Probiotic potential risk score

ARGs (CARD)	VFs (VFDB)	PGs (PHI-base)	PPRS
15	10	57	59.78

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:3003006	blt	100.00	100.00	blt	L32599.1
ARO:3003324	Bacillus subtilis mprF	99.77	100.00	Bsub_mprF	AL009126.3
ARO:3003007	bmr	99.74	100.00	bmr	M33768.1
ARO:3004663	FusF	99.53	100.00	FusF	CP027422.1
ARO:3002813	lmrB	98.74	100.42	lmrB	JYFL01000006.1
ARO:3000319	mphC	98.66	100.00	mphC	AB013298.1
ARO:3002627	aadK	98.59	100.00	aadK	AL009126.1
ARO:3000251	msrA	98.57	100.00	msrA	X52085.1
ARO:3004476	vmlR	98.36	100.18	vmlR	NC_000964.3
ARO:3003064	ykkD	98.10	100.00	ykkD	AL009126.1
ARO:3003063	ykkC	97.32	100.00	ykkC	AL009126.1
ARO:3003059	tmrB	96.95	100.00	tmrB	AL009126.3
ARO:3004541	mphK	96.42	100.33	mphK	CP010314.1
ARO:3007014	qacJ	88.79	100.00	qacJ	AJ512814.1
ARO:3000319	mphC	86.62	100.00	mphC	AB013298.1

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

ResFinder

Resistance gene	Identity	Coverage	Phenotype	Accession no.
mph(C)	100.00	100.00	Macrolide resistance	AF167161
tet(L)	99.35	100.00	Tetracycline resistance	X08034
msr(A)	99.05	100.00	Macrolide, Lincosamide and Streptogramin B resistance	X52085
aadK	98.71	100.00	Aminoglycoside resistance	M26879
mph(K)	96.97	100.00	Warning: gene is missing from Notes file. Please inform curator.	NC_000964

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

AMRFinderPlus

Gene symbol	Sequence name	Method	Identity	Coverage	Accession no.
mph(C)	Mph(C) family macrolide 2'-phosphotransferase	EXACTX	100.00	100.00	WP_000196697.1
msr(A)	ABC-F type ribosomal protection protein Msr(A)	BLASTX	99.80	100.00	WP_000438874.1
fusF	fusidic acid resistance EF-G-binding protein FusF	BLASTX	99.53	100.00	WP_063851262.1
tet(L)	tetracycline efflux MFS transporter Tet(L)	BLASTX	99.13	100.00	WP_003242953.1
aadK	aminoglycoside 6-adenylyltransferase AadK	BLASTX	98.59	100.00	WP_003229862.1
vmlR	ABC-F type ribosomal protection protein VmlR	BLASTX	98.36	100.00	WP_003234144.1
mphK	macrolide 2'-phosphotransferase MphK	BLASTX	96.42	100.00	WP_003246254.1
satA	streptothricin N-acetyltransferase SatA	BLASTX	90.17	100.00	WP_003242546.1
qacJ	quaternary ammonium compound efflux SMR transporter QacJ	BLASTX	88.79	100.00	WP_011100750.1
mph(C)	Mph(C) family macrolide 2'-phosphotransferase	BLASTX	87.29	100.00	WP_000196697.1

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.
VFG016299	capB	99.66	100.00	0.0	Capsule	Immune modulation	NP_391471
VFG016291	capA	99.65	100.00	0.0	Capsule	Immune modulation	NP_391469
VFG016295	capC	99.56	100.00	0.0	Capsule	Immune modulation	NP_391470
VFG016234	hlyIII	99.53	100.00	0.0	Hemolysin III	Exotoxin	NP_390062
VFG049999	dhbA	99.36	100.00	0.0	Bacillibactin	Nutritional/Metabolic factor	NP_391080
VFG016303	dep/capD	99.21	100.00	0.0	Capsule	Immune modulation	NP_389723
VFG050043	dhbF	98.61	100.00	0.0	Bacillibactin	Nutritional/Metabolic factor	NP_391076
VFG050010	dhbC	98.58	100.00	0.0	Bacillibactin	Nutritional/Metabolic factor	NP_391079
VFG050032	dhbB	98.30	100.00	0.0	Bacillibactin	Nutritional/Metabolic factor	NP_391077
VFG050021	dhbE	97.90	100.00	0.0	Bacillibactin	Nutritional/Metabolic factor	NP_391078

