safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

Probiotic potential risk score

ARGs	VFs	PGs	PPRS
0	27	29	39.62

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.
NIKLHPCJ_1	1111419	1112288	rfbA	Capsule	Immune modulation	100.00	100.00	WP_011681286
NIKLHPCJ_1	1110826	1111419	STER_RS06030	Capsule	Immune modulation	100.00	100.00	WP_011226149
NIKLHPCJ_1	1333768	1334574	STER_RS07060	Capsule	Immune modulation	100.00	100.00	WP_011681437
NIKLHPCJ_1	1341796	1343055	STER_RS07100	Capsule	Immune modulation	100.00	100.00	WP_011681445
NIKLHPCJ_1	1335512	1336660	STER_RS07070	Capsule	Immune modulation	99.91	100.00	WP_011681439
NIKLHPCJ_1	1110826	1111419	STR_RS05880	Capsule	Immune modulation	99.83	100.00	WP_011226149
NIKLHPCJ_1	1334574	1335515	STR_RS06905	Capsule	Immune modulation	99.68	100.00	WP_011227430
NIKLHPCJ_1	1110826	1111419	STU_RS15260	Capsule	Immune modulation	99.66	100.00	WP_011226149
NIKLHPCJ_1	1329436	1331181	STER_RS07045	Capsule	Immune modulation	99.60	100.00	WP_011681434
NIKLHPCJ_1	1340823	1341799	STER_RS07095	Capsule	Immune modulation	99.59	99.90	WP_011681444
NIKLHPCJ_1	1334574	1335515	STER_RS07065	Capsule	Immune modulation	99.58	100.00	WP_011681438
NIKLHPCJ_1	43690	44529	cbpD	Autolysin	Exoenzyme	99.52	100.00	WP_011226733
NIKLHPCJ_1	1333768	1334574	STR_RS06900	Capsule	Immune modulation	99.50	100.00	WP_011227429
NIKLHPCJ_1	877590	879248	fbp54	FBPs	Adherence	99.34	100.00	WP_011227179
NIKLHPCJ_1	1335512	1336660	STR_RS06910	Capsule	Immune modulation	99.30	100.00	WP_011227431
NIKLHPCJ_1	1339837	1340805	STER_RS07090	Capsule	Immune modulation	99.28	100.00	WP_011681443
NIKLHPCJ_1	1147612	1148373	srtA	Sortase A	Exoenzyme	99.08	100.00	-
NIKLHPCJ_1	1052498	1053288	cshA	Cell surface hydrophobicity proteins	Adherence	98.74	100.00	-
NIKLHPCJ_1	971100	972515	STER_RS05250	Capsule	Immune modulation	98.59	100.00	WP_011681165
NIKLHPCJ_1	983507	984238	STU_RS14645	Capsule	Immune modulation	98.36	100.00	WP_011226048
NIKLHPCJ_1	1339120	1339835	STER_RS07085	Capsule	Immune modulation	98.32	99.86	WP_011681442
NIKLHPCJ_1	1337998	1338774	STER_RS07075	Capsule	Immune modulation	98.20	100.00	WP_011681440
NIKLHPCJ_1	983507	984238	STER_RS05315	Capsule	Immune modulation	98.09	100.00	WP_011681176
NIKLHPCJ_1	1329436	1331181	STR_RS06885	Capsule	Immune modulation	97.94	100.00	WP_011227426
NIKLHPCJ_1	983507	984238	STR_RS05260	Capsule	Immune modulation	97.68	100.00	WP_011227248
NIKLHPCJ_1	984239	985699	STER_RS05320	Capsule	Immune modulation	97.47	100.00	WP_011681177
NIKLHPCJ_1	1343174	1344025	rfbD	Capsule	Immune modulation	97.42	100.00	WP_014621820
NIKLHPCJ_1	982056	982796	STU_RS14635	Capsule	Immune modulation	97.17	100.00	WP_011226046
NIKLHPCJ_1	984239	985699	STU_RS14650	Capsule	Immune modulation	96.85	100.21	WP_011226049
NIKLHPCJ_1	982056	982796	STER_RS05305	Capsule	Immune modulation	96.76	100.00	WP_011681174
NIKLHPCJ_1	982061	982796	STR_RS05250	Capsule	Immune modulation	96.20	98.13	WP_011227246
NIKLHPCJ_1	984239	985699	STR_RS05265	Capsule	Immune modulation	95.89	100.21	WP_041827043
NIKLHPCJ_1	982806	983498	STR_RS05255	Capsule	Immune modulation	95.40	99.86	WP_011227247
NIKLHPCJ_1	982806	983498	STU_RS14640	Capsule	Immune modulation	95.40	99.86	WP_011226047
NIKLHPCJ_1	980632	981999	STU_RS14630	Capsule	Immune modulation	95.32	100.00	WP_011226045
NIKLHPCJ_1	980634	981999	STER_RS05300	Capsule	Immune modulation	94.07	99.85	WP_011681173
NIKLHPCJ_1	982806	983498	STER_RS05310	Capsule	Immune modulation	89.47	100.00	WP_011681175
NIKLHPCJ_1	613068	614371	eno	Streptococcal enolase	Exoenzyme	88.10	99.46	WP_000022832
NIKLHPCJ_1	1632676	1633686	plr/gapA	Streptococcal plasmin receptor/GAPDH	Adherence	87.45	99.90	WP_002986042
NIKLHPCJ_1	1332545	1333768	SGO_RS05025	Capsule	Immune modulation	84.52	99.92	WP_012000441
NIKLHPCJ_1	1333768	1334574	SGO_RS05020	Capsule	Immune modulation	82.90	100.00	WP_012000440
NIKLHPCJ_1	142497	143780	tig/ropA	Trigger factor	Stress survival	80.65	99.77	WP_000107753
NIKLHPCJ_1	1109351	1110397	rfbB	Capsule	Immune modulation	80.61	100.00	WP_009659423
NIKLHPCJ_1	1333031	1333768	STER_RS07055	Capsule	Immune modulation	98.10	61.35	WP_011681436
NIKLHPCJ_1	1333031	1333768	STR_RS06895	Capsule	Immune modulation	97.83	61.35	WP_011227428

