BRESEQ :: Mutation Predictions

Predicted mutations
evidence	position	mutation	annotation	gene	description
MC JC	15,445	Δ1,459 bp		[insL1]–[mokC]	[insL1], [hokC], [mokC]
MC JC	19,646	Δ863 bp		insB1–[insA1]	insB1, [insA1]
MC JC	65,857	12940 bp→GA		[araD]–[setA]	[araD], araA, araB, araC, yabI, thiQ, thiP, thiB, sroA, sgrR, sgrS, sgrT, [setA]
RA	155,463	A→T	*247K (TAA→AAA)	yadV ←	putative fimbrial chaperone YadV
MC JC	167,401	Δ5,915 bp		fhuA–[fhuB]	fhuA, fhuC, fhuD, [fhuB]
MC JC	244,301	Δ9,446 bp		yafJ–yafP	yafJ, dpaA, yafQ, dinJ, yafL, rayT, dinB, yafN, yafO, yafP
RA	254,249	A→T	intergenic (+1088/+10)	yafP → / ← pepD	putative N‑acetyltransferase YafP/peptidase D
MC JC	257,908	Δ776 bp		insB9–[crl]	insB9, insA9, [crl]
MC JC	263,076	Δ125,568 bp		ykfI–[tauD]	127 genes ykfI, yafW, ykfH, ykfG, yafX, ykfF, ykfB, yafY, yafZ, ykfA, perR, insN, insI1, insN, eyeA, ykfC, insH1, mmuP, mmuM, afuC, insB2, insA2, yagB, yagA, yagE, yagF, yagG, yagH, xynR, argF, argL, ykgS, insB3, insA3, yagJ, yagK, yagL, yagM, ykgV, yagN, intF, yagP, paoD, paoC, paoB, paoA, yagU, ykgJ, ecpE, ecpD, ecpC, ecpB, ecpA, matA, ykgL, ykgO, ykgM, ykgR, insE1, insF1, rclC, rclB, rclA, rclR, ykgE, ykgF, ykgG, ykgH, betA, betB, betI, betT, yahV, pdeL, yahB, yahC, yahD, yahE, yahF, yahG, yahH, yahI, yahJ, yahK, yahL, yahM, yahN, yahO, prpR, prpB, prpC, prpD, prpE, codB, codA, cynR, cynT, cynS, cynX, lacA, lacY, lacZ, lacI, mhpR, mhpA, mhpB, mhpC, mhpD, mhpF, mhpE, mhpT, yaiL, frmB, frmA, frmR, yaiO, yaiX, insC1, insD1, yaiX, yaiP, ykiC, yaiS, tauA, tauB, tauC, [tauD]
RA	389,601	C→T	D43N (GAC→AAC)	hemB ←	porphobilinogen synthase
RA	389,867	T→C	intergenic (‑140/‑384)	hemB ← / → yaiT	porphobilinogen synthase/putative autotransporter YaiT
MC JC	390,251	Δ14,565 bp		[yaiT]–[dgcC]	16 genes [yaiT], ytiB, insF2, insE2, yaiT, iprA, ampH, sbmA, yaiW, yaiY, yaiZ, ddlA, iraP, phoA, psiF, [dgcC]
RA	498,917	T→C	F288S (TTC→TCC)	hemH →	ferrochelatase
MC JC	519,143	Δ14,682 bp		[ybbO]–[allZ]	[ybbO], [tesA], ybbA, ybbP, rhsD, ybbC, ylbG, selU, allS, allA, [allR], [allZ]
RA	535,337	T→C	A474A (GCT→GCC)	gcl →	glyoxylate carboligase
RA	536,173	T→C	L155P (CTC→CCC)	hyi →	hydroxypyruvate isomerase
RA	536,492	A→G	intergenic (+6/‑94)	hyi → / → glxR	hydroxypyruvate isomerase/tartronate semialdehyde reductase 2
RA	536,549	T→C	intergenic (+63/‑37)	hyi → / → glxR	hydroxypyruvate isomerase/tartronate semialdehyde reductase 2
MC JC	536,617	Δ14,712 bp		[glxR]–[ybcF]	[glxR], ybbW, allB, ybbY, glxK, allE, allC, allD, fdrA, ylbE, ylbF, [ybcF]
RA	557,635	A→T	L36Q (CTG→CAG)	folD ←	bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase
MC JC	565,054	44181 bp→TGA		[intD]–insL2	52 genes [intD], renD, insE3, insF3, renD, emrE, ylcJ, ybcK, ybcL, ybcM, ylcH, ybcN, ninE, ybcO, rusA, ylcG, quuD, nmpC, insH2, nmpC, essD, rrrD, rzpD, rzoD, borD, ybcV, ybcW, ylcI, nohD, tfaD, tfaX, appY, ompT, envY, ybcH, nfrA, nfrB, cusS, cusR, cusC, cusF, cusB, cusA, pheP, ybdG, nfsB, ybdF, ybdJ, ybdK, sokE, hokE, insL2
MC JC	641,446	Δ17,325 bp		[uspG]–crcB	18 genes [uspG], ybdR, yldA, rnk, rna, citT, citG, citX, citF, citE, citD, citC, dpiB, dpiA, dcuC, pagP, cspE, crcB
RA	674,518	G→A	A89V (GCG→GTG)	leuS ←	leucine‑‑tRNA ligase
RA	674,920	T→C	intergenic (‑137/‑98)	leuS ← / → ybeL	leucine‑‑tRNA ligase/DUF1451 domain‑containing protein YbeL
RA	674,992	C→A	intergenic (‑209/‑26)	leuS ← / → ybeL	leucine‑‑tRNA ligase/DUF1451 domain‑containing protein YbeL
MC JC	675,018	Δ14,271 bp		[ybeL]–insH3	15 genes [ybeL], ybeQ, ybeR, djlB, ybeT, ybeU, djlC, hscC, rihA, gltL, gltK, gltJ, sroC, gltI, insH3
MC JC	728,735	Δ10,773 bp		[kdpF]–[phr]	[kdpF], ybfA, rhsC, ybfB, ybfC, ybfQ, ybfD, [ybgA], [phr]
MC JC	832,467	Δ15,538 bp		ybiA–[glnH]	16 genes ybiA, dinG, ybiB, hcxB, zbiJ, ybiE, ybiJ, ybiI, ybiX, fiu, mcbA, rlmF, ybiO, glnQ, glnP, [glnH]
MC JC	867,553	Δ15,836 bp		[gsiA]–[ybjG]	[gsiA], gsiB, gsiC, gsiD, pdeI, dgcI, rimO, bssR, yliI, gstB, dacC, deoR, [ybjG]
MC JC	890,913	Δ18,382 bp		[ybjC]–[ltaE]	21 genes [ybjC], nfsA, rimK, ybjN, potF, potG, potH, potI, ybjO, rlmC, artJ, artM, artQ, artI, artP, ybjP, ybjQ, amiD, ybjS, ybjT, [ltaE]
RA	1,048,596	G→A	G32G (GGC→GGT)	gfcC ←	capsule biosynthesis GfcC family protein
MC JC	1,048,805	Δ48,085 bp		[gfcB]–ycdU	45 genes [gfcB], gfcA, insA4, insB4, cspH, cspG, ymcF, ymcE, gnsA, yccM, torS, torT, torR, torC, torA, torD, cbpM, cbpA, yccE, agp, yccJ, wrbA, ymdF, rutG, rutF, rutE, rutD, rutC, rutB, rutA, rutR, putA, ymdG, putP, efeO, efeB, phoH, pgaD, pgaC, pgaB, pgaA, dgcT, insF4, insE4, ycdU
MC JC	1,097,887	Δ17,605 bp		[ghrA]–mdtG	20 genes [ghrA], ycdX, ycdY, ycdZ, csgG, csgF, csgE, csgD, csgB, csgA, csgC, ymdA, ymdB, clsC, opgC, opgG, opgH, yceK, msyB, mdtG
RA	1,115,852	T→C	K244R (AAG→AGG)	lpxL ←	lauroyl acyltransferase
RA	1,196,861	A→G	intergenic (+79/+6)	C0293 → / ← ymfD	small regulatory RNA C0293/putative SAM‑dependent methyltransferase YmfD
MC JC	1,196,867	Δ27,041 bp		[ymfD]–ymgJ	37 genes [ymfD], ymfE, lit, intE, xisE, ymfH, ymfI, ymfJ, ymfK, ymfT, ymfL, ymfM, ymfN, ymfR, beeE, ymfQ, ycfK, tfaP, tfaE, pinE, mcrA, iraM, ymgK, ymgL, ycgX, bluR, bluF, ycgZ, ymgA, ariR, ymgC, pdeG, ymgF, ymgD, ymgG, ymgI, ymgJ
RA	1,269,250	A→G	I9T (ATT→ACT)	ldrA ←	small toxic polypeptide LdrA
MC JC	1,294,426	Δ12,725 bp		adhE–[yciU]	adhE, ychT, ychE, insH21, oppA, oppB, oppC, oppD, oppF, [yciU]
RA	1,337,394	A→G	S522G (AGC→GGC)	acnA →	aconitate hydratase 1
MC JC	1,357,803	Δ9,014 bp		[puuP]–puuE	[puuP], ymjE, puuA, puuD, puuR, puuC, puuB, puuE
MC JC	1,394,891	Δ2,732 bp		[ynaI]–[ynaJ]	[ynaI], insH4, [ynaJ]
RA	1,413,092	C→T	A48A (GCG→GCA)	intR ←	putative integrase
RA	1,413,450	C→T	M1M (ATG→ATA) †	xisR ←	excisionase
RA	1,413,558	G→T	S61S (TCC→TCA) noncoding (3/179 nt)	rcbA ← ralA →	double‑strand break reduction protein small regulatory RNA antitoxin RalA
MC JC	1,422,752	Δ14,142 bp		[ydaW]–[ompN]	16 genes [ydaW], rzoR, trkG, ynaK, ydaY, ynaA, lomR, insH5, lomR, stfR, tfaR, pinR, ynaE, ynaM, uspF, [ompN]
MC JC	1,465,392	Δ16,810 bp		[ydbA]–[ynbD]	[ydbA], insD2, insC2, ydbA, insI2, ydbA, pdxI, ydbD, ynbA, ynbB, ynbC, [ynbD]
MC JC	1,502,457	Δ15,875 bp		[ydcL]–[mnaT]	19 genes [ydcL], insQ, ydcO, sutR, rlhA, yncJ, hicA, hicB, ydcR, ydcS, ydcT, ydcU, ydcV, patD, yncL, ortT, ydcY, [ydcZ], [mnaT]
MC JC	1,520,673	Δ21,396 bp		[mcbR]–[narZ]	17 genes [mcbR], yncD, yncE, ansP, yncG, yncH, ydcD, yncO, ydcC, pptA, yddH, nhoA, yddE, narV, narW, narY, [narZ]
