safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

Probiotic potential risk score

ARGs	VFs	PGs	PPRS
0	27	33	42.64

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.
PFGAIEGL_6	52997	53590	STER_RS06030	Capsule	Immune modulation	100.00	100.00	WP_011226149
PFGAIEGL_9	132701	133417	STER_RS07085	Capsule	Immune modulation	100.00	100.00	WP_011681442
PFGAIEGL_9	133418	134386	STER_RS07090	Capsule	Immune modulation	100.00	100.00	WP_011681443
PFGAIEGL_9	123901	125646	STER_RS07045	Capsule	Immune modulation	99.94	100.00	WP_011681434
PFGAIEGL_9	125648	127348	STER_RS07050	Capsule	Immune modulation	99.94	100.00	WP_041827753
PFGAIEGL_9	135377	136636	STER_RS07100	Capsule	Immune modulation	99.92	100.00	WP_011681445
PFGAIEGL_9	130312	131460	STER_RS07070	Capsule	Immune modulation	99.91	100.00	WP_011681439
PFGAIEGL_6	53590	54459	rfbA	Capsule	Immune modulation	99.89	100.00	WP_011681286
PFGAIEGL_9	129374	130315	STER_RS07065	Capsule	Immune modulation	99.89	100.00	WP_011681438
PFGAIEGL_9	131579	132355	STER_RS07075	Capsule	Immune modulation	99.87	100.00	WP_011681440
PFGAIEGL_9	127366	128568	STER_RS07055	Capsule	Immune modulation	99.83	100.00	WP_011681436
PFGAIEGL_6	52997	53590	STR_RS05880	Capsule	Immune modulation	99.83	100.00	WP_011226149
PFGAIEGL_9	125648	127348	STR_RS06890	Capsule	Immune modulation	99.77	100.00	WP_041827077
PFGAIEGL_6	52997	53590	STU_RS15260	Capsule	Immune modulation	99.66	100.00	WP_011226149
PFGAIEGL_9	128568	129374	STER_RS07060	Capsule	Immune modulation	99.63	100.00	WP_011681437
PFGAIEGL_9	134404	135380	STER_RS07095	Capsule	Immune modulation	99.59	99.90	WP_011681444
PFGAIEGL_4	69997	71655	fbp54	FBPs	Adherence	99.58	100.00	WP_011227179
PFGAIEGL_9	127366	128568	STR_RS06895	Capsule	Immune modulation	99.58	100.00	WP_011227428
PFGAIEGL_1	20069	20908	cbpD	Autolysin	Exoenzyme	99.52	100.00	WP_011226733
PFGAIEGL_9	129374	130315	STR_RS06905	Capsule	Immune modulation	99.36	100.00	WP_011227430
PFGAIEGL_9	130312	131460	STR_RS06910	Capsule	Immune modulation	99.30	100.00	WP_011227431
PFGAIEGL_9	128568	129374	STR_RS06900	Capsule	Immune modulation	99.13	100.00	WP_011227429
PFGAIEGL_4	180880	181611	STER_RS05315	Capsule	Immune modulation	98.63	100.00	WP_011681176
PFGAIEGL_5	6797	7590	cshA	Cell surface hydrophobicity proteins	Adherence	98.36	100.25	-
PFGAIEGL_9	123901	125646	STR_RS06885	Capsule	Immune modulation	98.28	100.00	WP_011227426
PFGAIEGL_4	180880	181611	STR_RS05260	Capsule	Immune modulation	98.22	100.00	WP_011227248
PFGAIEGL_4	180880	181611	STU_RS14645	Capsule	Immune modulation	98.09	100.00	WP_011226048
PFGAIEGL_4	179429	180169	STER_RS05305	Capsule	Immune modulation	97.98	100.00	WP_011681174