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
W8TRT9	tufA	94.43	99.75	0.0	Elongation factor Tu	AHM69299
P95844	sigB	92.58	99.61	0.0	RNA polymerase sigma factor	AAP42796
Q2FWE8	atpA	92.03	99.80	0.0	ATP synthase subunit alpha	ABD31377
P99075	FbaA	91.61	99.65	0.0	Fructose-bisphosphate aldolase	BAB43211
Q2FZ08	cvfA	91.38	95.96	0.0	Virulence factor	BAF96735
W8U6D4	purR	90.88	99.64	0.0	Purine biosynthesis regulator	AUS75592
A6QHK8	ClpX	90.71	99.76	0.0	Part of proteolytic complex	BAF67840
T1YC56	Rho	90.64	98.65	0.0	Transcriptional regulator	AGU62228
A6QFR9	qoxB	90.33	99.85	0.0	Terminal Oxidases	BAF67201
Q2FFI7	PurB	90.00	99.54	0.0	Adenylosuccinate lyase	ABD20399
Q5HF73	accD	89.44	98.95	0.0	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta	AAW36851
A0A0H2XG07	PurA	88.99	99.77	0.0	Adenylosuccinate synthetase	ABD21364
Q2G2U4	walK	88.65	99.67	0.0	Sensor protein kinase	AF136709_2
A0A0B6XPF7	rsh	88.07	98.91	0.0	(P)ppGpp synthetase	AXP71580
P0A038	GAPDH	87.80	99.41	0.0	Glyceraldehyde-3-phosphate dehydrogenase	CAB38645
Q99SZ7	vraS	87.32	99.71	0.0	Sensor protein	BAB42971
A0A2S6D5Q7	PitA	86.79	99.11	0.0	Inorganic phosphate transporter	PPJ74719
P60392	rsmH	85.53	99.68	0.0	Ribosomal RNA small subunit methyltransferase H	BAB42274
W8US24	ndhC	84.83	99.75	0.0	NADH dehydrogenase	AHM68945
A0A0H3KEX5	ccpE	84.51	98.27	0.0	Regulates virulence determinant biosynthesis and pathogenesis	BAF66913
A0A2Y2A0B5	murA	84.32	99.76	0.0	UDP-N-acetylglucosamine 1-carboxyvinyltransferase	AHM70338
Q9X668	nupC	84.11	99.76	0.0	Nucleoside permease	AHM69205
W8TNJ3	ltaS	83.75	99.85	0.0	LTA synthase	AKJ48565
B3GXB6	pdxS	83.45	97.97	0.0	Encodes the putative pyridoxal 5�-phosphate synthase subunit PdxS	ACE61268
P99175	ccpA	81.76	99.70	0.0	Catabolite control protein A	BAB42825
Q5HCU5	Lqo	81.49	99.40	0.0	L-lactate-quinone oxidoreductases	AAW38622
Q2FYP3	cvfB	80.61	97.67	0.0	Virulence factor	ABD30486
Q2FH26	odhB	80.19	100.24	0.0	Dihydrolipoamide succinyltransferase	ABD22597
Q2FYQ0	PstB	86.47	93.31	3.56e-178	Phosphate import ATP-binding protein	ABD30480
W8U4S5	ctaB	82.12	99.34	3.86e-175	Protoheme IX farnesyltransferase	AHM68781
Q2FZQ3	fabI	87.11	99.61	2.60e-167	Enoyl-ACP reductase	ABD30072
Q2G2U6	yycF	95.28	99.57	3.39e-167	Transcriptional regulatory protein	AF136709_1
W8TTB7	srrA	87.55	99.59	2.48e-159	Transcriptional regulator	AHM70893
Q309Y7	agrA	84.03	99.58	2.75e-153	Accessory gene regulator protein A	ABB17358
W8TW76	ubiE	82.83	96.28	3.19e-153	Ubiquinone biosynthesis methyltransferase	AHM70914
B7HLG1	CodY	81.08	99.62	8.99e-148	Nutrient-responsive regulator	ACJ80679
P63786	ClpP	95.36	98.98	8.96e-140	Part of proteolytic complex	BAB94595
W8TMV6	relP	85.78	99.53	2.61e-139	(P)ppGpp synthetase	AUS75139
Q7A4R9	vraR	90.43	99.52	2.02e-126	Response regulator protein	BAB69827
P0A086	msrA2	81.87	96.07	7.43e-107	Methionine Sulfoxide Reductase	AF349112_1
Q2FZ97	mraZ	95.11	99.31	5.98e-102	Transcriptional regulator	ABD30252
P60378	spx	98.47	99.24	4.23e-95	Essential gene which is a thiol/oxidative stress sensor	BAB57159
Q2G282	PerR	82.64	96.64	6.95e-93	hydrogen peroxide sensor	ABD31053
P0A088	msrB	84.51	99.30	7.27e-93	Methionine Sulfoxide Reductase	AF349112_2
P0C1S0	MgrA	84.35	99.32	9.84e-87	global regulator; member of the MarR (multiple antibiotic resistance regulator)/SarA (staphylococcal accessory regulator A) family proteins	AAP48794
Q9RGX0	spxA1	83.97	99.24	1.45e-82	Redox-responsive transcription factor	AAF21893
Q7A1N5	sarA	86.29	99.20	5.36e-75	Transcriptional regulator	BAB94445
A6QIR4	mazF	85.59	97.52	1.64e-71	Endoribonuclease	BAF68246
P99143	ptsH	93.18	98.88	1.01e-57	Histidine-containing phosphocarrier protein	BAB42180
Q724L7	SpoVG	82.72	78.64	3.73e-47	RNA-Binding Protein	AAT02994
Q2FID9	nfu	94.03	82.72	8.57e-44	aids in the maturation of Iron-Sulphur proteins	ABD20438
Q2FH36	msaB	96.97	98.51	1.12e-42	Cold shock protein	ABD22065
P0A355	CspA	90.91	98.51	1.23e-39	Cold shock protein	CAA62903
Q92AD0	CspD	80.00	97.01	1.78e-35	Cold shock protein	CAC99957
P0A357	CspB	83.08	97.01	4.72e-34	Cold shock protein	CAD00094
Q2FI75	yjbI (SAUSA300_0904)	82.44	97.40	6.12e-154	Conserved hypothetical protein	ABD21733
Q2FIE9	lipA (SAUSA300_0829)	95.07	99.35	0.0	Lipoic acid synthetase	ABD22039

