safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

Probiotic potential risk score

ARGs	VFs	PGs	PPRS
0	25	29	38.29

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

Antibiotic resistance genes

Comprehensive Antibiotic Resistance Database (CARD)

Query ID	Begin	End	ARO name	ARO accession	CARD name	Identity	Coverage	Accession no.
No hit found

RGI v6.0.3 (Database: CARD Variants v4.0.2, Nov. 2023 release)

ResFinder

Query ID	Begin	End	Resistance gene	Phenotype	Identity	Coverage	Accession no.
No hit found

ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)

AMRFinderPlus

Query ID	Begin	End	Gene symbol	Sequence name	Method	Identity	Coverage	Accession no.
No hit found

AMRFinderPlus v4.0.3 (Database: Oct. 2024 release)

Virulence factors

Virulence Factor Database (VFDB)

Query ID	qstart	qend	Gene name	VF name	VF category	Identity	Coverage	Accession no.
MMPHFKCF_1	1121892	1122761	rfbA	Capsule	Immune modulation	100.00	100.00	WP_011681286
MMPHFKCF_1	1121299	1121892	STER_RS06030	Capsule	Immune modulation	100.00	100.00	WP_011226149
MMPHFKCF_1	1121299	1121892	STR_RS05880	Capsule	Immune modulation	99.83	100.00	WP_011226149
MMPHFKCF_1	1336664	1337620	STU_RS16250	Capsule	Immune modulation	99.79	100.00	WP_011226328
MMPHFKCF_1	1335871	1336680	STU_RS16245	Capsule	Immune modulation	99.75	100.00	WP_002948020
MMPHFKCF_1	1337617	1338765	STU_RS16255	Capsule	Immune modulation	99.74	100.00	WP_041828290
MMPHFKCF_1	1121299	1121892	STU_RS15260	Capsule	Immune modulation	99.66	100.00	WP_011226149
MMPHFKCF_1	1334666	1335871	STU_RS16240	Capsule	Immune modulation	99.58	100.00	WP_011226326
MMPHFKCF_1	1331810	1333594	STU_RS16230	Capsule	Immune modulation	99.55	100.00	WP_011226325
MMPHFKCF_1	1342261	1343112	rfbD	Capsule	Immune modulation	99.53	100.00	WP_014621820
MMPHFKCF_1	43690	44529	cbpD	Autolysin	Exoenzyme	99.52	100.00	WP_011226733
MMPHFKCF_1	1338874	1339884	STU_RS16260	Capsule	Immune modulation	99.50	100.00	WP_011226330
MMPHFKCF_1	1333591	1334646	STU_RS16235	Capsule	Immune modulation	99.43	100.00	WP_002948022
MMPHFKCF_1	886141	887799	fbp54	FBPs	Adherence	99.34	100.00	WP_011227179
MMPHFKCF_1	998350	999081	STER_RS05315	Capsule	Immune modulation	99.04	100.00	WP_011681176
MMPHFKCF_1	998350	999081	STU_RS14645	Capsule	Immune modulation	98.77	100.00	WP_011226048
MMPHFKCF_1	998350	999081	STR_RS05260	Capsule	Immune modulation	98.63	100.00	WP_011227248
MMPHFKCF_1	1065082	1065870	cshA	Cell surface hydrophobicity proteins	Adherence	98.36	99.75	-
MMPHFKCF_1	988409	989824	STER_RS05250	Capsule	Immune modulation	97.81	100.00	WP_011681165
MMPHFKCF_1	1158084	1158845	srtA	Sortase A	Exoenzyme	97.64	100.00	-
MMPHFKCF_1	1339887	1341158	STU_RS16265	Capsule	Immune modulation	97.48	99.76	WP_011226331
MMPHFKCF_1	999082	1000542	STER_RS05320	Capsule	Immune modulation	97.47	100.00	WP_011681177
MMPHFKCF_1	999082	1000542	STU_RS14650	Capsule	Immune modulation	96.85	100.21	WP_011226049
MMPHFKCF_1	999082	1000542	STR_RS05265	Capsule	Immune modulation	95.89	100.21	WP_041827043
MMPHFKCF_1	997649	998341	STR_RS05255	Capsule	Immune modulation	95.40	99.86	WP_011227247
MMPHFKCF_1	997649	998341	STU_RS14640	Capsule	Immune modulation	95.40	99.86	WP_011226047
MMPHFKCF_1	995459	996824	STER_RS05300	Capsule	Immune modulation	95.17	99.85	WP_011681173
MMPHFKCF_1	995457	996824	STU_RS14630	Capsule	Immune modulation	93.93	100.00	WP_011226045
MMPHFKCF_1	996881	997639	STER_RS05305	Capsule	Immune modulation	93.81	100.94	WP_011681174
MMPHFKCF_1	996881	997639	STU_RS14635	Capsule	Immune modulation	93.68	100.94	WP_011226046
MMPHFKCF_1	996886	997639	STR_RS05250	Capsule	Immune modulation	93.37	99.07	WP_011227246
MMPHFKCF_1	997649	998341	STER_RS05310	Capsule	Immune modulation	89.47	100.00	WP_011681175
MMPHFKCF_1	620832	622135	eno	Streptococcal enolase	Exoenzyme	88.10	99.46	WP_000022832
MMPHFKCF_1	1628450	1629460	plr/gapA	Streptococcal plasmin receptor/GAPDH	Adherence	87.45	99.90	WP_002986042
MMPHFKCF_1	1119824	1120870	rfbB	Capsule	Immune modulation	80.61	100.00	WP_009659423
MMPHFKCF_1	160781	162064	tig/ropA	Trigger factor	Stress survival	80.58	99.77	WP_000107753