MC JC	1,590,854	Δ7,233 bp		[hipA]–hipB	[hipA], hipB
RA	1,628,332	T→C	intergenic (+69/‑20)	ydfG → / → rspR	3‑hydroxy acid dehydrogenase YdfG/DNA‑binding transcriptional repressor RspR
MC JC	1,628,340	Δ10,127 bp		rspR–[cspI]	17 genes rspR, ydfZ, ydfI, ydfJ, ynfT, ydfK, pinQ, tfaQ, stfQ, nohA, ynfO, ydfO, gnsB, ynfN, ynfR, ynfQ, [cspI]
RA	1,638,571	G→A	H33Y (CAT→TAT)	cspI ←	cold shock‑like protein CspI
RA	1,640,045	+C	coding (13/534 nt)	rrrQ ←	putative lysozyme
MC JC	1,640,057	Δ7,591 bp		[rrrQ]–[dicC]	18 genes [rrrQ], [ydfR], essQ, ynfU, cspB, cspF, ynfS, ydfT, ydfU, rem, hokD, relE, relB, ydfV, flxA, ydfW, ydfX, [dicC]
MC JC	1,649,794	Δ6,356 bp		[dicB]–[ynfB]	[dicB], [ydfD], ynfP, rspB, rspA, ynfA, [ynfB]
RA	1,851,841	C→T	Q328* (CAA→TAA)	ansA →	L‑asparaginase 1
MC JC	1,851,866	Δ10,563 bp		[ansA]–[msrB]	[ansA], pncA, ydjE, ydjF, ydjG, ydjH, ydjI, ydjJ, ydjK, ydjL, yeaC, [msrB]
MC JC	1,873,574	13215 bp→TAG		[yeaK]–[yeaX]	19 genes [yeaK], yoaI, yeaL, nimR, nimT, yeaO, yoaF, dgcP, yoaK, yoaJ, yeaQ, yoaG, yeaR, leuE, dmlR, dmlA, yeaV, yeaW, [yeaX]
RA	1,887,158	C→A	L278L (CTG→CTT)	rnd ←	RNase D
RA	1,887,644	C→T	W116* (TGG→TGA)	rnd ←	RNase D
RA	1,946,876	C→A	L167L (CTG→CTT)	ruvC ←	crossover junction endodeoxyribonuclease RuvC
MC JC	1,961,950	Δ28,129 bp		yecT–[tyrP]	33 genes yecT, flhE, flhA, flhB, cheZ, cheY, cheB, cheR, tap, tar, cheW, cheA, cheA, motB, motA, motR, flhC, flhD, insB5, insA5, uspC, otsA, otsB, araH, araG, araF, ftnB, yecJ, azuC, yecR, ftnA, yecH, [tyrP]
MC JC	1,993,664	Δ31,548 bp		[uvrC]–[yodD]	40 genes [uvrC], uvrY, yecU, yecF, sdiA, sdsN, tcyN, tcyL, dcyD, tcyJ, fliZ, fliA, fliX, fliC, fliD, fliS, fliT, amyA, yedD, yedE, yedF, yedK, yedL, fliE, fliF, fliG, fliH, fliI, fliJ, fliK, fliL, fliM, fliN, fliO, fliP, fliQ, fliR, rcsA, dsrB, [yodD]
MC JC	2,030,451	Δ10,928 bp		[yedA]–[zinT]	[yedA], [vsr], dcm, yedJ, drpB, rseX, hchA, hprS, hprR, hiuH, msrP, msrQ, [zinT]
RA	2,041,467	A→G	K31K (AAA→AAG)	zinT →	metal‑binding protein ZinT
MC JC	2,066,152	Δ12,778 bp		insH6–[yoeF]	insH6, yoeA, insD3, insC3, yoeA, isrC, flu, yeeR, yeeS, yeeT, cbeA, cbtA, yeeW, [yoeF]
RA	2,078,954	A→G	intergenic (+23/+78)	yoeF → / ← tmaR	putative uncharacterized protein YoeF/PTS system regulator TmaR
MC JC	2,089,216	Δ255 bp		[yoeB]–[yefM]	[yoeB], [yefM]
RA	2,089,473	T→C	I81V (ATC→GTC)	yefM ←	YefM antitoxin of the YoeB‑YefM toxin‑antitoxin pair and DNA binding transcriptional repressor
RA	2,089,621	A→G	R31R (CGT→CGC)	yefM ←	YefM antitoxin of the YoeB‑YefM toxin‑antitoxin pair and DNA binding transcriptional repressor
RA	2,093,977	C→T	H170H (CAC→CAT)	hisB →	imidazoleglycerol‑phosphate dehydratase/histidinol‑phosphatase
MC JC	2,101,395	Δ11,672 bp		wbbL–rfbB	wbbL, insH7, wbbL, wbbK, wbbJ, wbbI, wbbH, glf, rfbX, rfbC, rfbA, rfbD, rfbB
RA	2,113,177	A→G	intergenic (‑116/+257)	rfbB ← / ← galF	dTDP‑glucose 4,6‑dehydratase 1/UTP:glucose‑1‑phosphate uridylyltransferase, low activity
MC JC	2,143,266	Δ40,395 bp		[dgcE]–yegX	38 genes [dgcE], alkA, yegD, yegI, yegJ, pphC, yegL, sibA, ibsA, sibB, ibsB, mdtA, mdtB, mdtC, mdtD, baeS, baeR, yegP, trhP, cyaR, ogrK, yegR, yegS, gatR, insE5, insF5, gatR, gatD, gatB, gatA, gatZ, gatY, fbaB, yegT, yegU, yegV, yegW, yegX
MC JC	2,196,474	Δ29,182 bp		[yehF]–yohC	21 genes [yehF], yehI, yehK, yehL, yehM, yehP, yehQ, yehR, yehS, btsR, btsS, mlrA, yohO, yehW, yehX, yehY, osmF, bglX, dld, pbpG, yohC
RA	2,251,586	G→A	Q249Q (CAG→CAA)	nfo →	endonuclease IV
MC JC	2,251,701	Δ7,597 bp		[yeiI]–psuK	[yeiI], nupX, rihB, yeiL, psuT, psuG, psuK
MC JC	2,286,390	Δ3,880 bp		[yejO]–yejO	[yejO], insH8, yejO
MC JC	2,380,731	Δ9,210 bp		[elaB]–[yfbP]	[elaB], elaA, rbn, elaD, yfbK, yfbL, yfbM, yfbN, yfbO, [yfbP]
RA	2,390,293	C→T	A405T (GCA→ACA)	nuoN ←	NADH:quinone oxidoreductase subunit N
RA	2,406,367	A→G	L92S (TTA→TCA)	lrhA ←	DNA‑binding transcriptional dual regulator LrhA
RA	2,406,861	T→A	intergenic (‑220/‑700)	lrhA ← / → alaA	DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA
RA	2,417,032	C→T	intergenic (+141/‑49)	pta → / → yfcC	phosphate acetyltransferase/putative transporter YfcC
RA	2,417,047	A→C	intergenic (+156/‑34)	pta → / → yfcC	phosphate acetyltransferase/putative transporter YfcC
MC JC	2,417,058	Δ10,734 bp		yfcC–[argT]	yfcC, yfcD, yfcE, yfcF, yfcG, folX, yfcH, rpnB, hisP, hisM, hisQ, hisJ, [argT]
MC JC	2,466,540	9636 bp→ACCC		intS–[ypdJ]	15 genes intS, yfdG, yfdH, yfdI, yodE, yfdK, yfdM, yfdN, yfdO, yfdP, yfdQ, yfdR, yfdS, [yfdT], [ypdJ]
RA	2,476,629	A→G	intergenic (+119/+65)	torI → / ← dsdC	prophage CPS‑53 recombination directionality factor and response regulator inhibitor/DNA‑binding transcriptional dual regulator DsdC
RA	2,481,795	G→A	Q128* (CAG→TAG)	emrY ←	tripartite efflux pump membrane subunit EmrY
MC JC	2,489,242	Δ19,001 bp		[yfdV]–[fryB]	17 genes [yfdV], oxc, frc, yfdX, ypdI, yfdY, lpxP, ypdK, alaC, pyrS, pyrR, ypdC, fryA, ypdE, ypdF, fryC, [fryB]
RA	2,508,268	T→C	intergenic (‑26/+193)	fryB ← / ← glk	putative PTS enzyme IIB component FryB/glucokinase
RA	2,508,293	A→G	intergenic (‑51/+168)	fryB ← / ← glk	putative PTS enzyme IIB component FryB/glucokinase
MC JC	2,514,272	Δ3,561 bp		insL3–[pdeA]	insL3, [pdeA]
MC JC	2,558,770	Δ6,560 bp		intZ–[yffS]	intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, [yffS]
MC JC	2,601,202	Δ13,582 bp		[hyfA]–focB	[hyfA], hyfB, hyfC, hyfD, hyfE, hyfF, hyfG, hyfH, hyfI, hyfJ, hyfR, focB
RA	2,730,870	T→C	noncoding (288/1542 nt)	rrsG ←	16S ribosomal RNA
MC JC	2,756,159	Δ33,804 bp		[intA]–[glaH]	28 genes [intA], yfjH, alpA, yfjI, yfjJ, abpB, abpA, yfjM, rnlA, rnlB, yfjP, yfjQ, yfjR, ypjK, yfjS, yfjT, yfjU, yfjW, yfjX, yfjY, ypjJ, yfjZ, ypjF, ypjA, ypjB, ypjC, ileY, [glaH]
RA	2,790,153	C→T	P58S (CCC→TCC)	lhgD →	L‑2‑hydroxyglutarate dehydrogenase
RA	2,790,310	C→T	A110V (GCG→GTG)	lhgD →	L‑2‑hydroxyglutarate dehydrogenase
MC JC	2,795,656	Δ5,717 bp		glaR–[nrdE]	glaR, kbp, yqaE, ygaV, ygaP, stpA, alaE, ygaC, ygaM, nrdH, [nrdI], [nrdE]
MC JC	2,804,790	Δ5,840 bp		proV–[ygaH]	proV, proW, proX, ygaZ, [ygaH]
MC JC	2,825,796	Δ4,947 bp		srlA–[gutQ]	srlA, srlE, srlB, srlD, gutM, srlR, [gutQ]
RA	2,867,454	2 bp→AA	coding (97‑98/993 nt)	rpoS ←	RNA polymerase sigma factor RpoS
MC JC	2,877,974	Δ183 bp	intergenic (+356/+413)	iap → / ← cas2	alkaline phosphatase isozyme conversion protein/CRISPR‑associated endoribonuclease Cas2
MC JC	2,910,754	Δ300 bp		[mazF]	[mazF]