PFGAIEGL_4	181612	183072	STER_RS05320	Capsule	Immune modulation	97.95	100.00	WP_011681177
PFGAIEGL_4	179429	180169	STU_RS14635	Capsule	Immune modulation	97.84	100.00	WP_011226046
PFGAIEGL_7	14652	15413	srtA	Sortase A	Exoenzyme	97.64	100.00	-
PFGAIEGL_9	136755	137606	rfbD	Capsule	Immune modulation	97.42	100.00	WP_014621820
PFGAIEGL_4	179434	180169	STR_RS05250	Capsule	Immune modulation	97.42	98.13	WP_011227246
PFGAIEGL_4	181612	183072	STU_RS14650	Capsule	Immune modulation	96.92	100.21	WP_011226049
PFGAIEGL_4	180179	180871	STR_RS05255	Capsule	Immune modulation	96.83	100.00	WP_011227247
PFGAIEGL_4	180179	180871	STU_RS14640	Capsule	Immune modulation	96.83	100.00	WP_011226047
PFGAIEGL_4	181612	183072	STR_RS05265	Capsule	Immune modulation	95.96	100.21	WP_041827043
PFGAIEGL_4	178007	179372	STER_RS05300	Capsule	Immune modulation	94.66	99.85	WP_011681173
PFGAIEGL_4	178005	179372	STU_RS14630	Capsule	Immune modulation	94.08	100.00	WP_011226045
PFGAIEGL_4	180179	180871	STER_RS05310	Capsule	Immune modulation	91.78	100.00	WP_011681175
PFGAIEGL_21	102861	104164	eno	Streptococcal enolase	Exoenzyme	88.10	99.46	WP_000022832
PFGAIEGL_11	106193	107203	plr/gapA	Streptococcal plasmin receptor/GAPDH	Adherence	86.54	99.41	WP_002986042
PFGAIEGL_9	128568	129374	SGO_RS05020	Capsule	Immune modulation	83.27	100.00	WP_012000440
PFGAIEGL_19	6304	7587	tig/ropA	Trigger factor	Stress survival	80.65	99.77	WP_000107753
PFGAIEGL_6	51522	52568	rfbB	Capsule	Immune modulation	80.61	100.00	WP_009659423
PFGAIEGL_9	127831	128568	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
PFGAIEGL_7	18100	19083	ldh(Sp_1220)	0.0	L-lactate dehydrogenase	94.82	100.00	AAK75326
PFGAIEGL_23	24971	26044	MntE	0.0	manganese homeostasis	94.41	99.72	ABF32167
PFGAIEGL_10	145907	148210	pfl2(Sp_0459)	0.0	formate acetyltransferase	92.97	99.22	AAK74619
PFGAIEGL_21	20616	21584	spr0084	0.0	pathogenitcity related	92.57	98.48	AAK98888
PFGAIEGL_9	29058	30539	SPD_0310	0.0	UPF0371 protein SPD_0310	92.11	100.00	ABJ54480
PFGAIEGL_23	61236	63482	metE	0.0	methionine biosynthesis enzymes	91.99	100.00	AAK74738
PFGAIEGL_1	39700	40698	recA	0.0	DNA recombination and repair	91.29	85.82	AAL00560
PFGAIEGL_1	3587	4558	prsA2	0.0	ribose-phosphate pyrophosphokinase	90.12	100.00	ABF36968
PFGAIEGL_10	31890	30739	potA	0.0	ABC transporter ATP-binding protein-spermidine/putrescine transport	89.32	99.74	AAL00050
PFGAIEGL_9	150645	148657	uvrB	0.0	excinuclease ABC, B subunit	88.84	100.00	AE014259_2
PFGAIEGL_7	1901	171	ptsI	0.0	phosphoenolpyruvate-protein phosphotransferase	88.04	100.00	AAK34199
PFGAIEGL_16	94208	92730	IMPDH	0.0	inosine-5'-monophosphate dehydrogenase	87.63	100.00	ADE32434
PFGAIEGL_21	102861	104162	Eno	0.0	enolase	86.21	99.77	ABP90468
