNA synthetase, alpha subunit
RA	3,722,763	C→A	intergenic (‑32/+40)	xylB ← / ← xylA	xylulokinase/D‑xylose isomerase
RA	3,722,949	C→A	E393* (GAA→TAA)	xylA ←	D‑xylose isomerase
RA	3,727,580	C→A	A167A (GCC→GCA)	xylH →	D‑xylose ABC transporter permease subunit
RA	3,729,221	C→A	R295S (CGT→AGT)	xylR →	xylose divergent operon transcriptional activator
RA	3,729,325	C→A	T329T (ACC→ACA)	xylR →	xylose divergent operon transcriptional activator
RA	3,732,549	G→T	D565Y (GAT→TAT)	malS →	alpha‑amylase
RA	3,736,722	C→A	G210G (GGC→GGA)	yiaK →	2,3‑diketo‑L‑gulonate reductase, NADH‑dependent
RA	3,738,088	T→A	F134Y (TTC→TAC)	yiaM →	2,3‑diketo‑L‑gulonate TRAP transporter small permease protein
RA	3,738,431	C→A	P90T (CCA→ACA)	yiaN →	2,3‑diketo‑L‑gulonate TRAP transporter large permease protein
RA	3,751,135	G→T	S18* (TCA→TAA)	yiaY ←	putative Fe‑containing alcohol dehydrogenase, Pfam00465 family
RA	3,751,360	C→T	intergenic (‑173/+17)	yiaY ← / ← selB	putative Fe‑containing alcohol dehydrogenase, Pfam00465 family/selenocysteinyl‑tRNA‑specific translation factor
RA	3,767,000	G→T	D454Y (GAC→TAC)	mtlA →	fused mannitol‑specific PTS enzymes: IIA components/IIB components/IIC components
RA	3,767,410	G→T	V590V (GTG→GTT)	mtlA →	fused mannitol‑specific PTS enzymes: IIA components/IIB components/IIC components
RA	3,772,732	G→T	A107S (GCC→TCC)	lldR →	dual role activator/repressor for lldPRD operon
RA	3,780,573	C→A	R126S (CGT→AGT)	envC →	activator of AmiB,C murein hydrolases, septal ring factor
RA	3,782,439	G→T	R335S (CGC→AGC)	waaH ←	LPS(HepIII)‑glucuronic acid glycosyltransferase
RA	3,783,727	C→A	A327S (GCT→TCT)	tdh ←	L‑threonine 3‑dehydrogenase, NAD(P)‑binding
RA	3,784,878	A→T	L345Q (CTG→CAG)	kbl ←	glycine C‑acetyltransferase
RA	3,785,915	G→T	intergenic (‑4/+271)	kbl ← / ← yibB	glycine C‑acetyltransferase/YibB family protein, function unknown
RA	3,789,381	C→A	L15I (CTC→ATC)	waaC →	ADP‑heptose:LPS heptosyl transferase I
RA	3,798,582	C→A	Q243H (CAG→CAT)	waaP ←	kinase that phosphorylates core heptose of lipopolysaccharide
RA	3,810,195	C→A	R54S (CGT→AGT)	yicC →	UPF0701 family protein
RA	3,816,601	A→T	H281L (CAC→CTC)	spoT →	bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
RA	3,817,604	G→T	V615V (GTG→GTT)	spoT →	bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
RA	3,818,010	C→A	H46N (CAT→AAT)	trmH →	tRNA mG18‑2'‑O‑methyltransferase, SAM‑dependent
RA	3,824,948	T→A	W378R (TGG→AGG)	yicH →	putative inner membrane‑anchored periplasmic AsmA family protein
RA	3,825,702	C→A	K732N (AAG→AAT)	yicI ←	putative alpha‑glucosidase
RA	3,828,206	T→A	S362C (AGT→TGT)	yicJ ←	putative transporter
RA	3,830,197	C→A	intergenic (+281/‑116)	yicT → / → setC	pseudogene/putative arabinose efflux transporter
RA	3,830,311	G→T	intergenic (+395/‑2)	yicT → / → setC	pseudogene/putative arabinose efflux transporter
RA	3,830,819	T→G	F169L (TTT→TTG)	setC →	putative arabinose efflux transporter
RA	3,832,308	G→C	S234T (AGT→ACT)	yicL →	EamA family inner membrane putative transporter
RA	3,839,798	C→A	D244Y (GAT→TAT)	uhpT ←	hexose phosphate transporter
