Probiotic potential risk score

ARGs (CARD)	VFs (VFDB)	PGs (PHI-base)	PPRS
3	17	29	33.75

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:3000375	ErmB	99.18	98.79	ErmB	AF242872.1
ARO:3000186	tet(M)	98.90	100.00	tet(M)	AB039845.1
ARO:3007011	mdeA	81.33	99.34	mdeA	NZ_CP044221.1

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

ResFinder

Resistance gene	Identity	Coverage	Phenotype	Accession no.
erm(B)	100.00	100.00	Macrolide resistance	X72021
tet(M)	99.58	100.00	Tetracycline resistance	X92947

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

AMRFinderPlus

Gene symbol	Sequence name	Method	Identity	Coverage	Accession no.
erm(B)	23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)	EXACTX	100.00	100.00	WP_001038795.1
tet(M)	tetracycline resistance ribosomal protection protein Tet(M)	EXACTX	100.00	100.00	WP_000691736.1

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.
VFG005556	tig/ropA	94.00	100.00	0.0	Trigger factor	Stress survival	WP_011680653
VFG006022	rfbB	92.74	100.00	0.0	Capsule	Immune modulation	WP_002947383
VFG006081	rfbD	92.49	100.00	0.0	Capsule	Immune modulation	WP_014621820
VFG006041	rfbA	91.61	100.00	0.0	Capsule	Immune modulation	WP_011681286
VFG006079	STER_RS07085	90.64	98.33	0.0	Capsule	Immune modulation	WP_011681442
VFG006046	STR_RS05880	90.24	100.00	0.0	Capsule	Immune modulation	WP_011226149
VFG005190	fbp54	90.12	99.94	0.0	FBPs	Adherence	WP_002952952
VFG018652	plr/gapA	90.06	100.00	0.0	Streptococcal plasmin receptor/GAPDH	Adherence	WP_006154814
VFG006075	STER_RS07075	88.89	98.97	0.0	Capsule	Immune modulation	WP_011681440
VFG005576	eno	87.86	99.39	0.0	Streptococcal enolase	Exoenzyme	WP_000022832
VFG005323	cbpD	86.89	90.60	0.0	Autolysin	Exoenzyme	WP_011225268
VFG006087	STER_RS07100	86.49	99.13	0.0	Capsule	Immune modulation	WP_011681445
VFG006083	STER_RS07090	85.16	99.90	0.0	Capsule	Immune modulation	WP_011681443
VFG006000	STER_RS05315	83.79	99.73	0.0	Capsule	Immune modulation	WP_011681176
VFG005964	STER_RS05300	83.47	99.78	0.0	Capsule	Immune modulation	WP_011681173
VFG005382	srtA	83.05	99.61	0.0	Sortase A	Exoenzyme	WP_011681303
VFG006004	SPD_RS01775	81.26	96.53	2.58e-134	Capsule	Immune modulation	WP_001819836

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
Q54970	spxB	96.95	99.83	0.0	Pyruvate Oxidase Gene	AAB40976
Q1JLQ2	MntE	94.69	99.44	0.0	Manganese Homeostasis	ABF32167
P67331	spr0084	93.19	98.18	0.0	pathogenitcity related	AAK98888
Q97S31	metE	92.52	99.87	0.0	Methionine biosynthesis enzymes	AAK74738
Q1J943	prsA2	91.88	98.46	0.0	Ribose-phosphate pyrophosphokinase	ABF36968
Q99Z66	ptsI	90.12	99.83	0.0	Phosphoenolpyruvate-protein phosphotransferase	AAK34199
Q8DYL6	uvrB	89.74	99.85	0.0	Excinuclease ABC, B subunit	AE014259_2
Q8DPC2	potA	89.58	99.48	0.0	ABC transporter ATP-binding protein - spermidine/putrescine transport	AAL00050
P0C0B9	bglB	87.54	99.33	0.0	Putative phospho--glucosidase	AAK33487
D5AF41	IMPDH	87.02	99.80	0.0	Inosine-5'-monophosphate dehydrogenase	ADE32434
Q97S30	metF	86.01	98.96	0.0	Methionine biosynthesis enzymes	AAK74739
A4VYE0	gidA	85.10	98.75	0.0	tRNA uridine 5-carboxymethylaminomethyl modification enzyme	ABP91129
P0A452	recA	84.67	98.71	0.0	DNA recombination and repair	AAL00560
B5TQV9	PGM	84.41	99.48	0.0	phosphoglucomutase	ACH87041
A4VWH9	Eno	84.14	99.31	0.0	Enolase	ABP90468
Q97RW0	SP_0676	83.44	93.50	0.0	Transcription facot	AAK74821
A4VWD1	mnmE	83.33	99.34	0.0	Central tRNA-modifying GTPase	ABP90420
A4VY17	pdh	81.90	99.41	0.0	Pyruvate dehydrogenase	ABP91006
Q93MY4	covR	86.44	99.58	4.05e-152	Responder protein	AAK71319
Q9S1K2	rr01	84.82	99.12	3.17e-145	Response regulator	CAB54566
P0A4H7	CiaR	87.89	99.11	1.21e-143	Two-component response regulator	AAK74935
B3VA60	CovR	81.66	99.56	1.39e-137	serves to repress GAS virulence factor-encoding genes	ACE75886
U2W9V3	SpxA2	91.67	99.25	1.86e-88	Transcriptional regulator	ERL21461
U2UML5	SpxA1	82.84	99.26	1.50e-82	Transcriptional regulator	ERL19273
Q8DQV4	spr0479	86.46	97.96	2.12e-58	essential gene	AAK99283
Q8DP67	spr1327	90.59	98.84	2.44e-53	essential gene	AAL00131
Q8CZ89	spr0175	85.23	98.88	4.27e-52	pathogenitcity related	AAK98979
Q8DRE1	spr0177	83.15	87.25	1.64e-50	essential gene	AAK98981
Q04M32	ilvC (SPD_0406)	84.41	99.71	0.0	Ketol-acid reductoisomerase (NADP(+))	ABJ55451

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

Plasmid

PlasmidFinder

Plasmid	Identity	Query / Template	Accession no.
repUS43	99.92	1203 / 1206	CP003584

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

Prophage

Phigaro

Scaffold	Begin	End	Transposable	Taxonomy	pVOGs
CABFMM010000009.1	870	31405	False	Siphoviridae	VOG10230, VOG0054, VOG0641, VOG5008, VOG4828, VOG4633, VOG3636, VOG0701, VOG8357, VOG0698, VOG0697, VOG0696, VOG0695, VOG5872, VOG4711, VOG4555, VOG0692, VOG0691, VOG4544, VOG0796, VOG0198, VOG0658, VOG0044, VOG0657, VOG4567, VOG4603, VOG7484, VOG0152, VOG0656, VOG0655, VOG4693, VOG0226, VOG0685, VOG0283

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