RA	2,985,726	A→G	intergenic (‑134/‑121)	yqeF ← / → yqeG	putative acyltransferase/putative transporter YqeG
RA	2,985,816	T→C	intergenic (‑224/‑31)	yqeF ← / → yqeG	putative acyltransferase/putative transporter YqeG
MC JC	2,985,842	Δ47,769 bp		yqeG–[idi]	39 genes yqeG, yqeH, yqeI, yqeJ, yqeL, yqeK, ygeG, ygeH, ygeI, insD4, insC4, ygeQ, glyU, actS, xdhA, xdhB, xdhC, ygeV, ygeW, ygeX, ygeY, hyuA, yqeA, yqeB, yqeC, mocA, ygfK, ssnA, ygfM, xdhD, xanQ, guaD, ghxQ, ygfS, ygfT, uacT, yqfG, yqfH, [idi]
MC JC	3,077,568	Δ1,832 bp		[cmtA]–cmtB	[cmtA], cmtB
RA	3,103,240	G→A	L76L (TTG→TTA)	mutY →	adenine DNA glycosylase
MC JC	3,110,591	Δ24,234 bp		[yghD]–yghT	20 genes [yghD], yghE, yqhJ, yghF, yghG, pppA, yghJ, glcA, glcB, glcG, glcF, glcE, glcD, glcC, yghO, insH9, yghQ, yghR, yghS, yghT
MC JC	3,166,114	Δ7,312 bp		[ygiS]–[ygiN]	[ygiS], mqsA, mqsR, ygiV, ygiW, qseB, qseC, ygiZ, mdaB, [ygiN]
RA	3,173,431	T→A	I97N (ATC→AAC)	ygiN →	putative quinol monooxygenase YgiN
MC JC	3,185,131	Δ4,735 bp		ygiL–[yqiG]	ygiL, yqiG, insC5, insD5, [yqiG]
RA	3,190,000	T→C	D40D (GAT→GAC)	yqiH →	putative fimbrial chaperone YqiH
RA	3,190,238	A→T	K120* (AAA→TAA)	yqiH →	putative fimbrial chaperone YqiH
RA	3,190,725	A→G	N32D (AAT→GAT)	yqiI →	putative fimbrial protein YqiI
RA	3,226,228	T→C	intergenic (+57/‑6)	ebgC → / → ygjI	DUF386 domain‑containing evolved beta‑D‑galactosidase subunit beta/putative transporter YgjI
MC JC	3,226,234	Δ15,511 bp		[ygjI]–[ygjV]	[ygjI], ygjJ, ygjK, fadH, higA, higB, rlmG, ygjP, ygjQ, ygjR, alx, sstT, [ygjV]
RA	3,252,464	T→C	I54T (ATC→ACC)	yhaH →	putative inner membrane protein
MC JC	3,361,226	Δ9,811 bp		[gltF]–[nanE]	[gltF], yhcA, yhcD, yhcE, insH10, yhcE, yhcF, yhcG, nanQ, nanK, [nanE]
RA	3,410,666	C→G	V129V (GTC→GTG)	dusB →	tRNA‑dihydrouridine synthase B
MC JC	3,411,645	9722 bp→A		yhdJ–[yhdY]	yhdJ, yhdU, envR, acrE, acrF, yhdV, yhdX, [yhdY]
RA	3,421,374	C→T	S17L (TCA→TTA)	yhdY →	putative ABC transporter membrane subunit YhdY
MC JC	3,453,509	Δ16,346 bp		[gspB]–chiA	17 genes [gspB], gspA, gspC, gspD, gspE, gspF, gspG, gspH, gspI, gspJ, gspK, gspL, gspM, gspO, bfr, bfd, chiA
RA	3,486,205	C→A	T29K (ACG→AAG)	crp →	DNA‑binding transcriptional dual regulator CRP
RA	3,499,391	G→T	intergenic (+190/‑57)	cysG → / → yhfL	siroheme synthase/DUF4223 domain‑containing lipoprotein YhfL
RA	3,499,393	T→G	intergenic (+192/‑55)	cysG → / → yhfL	siroheme synthase/DUF4223 domain‑containing lipoprotein YhfL
MC JC	3,499,401	Δ12,725 bp		yhfL–[yhfZ]	yhfL, frlA, frlB, frlC, frlD, frlR, yhfS, yhfT, yhfU, php, yhfW, yhfX, yhfY, [yhfZ]
RA	3,512,183	T→C	E54E (GAA→GAG)	yhfZ ←	putative DNA‑binding transcriptional regulator YhfZ
RA	3,560,455	+G	intergenic (+589/+167)	rtcR → / ← glpG	DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG
MC JC	3,578,950	Δ6,094 bp		[yhhW]–[yrhB]	[yhhW], yhhX, ryhB, yhhY, yhhZ, yrhA, insA6, insB6, yrhA, yrhD, [yrhB]
MC JC	3,619,069	Δ18,342 bp		rhsB–[yhiN]	rhsB, yhhH, yhhI, yhhJ, rbbA, yhiI, yhiY, yhiJ, yhiM, [yhiN]
RA	3,637,426	Δ1 bp	intergenic (‑16/‑216)	yhiN ← / → pitA	putative oxidoreductase YhiN/metal phosphate:H(+) symporter PitA
RA	3,637,436	G→A	intergenic (‑26/‑206)	yhiN ← / → pitA	putative oxidoreductase YhiN/metal phosphate:H(+) symporter PitA
MC JC	3,651,191	Δ2,158 bp		yhiS–[yhiS]	yhiS, insH11, [yhiS]
MC JC	3,701,865	Δ5,842 bp		[dppF]–dppA	[dppF], dppD, dppC, dppB, dppA
RA	3,708,172	(A)_7→6	intergenic (‑467/+444)	dppA ← / ← proK	dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro
MC JC	3,716,547	Δ5,503 bp		[yiaD]–[insK]	[yiaD], ghrB, yiaF, yiaG, cspA, ysaE, hokA, insJ, [insK]
RA	3,725,734	G→A	intergenic (‑22/‑153)	ysaB ← / → wecH	putative lipoprotein YsaB/O‑acetyltransferase WecH
RA	3,725,782	T→C	intergenic (‑70/‑105)	ysaB ← / → wecH	putative lipoprotein YsaB/O‑acetyltransferase WecH
MC JC	3,725,888	Δ42,752 bp		[wecH]–yibG	37 genes [wecH], yiaA, yiaB, xylB, xylZ, xylA, xylF, xylG, xylH, xylR, bax, baxL, malS, avtA, ysaA, plaR, yiaK, yiaL, yiaM, yiaN, yiaO, lyxK, sgbH, sgbU, sgbE, yiaT, yiaU, yiaV, yiaW, aldB, yiaY, selB, selA, yibF, rhsA, yibA, yibG
RA	3,768,988	C→T	intergenic (+350/‑357)	yibG → / → yibV	tetratricopeptide‑like domain‑containing protein YibG/PF15596 family protein YibV
RA	3,815,199	G→A	Y190Y (TAC→TAT)	pyrE ←	orotate phosphoribosyltransferase
RA	3,815,202	A→G	A189A (GCT→GCC)	pyrE ←	orotate phosphoribosyltransferase
RA	3,815,211	G→A	D186D (GAC→GAT)	pyrE ←	orotate phosphoribosyltransferase
RA	3,815,292	G→C	R159R (CGC→CGG)	pyrE ←	orotate phosphoribosyltransferase
RA	3,815,307	G→A	L154L (CTC→CTT)	pyrE ←	orotate phosphoribosyltransferase
RA	3,815,319	C→T	V150V (GTG→GTA)	pyrE ←	orotate phosphoribosyltransferase
RA	3,815,343	G→A	A142A (GCC→GCT)	pyrE ←	orotate phosphoribosyltransferase
RA	3,815,364	C→T	E135E (GAG→GAA)	pyrE ←	orotate phosphoribosyltransferase
RA	3,815,466	T→C	E101E (GAA→GAG)	pyrE ←	orotate phosphoribosyltransferase
RA	3,815,496	C→A	L91L (CTG→CTT)	pyrE ←	orotate phosphoribosyltransferase
RA	3,815,502	G→A	H89H (CAC→CAT)	pyrE ←	orotate phosphoribosyltransferase
RA	3,815,517	T→C	A84A (GCA→GCG)	pyrE ←	orotate phosphoribosyltransferase
RA	3,815,523	A→G	A82A (GCT→GCC)	pyrE ←	orotate phosphoribosyltransferase
RA	3,815,529	T→A	T80T (ACA→ACT)	pyrE ←	orotate phosphoribosyltransferase
RA	3,815,535	G→C	A78A (GCC→GCG)	pyrE ←	orotate phosphoribosyltransferase
RA	3,815,589	G→A	S60S (TCC→TCT)	pyrE ←	orotate phosphoribosyltransferase
RA	3,815,601	C→T	A56A (GCG→GCA)	pyrE ←	orotate phosphoribosyltransferase
RA	3,815,634	A→G	D45D (GAT→GAC)	pyrE ←	orotate phosphoribosyltransferase
RA	3,815,883	+C	coding (667/687 nt)	rph ←	truncated RNase PH
RA	3,815,893	A→C	A219A (GCT→GCG)	rph ←	truncated RNase PH
RA	3,815,903	A→G	I216T (ATC→ACC)	rph ←	truncated RNase PH
RA	3,816,007	A→T	S181S (TCT→TCA)	rph ←	truncated RNase PH
RA	3,816,036	2 bp→TT	coding (513‑514/687 nt)	rph ←	truncated RNase PH
RA	3,816,043	G→A	G169G (GGC→GGT)	rph ←	truncated RNase PH
RA	3,816,049	C→T	V167V (GTG→GTA)	rph ←	truncated RNase PH
RA	3,816,055	T→A	G165G (GGA→GGT)	rph ←	truncated RNase PH
RA	3,816,091	A→G	N153N (AAT→AAC)	rph ←	truncated RNase PH
RA	3,816,137	A→G	V138A (GTA→GCA)	rph ←	truncated RNase PH
MC JC	3,836,957	Δ8,771 bp		[setC]–[adeD]	[setC], yicL, yicU, nlpA, yicS, nepI, yicN, adeQ, [adeD]
MC JC	3,855,159	Δ11,170 bp		[yidF]–yidE	[yidF], yidG, yidH, yidI, yidJ, yidK, yidL, glvB, glvC, yidP, yidE