JC	3,841,419	(CCAGCAA)1→2	coding (566/1320 nt)	uhpC ←	membrane protein regulates uhpT expression
RA	3,842,467	C→A	G344W (GGG→TGG)	uhpB ←	sensory histidine kinase in two‑component regulatory sytem with UhpA
RA	3,860,159	C→A	P33P (CCG→CCT)	ibpB ←	heat shock chaperone
RA	3,860,327	C→A	intergenic (‑70/+42)	ibpB ← / ← ibpA	heat shock chaperone/heat shock chaperone
RA	3,860,653	C→A	E44* (GAA→TAA)	ibpA ←	heat shock chaperone
RA	3,861,553	C→A	G373C (GGC→TGC)	yidR ←	DUF3748 family protein
RA	3,863,438	G→T	M234I (ATG→ATT)	cbrA →	colicin M resistance protein; FAD‑binding protein, putative oxidoreductase
RA	3,865,120	C→A	intergenic (‑30/+90)	dgoT ← / ← dgoD	D‑galactonate transporter/galactonate dehydratase
RA	3,865,863	T→A	T166S (ACC→TCC)	dgoD ←	galactonate dehydratase
RA	3,869,711	A→C	V201G (GTG→GGG)	yidA ←	sugar phosphate phosphatase; substrates include erythrose 4‑P and mannose 1‑P phosphatase
RA	3,871,587	G→T	N631K (AAC→AAA)	gyrB ←	DNA gyrase, subunit B
RA	3,872,006	T→A	S492C (AGC→TGC)	gyrB ←	DNA gyrase, subunit B
RA	3,872,381	C→A	D367Y (GAC→TAC)	gyrB ←	DNA gyrase, subunit B
RA	3,875,148	C→A	A178A (GCG→GCT)	dnaN ←	DNA polymerase III, beta subunit
RA	3,875,671	G→A	T4I (ACC→ATC)	dnaN ←	DNA polymerase III, beta subunit
RA	3,880,731	G→T	D182Y (GAT→TAT)	mnmE →	tRNA U34 5‑methylaminomethyl‑2‑thiouridine modification GTPase
RA	3,886,162	T→G	L13R (CTG→CGG)	yidZ →	putative DNA‑binding transcriptional regulator
RA	3,890,808	A→T	intergenic (+9/‑58)	yieH → / → cbrB	phosphoenolpyruvate and 6‑phosphogluconate phosphatase/PRK09823 family inner membrane protein, creBC regulon
RA	3,890,960	T→A	F32Y (TTC→TAC)	cbrB →	PRK09823 family inner membrane protein, creBC regulon
RA	3,892,304	C→A	P150P (CCG→CCT)	yieK ←	putative 6‑phosphogluconolactonase
RA	3,901,415	C→A	P104P (CCG→CCT)	pstB ←	phosphate transporter subunit
RA	3,904,553	T→A	P111P (CCA→CCT)	pstS ←	periplasmic phosphate binding protein, high‑affinity
RA	3,906,384	G→T	I215I (ATC→ATA)	glmS ←	L‑glutamine:D‑fructose‑6‑phosphate aminotransferase
RA	3,910,416	C→A	R107L (CGT→CTT)	atpD ←	F1 sector of membrane‑bound ATP synthase, beta subunit
RA	3,910,448	G→T	V96V (GTC→GTA)	atpD ←	F1 sector of membrane‑bound ATP synthase, beta subunit
RA	3,910,894	C→A	M244I (ATG→ATT)	atpG ←	F1 sector of membrane‑bound ATP synthase, gamma subunit
RA	3,916,830	C→A	D71Y (GAT→TAT)	rsmG ←	16S rRNA m(7)G527 methyltransferase, SAM‑dependent; glucose‑inhibited cell‑division protein
RA	3,917,554	C→A	L480L (CTG→CTT)	mnmG ←	5‑methylaminomethyl‑2‑thiouridine modification at tRNA U34
RA	3,923,028	C→A	D476Y (GAC→TAC)	ravA ←	hexameric AAA+ MoxR family ATPase, putative molecular chaperone
RA	3,924,313	C→G	P47P (CCG→CCC)	ravA ←	hexameric AAA+ MoxR family ATPase, putative molecular chaperone
RA	3,925,821	G→T	S382S (TCG→TCT)	kup →	potassium transporter
RA	3,926,831	G→T	D41Y (GAT→TAT)	rbsD →	putative cytoplasmic sugar‑binding protein
RA	3,927,972	G→T	E279* (GAA→TAA)	rbsA →	fused D‑ribose transporter subunits of ABC superfamily: ATP‑binding components
RA	3,928,761	G→T	P38P (CCG→CCT)	rbsC →	D‑ribose transporter subunit
RA	3,930,738	G→T	E29* (GAA→TAA)	rbsK →	ribokinase