BLASTN v2.16.0 (Database: VFDB, Dec. 2024 release)

VirulenceFinder

Query ID	Begin	End	Database	Virulence factor	Protein function	Identity	Coverage	Accession no.
No hit found

VirulenceFinder v2.0. 4 (Database: virulencefinder_db, Feb . 2024 release)

Pathogenic genes

PHI-base

Query ID	qstart	qend	Gene name	e-value	Function	Identity	Coverage	Gene ID
MMPHFKCF_1	1161532	1162515	ldh(Sp_1220)	0.0	L-lactate dehydrogenase	94.82	100.00	AAK75326
MMPHFKCF_1	726558	727631	MntE	0.0	manganese homeostasis	94.41	99.72	ABF32167
MMPHFKCF_1	537434	538402	spr0084	0.0	pathogenitcity related	93.19	98.48	AAK98888
MMPHFKCF_1	1508077	1510380	pfl2(Sp_0459)	0.0	formate acetyltransferase	92.97	99.22	AAK74619
MMPHFKCF_1	1236896	1238377	SPD_0310	0.0	UPF0371 protein SPD_0310	92.31	100.00	ABJ54480
MMPHFKCF_1	763001	765247	metE	0.0	methionine biosynthesis enzymes	91.99	100.00	AAK74738
MMPHFKCF_1	65879	66871	recA	0.0	DNA recombination and repair	91.24	85.31	AAL00560
MMPHFKCF_1	27206	28177	prsA2	0.0	ribose-phosphate pyrophosphokinase	90.12	100.00	ABF36968
MMPHFKCF_1	1394292	1393141	potA	0.0	ABC transporter ATP-binding protein-spermidine/putrescine transport	89.32	99.74	AAL00050
MMPHFKCF_1	1358403	1356415	uvrB	0.0	excinuclease ABC, B subunit	88.99	100.00	AE014259_2
MMPHFKCF_1	1145336	1143606	ptsI	0.0	phosphoenolpyruvate-protein phosphotransferase	88.04	100.00	AAK34199
MMPHFKCF_1	1836466	1834988	IMPDH	0.0	inosine-5'-monophosphate dehydrogenase	87.42	100.00	ADE32434
MMPHFKCF_1	620832	622133	Eno	0.0	enolase	86.21	99.77	ABP90468
MMPHFKCF_1	1821277	1819385	gidA	0.0	tRNA uridine 5-carboxymethylaminomethyl modification enzyme	86.05	98.90	ABP91129
MMPHFKCF_1	768172	766463	PGM	0.0	phosphoglucomutase	83.89	99.65	ACH87041
MMPHFKCF_1	1672123	1673133	pdh	0.0	pyruvate dehydrogenase	83.09	99.70	ABP91006
MMPHFKCF_1	912094	910733	mnmE	0.0	central tRNA-modifying GTPase	82.24	99.56	ABP90420
MMPHFKCF_1	1723839	1721947	PepO	0.0	endopeptidase	80.03	100.00	ABF32980
MMPHFKCF_1	606397	607287	bglB	5.28e-177	putative phospho--glucosidase	88.22	99.66	AAK33487
MMPHFKCF_1	827465	826527	SP_0676	2.35e-167	transcription facot	81.15	97.20	AAK74821
MMPHFKCF_1	765439	766296	metF	8.62e-165	methionine biosynthesis enzymes	86.36	99.31	AAK74739
MMPHFKCF_1	1037250	1036546	covR	4.37e-131	responder protein	85.53	100.00	AAK71319
MMPHFKCF_1	1217920	1217249	rr01	2.99e-124	response regulator	83.93	99.56	CAB54566
MMPHFKCF_1	1037250	1036546	walR	1.84e-121	DNA-binding response regulator	82.13	100.00	ANC99504
MMPHFKCF_1	772126	772794	CiaR	9.38e-118	two-component response regulator	84.75	99.55	AAK74935
MMPHFKCF_1	315204	315890	CovR	1.00e-117	serves to repress GAS virulence factor-encoding genes	80.79	100.00	ACE75886
MMPHFKCF_1	772126	772797	ciaR	1.02e-115	two component system response regulator	82.59	99.12	AIK75708
MMPHFKCF_1	67183	67578	SpxA2	3.17e-73	transcriptional regulator	90.15	100.00	ERL21461
MMPHFKCF_1	923453	923854	SpxA1	3.75e-66	transcriptional regulator	80.60	100.00	ERL19273
MMPHFKCF_1	162222	162722	RopE (M5005_Spy_1611)	4.91e-75	probable DNA-directed RNA polymerase subunit delta	81.44	87.43	AAK34603
MMPHFKCF_1	1508077	1510374	PFL (B9H01_RS01125)	0.0	formate C-acetyltransferase	82.94	98.08	MYN69560
MMPHFKCF_1	1709430	1708411	ilvC (SPD_0406)	0.0	ketol-acid reductoisomerase (NADP(+))	95.88	100.00	ABJ55451

BLASTX v2.16.0 (Database: PHI base v4.16, May. 2024 release)

Plasmid

PlasmidFinder

Query ID	Begin	End	Plasmid	Query / Template	Identity	Accession no.
No hit found

PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)

PlasmidHunter

Query ID	Prediction	Chromosome	Plasmid
MMPHFKCF_1	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Prophage

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
No hit found