safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

ARGs	VFs	PGs	PPRS
14	10	4	17.66

PPRS is classified as low-risk (≤4), medium-risk (4-6), and high-risk (≥6).

Comprehensive Antibiotic Resistance Database (CARD)

Query ID	Begin	End	ARO name	ARO accession	CARD name	Identity	Coverage	Accession no.
LCKAGGKD_1	3045800	3046582	ANT(9)-Ia	ARO:3002630	ANT(9)-Ia	100.00	100.00	X02588.1
LCKAGGKD_1	2735674	2736528	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
LCKAGGKD_1	2716965	2718167	blt	ARO:3003006	blt	100.00	100.00	L32599.1
LCKAGGKD_1	2494647	2495816	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
LCKAGGKD_1	1376847	1377164	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
LCKAGGKD_1	1376509	1376847	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
LCKAGGKD_1	916767	919337	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3
LCKAGGKD_1	604724	606367	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3
LCKAGGKD_1	339155	339748	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
LCKAGGKD_1	288652	290085	lmrB	ARO:3002813	lmrB	100.00	100.00	JYFL01000006.1
LCKAGGKD_1	275837	276757	mphK	ARO:3004541	mphK	100.00	100.00	CP010314.1

RGI v6.0.3 (Database: CARD Variants v4.0.2, Nov. 2023 release)

ResFinder

Query ID	Begin	End	Resistance gene	Phenotype	Identity	Coverage	Accession no.
LCKAGGKD_1	2735674	2736528	aadK	Streptomycin	100.00	100.00	M26879
LCKAGGKD_1	3045800	3046582	ant(9)-Ia	Spectinomycin	100.00	100.00	X02588
LCKAGGKD_1	275837	276757	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
LCKAGGKD_1	4190020	4191396	tet(L)	Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline	100.00	100.00	X08034

ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)

AMRFinderPlus

Query ID	Begin	End	Gene symbol	Sequence name	Method	Identity	Coverage	Accession no.
LCKAGGKD_1	2735677	2736528	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
LCKAGGKD_1	3045803	3046582	ant(9)-Ia	aminoglycoside nucleotidyltransferase ANT(9)-Ia	EXACTX	100.00	100.00	WP_000067268.1
LCKAGGKD_1	275837	276754	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
LCKAGGKD_1	4187502	4188020	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
LCKAGGKD_1	4190023	4191396	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
LCKAGGKD_1	604727	606367	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
LCKAGGKD_1	2051327	2053921	rphC	rifamycin-inactivating phosphotransferase RphC	BLASTX	81.15	99.88	WP_087347987.1

AMRFinderPlus v4.0.3 (Database: Oct. 2024 release)

Virulence Factor Database (VFDB)

Query ID	qstart	qend	Gene name	VF name	VF category	Identity	Coverage	Accession no.
LCKAGGKD_1	3700159	3701301	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
LCKAGGKD_1	3701784	3702965	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
LCKAGGKD_1	3701320	3701769	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
LCKAGGKD_1	2004669	2006432	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
LCKAGGKD_1	3293849	3294634	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
LCKAGGKD_1	3290013	3290951	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
LCKAGGKD_1	3292627	3293823	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
LCKAGGKD_1	3290979	3292598	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
LCKAGGKD_1	3282857	3289993	dhbF	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391076
LCKAGGKD_1	2295295	2295936	hlyIII	Hemolysin III	Exotoxin	100.00	100.00	NP_390062

BLASTN v2.16.0 (Database: VFDB, Dec. 2024 release)

VirulenceFinder

Query ID	Begin	End	Database	Virulence factor	Protein function	Identity	Coverage	Accession no.
No hit found

VirulenceFinder v2.0. 4 (Database: virulencefinder_db, Feb . 2024 release)

PHI-base

Query ID	qstart	qend	Gene name	e-value	Function	Identity	Coverage	Gene ID
LCKAGGKD_1	132882	134018	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
LCKAGGKD_1	19074	19943	pdxS	3.13e-149	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
LCKAGGKD_1	1690111	1690887	CodY	3.42e-124	nutrient-responsive regulator	81.08	100.00	ACJ80679
LCKAGGKD_1	3548572	3549141	ClpP	2.54e-98	part of proteolytic complex	81.05	97.44	BAB94595

BLASTX v2.16.0 (Database: PHI base v4.16, May. 2024 release)

PlasmidFinder

Query ID	Begin	End	Plasmid	Query / Template	Identity	Accession no.
No hit found

PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)

PlasmidHunter

Query ID	Prediction	Chromosome	Plasmid
LCKAGGKD_1	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
LCKAGGKD_1	1320562	1346670	False	Myoviridae	VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG4705
LCKAGGKD_1	2667037	2697281	False	Myoviridae	VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG10227, VOG0796, VOG4673, VOG9587, VOG4693, VOG0189, VOG11060, VOG1309, VOG4600

Phigaro v2.4.0 (Database: Jan. 2024 release)