RA	3,931,021	C→A	A123E (GCG→GAG)	rbsK →	ribokinase
RA	3,935,100	G→T	intergenic (‑413/‑68)	yieP ← / → rrsC	putative transcriptional regulator/16S ribosomal RNA of rrnC operon
RA	3,936,831	C→A	noncoding (37/76 nt)	gltU →	tRNA‑Glu
RA	3,936,834	G→T	noncoding (40/76 nt)	gltU →	tRNA‑Glu
RA	3,945,181	G→T	pseudogene (280/663 nt)	ilvG →	pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive; acetolactate synthase II, large subunit, cryptic, interrupted
RA	3,959,351	G→T	P77P (CCG→CCT)	trxA →	thioredoxin 1
RA	3,960,036	G→A	R87H (CGC→CAC)	rho →	transcription termination factor
RA	3,966,854	C→A	R325S (CGT→AGT)	rffG →	dTDP‑glucose 4,6‑dehydratase
RA	3,967,474	G→T	A169A (GCG→GCT)	rffH →	glucose‑1‑phosphate thymidylyltransferase
RA	3,969,710	G→T	G25C (GGT→TGT)	wzxE →	O‑antigen translocase
RA	3,972,296	G→T	E112D (GAG→GAT)	wzyE →	putative ECA polysaccharide chain elongation protein
RA	3,973,393	C→A	A26A (GCC→GCA)	wecG →	UDP‑N‑acetyl‑D‑mannosaminuronic acid transferase
RA	3,983,298	G→T	R277S (CGC→AGC)	hemC ←	hydroxymethylbilane synthase
RA	3,988,075	T→A	V65E (GTG→GAG)	yifL →	putative lipoprotein
RA	3,993,534	A→G	intergenic (+29/+118)	uvrD → / ← yigE	DNA‑dependent ATPase I and helicase II/DUF2233 family protein
RA	3,993,566	A→G	intergenic (+61/+86)	uvrD → / ← yigE	DNA‑dependent ATPase I and helicase II/DUF2233 family protein
RA	3,994,076	A→T	L114* (TTA→TAA)	yigE ←	DUF2233 family protein
RA	3,994,247	A→T	V57E (GTG→GAG)	yigE ←	DUF2233 family protein
RA	3,996,346	T→A	I70F (ATC→TTC)	yigG ←	PRK11371 family inner membrane protein
RA	4,009,705	G→A	intergenic (‑176/‑86)	ysgA ← / → udp	putative carboxymethylenebutenolidase/uridine phosphorylase
RA	4,020,049	C→G	P55A (CCG→GCG)	fre →	NAD(P)H‑flavin reductase
RA	4,024,827	G→T	D103Y (GAT→TAT)	pepQ →	proline dipeptidase
RA	4,034,118	G→T	intergenic (+122/+148)	rrfA → / ← mobB	5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B
RA	4,035,421	G→T	intergenic (‑62/‑8)	mobA ← / → yihD	molybdopterin‑guanine dinucleotide synthase/DUF1040 protein YihD
RA	4,036,012	G→T	D80Y (GAT→TAT)	srkA →	stress response kinase A; MazF antagonist; Thr/Ser kinase involved in Cpx stress response
RA	4,037,484	T→A	intergenic (+80/‑75)	dsbA → / → yihF	periplasmic protein disulfide isomerase I/DUF945 family protein
RA	4,040,044	A→C	intergenic (‑82/‑282)	yihG ← / → polA	inner membrane protein, inner membrane acyltransferase/fused DNA polymerase I 5'‑>3' polymerase/3'‑>5' exonuclease/5'‑>3' exonuclease
RA	4,045,302	G→T	intergenic (+86/‑103)	yihI → / → hemN	activator of Der GTPase/coproporphyrinogen III oxidase, SAM and NAD(P)H dependent, oxygen‑independent
RA	4,045,386	G→T	intergenic (+170/‑19)	yihI → / → hemN	activator of Der GTPase/coproporphyrinogen III oxidase, SAM and NAD(P)H dependent, oxygen‑independent
RA	4,046,172	A→T	K256N (AAA→AAT)	hemN →	coproporphyrinogen III oxidase, SAM and NAD(P)H dependent, oxygen‑independent
RA	4,053,774	G→T	intergenic (+184/‑33)	typA → / → yihL	GTP‑binding protein/putative DNA‑binding transcriptional regulator
RA	4,056,018	T→A	F138I (TTC→ATC)	yihN →	MFS transporter family protein
RA	4,057,396	A→T	L87* (TTA→TAA)	ompL ←	outer membrane porin L
