safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

Probiotic potential risk score

ARGs	VFs	PGs	PPRS
0	35	33	48.10

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.
ICPEPJGA_29	9521	10390	rfbA	Capsule	Immune modulation	100.00	100.00	WP_011681286
ICPEPJGA_47	88494	89909	STER_RS05250	Capsule	Immune modulation	100.00	100.00	WP_011681165
ICPEPJGA_47	86313	87293	STER_RS05260	Capsule	Immune modulation	100.00	100.00	WP_011681166
ICPEPJGA_47	85136	86320	STER_RS05265	Capsule	Immune modulation	100.00	100.00	WP_011681167
ICPEPJGA_47	84067	85119	STER_RS05270	Capsule	Immune modulation	100.00	100.00	WP_011681168
ICPEPJGA_47	83144	84052	STER_RS05275	Capsule	Immune modulation	100.00	100.00	WP_011681169
ICPEPJGA_47	82062	83123	STER_RS05280	Capsule	Immune modulation	100.00	100.00	WP_202964935
ICPEPJGA_47	81534	82025	STER_RS05285	Capsule	Immune modulation	100.00	100.00	WP_011681171
ICPEPJGA_47	81046	81522	STER_RS05290	Capsule	Immune modulation	100.00	100.00	WP_011681172
ICPEPJGA_47	78126	78866	STER_RS05305	Capsule	Immune modulation	100.00	100.00	WP_011681174
ICPEPJGA_47	77424	78116	STER_RS05310	Capsule	Immune modulation	100.00	100.00	WP_011681175
ICPEPJGA_47	76684	77415	STER_RS05315	Capsule	Immune modulation	100.00	100.00	WP_011681176
ICPEPJGA_47	75223	76683	STER_RS05320	Capsule	Immune modulation	100.00	100.00	WP_011681177
ICPEPJGA_29	8928	9521	STER_RS06030	Capsule	Immune modulation	100.00	100.00	WP_011226149
ICPEPJGA_45	105038	106783	STER_RS07045	Capsule	Immune modulation	100.00	100.00	WP_011681434
ICPEPJGA_45	103336	105036	STER_RS07050	Capsule	Immune modulation	100.00	100.00	WP_041827753
ICPEPJGA_45	102116	103318	STER_RS07055	Capsule	Immune modulation	100.00	100.00	WP_011681436
ICPEPJGA_45	101310	102116	STER_RS07060	Capsule	Immune modulation	100.00	100.00	WP_011681437
ICPEPJGA_45	100369	101310	STER_RS07065	Capsule	Immune modulation	100.00	100.00	WP_011681438
ICPEPJGA_45	99224	100372	STER_RS07070	Capsule	Immune modulation	100.00	100.00	WP_011681439
ICPEPJGA_45	98329	99105	STER_RS07075	Capsule	Immune modulation	100.00	100.00	WP_011681440
ICPEPJGA_45	97267	97983	STER_RS07085	Capsule	Immune modulation	100.00	100.00	WP_011681442
ICPEPJGA_45	96298	97266	STER_RS07090	Capsule	Immune modulation	100.00	100.00	WP_011681443
ICPEPJGA_45	95303	96280	STER_RS07095	Capsule	Immune modulation	100.00	100.00	WP_011681444
ICPEPJGA_45	94047	95306	STER_RS07100	Capsule	Immune modulation	100.00	100.00	WP_011681445
ICPEPJGA_47	78923	80290	STER_RS05300	Capsule	Immune modulation	99.85	100.00	WP_011681173
ICPEPJGA_29	8928	9521	STR_RS05880	Capsule	Immune modulation	99.83	100.00	WP_011226149
ICPEPJGA_45	103336	105036	STR_RS06890	Capsule	Immune modulation	99.71	100.00	WP_041827077
ICPEPJGA_29	8928	9521	STU_RS15260	Capsule	Immune modulation	99.66	100.00	WP_011226149
ICPEPJGA_46	89717	91375	fbp54	FBPs	Adherence	99.64	100.00	WP_011227179
ICPEPJGA_45	101310	102116	STR_RS06900	Capsule	Immune modulation	99.50	100.00	WP_011227429
ICPEPJGA_45	100369	101310	STR_RS06905	Capsule	Immune modulation	99.47	100.00	WP_011227430
