safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

ARGs	VFs	PGs	PPRS
13	10	8	18.25

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.
NCJEPNOG_12	676663	677832	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
NCJEPNOG_1	590811	591149	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
NCJEPNOG_1	590494	590811	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
NCJEPNOG_12	454337	455539	blt	ARO:3003006	blt	100.00	100.00	L32599.1
NCJEPNOG_12	435976	436830	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
NCJEPNOG_28	276565	279135	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3
NCJEPNOG_30	107961	108881	mphK	ARO:3004541	mphK	100.00	100.00	CP010314.1
NCJEPNOG_30	94627	96066	lmrB	ARO:3002813	lmrB	99.79	100.42	JYFL01000006.1
NCJEPNOG_30	44970	45563	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
NCJEPNOG_33	29126	30769	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3

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.
NCJEPNOG_12	435976	436830	aadK	Streptomycin	100.00	100.00	M26879
NCJEPNOG_30	107961	108881	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
NCJEPNOG_32	90362	91738	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.
NCJEPNOG_12	435976	436827	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
NCJEPNOG_30	107964	108881	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
NCJEPNOG_32	87844	88362	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
NCJEPNOG_32	90365	91738	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
NCJEPNOG_33	29126	30766	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
NCJEPNOG_29	192794	195388	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.
NCJEPNOG_23	519091	520233	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
NCJEPNOG_23	520716	521897	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
NCJEPNOG_23	520252	520701	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
NCJEPNOG_29	240283	242046	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
NCJEPNOG_23	112782	113567	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
NCJEPNOG_23	108946	109884	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
NCJEPNOG_23	111560	112756	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
NCJEPNOG_23	109912	111531	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
NCJEPNOG_12	876558	877199	hlyIII	Hemolysin III	Exotoxin	100.00	100.00	NP_390062
NCJEPNOG_23	101790	108926	dhbF	Bacillibactin	Nutritional/Metabolic factor	99.97	100.00	NP_391076

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
NCJEPNOG_2	27975	26839	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
NCJEPNOG_4	4231	5100	pdxS	1.10e-151	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
NCJEPNOG_1	277547	276771	CodY	8.24e-125	nutrient-responsive regulator	81.08	100.00	ACJ80679
NCJEPNOG_23	367505	368074	ClpP	5.52e-99	part of proteolytic complex	81.05	97.44	BAB94595
NCJEPNOG_1	739972	739580	spxA1	2.44e-69	redox-responsive transcription factor	83.21	100.00	AAF21893
NCJEPNOG_3	20512	20754	SpoVG	2.72e-38	RNA-binding protein	80.25	79.41	AAT02994
NCJEPNOG_33	76241	76044	CspA	3.37e-32	cold shock protein	90.91	100.00	CAA62903
NCJEPNOG_12	864596	864402	CspD	5.69e-28	cold shock protein	81.54	98.48	CAC99957

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
NCJEPNOG_1	0.0	1.0	0.0
NCJEPNOG_2	0.0	1.0	0.0
NCJEPNOG_3	0.0	1.0	0.0
NCJEPNOG_4	0.0	1.0	0.0
NCJEPNOG_5	0.0	1.0	0.0
NCJEPNOG_6	0.0	1.0	0.0
NCJEPNOG_7	0.0	1.0	0.0
NCJEPNOG_12	0.0	1.0	0.0
NCJEPNOG_23	0.0	1.0	0.0
NCJEPNOG_28	0.0	1.0	0.0
NCJEPNOG_29	0.0	1.0	0.0
NCJEPNOG_30	0.0	1.0	0.0
NCJEPNOG_31	0.0	1.0	0.0
NCJEPNOG_32	0.0	1.0	0.0
NCJEPNOG_33	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
NCJEPNOG_1	620988	647096	False	Myoviridae	VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667
NCJEPNOG_12	475090	505467	False	Myoviridae	VOG4600, VOG1309, VOG11060, VOG0189, VOG4693, VOG9587, VOG4673, VOG0796, VOG10227, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718

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