RA	3,867,576	G→T	intergenic (‑154/‑152)	ibpA ← / → yidQ	small heat shock protein IbpA/DUF1375 domain‑containing putative lipoprotein YidQ
MC JC	3,867,599	Δ9,908 bp		yidQ–yidB	yidQ, yidR, cbrA, dgoT, dgoD, dgoA, dgoK, dgoR, yidX, yidA, yidB
MC JC	3,888,435	Δ3,155 bp		[tnaC]–tnaB	[tnaC], tnaA, tnaB
MC JC	3,927,155	Δ12,222 bp		[asnA]–[hsrA]	[asnA], viaA, ravA, kup, rbsD, rbsA, rbsC, rbsB, rbsZ, rbsK, rbsR, [hsrA]
RA	3,951,306	G→A	intergenic (+749/‑895)	ilvX → / → ilvM	uncharacterized protein IlvX/acetolactate synthase II subunit IlvM
RA	3,951,312	C→T	intergenic (+755/‑889)	ilvX → / → ilvM	uncharacterized protein IlvX/acetolactate synthase II subunit IlvM
RA	3,951,327	A→G	intergenic (+770/‑874)	ilvX → / → ilvM	uncharacterized protein IlvX/acetolactate synthase II subunit IlvM
RA	3,951,348	T→C	intergenic (+791/‑853)	ilvX → / → ilvM	uncharacterized protein IlvX/acetolactate synthase II subunit IlvM
RA	3,951,352	C→T	intergenic (+795/‑849)	ilvX → / → ilvM	uncharacterized protein IlvX/acetolactate synthase II subunit IlvM
RA	3,951,369	C→T	intergenic (+812/‑832)	ilvX → / → ilvM	uncharacterized protein IlvX/acetolactate synthase II subunit IlvM
RA	3,951,414	G→A	intergenic (+857/‑787)	ilvX → / → ilvM	uncharacterized protein IlvX/acetolactate synthase II subunit IlvM
RA	3,951,537	+AT	intergenic (+980/‑664)	ilvX → / → ilvM	uncharacterized protein IlvX/acetolactate synthase II subunit IlvM
RA	3,951,552	A→T	intergenic (+995/‑649)	ilvX → / → ilvM	uncharacterized protein IlvX/acetolactate synthase II subunit IlvM
RA	3,951,581	T→G	intergenic (+1024/‑620)	ilvX → / → ilvM	uncharacterized protein IlvX/acetolactate synthase II subunit IlvM
RA	3,951,643	G→A	intergenic (+1086/‑558)	ilvX → / → ilvM	uncharacterized protein IlvX/acetolactate synthase II subunit IlvM
RA	3,951,754	T→C	intergenic (+1197/‑447)	ilvX → / → ilvM	uncharacterized protein IlvX/acetolactate synthase II subunit IlvM
RA	3,951,760	T→C	intergenic (+1203/‑441)	ilvX → / → ilvM	uncharacterized protein IlvX/acetolactate synthase II subunit IlvM
RA	3,951,796	A→G	intergenic (+1239/‑405)	ilvX → / → ilvM	uncharacterized protein IlvX/acetolactate synthase II subunit IlvM
RA	3,951,811	G→A	intergenic (+1254/‑390)	ilvX → / → ilvM	uncharacterized protein IlvX/acetolactate synthase II subunit IlvM
RA	3,951,823	T→C	intergenic (+1266/‑378)	ilvX → / → ilvM	uncharacterized protein IlvX/acetolactate synthase II subunit IlvM
RA	3,951,964	T→C	intergenic (+1407/‑237)	ilvX → / → ilvM	uncharacterized protein IlvX/acetolactate synthase II subunit IlvM
RA	3,951,976	C→T	intergenic (+1419/‑225)	ilvX → / → ilvM	uncharacterized protein IlvX/acetolactate synthase II subunit IlvM
RA	3,951,994	T→C	intergenic (+1437/‑207)	ilvX → / → ilvM	uncharacterized protein IlvX/acetolactate synthase II subunit IlvM
RA	3,952,038	A→C	intergenic (+1481/‑163)	ilvX → / → ilvM	uncharacterized protein IlvX/acetolactate synthase II subunit IlvM
RA	3,952,057	G→T	intergenic (+1500/‑144)	ilvX → / → ilvM	uncharacterized protein IlvX/acetolactate synthase II subunit IlvM
RA	3,952,168	C→T	intergenic (+1611/‑33)	ilvX → / → ilvM	uncharacterized protein IlvX/acetolactate synthase II subunit IlvM
RA	3,968,248	G→A	M111I (ATG→ATA)	rfe →	UDP‑N‑acetylglucosamine‑‑undecaprenyl‑phosphate N‑acetylglucosaminephosphotransferase
MC JC	4,060,444	Δ19,761 bp		yihL–yiiF	19 genes yihL, yihM, yihN, ompL, yihO, yihP, yihQ, yihR, yihS, yihT, yihU, yihV, csqR, yihX, yihY, dtd, fabY, yiiE, yiiF
MC JC	4,086,996	Δ13,531 bp		yiiG–rhaT	yiiG, frvR, frvX, frvB, frvA, rhaM, rhaD, rhaA, rhaB, rhaS, rhaR, rhaT
RA	4,100,653	G→T	intergenic (‑128/‑157)	rhaT ← / → sodA	rhamnose/lyxose:H(+) symporter/superoxide dismutase (Mn)
RA	4,139,288	C→T	D141N (GAC→AAC)	fsaB ←	fructose‑6‑phosphate aldolase 2
RA	4,139,511	Δ1 bp	coding (198/663 nt)	fsaB ←	fructose‑6‑phosphate aldolase 2
MC JC	4,139,771	10483 bp→TG		[ptsA]–[eptC]	[ptsA], frwC, frwB, pflD, pflC, frwD, yijO, [eptC]
RA	4,212,973	Δ1 bp	intergenic (+27/‑67)	rrlE → / → rrfE	23S ribosomal RNA/5S ribosomal RNA
RA	4,235,651	T→C	intergenic (+244/‑255)	pgi → / → yjbE	glucose‑6‑phosphate isomerase/uncharacterized protein YjbE
MC JC	4,235,905	16376 bp→52 bp		yjbE–malM	yjbE, yjbF, yjbG, yjbH, yjbT, psiE, xylE, malH, malG, malF, malE, malK, lamB, malM
RA	4,296,381	+GC	intergenic (+587/+55)	gltP → / ← yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
MC JC	4,299,522	Δ12,535 bp		mdtP–alsB	mdtP, mdtO, mdtN, ytcA, yjcS, alsK, alsE, alsC, alsA, alsB
RA	4,312,070	Δ1 bp	intergenic (‑28/+31)	alsB ← / ← alsR	D‑allose ABC transporter periplasmic binding protein/DNA‑binding transcriptional repressor AlsR
RA	4,312,151	G→C	Q281E (CAA→GAA)	alsR ←	DNA‑binding transcriptional repressor AlsR
RA	4,312,215	A→G	T259T (ACT→ACC)	alsR ←	DNA‑binding transcriptional repressor AlsR
RA	4,312,219	A→G	L258P (CTA→CCA)	alsR ←	DNA‑binding transcriptional repressor AlsR
RA	4,312,289	A→G	Y235H (TAT→CAT)	alsR ←	DNA‑binding transcriptional repressor AlsR
RA	4,312,498	C→G	R165P (CGC→CCC)	alsR ←	DNA‑binding transcriptional repressor AlsR
RA	4,313,027	T→G	intergenic (‑36/‑323)	alsR ← / → rpiB	DNA‑binding transcriptional repressor AlsR/allose‑6‑phosphate isomerase/ribose‑5‑phosphate isomerase B
MC JC	4,313,864	Δ16,405 bp		yjdP–rdcB	18 genes yjdP, phnP, phnO, phnN, phnM, phnL, phnK, phnJ, phnI, phnH, phnG, phnF, phnD, phnC, yjdN, yjdM, rdcA, rdcB
MC JC	4,410,081	13624 bp→ATGC		yjfI–[ulaF]	18 genes yjfI, yjfJ, yjfK, yjfL, yjfM, yjfC, aidB, yjfN, bsmA, yjfP, ulaR, ulaG, ulaA, ulaB, ulaC, ulaD, ulaE, [ulaF]
MC JC	4,442,382	Δ6,658 bp		[tamA]–[chpB]	[tamA], tamB, ytfP, chpS, [chpB]
RA	4,450,030	A→C	P23P (CCA→CCC)	ytfQ →	galactofuranose ABC transporter periplasmic binding protein
MC JC	4,496,758	Δ13,333 bp		insC6–insO	insC6, insD6, yjgZ, insG, nanX, nanY, ythA, insO, insI3, insO, insO
RA	4,518,356	A→G	intergenic (‑121/‑16)	fecI ← / → ykiE	RNA polymerase sigma factor FecI/protein YkiE
MC JC	4,518,434	Δ81,761 bp		[ykiE]–yjjA	74 genes [ykiE], insA7, yjhU, yjhF, yjhG, yjhH, yjhI, sgcR, sgcE, sgcA, ryjB, sgcQ, sgcC, sgcB, sgcX, yjhP, yjhQ, topAI, ythB, nanS, nanM, nanC, fimB, fimE, fimA, fimI, fimC, fimD, fimF, fimG, fimH, gntP, uxuA, uxuB, uxuR, yjiC, ytiC, ytiD, idlP, iraD, hypT, iadA, yjiG, yjiH, kptA, yjiJ, yjiK, ytiA, yjiL, yjiM, yjiN, mdtM, ytiE, yjiR, yjiS, yjiT, mcrC, mcrB, mcrB, symE, symR, hsdS, hsdM, hsdR, mrr, yjiA, yjiX, btsT, tsr, lgoT, lgoR, lgoD, opgB, yjjA

