Probiotic potential risk score

ARGs (CARD)	VFs (VFDB)	PGs (PHI-base)	PPRS
1	22	28	35.62

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:3000979	TEM-116	100.00	100.00	TEM-116	U36911.1

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

ResFinder

Resistance gene	Identity	Coverage	Phenotype	Accession no.
blaTEM-116	100.00	100.00	Beta-lactam resistance	AY425988
mef(A)	100.00	100.00	Macrolide resistance	U83667
msr(D)	100.00	100.00	Macrolide, Lincosamide and Streptogramin B resistance	AF274302

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

AMRFinderPlus

Gene symbol	Sequence name	Method	Identity	Coverage	Accession no.
blaTEM-116	broad-spectrum class A beta-lactamase TEM-116	ALLELEX	100.00	100.00	WP_000027050.1
mef(A)	macrolide efflux MFS transporter Mef(A)	EXACTX	100.00	100.00	WP_000417519.1
msr(D)	ABC-F type ribosomal protection protein Msr(D)	EXACTX	100.00	100.00	WP_000420313.1

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.
VFG006074	STU_RS16230	96.19	100.00	0.0	Capsule	Immune modulation	WP_011226325
VFG006088	STU_RS16255	95.91	99.91	0.0	Capsule	Immune modulation	WP_041828290
VFG006011	STER_RS05320	95.41	100.00	0.0	Capsule	Immune modulation	WP_011681177
VFG006081	rfbD	95.31	100.00	0.0	Capsule	Immune modulation	WP_014621820
VFG005964	STER_RS05300	95.31	99.85	0.0	Capsule	Immune modulation	WP_011681173
VFG005976	STER_RS05305	94.87	100.00	0.0	Capsule	Immune modulation	WP_011681174
VFG005556	tig/ropA	94.39	100.00	0.0	Trigger factor	Stress survival	WP_011680653
VFG006078	STU_RS16235	94.32	99.34	0.0	Capsule	Immune modulation	WP_002948022
VFG006086	STU_RS16250	94.04	100.00	0.0	Capsule	Immune modulation	WP_011226328
VFG006022	rfbB	93.89	100.00	0.0	Capsule	Immune modulation	WP_002947383
VFG005359	plr/gapA	93.87	100.10	0.0	Streptococcal plasmin receptor/GAPDH	Adherence	WP_002899102
VFG006000	STER_RS05315	93.85	100.00	0.0	Capsule	Immune modulation	WP_011681176
VFG006091	STU_RS16265	93.79	99.76	0.0	Capsule	Immune modulation	WP_011226331
VFG006082	STU_RS16240	92.79	100.00	0.0	Capsule	Immune modulation	WP_011226326
VFG006084	STU_RS16245	92.72	99.88	0.0	Capsule	Immune modulation	WP_002948020
VFG006046	STR_RS05880	91.92	100.00	0.0	Capsule	Immune modulation	WP_011226149
VFG005323	cbpD	91.19	100.00	0.0	Autolysin	Exoenzyme	WP_011225268
VFG006041	rfbA	91.03	100.00	0.0	Capsule	Immune modulation	WP_011681286
VFG005579	eno	90.58	100.00	0.0	Streptococcal enolase	Exoenzyme	WP_000022815
VFG005190	fbp54	90.42	99.94	0.0	FBPs	Adherence	WP_002952952
VFG006047	STU_RS14640	88.33	99.86	0.0	Capsule	Immune modulation	WP_011226047
VFG005382	srtA	84.27	99.87	0.0	Sortase A	Exoenzyme	WP_011681303

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	95.53	99.44	0.0	Manganese Homeostasis	ABF32167
Q97S31	metE	92.92	99.87	0.0	Methionine biosynthesis enzymes	AAK74738
P67331	spr0084	92.88	98.18	0.0	pathogenitcity related	AAK98888
Q1J943	prsA2	92.19	98.46	0.0	Ribose-phosphate pyrophosphokinase	ABF36968
Q99Z66	ptsI	89.95	99.83	0.0	Phosphoenolpyruvate-protein phosphotransferase	AAK34199
Q8DPC2	potA	89.84	99.48	0.0	ABC transporter ATP-binding protein - spermidine/putrescine transport	AAL00050
Q8DYL6	uvrB	89.59	99.85	0.0	Excinuclease ABC, B subunit	AE014259_2
P0C0B9	bglB	88.22	99.33	0.0	Putative phospho--glucosidase	AAK33487
Q97S30	metF	88.11	98.96	0.0	Methionine biosynthesis enzymes	AAK74739
D5AF41	IMPDH	87.63	99.80	0.0	Inosine-5'-monophosphate dehydrogenase	ADE32434
A4VWH9	Eno	86.44	99.54	0.0	Enolase	ABP90468
A4VYE0	gidA	85.42	98.75	0.0	tRNA uridine 5-carboxymethylaminomethyl modification enzyme	ABP91129
P0A452	recA	85.19	98.46	0.0	DNA recombination and repair	AAL00560
B5TQV9	PGM	84.76	99.48	0.0	phosphoglucomutase	ACH87041
Q97RW0	SP_0676	83.44	93.50	0.0	Transcription facot	AAK74821
A4VY17	pdh	83.09	99.41	0.0	Pyruvate dehydrogenase	ABP91006
A4VWD1	mnmE	82.46	99.34	0.0	Central tRNA-modifying GTPase	ABP90420
Q93MY4	covR	85.53	99.58	4.32e-151	Responder protein	AAK71319
Q9S1K2	rr01	84.82	99.12	2.07e-145	Response regulator	CAB54566
R4Z8M6	ciaR	86.16	98.68	9.44e-144	Two component system response regulator	AIK75708
B3VA60	CovR	81.66	99.56	1.33e-137	serves to repress GAS virulence factor-encoding genes	ACE75886
U2W9V3	SpxA2	91.67	99.25	1.79e-88	Transcriptional regulator	ERL21461
U2UML5	SpxA1	82.84	99.26	1.65e-82	Transcriptional regulator	ERL19273
Q8DQV4	spr0479	85.42	97.96	6.73e-58	essential gene	AAK99283
Q8DP67	spr1327	92.94	98.84	1.76e-54	essential gene	AAL00131
Q8CZ89	spr0175	85.23	98.88	1.21e-52	pathogenitcity related	AAK98979
Q8DRE1	spr0177	83.15	87.25	1.57e-50	essential gene	AAK98981
Q04M32	ilvC (SPD_0406)	97.35	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.
ColRNAI	87.02	131 / 130	DQ298019

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

Prophage

Phigaro

Scaffold	Begin	End	Transposable	Taxonomy	pVOGs
No hit found

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