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
NIKLHPCJ_1	1151060	1152043	ldh(Sp_1220)	0.0	L-lactate dehydrogenase	94.82	100.00	AAK75326
NIKLHPCJ_1	716732	717805	MntE	0.0	manganese homeostasis	94.41	99.72	ABF32167
NIKLHPCJ_1	529668	530636	spr0084	0.0	pathogenitcity related	93.19	98.48	AAK98888
NIKLHPCJ_1	1509611	1511914	pfl2(Sp_0459)	0.0	formate acetyltransferase	92.97	99.22	AAK74619
NIKLHPCJ_1	1226456	1227937	SPD_0310	0.0	UPF0371 protein SPD_0310	92.31	100.00	ABJ54480
NIKLHPCJ_1	746605	748851	metE	0.0	methionine biosynthesis enzymes	91.99	100.00	AAK74738
NIKLHPCJ_1	65880	66872	recA	0.0	DNA recombination and repair	91.24	85.31	AAL00560
NIKLHPCJ_1	27206	28177	prsA2	0.0	ribose-phosphate pyrophosphokinase	90.12	100.00	ABF36968
NIKLHPCJ_1	1395824	1394673	potA	0.0	ABC transporter ATP-binding protein-spermidine/putrescine transport	89.32	99.74	AAL00050
NIKLHPCJ_1	1357064	1355076	uvrB	0.0	excinuclease ABC, B subunit	88.99	100.00	AE014259_2
NIKLHPCJ_1	1134863	1133133	ptsI	0.0	phosphoenolpyruvate-protein phosphotransferase	88.04	100.00	AAK34199
NIKLHPCJ_1	1846253	1844775	IMPDH	0.0	inosine-5'-monophosphate dehydrogenase	87.42	100.00	ADE32434
NIKLHPCJ_1	613068	614369	Eno	0.0	enolase	86.21	99.77	ABP90468
NIKLHPCJ_1	1831063	1829171	gidA	0.0	tRNA uridine 5-carboxymethylaminomethyl modification enzyme	86.05	98.90	ABP91129
NIKLHPCJ_1	751776	750067	PGM	0.0	phosphoglucomutase	83.89	99.65	ACH87041
NIKLHPCJ_1	1679203	1680213	pdh	0.0	pyruvate dehydrogenase	83.09	99.70	ABP91006
NIKLHPCJ_1	905056	903695	mnmE	0.0	central tRNA-modifying GTPase	81.80	99.56	ABP90420
NIKLHPCJ_1	1730892	1729000	PepO	0.0	endopeptidase	80.03	100.00	ABF32980
NIKLHPCJ_1	598634	599524	bglB	1.33e-178	putative phospho--glucosidase	88.89	99.66	AAK33487
NIKLHPCJ_1	817195	816257	SP_0676	2.36e-167	transcription facot	81.15	97.20	AAK74821
NIKLHPCJ_1	749043	749900	metF	8.67e-165	methionine biosynthesis enzymes	86.36	99.31	AAK74739
NIKLHPCJ_1	1022407	1021703	covR	4.39e-131	responder protein	85.53	100.00	AAK71319
NIKLHPCJ_1	1207453	1206782	rr01	1.09e-121	response regulator	82.59	99.56	CAB54566
NIKLHPCJ_1	1022407	1021703	walR	1.85e-121	DNA-binding response regulator	82.13	100.00	ANC99504
NIKLHPCJ_1	755730	756398	CiaR	9.43e-118	two-component response regulator	84.75	99.55	AAK74935
NIKLHPCJ_1	296921	297607	CovR	1.01e-117	serves to repress GAS virulence factor-encoding genes	80.79	100.00	ACE75886
NIKLHPCJ_1	755730	756401	ciaR	1.02e-115	two component system response regulator	82.59	99.12	AIK75708
NIKLHPCJ_1	67184	67579	SpxA2	3.19e-73	transcriptional regulator	90.15	100.00	ERL21461
NIKLHPCJ_1	916414	916815	SpxA1	3.77e-66	transcriptional regulator	80.60	100.00	ERL19273
NIKLHPCJ_1	143938	144438	RopE (M5005_Spy_1611)	4.93e-75	probable DNA-directed RNA polymerase subunit delta	81.44	87.43	AAK34603
NIKLHPCJ_1	1509611	1511908	PFL (B9H01_RS01125)	0.0	formate C-acetyltransferase	82.94	98.08	MYN69560
NIKLHPCJ_1	1716483	1715464	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
NIKLHPCJ_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