Predicted mutations

evidence

position

mutation

annotation

gene

description

MC JC

15,445

Δ1,459 bp

[insL1]–[mokC]

[insL1], [hokC], [mokC]

MC JC

19,646

Δ863 bp

insB1–[insA1]

insB1, [insA1]

MC JC

65,857

12940 bp→GA

[araD]–[setA]

[araD], araA, araB, araC, yabI, thiQ, thiP, thiB, sroA, sgrR, sgrS, sgrT, [setA]

155,463

A→T

*247K (TAA→AAA)

yadV ←

putative fimbrial chaperone YadV

MC JC

167,401

Δ5,915 bp

fhuA–[fhuB]

fhuA, fhuC, fhuD, [fhuB]

MC JC

244,301

Δ9,446 bp

yafJ–yafP

yafJ, dpaA, yafQ, dinJ, yafL, rayT, dinB, yafN, yafO, yafP

254,249

A→T

intergenic (+1088/+10)

yafP → / ← pepD

putative N‑acetyltransferase YafP/peptidase D

MC JC

257,908

Δ776 bp

insB9–[crl]

insB9, insA9, [crl]

MC JC

263,076

Δ125,568 bp

ykfI–[tauD]

127 genes

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[tauD]

389,601

C→T

D43N (GAC→AAC)

hemB ←

porphobilinogen synthase

389,867

T→C

intergenic (‑140/‑384)

hemB ← / → yaiT

porphobilinogen synthase/putative autotransporter YaiT

MC JC

390,251

Δ14,565 bp

[yaiT]–[dgcC]

16 genes

[yaiT]ytiBinsF2insE2yaiTiprAampHsbmAyaiWyaiYyaiZddlAiraPphoApsiF[dgcC]

498,917

T→C

F288S (TTC→TCC)

hemH →

ferrochelatase

MC JC

519,143

Δ14,682 bp

[ybbO]–[allZ]

[ybbO], [tesA], ybbA, ybbP, rhsD, ybbC, ylbG, selU, allS, allA, [allR], [allZ]