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

Plasmid

PlasmidFinder

Plasmid	Identity	Query / Template	Accession no.
rep21	95.22	1005 / 1005	GQ900464

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

Prophage

Phigaro

Scaffold	Begin	End	Transposable	Taxonomy	pVOGs
VDUC01000011.1	47486	70683	False	Myoviridae	VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4691, VOG4862, VOG7718, VOG4705
VDUC01000013.1	1569	9629	False	Siphoviridae	VOG0327, VOG4606, VOG6545, VOG4548, VOG0322, VOG0808, VOG2222, VOG7608, VOG3453, VOG2338, VOG9667
VDUC01000018.1	83868	108865	False	Siphoviridae	VOG0054, VOG5100, VOG9900, VOG0311, VOG4705, VOG4334, VOG4612, VOG4868, VOG3463, VOG3462, VOG0801, VOG4545, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0562, VOG3438, VOG4553, VOG4573, VOG4556, VOG4544, VOG0519, VOG4841, VOG0813, VOG1183, VOG0559, VOG0557
VDUC01000001.1	1870	27842	False	Siphoviridae	VOG0559, VOG0198, VOG4581, VOG4544, VOG4556, VOG4568, VOG4553, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG4545, VOG0801, VOG3462, VOG7906, VOG7900, VOG4612, VOG4334, VOG4705, VOG0311, VOG9900, VOG5100, VOG0054
VDUC01000031.1	21570	46964	False	Siphoviridae	VOG4714, VOG2703, VOG4574, VOG0136, VOG0753, VOG10940, VOG5535, VOG4599, VOG4605, VOG4545, VOG0725, VOG2621, VOG0799, VOG0724, VOG5660, VOG0816, VOG4623, VOG3480, VOG1329, VOG4555, VOG4564, VOG0720, VOG10227
VDUC01000031.1	54420	63277	False	Siphoviridae	VOG1309, VOG4600, VOG4552, VOG0650, VOG4603, VOG9667, VOG3304, VOG4602
VDUC01000004.1	163739	169488	False	Siphoviridae	VOG4552, VOG4603, VOG4600, VOG1309, VOG4566, VOG0189
VDUC01000004.1	177506	201195	False	Myoviridae	VOG0796, VOG0720, VOG4555, VOG4553, VOG4564, VOG4623, VOG1353, VOG1881, VOG1883, VOG1352, VOG4699, VOG6163, VOG1956, VOG1433, VOG1348, VOG0573, VOG4550, VOG4691, VOG4845, VOG7718, VOG3390, VOG4705, VOG0641, VOG4707
VDUC01000005.1	27838	48657	False	Siphoviridae	VOG7718, VOG3390, VOG4705, VOG5008, VOG8610, VOG7930, VOG0275, VOG9312, VOG4910, VOG3389, VOG5042, VOG9712
VDUC01000008.1	429	9322	False	Siphoviridae	VOG4559, VOG4716, VOG8575, VOG0327, VOG4606, VOG6545, VOG3777, VOG4548, VOG0322, VOG0808, VOG0534, VOG3453, VOG11003

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