Probiotic potential risk score

ARGs (CARD)	VFs (VFDB)	PGs (PHI-base)	PPRS
4	18	58	60.86

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

Antibiotic resistance genes

Comprehensive Antibiotic Resistance Database (CARD)

ARO accession	ARO name	Identity	Coverage	CARD name	Accession no.
ARO:3000838	arlR	100.00	100.00	arlR	CP023390.1
ARO:3000839	arlS	100.00	100.00	arlS	CP000253.1
ARO:3003312	Staphylococcus aureus parC conferring resistance to fluoroquinolones	99.75	100.00	Saur_parC_FLO	NC_002951.2
ARO:3002814	clbA	97.42	100.00	clbA	CP006845.1

RGI v6.0.0 (Database: CARD Variants v4.0.0, Jul. 2022 release)

ResFinder

Resistance gene	Identity	Coverage	Phenotype	Accession no.
cfr(B)	87.64	98.67	Warning: gene is missing from Notes file. Please inform curator.	KR610408
tet(L)	87.07	100.00	Tetracycline resistance	X08034

ResFinder v4.0 (Database: resfinder_db, May 2022 release)

AMRFinderPlus

Gene symbol	Sequence name	Method	Identity	Coverage	Accession no.
clbA	23S rRNA (adenine(2503)-C(8))-methyltransferase ClbA	BLASTX	97.42	100.00	WP_012116915.1
tet(L)	tetracycline efflux MFS transporter Tet(L)	BLASTX	87.09	99.78	WP_003242953.1

AMRFinderPlus v3.10.42 (Database: Oct. 2022 release)

Virulence factors

Virulence Factor Database (VFDB)

Gene ID	Gene name	Identity	Coverage	e-value	VF name	VF category	Accession no.
VFG017229	eap/map	100.00	100.00	0.0	Eap/Map	Adherence	WP_000769694
VFG017113	ebp	100.00	100.00	0.0	EbpS	Adherence	WP_000069291
VFG004494	efb	100.00	100.00	0.0	Fibrinogen binding protein efb	Immune modulation	WP_000791581
VFG004845	hly/hla	100.00	100.00	0.0	-hemolysin	Exotoxin	WP_000857488
VFG001318	isdA	100.00	100.00	0.0	Isd	Nutritional/Metabolic factor	WP_000160859
VFG001319	isdC	100.00	100.00	0.0	Isd	Nutritional/Metabolic factor	WP_000789821
VFG001321	isdE	100.00	100.00	0.0	Isd	Nutritional/Metabolic factor	WP_001220199
VFG044268	isdF	100.00	100.00	0.0	Isd	Nutritional/Metabolic factor	WP_000594530
VFG004735	nuc	100.00	100.00	0.0	Thermonuclease nuc	Exoenzyme	WP_000841351
VFG004722	sspB	100.00	100.00	0.0	Staphopain	Exoenzyme	WP_001089094
VFG004485	atl	99.97	100.00	0.0	Autolysin alt	Adherence	WP_001074534
VFG044266	isdD	99.91	100.00	0.0	Isd	Nutritional/Metabolic factor	WP_001246698
VFG004781	sspA	99.81	100.00	0.0	V8 protease	Exoenzyme	WP_000676539
VFG044269	srtB	99.73	100.00	0.0	Isd	Nutritional/Metabolic factor	WP_001242429
VFG001317	isdB	99.02	99.95	0.0	Isd	Nutritional/Metabolic factor	WP_001041586
VFG016299	capB	82.46	99.66	0.0	Capsule	Immune modulation	NP_391471
VFG004711	sspC	99.70	100.00	8.65e-174	Staphopain	Exoenzyme	WP_000284458
VFG001324	isdG	99.69	100.00	1.84e-170	Isd	Nutritional/Metabolic factor	WP_000670950

BLASTN v2.8.1+ (Database: VFDB, Jun. 2022 release)

VirulenceFinder

Database	Virulence factor	Identity	Coverage	Protein function	Accession no.
No hit found

VirulenceFinder v2.0.3 (Database: virulencefinder_db, Dec. 2022 release)