535,337

T→C

A474A (GCT→GCC)

gcl →

glyoxylate carboligase

536,173

T→C

L155P (CTC→CCC)

hyi →

hydroxypyruvate isomerase

536,492

A→G

intergenic (+6/‑94)

hyi → / → glxR

hydroxypyruvate isomerase/tartronate semialdehyde reductase 2

536,549

T→C

intergenic (+63/‑37)

hyi → / → glxR

hydroxypyruvate isomerase/tartronate semialdehyde reductase 2

MC JC

536,617

Δ14,712 bp

[glxR]–[ybcF]

[glxR], ybbW, allB, ybbY, glxK, allE, allC, allD, fdrA, ylbE, ylbF, [ybcF]

557,635

A→T

L36Q (CTG→CAG)

folD ←

bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase

MC JC

565,054

44181 bp→TGA

[intD]–insL2

52 genes

[intD]renDinsE3insF3renDemrEylcJybcKybcLybcMylcHybcNninEybcOrusAylcGquuDnmpCinsH2nmpCessDrrrDrzpDrzoDborDybcVybcWylcInohDtfaDtfaXappYompTenvYybcHnfrAnfrBcusScusRcusCcusFcusBcusAphePybdGnfsBybdFybdJybdKsokEhokEinsL2

MC JC

641,446

Δ17,325 bp

[uspG]–crcB

18 genes

[uspG]ybdRyldArnkrnacitTcitGcitXcitFcitEcitDcitCdpiBdpiAdcuCpagPcspEcrcB

674,518

G→A

A89V (GCG→GTG)

leuS ←

leucine‑‑tRNA ligase

674,920

T→C

intergenic (‑137/‑98)

leuS ← / → ybeL

leucine‑‑tRNA ligase/DUF1451 domain‑containing protein YbeL

674,992

C→A

intergenic (‑209/‑26)

leuS ← / → ybeL

leucine‑‑tRNA ligase/DUF1451 domain‑containing protein YbeL

MC JC

675,018

Δ14,271 bp

[ybeL]–insH3

15 genes

MC JC

728,735

Δ10,773 bp

[kdpF]–[phr]

[kdpF], ybfA, rhsC, ybfB, ybfC, ybfQ, ybfD, [ybgA], [phr]

MC JC

832,467

Δ15,538 bp

ybiA–[glnH]

16 genes

ybiAdinGybiBhcxBzbiJybiEybiJybiIybiXfiumcbArlmFybiOglnQglnP[glnH]

MC JC

867,553

Δ15,836 bp

[gsiA]–[ybjG]

[gsiA], gsiB, gsiC, gsiD, pdeI, dgcI, rimO, bssR, yliI, gstB, dacC, deoR, [ybjG]

MC JC

890,913

Δ18,382 bp

[ybjC]–[ltaE]

21 genes

[ybjC]nfsArimKybjNpotFpotGpotHpotIybjOrlmCartJartMartQartIartPybjPybjQamiDybjSybjT[ltaE]

1,048,596

G→A

G32G (GGC→GGT)

gfcC ←

capsule biosynthesis GfcC family protein

MC JC

1,048,805

Δ48,085 bp

[gfcB]–ycdU

45 genes

[gfcB]gfcAinsA4insB4cspHcspGymcFymcEgnsAyccMtorStorTtorRtorCtorAtorDcbpMcbpAyccEagpyccJwrbAymdFrutGrutFrutErutDrutCrutBrutArutRputAymdGputPefeOefeBphoHpgaDpgaCpgaBpgaAdgcTinsF4insE4ycdU

MC JC

1,097,887

Δ17,605 bp

[ghrA]–mdtG

20 genes

[ghrA]ycdXycdYycdZcsgGcsgFcsgEcsgDcsgBcsgAcsgCymdAymdBclsCopgCopgGopgHyceKmsyBmdtG

1,115,852

T→C

K244R (AAG→AGG)

lpxL ←

lauroyl acyltransferase

1,196,861

A→G

intergenic (+79/+6)

C0293 → / ← ymfD

small regulatory RNA C0293/putative SAM‑dependent methyltransferase YmfD

MC JC

1,196,867

Δ27,041 bp

[ymfD]–ymgJ

37 genes

[ymfD]ymfElitintExisEymfHymfIymfJymfKymfTymfLymfMymfNymfRbeeEymfQycfKtfaPtfaEpinEmcrAiraMymgKymgLycgXbluRbluFycgZymgAariRymgCpdeGymgFymgDymgGymgIymgJ

1,269,250

A→G

I9T (ATT→ACT)

ldrA ←

small toxic polypeptide LdrA

MC JC

1,294,426

Δ12,725 bp

adhE–[yciU]

adhE, ychT, ychE, insH21, oppA, oppB, oppC, oppD, oppF, [yciU]

1,337,394

A→G

S522G (AGC→GGC)

acnA →

aconitate hydratase 1

MC JC

1,357,803

Δ9,014 bp

[puuP]–puuE

[puuP], ymjE, puuA, puuD, puuR, puuC, puuB, puuE

MC JC

1,394,891

Δ2,732 bp

[ynaI]–[ynaJ]

[ynaI], insH4, [ynaJ]

1,413,092

C→T

A48A (GCG→GCA)

intR ←

putative integrase

1,413,450

C→T

M1M (ATG→ATA) †

xisR ←

excisionase

1,413,558

G→T

S61S (TCC→TCA)
noncoding (3/179 nt)

rcbA ←
ralA →

double‑strand break reduction protein
small regulatory RNA antitoxin RalA

MC JC

1,422,752

Δ14,142 bp

[ydaW]–[ompN]

16 genes

[ydaW]rzoRtrkGynaKydaYynaAlomRinsH5lomRstfRtfaRpinRynaEynaMuspF[ompN]

MC JC

1,465,392

Δ16,810 bp

[ydbA]–[ynbD]

[ydbA], insD2, insC2, ydbA, insI2, ydbA, pdxI, ydbD, ynbA, ynbB, ynbC, [ynbD]

MC JC

1,502,457

Δ15,875 bp

[ydcL]–[mnaT]

19 genes

[ydcL]insQydcOsutRrlhAyncJhicAhicBydcRydcSydcTydcUydcVpatDyncLortTydcY[ydcZ][mnaT]

MC JC

1,520,673

Δ21,396 bp

[mcbR]–[narZ]

17 genes

[mcbR]yncDyncEansPyncGyncHydcDyncOydcCpptAyddHnhoAyddEnarVnarWnarY[narZ]

MC JC

1,590,854

Δ7,233 bp

[hipA]–hipB

[hipA], hipB

1,628,332

T→C

intergenic (+69/‑20)

ydfG → / → rspR

3‑hydroxy acid dehydrogenase YdfG/DNA‑binding transcriptional repressor RspR

MC JC

1,628,340

Δ10,127 bp

rspR–[cspI]

17 genes

rspRydfZydfIydfJynfTydfKpinQtfaQstfQnohAynfOydfOgnsBynfNynfRynfQ[cspI]

1,638,571

G→A

H33Y (CAT→TAT)

cspI ←

cold shock‑like protein CspI

1,640,045

coding (13/534 nt)

rrrQ ←

putative lysozyme

MC JC

1,640,057

Δ7,591 bp

[rrrQ]–[dicC]

18 genes

[rrrQ][ydfR]essQynfUcspBcspFynfSydfTydfUremhokDrelErelBydfVflxAydfWydfX[dicC]

MC JC

1,649,794

Δ6,356 bp

[dicB]–[ynfB]

[dicB], [ydfD], ynfP, rspB, rspA, ynfA, [ynfB]

1,851,841

C→T

Q328* (CAA→TAA)

ansA →

L‑asparaginase 1

MC JC

1,851,866

Δ10,563 bp

[ansA]–[msrB]

[ansA], pncA, ydjE, ydjF, ydjG, ydjH, ydjI, ydjJ, ydjK, ydjL, yeaC, [msrB]

MC JC

1,873,574

13215 bp→TAG

[yeaK]–[yeaX]

19 genes

[yeaK]yoaIyeaLnimRnimTyeaOyoaFdgcPyoaKyoaJyeaQyoaGyeaRleuEdmlRdmlAyeaVyeaW[yeaX]

1,887,158

C→A

L278L (CTG→CTT)

rnd ←

RNase D

1,887,644

C→T

W116* (TGG→TGA)

rnd ←

RNase D

1,946,876

C→A

L167L (CTG→CTT)

ruvC ←

crossover junction endodeoxyribonuclease RuvC

MC JC

1,961,950

Δ28,129 bp

yecT–[tyrP]

33 genes

yecTflhEflhAflhBcheZcheYcheBcheRtaptarcheWcheAcheAmotBmotAmotRflhCflhDinsB5insA5uspCotsAotsBaraHaraGaraFftnByecJazuCyecRftnAyecH[tyrP]

MC JC

1,993,664

Δ31,548 bp

[uvrC]–[yodD]

