BRESEQ :: Mutation Predictions

Predicted mutations
evidence	position	mutation	annotation	gene	description
RA	155,463	A→T	*247K (TAA→AAA)	yadV ←	putative fimbrial chaperone YadV
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
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]
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
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
JC JC	1,105,376	IS2 (–) +5 bp	intergenic (+83/‑34)	csgC → / → ymdA	curlin chaperone/uncharacterized protein YmdA
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
MC JC	1,299,499	Δ1,199 bp		insH21	insH21
RA	1,301,917	C→T	Q246Y (CAG→TAT)	oppA →	oligopeptide ABC transporter periplasmic binding protein
RA	1,301,919	G→T	Q246Y (CAG→TAT)	oppA →	oligopeptide ABC transporter periplasmic binding protein
RA	1,337,394	A→G	S522G (AGC→GGC)	acnA →	aconitate hydratase 1
RA	1,413,092	C→T	A48A (GCG→GCA)	intR ←	putative integrase
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]
RA	1,652,331	T→C	intergenic (+2346/+397)	ydfD → / ← ynfP	lysis protein/protein YnfP
JC JC	1,853,797	IS1 (–) +9 bp	coding (175‑183/1359 nt)	ydjE ←	putative transporter YdjE
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	2,101,395	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	2,380,731	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	2,417,032	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	2,498,768	9486 bp→CCC		[pyrS]–fryB	[pyrS], pyrR, ypdC, fryA, ypdE, ypdF, fryC, fryB
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
RA	2,926,772	C→A	G155G (GGC→GGA)	ppnN →	nucleotide 5'‑monophosphate nucleosidase
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
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	3,361,226	Δ9,811 bp		[gltF]–[nanE]	[gltF], yhcA, yhcD, yhcE, insH10, yhcE, yhcF, yhcG, nanQ, nanK, [nanE]
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	3,560,455	+G	intergenic (+589/+167)	rtcR → / ← glpG	DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG
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
JC JC	3,707,484	+GA :: IS3 (+) +4 bp	coding (219‑222/1608 nt)	dppA ←	dipeptide ABC transporter periplasmic binding protein
JC JC	3,720,136	IS3 (–) +3 bp :: +TCA	coding (88‑90/213 nt)	cspA →	cold shock protein CspA
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
JC JC	3,890,411	IS1 (–) +9 bp	coding (176‑184/1248 nt)	tnaB →	tryptophan:H(+) symporter TnaB
MC JC	3,927,155	Δ12,222 bp		[asnA]–[hsrA]	[asnA], viaA, ravA, kup, rbsD, rbsA, rbsC, rbsB, rbsZ, rbsK, rbsR, [hsrA]
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	4,139,288	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	4,235,651	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	4,496,758	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

155,463

A→T

*247K (TAA→AAA)

yadV ←

putative fimbrial chaperone YadV

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

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]

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

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

JC JC

1,105,376

IS2 (–) +5 bp

intergenic (+83/‑34)

csgC → / → ymdA

curlin chaperone/uncharacterized protein YmdA

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

MC JC

1,299,499

Δ1,199 bp

insH21

insH21

1,301,917

C→T

Q246Y (CAG→TAT)

oppA →

oligopeptide ABC transporter periplasmic binding protein

1,301,919

G→T

Q246Y (CAG→TAT)

oppA →

oligopeptide ABC transporter periplasmic binding protein

1,337,394

A→G

S522G (AGC→GGC)

acnA →

aconitate hydratase 1

1,413,092

C→T

A48A (GCG→GCA)

intR ←

putative integrase

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]

1,652,331

T→C

intergenic (+2346/+397)

ydfD → / ← ynfP

lysis protein/protein YnfP

JC JC

1,853,797

IS1 (–) +9 bp

coding (175‑183/1359 nt)

ydjE ←

putative transporter YdjE

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

2,101,395

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

2,380,731

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

2,417,032

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

2,498,768

9486 bp→CCC

[pyrS]–fryB

[pyrS], pyrR, ypdC, fryA, ypdE, ypdF, fryC, fryB

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

2,926,772

C→A

G155G (GGC→GGA)

ppnN →

nucleotide 5'‑monophosphate nucleosidase

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

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

3,361,226

Δ9,811 bp

[gltF]–[nanE]

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

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

3,560,455

intergenic (+589/+167)

rtcR → / ← glpG

DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG

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

JC JC

3,707,484

+GA :: IS3 (+) +4 bp

coding (219‑222/1608 nt)

dppA ←

dipeptide ABC transporter periplasmic binding protein

JC JC

3,720,136

IS3 (–) +3 bp :: +TCA

coding (88‑90/213 nt)

cspA →

cold shock protein CspA

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

JC JC

3,890,411

IS1 (–) +9 bp

coding (176‑184/1248 nt)

tnaB →

tryptophan:H(+) symporter TnaB

MC JC

3,927,155

Δ12,222 bp

[asnA]–[hsrA]

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

MC JC

4,060,444

Δ19,761 bp

yihL–yiiF

19 genes

yihLyihMyihNompLyihOyihPyihQyihRyihSyihTyihUyihVcsqRyihXyihYdtdfabYyiiEyiiF

MC JC

4,086,996

Δ13,531 bp

yiiG–rhaT

yiiG, frvR, frvX, frvB, frvA, rhaM, rhaD, rhaA, rhaB, rhaS, rhaR, rhaT

4,139,288

C→T

D141N (GAC→AAC)

fsaB ←

fructose‑6‑phosphate aldolase 2

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]

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

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

4,312,070

Δ1 bp

intergenic (‑28/+31)

alsB ← / ← alsR

D‑allose ABC transporter periplasmic binding protein/DNA‑binding transcriptional repressor AlsR

4,312,151

G→C

Q281E (CAA→GAA)

alsR ←