ICPEPJGA_45	102116	103318	STR_RS06895	Capsule	Immune modulation	99.42	100.00	WP_011227428
ICPEPJGA_45	99224	100372	STR_RS06910	Capsule	Immune modulation	99.22	100.00	WP_011227431
ICPEPJGA_16	7324	8292	cbpD	Autolysin	Exoenzyme	98.86	100.00	WP_082302295
ICPEPJGA_47	1301	2091	cshA	Cell surface hydrophobicity proteins	Adherence	98.74	100.00	-
ICPEPJGA_47	78126	78861	STR_RS05250	Capsule	Immune modulation	98.50	98.13	WP_011227246
ICPEPJGA_47	78126	78866	STU_RS14635	Capsule	Immune modulation	98.25	100.00	WP_011226046
ICPEPJGA_47	76684	77415	STR_RS05260	Capsule	Immune modulation	98.22	100.00	WP_011227248
ICPEPJGA_45	105038	106783	STR_RS06885	Capsule	Immune modulation	98.22	100.00	WP_011227426
ICPEPJGA_47	76684	77415	STU_RS14645	Capsule	Immune modulation	98.09	100.00	WP_011226048
ICPEPJGA_29	44290	45051	srtA	Sortase A	Exoenzyme	97.64	100.00	-
ICPEPJGA_47	75223	76683	STU_RS14650	Capsule	Immune modulation	97.47	100.21	WP_011226049
ICPEPJGA_47	75223	76683	STR_RS05265	Capsule	Immune modulation	96.92	100.21	WP_041827043
ICPEPJGA_45	93077	93928	rfbD	Capsule	Immune modulation	96.83	100.00	WP_014621820
ICPEPJGA_47	78923	80286	STU_RS14630	Capsule	Immune modulation	94.94	99.71	WP_011226045
ICPEPJGA_47	77424	78116	STU_RS14640	Capsule	Immune modulation	89.90	100.00	WP_011226047
ICPEPJGA_47	77424	78116	STR_RS05255	Capsule	Immune modulation	89.61	100.00	WP_011227247
ICPEPJGA_38	46460	47763	eno	Streptococcal enolase	Exoenzyme	88.10	99.46	WP_000022832
ICPEPJGA_24	14294	15304	plr/gapA	Streptococcal plasmin receptor/GAPDH	Adherence	86.54	99.41	WP_002986042
ICPEPJGA_45	101310	102116	SGO_RS05020	Capsule	Immune modulation	82.90	100.00	WP_012000440
ICPEPJGA_18	159345	160628	tig/ropA	Trigger factor	Stress survival	80.73	99.77	WP_000107753
ICPEPJGA_29	7453	8499	rfbB	Capsule	Immune modulation	80.61	100.00	WP_009659423
ICPEPJGA_45	102116	102853	SGO_RS05025	Capsule	Immune modulation	84.96	60.29	WP_012000441

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
ICPEPJGA_29	47738	48721	ldh(Sp_1220)	0.0	L-lactate dehydrogenase	94.82	100.00	AAK75326
ICPEPJGA_48	27639	28712	MntE	0.0	manganese homeostasis	94.41	99.72	ABF32167
ICPEPJGA_43	57528	59831	pfl2(Sp_0459)	0.0	formate acetyltransferase	92.97	99.22	AAK74619
ICPEPJGA_5	37294	36326	spr0084	0.0	pathogenitcity related	92.88	98.48	AAK98888
ICPEPJGA_29	124494	125975	SPD_0310	0.0	UPF0371 protein SPD_0310	92.51	100.00	ABJ54480
ICPEPJGA_48	59550	61796	metE	0.0	methionine biosynthesis enzymes	91.99	100.00	AAK74738
ICPEPJGA_17	40292	41290	recA	0.0	DNA recombination and repair	91.29	85.82	AAL00560
ICPEPJGA_17	4177	5148	prsA2	0.0	ribose-phosphate pyrophosphokinase	90.12	100.00	ABF36968
ICPEPJGA_45	44939	46090	potA	0.0	ABC transporter ATP-binding protein-spermidine/putrescine transport	89.32	99.74	AAL00050
ICPEPJGA_45	80038	82026	uvrB	0.0	excinuclease ABC, B subunit	89.14	100.00	AE014259_2
ICPEPJGA_29	31539	29809	ptsI	0.0	phosphoenolpyruvate-protein phosphotransferase	87.87	100.00	AAK34199
ICPEPJGA_4	13824	15302	IMPDH	0.0	inosine-5'-monophosphate dehydrogenase	87.63	100.00	ADE32434