RA	4,058,809	G→T	I106I (ATC→ATA)	yihO ←	putative transporter
RA	4,059,896	G→T	T220N (ACC→AAC)	yihP ←	putative transporter
RA	4,062,424	G→T	I71I (ATC→ATA)	yihQ ←	alpha‑glucosidase
RA	4,063,127	T→A	N212I (AAT→ATT)	yihR ←	mutarotase superfamily protein, YihR family
RA	4,066,133	T→G	S267R (AGC→CGC)	yihU ←	gamma‑hydroxybutyrate dehydrogenase, NADH‑dependent
RA	4,068,208	C→A	G60G (GGC→GGA)	yihW →	DeoR family putative transcriptional regulator
RA	4,070,543	G→T	D57Y (GAT→TAT)	dtd →	D‑tyr‑tRNA(Tyr) deacylase
RA	4,074,579	G→T	R4S (CGC→AGC)	fdhE ←	formate dehydrogenase formation protein
RA	4,075,234	C→A	D296Y (GAC→TAC)	fdoH ←	formate dehydrogenase‑O, Fe‑S subunit
RA	4,088,850	C→A	R93S (CGT→AGT)	rhaR →	transcriptional activator of rhaSR
RA	4,094,362	C→A	W181L (TGG→TTG)	cpxA ←	sensory histidine kinase in two‑component regulatory system with CpxR
RA	4,097,822	G→T	E115* (GAA→TAA)	pfkA →	6‑phosphofructokinase I
RA	4,108,175	C→T	intergenic (‑157/‑268)	glpF ← / → zapB	glycerol facilitator/FtsZ stabilizer; septal ring assembly factor, stimulates cell division
RA	4,109,064	G→T	G65G (GGC→GGA)	rraA ←	ribonuclease E (RNase E) inhibitor protein
RA	4,117,673	G→T	T50T (ACC→ACA)	yiiX ←	putative lipid binding hydrolase, DUF830 family protein
RA	4,122,248	A→T	intergenic (+53/‑296)	metL → / → metF	Bifunctional aspartokinase/homoserine dehydrogenase 2/5,10‑methylenetetrahydrofolate reductase
RA	4,124,384	C→A	H208N (CAT→AAT)	katG →	catalase‑peroxidase HPI, heme b‑containing
RA	4,125,407	C→A	H549N (CAT→AAT)	katG →	catalase‑peroxidase HPI, heme b‑containing
RA	4,127,022	T→G	E188D (GAA→GAC)	yijF ←	DUF1287 family protein
RA	4,135,168	G→T	V416L (GTA→TTA)	pflD →	putative glycine radical domain‑containing pyruvate formate‑lyase
RA	4,150,054	G→T	S222Y (TCT→TAT)	sthA ←	pyridine nucleotide transhydrogenase, soluble
RA	4,161,564	T→G	intergenic (+92/‑1)	rrlB → / → rrfB	23S ribosomal RNA of rrnB operon/5S ribosomal RNA of rrnB operon
RA	4,172,507	C→A	I445I (ATC→ATA)	rpoB →	RNA polymerase, beta subunit
RA	4,173,145	A→T	Q658L (CAG→CTG)	rpoB →	RNA polymerase, beta subunit
RA	4,173,179	G→T	P669P (CCG→CCT)	rpoB →	RNA polymerase, beta subunit
RA	4,176,823	G→T	D516Y (GAC→TAC)	rpoC →	RNA polymerase, beta prime subunit
RA	4,178,969	G→T	R1231L (CGT→CTT)	rpoC →	RNA polymerase, beta prime subunit
RA	4,185,155	G→T	I291I (ATC→ATA)	thiC ←	phosphomethylpyrimidine synthase
RA	4,193,578	G→T	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	M172I (ATG→ATT)	aceA →	isocitrate lyase
RA	4,210,753	C→A	E555* (GAA→TAA)	arpA ←	ankyrin repeat protein
RA	4,211,576	G→T	S280R (AGC→AGA)	arpA ←	ankyrin repeat protein
RA	4,211,803	G→A	P205S (CCT→TCT)	arpA ←	ankyrin repeat protein
RA	4,213,578	C→A	intergenic (‑22/‑178)	iclR ← / → metH	transcriptional repressor/homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent
RA	4,214,563	A→T	T270S (ACC→TCC)	metH →	homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent
RA	4,214,809	G→T	E352* (GAA→TAA)	metH →	homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent
RA	4,224,685	G→T	A334S (GCG→TCG)	pgi →	glucosephosphate isomerase