Pathogenic genes

PHI-base

Protein ID	Gene name	Identity	Coverage	e-value	Function	Gene ID
Q7A656	IsdB	100.00	99.85	0.0	Iron-regulated surface determinant protein B	BAB42225
A6QFR9	qoxB	100.00	99.85	0.0	Terminal Oxidases	BAF67201
A0A390C306	menD	100.00	99.82	0.0	2-Succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase	AHM68850
Q2FZ08	cvfA	100.00	99.81	0.0	Virulence factor	BAF96735
W8TWD5	brnQ2	100.00	99.78	0.0	Branched-chain amino acid ABC transporter	AHM70974
W8US24	ndhC	100.00	99.75	0.0	NADH dehydrogenase	AHM68945
Q7A5Q2	PstS	100.00	99.70	0.0	Phosphate-binding protein/ thioredoxine reductase	BAB42481
Q99UN8	fabD	100.00	99.68	0.0	Malonyl CoA-acyl carrier protein transacylase	BAB57392
P60392	rsmH	100.00	99.68	0.0	Ribosomal RNA small subunit methyltransferase H	BAB42274
W8U4S5	ctaB	100.00	99.67	0.0	Protoheme IX farnesyltransferase	AHM68781
Q2FYQ0	PstB	100.00	99.65	0.0	Phosphate import ATP-binding protein	ABD30480
A0A4T9YUF5	fakB2	100.00	99.64	0.0	Fatty acid kinase	QBZ85624
W8TW76	ubiE	100.00	99.59	0.0	Ubiquinone biosynthesis methyltransferase	AHM70914
A6QFG2	MnhA1	99.88	99.88	0.0	Multi-subunit Na+/H+ (Mnh) antiporter	BAF67094
Q2G2M2	mprF	99.88	99.88	0.0	Phosphatidylglycerol lysyltransferase	AF145699_2
Q2FIB5	argH	99.78	99.78	0.0	Argininosuccinate lyase	ABD20820.1
Q5HFZ4	cvfC	99.73	99.73	0.0	Virulence factor	AAW36665
A6QFU3	cydB	99.70	99.71	0.0	Terminal Oxidases	BAF67225
A0A0H2XHH2	argF	99.70	99.70	0.0	Ornithine carbamoyltransferase	abd21287
A6QGB6	FMT	99.68	99.68	0.0	formyl methionyl transferase	BAF67398
Q2FZQ3	fabI	99.61	99.61	0.0	Enoyl-ACP reductase	ABD30072
Q9RL81	Stp1	99.59	99.60	0.0	Protein-serine/threonine phosphatase	AUS74922
Q2FH26	odhB	99.53	99.76	0.0	Dihydrolipoamide succinyltransferase	ABD22597
Q2FZL3	sspB	99.49	99.75	0.0	Glutamyl endopeptidase	ABD30112
Q6GAE8	purK	99.47	99.73	0.0	Purine biosynthesis regulator	CAG42775
A0A0H2XGW3	ctpA	99.39	99.80	0.0	Lone S41 family C-terminal processing protease	ABD21090
P09616	hla	99.37	99.69	0.0	Alpha-hemolysin	CAA25801
A0A0H3KBS1	NWMN_0826	99.20	99.73	0.0	NADH-dependent flavin oxidoreductase	BAF67098
Q2FYP3	cvfB	99.00	99.67	0.0	Virulence factor	ABD30486
A0A0H2XIJ3	atl	98.97	99.84	0.0	Autolysin	ABD22514
X5ELF9	plsX	98.48	99.70	0.0	Phosphate acyltransferase	AUS74912
Q2FZL2	sspA	97.95	101.19	0.0	Staphopain B	ABD30113
A6QHK8	ClpX	93.57	99.76	0.0	Part of proteolytic complex	BAF67840
A0A0B6XPF7	rsh	92.87	98.91	0.0	(P)ppGpp synthetase	AXP71580
Q5HF73	accD	89.05	98.95	0.0	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta	AAW36851
Q2FI79	mecA	99.58	99.58	5.68e-180	Adaptor protein	ABD21664
W8TTB7	srrA	92.12	99.59	6.80e-170	Transcriptional regulator	AHM70893
W8TMV6	relP	100.00	99.53	6.87e-159	(P)ppGpp synthetase	AUS75139
B7HLG1	CodY	81.08	99.62	8.47e-148	Nutrient-responsive regulator	ACJ80679
A0A0H3JRA8	SAV1322	100.00	99.50	1.65e-147	Two-component response regulator	BAB57484
P0A086	msrA2	99.44	99.44	6.07e-134	Methionine Sulfoxide Reductase	AF349112_1
P0A082	msrA1	100.00	99.41	3.41e-128	Methionine Sulfoxide Reductase	BAB42453
Q2FZ97	mraZ	100.00	99.31	3.26e-106	Transcriptional regulator	ABD30252
P0A088	msrB	99.30	99.30	3.20e-105	Methionine Sulfoxide Reductase	AF349112_2
P60378	spx	100.00	99.24	2.04e-96	Essential gene which is a thiol/oxidative stress sensor	BAB57159
Q9RGX0	spxA1	83.21	99.24	3.76e-82	Redox-responsive transcription factor	AAF21893
A0A0H2XED4	SAUSA300_0964	100.00	99.06	8.96e-73	Chitinase-related protein	ABD20642
W8U4X9	qoxD	100.00	98.97	5.13e-65	Quinol oxidase subunit 4	AHM68836
P99143	ptsH	100.00	98.88	5.63e-61	Histidine-containing phosphocarrier protein	BAB42180
Q2FID9	nfu	100.00	98.77	3.13e-55	aids in the maturation of Iron-Sulphur proteins	ABD20438
Q2FH36	msaB	100.00	98.51	5.73e-44	Cold shock protein	ABD22065
P0A355	CspA	90.91	98.51	8.23e-40	Cold shock protein	CAA62903
Q92AD0	CspD	80.00	97.01	1.16e-35	Cold shock protein	CAC99957
P0A357	CspB	84.61	97.01	1.01e-34	Cold shock protein	CAD00094
Q2FI75	yjbI (SAUSA300_0904)	100.00	97.03	0.0	Conserved hypothetical protein	ABD21733
A0A0H2XHR2	yjbH (SAUSA300_0903)	98.35	99.18	4.62e-89	Protozoan/cyanobacterial globin family protein	ABD22445
Q2FIE9	lipA (SAUSA300_0829)	100.00	99.67	0.0	Lipoic acid synthetase	ABD22039
A0A0H2XJD2	eep (SAUSA300_1155)	98.73	99.75	0.0	Putative membrane associated zinc metalloprotease	ABD22912

BLASTP v2.8.1+ (Database: PHI-base v4.14, Nov. 2022 release)

Plasmid

PlasmidFinder

Plasmid	Identity	Query / Template	Accession no.
No hit found

PlasmidFinder 2.0.1 (Database: plasmidfinder_db, Jan. 2023 release)

Prophage

Phigaro

Scaffold	Begin	End	Transposable	Taxonomy	pVOGs
PQCN01000001.1	718279	743937	False	Myoviridae	VOG0753, VOG4705, VOG3390, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189

Phigaro v2.3.0 (Database: Aug. 2017 release)