PFGAIEGL_16	79019	77127	gidA	0.0	tRNA uridine 5-carboxymethylaminomethyl modification enzyme	85.89	98.90	ABP91129
PFGAIEGL_23	66406	64697	PGM	0.0	phosphoglucomutase	84.06	99.65	ACH87041
PFGAIEGL_14	18867	19877	pdh	0.0	pyruvate dehydrogenase	83.09	99.70	ABP91006
PFGAIEGL_4	97020	95659	mnmE	0.0	central tRNA-modifying GTPase	82.24	99.56	ABP90420
PFGAIEGL_14	69199	67307	PepO	0.0	endopeptidase	80.19	100.00	ABF32980
PFGAIEGL_21	88425	89315	bglB	1.32e-179	putative phospho--glucosidase	88.89	99.66	AAK33487
PFGAIEGL_4	11838	10900	SP_0676	3.06e-168	transcription facot	81.15	97.20	AAK74821
PFGAIEGL_23	63674	64531	metF	3.36e-166	methionine biosynthesis enzymes	86.36	99.31	AAK74739
PFGAIEGL_4	219910	219206	covR	5.69e-132	responder protein	85.53	100.00	AAK71319
PFGAIEGL_9	10084	9413	rr01	2.48e-126	response regulator	84.38	99.56	CAB54566
PFGAIEGL_23	70361	71029	CiaR	3.40e-124	two-component response regulator	86.10	99.55	AAK74935
PFGAIEGL_4	219910	219206	walR	2.40e-122	DNA-binding response regulator	82.13	100.00	ANC99504
PFGAIEGL_23	70361	71032	ciaR	4.61e-122	two component system response regulator	83.93	99.12	AIK75708
PFGAIEGL_19	159256	159942	CovR	1.12e-118	serves to repress GAS virulence factor-encoding genes	80.79	100.00	ACE75886
PFGAIEGL_1	40974	41348	SpxA2	2.59e-71	transcriptional regulator	91.20	94.70	ERL21461
PFGAIEGL_4	108382	108783	SpxA1	4.89e-67	transcriptional regulator	80.60	100.00	ERL19273
PFGAIEGL_19	181654	181941	spr0479	1.58e-48	essential gene	86.46	98.97	AAK99283
PFGAIEGL_20	120961	121215	spr1327	2.10e-45	essential gene	95.29	100.00	AAL00131
PFGAIEGL_16	45392	45655	spr0175	4.73e-42	pathogenitcity related	84.09	100.00	AAK98979
PFGAIEGL_16	46219	46485	spr0177	1.03e-33	essential gene	84.27	88.12	AAK98981
PFGAIEGL_19	7745	8245	RopE (M5005_Spy_1611)	5.50e-76	probable DNA-directed RNA polymerase subunit delta	81.44	87.43	AAK34603
PFGAIEGL_10	145907	148204	PFL (B9H01_RS01125)	0.0	formate C-acetyltransferase	82.94	98.08	MYN69560
PFGAIEGL_14	54730	53711	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
PFGAIEGL_1	0.0	1.0	0.0
PFGAIEGL_2	1.0	0.0	1.0
PFGAIEGL_3	1.0	0.0	1.0
PFGAIEGL_4	0.0	1.0	0.0
PFGAIEGL_5	0.0	1.0	0.0
PFGAIEGL_6	0.0	1.0	0.0
PFGAIEGL_7	0.0	1.0	0.0
PFGAIEGL_8	0.0	1.0	0.0
PFGAIEGL_9	0.0	1.0	0.0
PFGAIEGL_10	0.0	1.0	0.0
PFGAIEGL_11	0.0	1.0	0.0
PFGAIEGL_12	0.0	1.0	0.0
PFGAIEGL_13	0.0	1.0	0.0
PFGAIEGL_14	0.0	1.0	0.0
PFGAIEGL_15	1.0	0.0	1.0
PFGAIEGL_16	0.0	1.0	0.0
PFGAIEGL_18	0.0	1.0	0.0
PFGAIEGL_19	0.0	1.0	0.0
PFGAIEGL_20	0.0	1.0	0.0
PFGAIEGL_21	0.0	1.0	0.0
PFGAIEGL_22	0.0	1.0	0.0
PFGAIEGL_23	0.0	1.0	0.0
PFGAIEGL_24	0.0	1.0	0.0
PFGAIEGL_25	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