RA	4,225,741	G→T	intergenic (+406/‑93)	pgi → / → yjbE	glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein
RA	4,225,841	A→C	K3T (AAA→ACA)	yjbE →	extracellular polysaccharide production threonine‑rich protein
RA	4,230,049	G→T	intergenic (‑66/‑204)	yjbT ← / → psiE	putative periplasmic protein/phosphate starvation inducible protein
RA	4,230,913	A→T	W424R (TGG→AGG)	xylE ←	D‑xylose transporter
RA	4,235,869	G→T	A160E (GCG→GAG)	malE ←	maltose transporter subunit
RA	4,235,916	G→T	N144K (AAC→AAA)	malE ←	maltose transporter subunit
RA	4,236,666	C→A	intergenic (‑319/‑46)	malE ← / → malK	maltose transporter subunit/fused maltose transport subunit, ATP‑binding component of ABC superfamily/regulatory protein
RA	4,241,153	G→T	pseudogene (265/1323 nt)	yjbI →	pseudogene, SopA‑related, pentapeptide repeats‑containing
RA	4,242,509	C→T	L26F (CTC→TTC)	ubiC →	chorismate‑‑pyruvate lyase
RA	4,245,537	G→T	N286K (AAC→AAA)	plsB ←	glycerol‑3‑phosphate O‑acyltransferase
RA	4,247,370	G→T	D110Y (GAT→TAT)	lexA →	transcriptional repressor of SOS regulon
RA	4,249,117	G→T	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	V256V (GTA→GTT)	dnaB →	replicative DNA helicase
RA	4,258,754	T→A	T63S (ACG→TCG)	yjbS ←	uncharacterized protein
RA	4,265,064	C→A	intergenic (‑95/‑335)	yjcB ← / → yjcC	putative inner membrane protein/putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	4,265,089	T→A	intergenic (‑120/‑310)	yjcB ← / → yjcC	putative inner membrane protein/putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	4,266,208	T→A	S270S (TCT→TCA)	yjcC →	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	4,266,318	G→T	R307L (CGT→CTT)	yjcC →	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	4,269,869	C→A	intergenic (+113/‑39)	yjcD → / → yjcE	inner membrane putative guanine permease/putative cation/proton antiporter
RA	4,274,926	A→C	I72M (ATT→ATG)	yjcH ←	DUF485 family inner membrane protein
RA	4,275,142	C→A	intergenic (‑1/+199)	yjcH ← / ← acs	DUF485 family inner membrane protein/acetyl‑CoA synthetase
RA	4,275,862	C→A	D480Y (GAT→TAT)	acs ←	acetyl‑CoA synthetase
RA	4,288,086	G→T	F366L (TTC→TTA)	fdhF ←	formate dehydrogenase‑H, selenopolypeptide subunit
RA	4,290,080	G→T	I256I (ATC→ATA)	mdtP ←	outer membrane factor of efflux pump
RA	4,297,485	G→C	G44G (GGC→GGG)	alsK ←	D‑allose kinase
RA	4,297,846	C→A	M150I (ATG→ATT)	alsE ←	allulose‑6‑phosphate 3‑epimerase
RA	4,303,614	T→A	*150R (TGA→AGA)	rpiB →	ribose 5‑phosphate isomerase B/allose 6‑phosphate isomerase
RA	4,318,517	A→T	T522T (ACA→ACT)	crfC →	clamp‑binding sister replication fork colocalization protein, dynamin‑related
RA	4,321,863	A→T	intergenic (+42/‑70)	proP → / → pmrR	proline/glycine betaine transporter/putative membrane‑bound BasS regulator
RA	4,329,774	C→A	D189Y (GAC→TAC)	adiA ←	arginine decarboxylase
RA	4,330,430	(T)5→4	intergenic (‑92/+107)	adiA ← / ← melR	arginine decarboxylase/melibiose operon transcriptional regulator; autoregulator
RA	4,337,551	C→A	V337V (GTG→GTT)	dcuB ←	C4‑dicarboxylate transporter, anaerobic; DcuS co‑sensor
