Probiotic potential risk score

ARGs (CARD)	VFs (VFDB)	PGs (PHI-base)	PPRS
0	11	21	23.71

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.
No hit found

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

ResFinder

Resistance gene	Identity	Coverage	Phenotype	Accession no.
No hit found

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

AMRFinderPlus

Gene symbol	Sequence name	Method	Identity	Coverage	Accession no.
No hit found

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	94.86	100.00	0.0	Trigger factor	Stress survival	WP_011680653
VFG006081	rfbD	94.13	100.00	0.0	Capsule	Immune modulation	WP_014621820
VFG006074	STU_RS16230	92.60	98.43	0.0	Capsule	Immune modulation	WP_011226325
VFG006084	STU_RS16245	92.48	99.88	0.0	Capsule	Immune modulation	WP_002948020
VFG006082	STU_RS16240	92.45	100.00	0.0	Capsule	Immune modulation	WP_011226326
VFG006086	STU_RS16250	91.85	100.00	0.0	Capsule	Immune modulation	WP_011226328
VFG005579	eno	91.64	99.92	0.0	Streptococcal enolase	Exoenzyme	WP_000022815
VFG006088	STU_RS16255	91.57	99.83	0.0	Capsule	Immune modulation	WP_041828290
VFG006078	STU_RS16235	91.00	99.15	0.0	Capsule	Immune modulation	WP_002948022
VFG006052	rfbA	90.92	100.00	0.0	Capsule	Immune modulation	WP_011226150
VFG005323	cbpD	89.18	99.88	0.0	Autolysin	Exoenzyme	WP_011225268
VFG006032	STER_RS06030	91.98	62.96	4.74e-150	Capsule	Immune modulation	WP_011226149

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
Q1JLQ2	MntE	96.09	99.44	0.0	Manganese Homeostasis	ABF32167
P67331	spr0084	92.57	98.18	0.0	pathogenitcity related	AAK98888
Q1J943	prsA2	92.19	98.46	0.0	Ribose-phosphate pyrophosphokinase	ABF36968
Q8DPC2	potA	89.84	99.48	0.0	ABC transporter ATP-binding protein - spermidine/putrescine transport	AAL00050
P0C0B9	bglB	87.88	99.33	0.0	Putative phospho--glucosidase	AAK33487
D5AF41	IMPDH	87.83	99.80	0.0	Inosine-5'-monophosphate dehydrogenase	ADE32434
A4VWH9	Eno	86.67	99.54	0.0	Enolase	ABP90468
A4VYE0	gidA	85.74	98.75	0.0	tRNA uridine 5-carboxymethylaminomethyl modification enzyme	ABP91129
P0A452	recA	85.19	98.46	0.0	DNA recombination and repair	AAL00560
Q97RW0	SP_0676	83.44	93.50	0.0	Transcription facot	AAK74821
A4VY17	pdh	83.38	99.41	0.0	Pyruvate dehydrogenase	ABP91006
Q93MY4	covR	85.53	99.58	6.55e-151	Responder protein	AAK71319
Q9S1K2	rr01	84.82	99.12	1.49e-145	Response regulator	CAB54566
R4Z8M6	ciaR	86.16	98.68	6.78e-144	Two component system response regulator	AIK75708
B3VA60	CovR	81.66	99.56	2.21e-137	serves to repress GAS virulence factor-encoding genes	ACE75886
U2W9V3	SpxA2	91.67	99.25	1.28e-88	Transcriptional regulator	ERL21461
U2UML5	SpxA1	82.09	99.26	5.32e-82	Transcriptional regulator	ERL19273
Q8DQV4	spr0479	85.42	97.96	4.84e-58	essential gene	AAK99283
Q8DP67	spr1327	90.59	98.84	1.35e-53	essential gene	AAL00131
Q8CZ89	spr0175	85.23	98.88	2.94e-52	pathogenitcity related	AAK98979
Q8DRE1	spr0177	83.15	87.25	1.13e-50	essential gene	AAK98981

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
JABZYR010000001.1	2878	37446	False	Siphoviridae	VOG0152, VOG0152, VOG0152, VOG1446, VOG2788, VOG9610, VOG4566, VOG0226, VOG4559, VOG0943, VOG1837, VOG8336, VOG4988, VOG1564, VOG1447, VOG6179, VOG2786, VOG8520, VOG4602, VOG0275, VOG3303, VOG7557, VOG5034, VOG4941, VOG0054, VOG3424, VOG4684, VOG1799, VOG4763, VOG4633, VOG0541, VOG10499, VOG4586, VOG0704, VOG0539, VOG4589, VOG5606, VOG0562, VOG4553, VOG4573, VOG4556
JABZYR010000002.1	8940	15615	False	Unknown	VOG9876, VOG10558, VOG2090, VOG7340

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