40 genes

[uvrC]uvrYyecUyecFsdiAsdsNtcyNtcyLdcyDtcyJfliZfliAfliXfliCfliDfliSfliTamyAyedDyedEyedFyedKyedLfliEfliFfliGfliHfliIfliJfliKfliLfliMfliNfliOfliPfliQfliRrcsAdsrB[yodD]

MC JC

2,030,451

Δ10,928 bp

[yedA]–[zinT]

[yedA], [vsr], dcm, yedJ, drpB, rseX, hchA, hprS, hprR, hiuH, msrP, msrQ, [zinT]

2,041,467

A→G

K31K (AAA→AAG)

zinT →

metal‑binding protein ZinT

MC JC

2,066,152

Δ12,778 bp

insH6–[yoeF]

insH6, yoeA, insD3, insC3, yoeA, isrC, flu, yeeR, yeeS, yeeT, cbeA, cbtA, yeeW, [yoeF]

2,078,954

A→G

intergenic (+23/+78)

yoeF → / ← tmaR

putative uncharacterized protein YoeF/PTS system regulator TmaR

MC JC

2,089,216

Δ255 bp

[yoeB]–[yefM]

[yoeB], [yefM]

2,089,473

T→C

I81V (ATC→GTC)

yefM ←

YefM antitoxin of the YoeB‑YefM toxin‑antitoxin pair and DNA binding transcriptional repressor

2,089,621

A→G

R31R (CGT→CGC)

yefM ←

YefM antitoxin of the YoeB‑YefM toxin‑antitoxin pair and DNA binding transcriptional repressor

2,093,977

C→T

H170H (CAC→CAT)

hisB →

imidazoleglycerol‑phosphate dehydratase/histidinol‑phosphatase

MC JC

2,101,395

Δ11,672 bp

wbbL–rfbB

wbbL, insH7, wbbL, wbbK, wbbJ, wbbI, wbbH, glf, rfbX, rfbC, rfbA, rfbD, rfbB

2,113,177

A→G

intergenic (‑116/+257)

rfbB ← / ← galF

dTDP‑glucose 4,6‑dehydratase 1/UTP:glucose‑1‑phosphate uridylyltransferase, low activity

MC JC

2,143,266

Δ40,395 bp

[dgcE]–yegX

38 genes

[dgcE]alkAyegDyegIyegJpphCyegLsibAibsAsibBibsBmdtAmdtBmdtCmdtDbaeSbaeRyegPtrhPcyaRogrKyegRyegSgatRinsE5insF5gatRgatDgatBgatAgatZgatYfbaByegTyegUyegVyegWyegX

MC JC

2,196,474

Δ29,182 bp

[yehF]–yohC

21 genes

[yehF]yehIyehKyehLyehMyehPyehQyehRyehSbtsRbtsSmlrAyohOyehWyehXyehYosmFbglXdldpbpGyohC

2,251,586

G→A

Q249Q (CAG→CAA)

nfo →

endonuclease IV

MC JC

2,251,701

Δ7,597 bp

[yeiI]–psuK

[yeiI], nupX, rihB, yeiL, psuT, psuG, psuK

MC JC

2,286,390

Δ3,880 bp

[yejO]–yejO

[yejO], insH8, yejO

MC JC

2,380,731

Δ9,210 bp

[elaB]–[yfbP]

[elaB], elaA, rbn, elaD, yfbK, yfbL, yfbM, yfbN, yfbO, [yfbP]

2,390,293

C→T

A405T (GCA→ACA)

nuoN ←

NADH:quinone oxidoreductase subunit N

2,406,367

A→G

L92S (TTA→TCA)

lrhA ←

DNA‑binding transcriptional dual regulator LrhA

2,406,861

T→A

intergenic (‑220/‑700)

lrhA ← / → alaA

DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA

2,417,032

C→T

intergenic (+141/‑49)

pta → / → yfcC

phosphate acetyltransferase/putative transporter YfcC

2,417,047

A→C

intergenic (+156/‑34)

pta → / → yfcC

phosphate acetyltransferase/putative transporter YfcC

MC JC

2,417,058

Δ10,734 bp

yfcC–[argT]

yfcC, yfcD, yfcE, yfcF, yfcG, folX, yfcH, rpnB, hisP, hisM, hisQ, hisJ, [argT]

MC JC

2,466,540

9636 bp→ACCC

intS–[ypdJ]

15 genes

2,476,629

A→G

intergenic (+119/+65)

torI → / ← dsdC

prophage CPS‑53 recombination directionality factor and response regulator inhibitor/DNA‑binding transcriptional dual regulator DsdC

2,481,795

G→A

Q128* (CAG→TAG)

emrY ←

tripartite efflux pump membrane subunit EmrY

MC JC

2,489,242

Δ19,001 bp

[yfdV]–[fryB]

17 genes

[yfdV]oxcfrcyfdXypdIyfdYlpxPypdKalaCpyrSpyrRypdCfryAypdEypdFfryC[fryB]

2,508,268

T→C

intergenic (‑26/+193)

fryB ← / ← glk

putative PTS enzyme IIB component FryB/glucokinase

2,508,293

A→G

intergenic (‑51/+168)

fryB ← / ← glk

putative PTS enzyme IIB component FryB/glucokinase

MC JC

2,514,272

Δ3,561 bp

insL3–[pdeA]

insL3, [pdeA]

MC JC

2,558,770

Δ6,560 bp

intZ–[yffS]

intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, [yffS]

MC JC

2,601,202

Δ13,582 bp

[hyfA]–focB

[hyfA], hyfB, hyfC, hyfD, hyfE, hyfF, hyfG, hyfH, hyfI, hyfJ, hyfR, focB

2,730,870

T→C

noncoding (288/1542 nt)

rrsG ←

16S ribosomal RNA

MC JC

2,756,159

Δ33,804 bp

[intA]–[glaH]

28 genes

[intA]yfjHalpAyfjIyfjJabpBabpAyfjMrnlArnlByfjPyfjQyfjRypjKyfjSyfjTyfjUyfjWyfjXyfjYypjJyfjZypjFypjAypjBypjCileY[glaH]

2,790,153

C→T

P58S (CCC→TCC)

lhgD →

L‑2‑hydroxyglutarate dehydrogenase

2,790,310

C→T

A110V (GCG→GTG)

lhgD →

L‑2‑hydroxyglutarate dehydrogenase

MC JC

2,795,656

Δ5,717 bp

glaR–[nrdE]

glaR, kbp, yqaE, ygaV, ygaP, stpA, alaE, ygaC, ygaM, nrdH, [nrdI], [nrdE]

MC JC

2,804,790

Δ5,840 bp

proV–[ygaH]

proV, proW, proX, ygaZ, [ygaH]

MC JC

2,825,796

Δ4,947 bp

srlA–[gutQ]

srlA, srlE, srlB, srlD, gutM, srlR, [gutQ]

2,867,454

2 bp→AA

coding (97‑98/993 nt)

rpoS ←

RNA polymerase sigma factor RpoS

MC JC

2,877,974

Δ183 bp

intergenic (+356/+413)

iap → / ← cas2

alkaline phosphatase isozyme conversion protein/CRISPR‑associated endoribonuclease Cas2

MC JC

2,910,754

Δ300 bp

[mazF]

2,985,726

A→G

intergenic (‑134/‑121)

yqeF ← / → yqeG

putative acyltransferase/putative transporter YqeG

2,985,816

T→C

intergenic (‑224/‑31)

yqeF ← / → yqeG

putative acyltransferase/putative transporter YqeG

MC JC

2,985,842

Δ47,769 bp

yqeG–[idi]

39 genes

yqeGyqeHyqeIyqeJyqeLyqeKygeGygeHygeIinsD4insC4ygeQglyUactSxdhAxdhBxdhCygeVygeWygeXygeYhyuAyqeAyqeByqeCmocAygfKssnAygfMxdhDxanQguaDghxQygfSygfTuacTyqfGyqfH[idi]

MC JC

3,077,568

Δ1,832 bp

[cmtA]–cmtB

[cmtA], cmtB

3,103,240

G→A

L76L (TTG→TTA)

mutY →

adenine DNA glycosylase

MC JC

3,110,591

Δ24,234 bp

[yghD]–yghT

20 genes

[yghD]yghEyqhJyghFyghGpppAyghJglcAglcBglcGglcFglcEglcDglcCyghOinsH9yghQyghRyghSyghT

MC JC

3,166,114

Δ7,312 bp

[ygiS]–[ygiN]

[ygiS], mqsA, mqsR, ygiV, ygiW, qseB, qseC, ygiZ, mdaB, [ygiN]

3,173,431

T→A

I97N (ATC→AAC)

ygiN →

putative quinol monooxygenase YgiN

MC JC

3,185,131

Δ4,735 bp

ygiL–[yqiG]

ygiL, yqiG, insC5, insD5, [yqiG]

