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.
GKFLCFJD_1	2735284	2736138	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
GKFLCFJD_1	2716575	2717777	blt	ARO:3003006	blt	100.00	100.00	L32599.1
GKFLCFJD_1	2494256	2495425	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
GKFLCFJD_1	1376459	1376776	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
GKFLCFJD_1	1376121	1376459	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
GKFLCFJD_1	916377	918947	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3
GKFLCFJD_1	604334	605977	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3
GKFLCFJD_1	338755	339348	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
GKFLCFJD_1	288252	289685	lmrB	ARO:3002813	lmrB	100.00	100.00	JYFL01000006.1
GKFLCFJD_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.
GKFLCFJD_1	2735284	2736138	aadK	Streptomycin	100.00	100.00	M26879
GKFLCFJD_1	275437	276357	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
GKFLCFJD_1	4187309	4188685	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.
GKFLCFJD_1	2735287	2736138	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
GKFLCFJD_1	275437	276354	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
GKFLCFJD_1	4184791	4185309	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
GKFLCFJD_1	4187312	4188685	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
GKFLCFJD_1	604337	605977	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
GKFLCFJD_1	2050941	2053535	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.
GKFLCFJD_1	3697448	3698590	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
GKFLCFJD_1	3699073	3700254	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
GKFLCFJD_1	3698609	3699058	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
GKFLCFJD_1	2004283	2006046	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
GKFLCFJD_1	3291113	3291898	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
GKFLCFJD_1	3287277	3288215	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
GKFLCFJD_1	3289891	3291087	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
GKFLCFJD_1	3288243	3289862	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
GKFLCFJD_1	3280121	3287257	dhbF	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391076
GKFLCFJD_1	2294909	2295550	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
GKFLCFJD_1	132473	133609	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
GKFLCFJD_1	18664	19533	pdxS	3.13e-149	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
GKFLCFJD_1	1689723	1690499	CodY	3.42e-124	nutrient-responsive regulator	81.08	100.00	ACJ80679
GKFLCFJD_1	3545836	3546405	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
GKFLCFJD_1	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
GKFLCFJD_1	1320174	1346282	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
GKFLCFJD_1	2666646	2696890	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)