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.
JJPNJFNG_1	3363994	3364731	ErmB	ARO:3000375	ErmB	98.78	98.79	AF242872.1
JJPNJFNG_1	2594566	2595420	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
JJPNJFNG_1	2575857	2577059	blt	ARO:3003006	blt	100.00	100.00	L32599.1
JJPNJFNG_1	2353539	2354708	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
JJPNJFNG_1	1356345	1356662	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
JJPNJFNG_1	1356007	1356345	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
JJPNJFNG_1	896274	898844	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3
JJPNJFNG_1	584232	585875	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3
JJPNJFNG_1	339164	339757	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
JJPNJFNG_1	288661	290094	lmrB	ARO:3002813	lmrB	100.00	100.00	JYFL01000006.1
JJPNJFNG_1	275846	276766	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.
JJPNJFNG_1	2594566	2595420	aadK	Streptomycin	100.00	100.00	M26879
JJPNJFNG_1	3363994	3364731	erm(B)	Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin IA, Virginiamycin S	100.00	100.00	U18931
JJPNJFNG_1	275846	276766	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
JJPNJFNG_1	4048811	4050187	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.
JJPNJFNG_1	2594569	2595420	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
JJPNJFNG_1	3363994	3364728	erm(B)	23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)	EXACTX	100.00	100.00	WP_002292226.1
JJPNJFNG_1	275846	276763	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
JJPNJFNG_1	4046293	4046811	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
JJPNJFNG_1	4048814	4050187	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
JJPNJFNG_1	584235	585875	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
JJPNJFNG_1	2044620	2047214	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.
JJPNJFNG_1	3558431	3559573	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
JJPNJFNG_1	3560056	3561237	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
JJPNJFNG_1	3559592	3560041	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
JJPNJFNG_1	2002085	2003848	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
JJPNJFNG_1	3150395	3151180	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
JJPNJFNG_1	3146559	3147497	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
JJPNJFNG_1	3149173	3150369	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
JJPNJFNG_1	3147525	3149144	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
JJPNJFNG_1	3139403	3146539	dhbF	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391076
JJPNJFNG_1	2154184	2154825	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
JJPNJFNG_1	132882	134018	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
JJPNJFNG_1	19074	19943	pdxS	3.03e-149	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
JJPNJFNG_1	1669617	1670393	CodY	3.31e-124	nutrient-responsive regulator	81.08	100.00	ACJ80679
JJPNJFNG_1	3406844	3407413	ClpP	2.45e-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
JJPNJFNG_1	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
JJPNJFNG_1	1300060	1326168	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
JJPNJFNG_1	2525929	2556173	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)