3,190,000

T→C

D40D (GAT→GAC)

yqiH →

putative fimbrial chaperone YqiH

3,190,238

A→T

K120* (AAA→TAA)

yqiH →

putative fimbrial chaperone YqiH

3,190,725

A→G

N32D (AAT→GAT)

yqiI →

putative fimbrial protein YqiI

3,226,228

T→C

intergenic (+57/‑6)

ebgC → / → ygjI

DUF386 domain‑containing evolved beta‑D‑galactosidase subunit beta/putative transporter YgjI

MC JC

3,226,234

Δ15,511 bp

[ygjI]–[ygjV]

[ygjI], ygjJ, ygjK, fadH, higA, higB, rlmG, ygjP, ygjQ, ygjR, alx, sstT, [ygjV]

3,252,464

T→C

I54T (ATC→ACC)

yhaH →

putative inner membrane protein

MC JC

3,361,226

Δ9,811 bp

[gltF]–[nanE]

[gltF], yhcA, yhcD, yhcE, insH10, yhcE, yhcF, yhcG, nanQ, nanK, [nanE]

3,410,666

C→G

V129V (GTC→GTG)

dusB →

tRNA‑dihydrouridine synthase B

MC JC

3,411,645

9722 bp→A

yhdJ–[yhdY]

yhdJ, yhdU, envR, acrE, acrF, yhdV, yhdX, [yhdY]

3,421,374

C→T

S17L (TCA→TTA)

yhdY →

putative ABC transporter membrane subunit YhdY

MC JC

3,453,509

Δ16,346 bp

[gspB]–chiA

17 genes

[gspB]gspAgspCgspDgspEgspFgspGgspHgspIgspJgspKgspLgspMgspObfrbfdchiA

3,486,205

C→A

T29K (ACG→AAG)

crp →

DNA‑binding transcriptional dual regulator CRP

3,499,391

G→T

intergenic (+190/‑57)

cysG → / → yhfL

siroheme synthase/DUF4223 domain‑containing lipoprotein YhfL

3,499,393

T→G

intergenic (+192/‑55)

cysG → / → yhfL

siroheme synthase/DUF4223 domain‑containing lipoprotein YhfL

MC JC

3,499,401

Δ12,725 bp

yhfL–[yhfZ]

yhfL, frlA, frlB, frlC, frlD, frlR, yhfS, yhfT, yhfU, php, yhfW, yhfX, yhfY, [yhfZ]

3,512,183

T→C

E54E (GAA→GAG)

yhfZ ←

putative DNA‑binding transcriptional regulator YhfZ

3,560,455

intergenic (+589/+167)

rtcR → / ← glpG

DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG

MC JC

3,578,950

Δ6,094 bp

[yhhW]–[yrhB]

[yhhW], yhhX, ryhB, yhhY, yhhZ, yrhA, insA6, insB6, yrhA, yrhD, [yrhB]

MC JC

3,619,069

Δ18,342 bp

rhsB–[yhiN]

rhsB, yhhH, yhhI, yhhJ, rbbA, yhiI, yhiY, yhiJ, yhiM, [yhiN]

3,637,426

Δ1 bp

intergenic (‑16/‑216)

yhiN ← / → pitA

putative oxidoreductase YhiN/metal phosphate:H(+) symporter PitA

3,637,436

G→A

intergenic (‑26/‑206)

yhiN ← / → pitA

putative oxidoreductase YhiN/metal phosphate:H(+) symporter PitA

MC JC

3,651,191

Δ2,158 bp

yhiS–[yhiS]

yhiS, insH11, [yhiS]

MC JC

3,701,865

Δ5,842 bp

[dppF]–dppA

[dppF], dppD, dppC, dppB, dppA

3,708,172

(A)_7→6

intergenic (‑467/+444)

dppA ← / ← proK

dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro

MC JC

3,716,547

Δ5,503 bp

[yiaD]–[insK]

[yiaD], ghrB, yiaF, yiaG, cspA, ysaE, hokA, insJ, [insK]

3,725,734

G→A

intergenic (‑22/‑153)

ysaB ← / → wecH

putative lipoprotein YsaB/O‑acetyltransferase WecH

3,725,782

T→C

intergenic (‑70/‑105)

ysaB ← / → wecH

putative lipoprotein YsaB/O‑acetyltransferase WecH

MC JC

3,725,888

Δ42,752 bp

[wecH]–yibG

37 genes

[wecH]yiaAyiaBxylBxylZxylAxylFxylGxylHxylRbaxbaxLmalSavtAysaAplaRyiaKyiaLyiaMyiaNyiaOlyxKsgbHsgbUsgbEyiaTyiaUyiaVyiaWaldByiaYselBselAyibFrhsAyibAyibG

3,768,988

C→T

intergenic (+350/‑357)

yibG → / → yibV

tetratricopeptide‑like domain‑containing protein YibG/PF15596 family protein YibV

3,815,199

G→A

Y190Y (TAC→TAT)

pyrE ←

orotate phosphoribosyltransferase

3,815,202

A→G

A189A (GCT→GCC)

pyrE ←

orotate phosphoribosyltransferase

3,815,211

G→A

D186D (GAC→GAT)

pyrE ←

orotate phosphoribosyltransferase

3,815,292

G→C

R159R (CGC→CGG)

pyrE ←

orotate phosphoribosyltransferase

3,815,307

G→A

L154L (CTC→CTT)

pyrE ←

orotate phosphoribosyltransferase

3,815,319

C→T

V150V (GTG→GTA)

pyrE ←

orotate phosphoribosyltransferase

3,815,343

G→A

A142A (GCC→GCT)

pyrE ←

orotate phosphoribosyltransferase

3,815,364

C→T

E135E (GAG→GAA)

pyrE ←

orotate phosphoribosyltransferase

3,815,466

T→C

E101E (GAA→GAG)

pyrE ←

orotate phosphoribosyltransferase

3,815,496

C→A

L91L (CTG→CTT)

pyrE ←

orotate phosphoribosyltransferase

3,815,502

G→A

H89H (CAC→CAT)

pyrE ←

orotate phosphoribosyltransferase

3,815,517

T→C

A84A (GCA→GCG)

pyrE ←

orotate phosphoribosyltransferase

3,815,523

A→G

A82A (GCT→GCC)

pyrE ←

orotate phosphoribosyltransferase

3,815,529

T→A

T80T (ACA→ACT)

pyrE ←

orotate phosphoribosyltransferase

3,815,535

G→C

A78A (GCC→GCG)

pyrE ←

orotate phosphoribosyltransferase

3,815,589

G→A

S60S (TCC→TCT)

pyrE ←

orotate phosphoribosyltransferase

3,815,601

C→T

A56A (GCG→GCA)

pyrE ←

orotate phosphoribosyltransferase

3,815,634

A→G

D45D (GAT→GAC)

pyrE ←

orotate phosphoribosyltransferase

3,815,883

coding (667/687 nt)

rph ←

truncated RNase PH

3,815,893

A→C

A219A (GCT→GCG)

rph ←

truncated RNase PH

3,815,903

A→G

I216T (ATC→ACC)

rph ←

truncated RNase PH

3,816,007

A→T

S181S (TCT→TCA)

rph ←

truncated RNase PH

3,816,036

2 bp→TT

coding (513‑514/687 nt)

rph ←

truncated RNase PH

3,816,043

G→A

G169G (GGC→GGT)

rph ←

truncated RNase PH

3,816,049

C→T

V167V (GTG→GTA)

rph ←

truncated RNase PH

3,816,055

T→A

G165G (GGA→GGT)

rph ←

truncated RNase PH

3,816,091

A→G

N153N (AAT→AAC)

rph ←

truncated RNase PH

3,816,137

A→G

V138A (GTA→GCA)

rph ←

truncated RNase PH

MC JC

3,836,957

Δ8,771 bp

[setC]–[adeD]

[setC], yicL, yicU, nlpA, yicS, nepI, yicN, adeQ, [adeD]

MC JC

3,855,159

Δ11,170 bp

[yidF]–yidE

[yidF], yidG, yidH, yidI, yidJ, yidK, yidL, glvB, glvC, yidP, yidE

3,867,576

G→T

intergenic (‑154/‑152)

ibpA ← / → yidQ

small heat shock protein IbpA/DUF1375 domain‑containing putative lipoprotein YidQ

MC JC

3,867,599

Δ9,908 bp

yidQ–yidB

yidQ, yidR, cbrA, dgoT, dgoD, dgoA, dgoK, dgoR, yidX, yidA, yidB

MC JC

3,888,435

Δ3,155 bp

[tnaC]–tnaB

[tnaC], tnaA, tnaB

MC JC

3,927,155

Δ12,222 bp

[asnA]–[hsrA]

[asnA], viaA, ravA, kup, rbsD, rbsA, rbsC, rbsB, rbsZ, rbsK, rbsR, [hsrA]

3,951,306

G→A

intergenic (+749/‑895)

ilvX → / → ilvM