safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

Probiotic potential risk score

ARGs	VFs	PGs	PPRS
0	27	31	41.11

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.
INIGJNDL_1	1186409	1187278	rfbA	Capsule	Immune modulation	100.00	100.00	WP_011681286
INIGJNDL_1	1185816	1186409	STER_RS06030	Capsule	Immune modulation	100.00	100.00	WP_011226149
INIGJNDL_1	1419238	1420047	STU_RS16245	Capsule	Immune modulation	99.88	100.00	WP_002948020
INIGJNDL_1	1185816	1186409	STR_RS05880	Capsule	Immune modulation	99.83	100.00	WP_011226149
INIGJNDL_1	1420031	1420987	STU_RS16250	Capsule	Immune modulation	99.79	100.00	WP_011226328
INIGJNDL_1	1420984	1422132	STU_RS16255	Capsule	Immune modulation	99.74	100.00	WP_041828290
INIGJNDL_1	1185816	1186409	STU_RS15260	Capsule	Immune modulation	99.66	100.00	WP_011226149
INIGJNDL_1	1425628	1426479	rfbD	Capsule	Immune modulation	99.65	100.00	WP_014621820
INIGJNDL_1	945031	946689	fbp54	FBPs	Adherence	99.58	100.00	WP_011227179
INIGJNDL_1	1418033	1419238	STU_RS16240	Capsule	Immune modulation	99.58	100.00	WP_011226326
INIGJNDL_1	43686	44525	cbpD	Autolysin	Exoenzyme	99.52	100.00	WP_011226733
INIGJNDL_1	1059254	1059853	STR_RS05245	Capsule	Immune modulation	99.50	100.00	WP_196767671
INIGJNDL_1	1422241	1423251	STU_RS16260	Capsule	Immune modulation	99.50	100.00	WP_011226330
INIGJNDL_1	1415177	1416961	STU_RS16230	Capsule	Immune modulation	99.44	100.00	WP_011226325
INIGJNDL_1	1416958	1418013	STU_RS16235	Capsule	Immune modulation	99.43	100.00	WP_002948022
INIGJNDL_1	1038554	1039969	STER_RS05250	Capsule	Immune modulation	99.15	100.00	WP_011681165
INIGJNDL_1	1060005	1060740	STER_RS05305	Capsule	Immune modulation	98.91	99.33	WP_011681174
INIGJNDL_1	1222603	1223364	srtA	Sortase A	Exoenzyme	98.82	100.00	-
INIGJNDL_1	1061451	1062182	STER_RS05315	Capsule	Immune modulation	98.77	100.00	WP_011681176
INIGJNDL_1	1062183	1063637	STR_RS05265	Capsule	Immune modulation	98.76	100.00	WP_041827043
INIGJNDL_1	1058130	1059089	STR_RS05240	Capsule	Immune modulation	98.54	100.00	WP_041827042
INIGJNDL_1	1061451	1062182	STU_RS14645	Capsule	Immune modulation	98.50	100.00	WP_011226048
INIGJNDL_1	1128161	1128954	cshA	Cell surface hydrophobicity proteins	Adherence	98.36	100.25	-
INIGJNDL_1	1061451	1062182	STR_RS05260	Capsule	Immune modulation	98.36	100.00	WP_011227248
INIGJNDL_1	1059991	1060740	STR_RS05250	Capsule	Immune modulation	98.27	100.00	WP_011227246
INIGJNDL_1	1062183	1063637	STU_RS14650	Capsule	Immune modulation	98.21	100.00	WP_011226049
INIGJNDL_1	1060005	1060740	STU_RS14635	Capsule	Immune modulation	98.10	99.33	WP_011226046
INIGJNDL_1	1423254	1424525	STU_RS16265	Capsule	Immune modulation	97.48	99.76	WP_011226331
INIGJNDL_1	1062183	1063637	STER_RS05320	Capsule	Immune modulation	96.65	99.79	WP_011681177
INIGJNDL_1	539955	544849	SAG_RS09105	Agglutinin receptor	Adherence	92.87	99.98	WP_000167699
INIGJNDL_1	539907	544849	SSU98_0978	Agglutinin receptor	Adherence	92.82	99.78	YP_001200536
INIGJNDL_1	539907	544849	SSU05_0965	Agglutinin receptor	Adherence	92.80	99.78	YP_001198331
INIGJNDL_1	1060750	1061442	STER_RS05310	Capsule	Immune modulation	89.75	100.00	WP_011681175
INIGJNDL_1	1060750	1061442	STU_RS14640	Capsule	Immune modulation	89.61	100.00	WP_011226047
INIGJNDL_1	1060750	1061442	STR_RS05255	Capsule	Immune modulation	89.32	100.00	WP_011227247
INIGJNDL_1	685933	687236	eno	Streptococcal enolase	Exoenzyme	88.10	99.46	WP_000022832
INIGJNDL_1	1717445	1718455	plr/gapA	Streptococcal plasmin receptor/GAPDH	Adherence	86.54	99.41	WP_002986042
INIGJNDL_1	152340	153623	tig/ropA	Trigger factor	Stress survival	80.73	99.77	WP_000107753
INIGJNDL_1	1184341	1185387	rfbB	Capsule	Immune modulation	80.61	100.00	WP_009659423