RA	4,341,023	A→T	Y153N (TAC→AAC)	dcuS ←	sensory histidine kinase in two‑component regulatory system with DcuR, regulator of anaerobic fumarate respiration
RA	4,350,223	G→A	A510V (GCT→GTT)	cadC ←	cadBA operon transcriptional activator
RA	4,352,529	C→A	intergenic (‑86/+21)	pheU ← / ← yjdC	tRNA‑Phe/putative transcriptional regulator
RA	4,358,390	A→C	intergenic (‑246/‑91)	aspA ← / → fxsA	aspartate ammonia‑lyase/suppressor of F exclusion of phage T7
RA	4,358,920	G→T	R147L (CGC→CTC)	fxsA →	suppressor of F exclusion of phage T7
RA	4,366,322	A→C	intergenic (+63/‑48)	ecnA → / → ecnB	entericidin A membrane lipoprotein, antidote entericidin B/entericidin B membrane lipoprotein
RA	4,376,178	C→A	E1004* (GAA→TAA)	mscM ←	mechanosensitive channel protein, miniconductance
RA	4,378,778	G→T	S137* (TCG→TAG)	mscM ←	mechanosensitive channel protein, miniconductance
RA	4,380,610	G→T	I239I (ATC→ATA)	rsgA ←	ribosome small subunit‑dependent GTPase A
RA	4,381,504	T→A	I28I (ATT→ATA)	orn →	oligoribonuclease
RA	4,382,218	C→A	noncoding (42/76 nt)	glyV →	tRNA‑Gly
RA	4,384,268	C→A	S129* (TCG→TAG)	nnr →	bifunctional NAD(P)H‑hydrate repair enzyme; C‑terminal domain ADP‑dependent (S)‑NAD(P)H‑hydrate dehydratase and N‑terminal domain NAD(P)H‑hydrate epimerase
RA	4,388,902	G→T	A558A (GCG→GCT)	mutL →	methyl‑directed mismatch repair protein
RA	4,394,875	G→T	A124A (GCG→GCT)	purA →	adenylosuccinate synthetase
RA	4,396,598	A→T	E43V (GAA→GTA)	rnr →	exoribonuclease R, RNase R
RA	4,402,850	G→T	L2L (CTG→CTT)	yjfC →	ATP‑Grasp family ATPase
RA	4,404,169	G→T	A26A (GCG→GCT)	aidB →	DNA alkylation damage repair protein; flavin‑containing DNA binding protein, weak isovaleryl CoA dehydrogenase
RA	4,405,730	G→T	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	R12L (CGG→CTG)	bsmA ←	bioflm peroxide resistance protein
RA	4,410,964	A→C	I390L (ATC→CTC)	ulaA →	L‑ascorbate‑specific enzyme IIC permease component of PTS
RA	4,412,786	G→T	E42* (GAA→TAA)	ulaE →	L‑xylulose 5‑phosphate 3‑epimerase
RA	4,417,122	G→T	R40S (CGT→AGT)	yjfZ ←	uncharacterized protein
RA	4,417,551	A→C	pseudogene (41/402 nt)	ytfA →	pseudogene, related to transcriptional regulators
RA	4,427,647	G→A	D42N (GAT→AAT)	ytfI →	uncharacterized protein
RA	4,428,092	G→T	G190V (GGA→GTA)	ytfI →	uncharacterized protein
RA	4,432,031	G→A	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	P111H (CCT→CAT)	tamB →	translocation and assembly module for autotransporter export, inner membrane subunit
RA	4,436,662	G→T	G912C (GGT→TGT)	tamB →	translocation and assembly module for autotransporter export, inner membrane subunit
RA	4,445,719	A→T	T40S (ACC→TCC)	mpl →	UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase
RA	4,452,700	G→T	intergenic (‑223/+171)	nrdD ← / ← treC	anaerobic ribonucleoside‑triphosphate reductase/trehalose‑6‑P hydrolase
RA	4,456,233	G→T	I277I (ATC→ATA)	treR ←	trehalose 6‑phosphate‑inducible trehalose regulon transcriptional repressor
RA	4,457,282	G→T	R12I (AGA→ATA)	mgtL →	regulatory leader peptide for mgtA
RA	4,457,499	C→A	R20S (CGT→AGT)	mgtA →	magnesium transporter
RA	4,458,254	T→A	V271V (GTT→GTA)	mgtA →	magnesium transporter
RA	4,458,609	G→T	D390Y (GAT→TAT)	mgtA →	magnesium transporter