ICPEPJGA_38	46460	47761	Eno	0.0	enolase	86.21	99.77	ABP90468
ICPEPJGA_4	28559	30451	gidA	0.0	tRNA uridine 5-carboxymethylaminomethyl modification enzyme	85.74	98.90	ABP91129
ICPEPJGA_48	64721	63012	PGM	0.0	phosphoglucomutase	84.06	99.65	ACH87041
ICPEPJGA_1	22463	23473	pdh	0.0	pyruvate dehydrogenase	83.09	99.70	ABP91006
ICPEPJGA_46	65282	66643	mnmE	0.0	central tRNA-modifying GTPase	82.24	99.56	ABP90420
ICPEPJGA_13	37056	38948	PepO	0.0	endopeptidase	80.19	100.00	ABF32980
ICPEPJGA_38	32024	32914	bglB	3.47e-179	putative phospho--glucosidase	88.55	99.66	AAK33487
ICPEPJGA_6	12490	11552	SP_0676	2.26e-169	transcription facot	81.47	97.20	AAK74821
ICPEPJGA_48	61988	62845	metF	5.82e-166	methionine biosynthesis enzymes	86.36	99.31	AAK74739
ICPEPJGA_47	38400	39104	covR	2.12e-132	responder protein	85.53	100.00	AAK71319
ICPEPJGA_29	99887	99216	rr01	2.21e-125	response regulator	83.93	99.56	CAB54566
ICPEPJGA_47	38400	39104	walR	8.95e-123	DNA-binding response regulator	82.13	100.00	ANC99504
ICPEPJGA_48	68676	69344	CiaR	7.70e-119	two-component response regulator	84.31	99.55	AAK74935
ICPEPJGA_18	7669	6983	CovR	8.82e-119	serves to repress GAS virulence factor-encoding genes	80.79	100.00	ACE75886
ICPEPJGA_48	68676	69347	ciaR	7.58e-117	two component system response regulator	82.14	99.12	AIK75708
ICPEPJGA_17	41566	41940	SpxA2	2.61e-71	transcriptional regulator	91.20	94.70	ERL21461
ICPEPJGA_46	53919	53518	SpxA1	2.12e-67	transcriptional regulator	80.60	100.00	ERL19273
ICPEPJGA_20	25972	25685	spr0479	2.97e-49	essential gene	86.46	98.97	AAK99283
ICPEPJGA_19	6517	6263	spr1327	4.16e-45	essential gene	94.12	100.00	AAL00131
ICPEPJGA_35	1215	952	spr0175	1.86e-43	pathogenitcity related	84.09	100.00	AAK98979
ICPEPJGA_35	388	122	spr0177	4.02e-35	essential gene	84.27	88.12	AAK98981
ICPEPJGA_18	159187	158687	RopE (M5005_Spy_1611)	4.32e-76	probable DNA-directed RNA polymerase subunit delta	81.44	87.43	AAK34603
ICPEPJGA_43	57528	59825	PFL (B9H01_RS01125)	0.0	formate C-acetyltransferase	82.94	98.08	MYN69560
ICPEPJGA_1	58324	57305	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
ICPEPJGA_1	0.0	1.0	0.0
ICPEPJGA_2	0.0	1.0	0.0
ICPEPJGA_4	0.0	1.0	0.0
ICPEPJGA_5	0.0	1.0	0.0
ICPEPJGA_6	0.0	1.0	0.0
ICPEPJGA_13	0.0	1.0	0.0
ICPEPJGA_14	0.0	1.0	0.0
ICPEPJGA_15	0.0	1.0	0.0
ICPEPJGA_16	0.0	1.0	0.0
ICPEPJGA_17	0.0	1.0	0.0
ICPEPJGA_18	0.0	1.0	0.0
ICPEPJGA_19	0.0	1.0	0.0
ICPEPJGA_20	0.0	1.0	0.0
ICPEPJGA_21	0.0	1.0	0.0
ICPEPJGA_22	0.0	1.0	0.0
ICPEPJGA_23	0.0	1.0	0.0
ICPEPJGA_24	0.0	1.0	0.0
ICPEPJGA_25	0.0	1.0	0.0
ICPEPJGA_26	0.0	1.0	0.0
ICPEPJGA_27	0.0	1.0	0.0
ICPEPJGA_28	0.0	1.0	0.0
ICPEPJGA_29	0.0	1.0	0.0
ICPEPJGA_30	0.0	1.0	0.0
ICPEPJGA_31	0.0	1.0	0.0
ICPEPJGA_32	0.0	1.0	0.0
ICPEPJGA_33	0.0	1.0	0.0
ICPEPJGA_34	1.0	0.0	1.0
ICPEPJGA_35	0.0	1.0	0.0
ICPEPJGA_36	0.0	1.0	0.0
ICPEPJGA_37	1.0	0.0	1.0
ICPEPJGA_38	0.0	1.0	0.0
ICPEPJGA_39	0.0	1.0	0.0
ICPEPJGA_40	0.0	1.0	0.0
ICPEPJGA_43	0.0	1.0	0.0
ICPEPJGA_45	0.0	1.0	0.0
ICPEPJGA_46	0.0	1.0	0.0
ICPEPJGA_47	0.0	1.0	0.0
ICPEPJGA_48	0.0	1.0	0.0
ICPEPJGA_49	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