safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

ARGs	VFs	PGs	PPRS
13	10	4	16.88

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.
LKCGKMCK_1	2621319	2622173	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
LKCGKMCK_1	2602610	2603812	blt	ARO:3003006	blt	100.00	100.00	L32599.1
LKCGKMCK_1	2380291	2381460	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
LKCGKMCK_1	1355942	1356259	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
LKCGKMCK_1	1355604	1355942	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
LKCGKMCK_1	895863	898433	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3
LKCGKMCK_1	583823	585466	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3
LKCGKMCK_1	338755	339348	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
LKCGKMCK_1	288252	289685	lmrB	ARO:3002813	lmrB	100.00	100.00	JYFL01000006.1
LKCGKMCK_1	275437	276357	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.
LKCGKMCK_1	2621319	2622173	aadK	Streptomycin	100.00	100.00	M26879
LKCGKMCK_1	275437	276357	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
LKCGKMCK_1	4073342	4074718	tet(L)	Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline	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.
LKCGKMCK_1	2621322	2622173	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
LKCGKMCK_1	275437	276354	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
LKCGKMCK_1	4070824	4071342	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
LKCGKMCK_1	4073345	4074718	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
LKCGKMCK_1	583826	585466	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
LKCGKMCK_1	2071379	2073973	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.
LKCGKMCK_1	3583486	3584628	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
LKCGKMCK_1	3585111	3586292	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
LKCGKMCK_1	3584647	3585096	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
LKCGKMCK_1	2024721	2026484	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
LKCGKMCK_1	3177150	3177935	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
LKCGKMCK_1	3173314	3174252	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
LKCGKMCK_1	3175928	3177124	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
LKCGKMCK_1	3174280	3175899	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
LKCGKMCK_1	3166158	3173294	dhbF	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391076
LKCGKMCK_1	2180945	2181586	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
LKCGKMCK_1	132473	133609	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
LKCGKMCK_1	18665	19534	pdxS	3.05e-149	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
LKCGKMCK_1	1669206	1669982	CodY	3.33e-124	nutrient-responsive regulator	81.08	100.00	ACJ80679
LKCGKMCK_1	3431874	3432443	ClpP	2.47e-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
LKCGKMCK_1	0.0	1.0	0.0
LKCGKMCK_2	1.0	0.0	1.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
LKCGKMCK_1	1299657	1325765	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
LKCGKMCK_1	1860154	1895686	False	Siphoviridae	VOG4602, VOG9667, VOG5353, VOG0181, VOG4552, VOG4566, VOG9600, VOG0025, VOG1884, VOG0198, VOG6093, VOG7462, VOG4581, VOG1886, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG4705, VOG0641, VOG4918
LKCGKMCK_1	2552681	2582925	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)