RA	4,458,948	G→T	D503Y (GAT→TAT)	mgtA →	magnesium transporter
RA	4,465,936	T→A	L228* (TTA→TAA)	yjgL →	uncharacterized protein
RA	4,468,165	A→G	intergenic (‑37/‑125)	argI ← / → rraB	ornithine carbamoyltransferase 1/protein inhibitor of RNase E
RA	4,469,550	G→A	A2T (GCT→ACT)	yjgN →	DUF898 family inner membrane protein
RA	4,470,017	G→A	M157I (ATG→ATA)	yjgN →	DUF898 family inner membrane protein
RA	4,470,873	G→T	R928S (CGT→AGT)	valS ←	valyl‑tRNA synthetase
RA	4,471,930	T→A	P575P (CCA→CCT)	valS ←	valyl‑tRNA synthetase
RA	4,480,139	G→T	A273E (GCG→GAG)	idnR ←	transcriptional repressor, 5‑gluconate‑binding
RA	4,493,435	T→C	intergenic (‑187/‑440)	insG ← / → yjhB	IS4 transposase/putative transporter
RA	4,494,721	G→A	A283T (GCC→ACC)	yjhB →	putative transporter
RA	4,495,859	T→G	D252E (GAT→GAG)	yjhC →	putative oxidoreductase
RA	4,499,530	G→T	pseudogene (705/785 nt)	insO →	pseudogene, IS911 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related
RA	4,505,141	G→T	R452S (CGT→AGT)	fecA ←	ferric citrate outer membrane transporter
RA	4,512,693	T→A	K407* (AAG→TAG)	yjhG ←	putative dehydratase
RA	4,520,701	G→T	G256G (GGC→GGA)	sgcX ←	putative endoglucanase with Zn‑dependent exopeptidase domain
RA	4,523,001	T→A	intergenic (‑1/+55)	yjhP ← / ← yjhQ	putative methyltransferase/putative acetyltransferase
RA	4,525,234	G→A	pseudogene (415/1029 nt)	yjhR →	pseudogene, helicase family; putative frameshift suppressor
RA	4,531,143	A→T	I124F (ATT→TTT)	fimB →	tyrosine recombinase/inversion of on/off regulator of fimA
RA	4,533,538	A→T	intergenic (+58/‑7)	fimA → / → fimI	major type 1 subunit fimbrin (pilin)/fimbrial protein involved in type 1 pilus biosynthesis
RA	4,536,446	A→T	K512* (AAG→TAG)	fimD →	fimbrial usher outer membrane porin protein; FimCD chaperone‑usher
RA	4,541,306	C→T	intergenic (‑193/‑147)	gntP ← / → uxuA	fructuronate transporter/mannonate hydrolase
RA	4,541,449	A→T	intergenic (‑336/‑4)	gntP ← / → uxuA	fructuronate transporter/mannonate hydrolase
RA	4,545,107	G→T	D239Y (GAT→TAT)	uxuR →	fructuronate‑inducible hexuronate regulon transcriptional repressor; autorepressor
RA	4,545,608	C→A	R177I (AGA→ATA)	yjiC ←	uncharacterized protein
RA	4,546,672	G→T	intergenic (‑535/‑138)	yjiC ← / → iraD	uncharacterized protein/RpoS stabilzer after DNA damage, anti‑RssB factor
RA	4,547,818	C→A	D97Y (GAT→TAT)	hypT ←	hypochlorite‑responsive transcription factor
RA	4,555,156	G→T	A171E (GCG→GAG)	yjiM ←	putative 2‑hydroxyglutaryl‑CoA dehydratase
RA	4,562,043	C→A	intergenic (+311/‑188)	yjiS → / → yjiT	DUF1127 family protein/pseudogene
RA	4,567,278	G→T	I166I (ATC→ATA)	mcrC ←	5‑methylcytosine‑specific restriction enzyme McrBC, subunit McrC
RA	4,571,233	G→A	S16F (TCT→TTT)	hsdS ←	specificity determinant for hsdM and hsdR
RA	4,572,520	A→T	Y116N (TAC→AAC)	hsdM ←	DNA methyltransferase M
RA	4,584,255	A→C	L95L (CTT→CTG)	yjjL ←	L‑galactonate transporter
RA	4,584,381	G→T	I53I (ATC→ATA)	yjjL ←	L‑galactonate transporter
RA	4,584,756	A→T	*305K (TAA→AAA)	yjjM ←	yjjMN operon transcriptional activator
RA	4,584,775	C→A	E298D (GAG→GAT)	yjjM ←	yjjMN operon transcriptional activator