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
INIGJNDL_1	1226051	1227034	ldh(Sp_1220)	0.0	L-lactate dehydrogenase	94.82	100.00	AAK75326
INIGJNDL_1	798815	799888	MntE	0.0	manganese homeostasis	94.41	99.72	ABF32167
INIGJNDL_1	539934	544844	B9H01_RS04765	0.0	glucan-binding protein	93.40	99.63	AUS90958
INIGJNDL_1	602248	603216	spr0084	0.0	pathogenitcity related	93.19	98.48	AAK98888
INIGJNDL_1	1594284	1596587	pfl2(Sp_0459)	0.0	formate acetyltransferase	92.97	99.22	AAK74619
INIGJNDL_1	1315415	1316896	SPD_0310	0.0	UPF0371 protein SPD_0310	92.31	100.00	ABJ54480
INIGJNDL_1	820757	823003	metE	0.0	methionine biosynthesis enzymes	91.72	100.00	AAK74738
INIGJNDL_1	72295	73293	recA	0.0	DNA recombination and repair	91.29	85.82	AAL00560
INIGJNDL_1	27203	28174	prsA2	0.0	ribose-phosphate pyrophosphokinase	90.12	100.00	ABF36968
INIGJNDL_1	1479266	1478115	potA	0.0	ABC transporter ATP-binding protein-spermidine/putrescine transport	89.32	99.74	AAL00050
INIGJNDL_1	1441449	1439461	uvrB	0.0	excinuclease ABC, B subunit	88.99	100.00	AE014259_2
INIGJNDL_1	1209852	1208122	ptsI	0.0	phosphoenolpyruvate-protein phosphotransferase	88.04	100.00	AAK34199
INIGJNDL_1	1925759	1924281	IMPDH	0.0	inosine-5'-monophosphate dehydrogenase	87.02	100.00	ADE32434
INIGJNDL_1	685933	687234	Eno	0.0	enolase	86.21	99.77	ABP90468
INIGJNDL_1	1910557	1908665	gidA	0.0	tRNA uridine 5-carboxymethylaminomethyl modification enzyme	86.05	98.90	ABP91129
INIGJNDL_1	825928	824219	PGM	0.0	phosphoglucomutase	83.71	99.65	ACH87041
INIGJNDL_1	1759935	1760945	pdh	0.0	pyruvate dehydrogenase	83.09	99.70	ABP91006
INIGJNDL_1	973103	971742	mnmE	0.0	central tRNA-modifying GTPase	82.24	99.56	ABP90420
INIGJNDL_1	1811979	1810087	PepO	0.0	endopeptidase	80.19	100.00	ABF32980
INIGJNDL_1	671498	672388	bglB	1.39e-178	putative phospho--glucosidase	88.89	99.66	AAK33487
INIGJNDL_1	886983	886045	SP_0676	2.46e-167	transcription facot	81.15	97.20	AAK74821
INIGJNDL_1	823195	824052	metF	1.60e-164	methionine biosynthesis enzymes	86.36	99.31	AAK74739
INIGJNDL_1	1100480	1099776	covR	4.58e-131	responder protein	85.53	100.00	AAK71319
INIGJNDL_1	1274223	1273552	rr01	3.14e-124	response regulator	83.93	99.56	CAB54566
INIGJNDL_1	1100480	1099776	walR	1.93e-121	DNA-binding response regulator	82.13	100.00	ANC99504
INIGJNDL_1	310380	311066	CovR	1.05e-117	serves to repress GAS virulence factor-encoding genes	80.79	100.00	ACE75886
INIGJNDL_1	829882	830550	CiaR	2.11e-117	two-component response regulator	84.31	99.55	AAK74935
INIGJNDL_1	829882	830553	ciaR	2.08e-115	two component system response regulator	82.14	99.12	AIK75708
INIGJNDL_1	73569	73943	SpxA2	1.21e-69	transcriptional regulator	91.20	94.70	ERL21461
INIGJNDL_1	984462	984863	SpxA1	3.93e-66	transcriptional regulator	80.60	100.00	ERL19273
INIGJNDL_1	153781	154281	RopE (M5005_Spy_1611)	5.14e-75	probable DNA-directed RNA polymerase subunit delta	81.44	87.43	AAK34603
INIGJNDL_1	1594284	1596581	PFL (B9H01_RS01125)	0.0	formate C-acetyltransferase	82.94	98.08	MYN69560
INIGJNDL_1	574557	575753	AUS90997 (B9H01_RS07385)	0.0	site-specific integrase	97.74	100.00	AUS90997
INIGJNDL_1	1797507	1796488	ilvC (SPD_0406)	0.0	ketol-acid reductoisomerase (NADP(+))	96.47	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
INIGJNDL_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