RA	4,585,338	A→T	S111T (TCT→ACT)	yjjM ←	yjjMN operon transcriptional activator
RA	4,588,180	G→T	S360* (TCA→TAA)	opgB ←	phosphoglycerol transferases I and II
RA	4,589,130	G→T	I43I (ATC→ATA)	opgB ←	phosphoglycerol transferases I and II
RA	4,591,139	C→A	D66Y (GAT→TAT)	dnaT ←	DNA biosynthesis protein (primosomal protein I)
RA	4,596,243	T→A	intergenic (‑25/+243)	leuQ ← / ← rsmC	tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase, SAM‑dependent
RA	4,600,972	G→T	intergenic (+152/‑241)	prfC → / → osmY	peptide chain release factor RF‑3/periplasmic protein
RA	4,609,543	G→T	E42* (GAA→TAA)	deoB →	phosphopentomutase
RA	4,615,947	G→T	E73D (GAG→GAT)	radA →	DNA repair protein
RA	4,617,341	C→A	F70L (TTC→TTA)	nadR →	trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor
RA	4,625,288	T→C	intergenic (‑161/‑50)	rob ← / → creA	right oriC‑binding transcriptional activator, AraC family/putative periplasmic protein
RA	4,630,770	G→T	T4T (ACG→ACT)	yjtD →	putative methyltransferase

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	CP009273	373860	375108	1249	144 [140]	[142] 145	frmA–[frmR]	frmA,[frmR]
*	*	÷	CP009273	1191676	1206956	15281	144 [140]	[142] 148	[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	4100592	4101538	947	144 [141]	[141] 144	[cdh]–tpiA	[cdh],tpiA

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	360104 =	220 (0.940)	272 (1.170)	139/298	0.2	55.3%	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)	7054 (32.030) +TTAATTAA	205/282	0.0	97.5%	intergenic (‑212/+383)	lacZ/lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
	?	CP009273	= 361823	193 (0.830)					coding (831/834 nt)	mhpR	mhp operon transcriptional activator
*	?	CP009273	360652 =	242 (1.040)	6707 (41.800) +46 bp	204/206	0.0	97.7%	intergenic (‑586/+9)	lacZ/lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
	?	CP009273	= 1317577	216 (0.930)					coding (101/882 nt)	yciV	PHP domain protein
*	?	CP009273	376716 =	NA (NA)	275 (1.180)	156/298	0.0	97.9%	intergenic (‑1/‑91)	yaiX/insC1	pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase/IS2 repressor TnpA
	?	CP009273	566411 =	6 (0.030)					coding (63/552 nt)	ybcL	inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
*	?	CP009273	= 378046	NA (NA)	223 (0.960)	132/298	0.3	95.7%	intergenic (+11/+1)	insD1/yaiX	IS2 transposase TnpB/pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase
	?	CP009273	= 566415	10 (0.040)					coding (67/552 nt)	ybcL	inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
*	?	CP009273	1635219 =	12 (0.050)	216 (0.940)	122/294	0.6	94.7%	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	7 (0.030)	246 (1.060)	139/298	0.2	97.2%	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)	237 (1.030)	136/294	0.2	95.2%	pseudogene (4/2445 nt)	yqiG	pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein
	?	CP009273	= 3833569	12 (0.050)					intergenic (‑216/‑6)	nlpA/yicS	cytoplasmic membrane lipoprotein‑28/putative periplasmic protein
*	?	CP009273	3833562 =	11 (0.050)	223 (0.960)	130/296	0.3	95.3%	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