safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

Probiotic potential risk score

ARGs	VFs	PGs	PPRS
0	24	29	37.64

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	e-value	VF name	VF category	Identity	Coverage	Accession no.
LPJJPAEB_1	513940	514908	STER_RS07090	0.0	Capsule	Immune modulation	97.32	100.00	WP_011681443
LPJJPAEB_1	514910	515625	STER_RS07085	0.0	Capsule	Immune modulation	94.55	99.86	WP_011681442
LPJJPAEB_1	1185813	1186544	STR_RS05260	0.0	Capsule	Immune modulation	94.54	100.00	WP_011227248
LPJJPAEB_1	510702	511553	rfbD	0.0	Capsule	Immune modulation	94.37	100.00	WP_014621820
LPJJPAEB_1	1185813	1186544	STU_RS14645	0.0	Capsule	Immune modulation	93.85	100.00	WP_011226048
LPJJPAEB_1	1185813	1186544	STER_RS05315	0.0	Capsule	Immune modulation	93.58	100.00	WP_011681176
LPJJPAEB_1	515971	516747	STER_RS07075	0.0	Capsule	Immune modulation	93.06	99.87	WP_011681440
LPJJPAEB_1	511672	512930	STER_RS07100	0.0	Capsule	Immune modulation	92.46	99.92	WP_011681445
LPJJPAEB_1	518952	519758	STER_RS07060	0.0	Capsule	Immune modulation	92.07	100.00	WP_011681437
LPJJPAEB_1	518952	519758	STR_RS06900	0.0	Capsule	Immune modulation	91.82	100.00	WP_011227429
LPJJPAEB_1	518011	518952	STER_RS07065	0.0	Capsule	Immune modulation	91.30	100.00	WP_011681438
LPJJPAEB_1	518011	518952	STR_RS06905	0.0	Capsule	Immune modulation	91.19	100.00	WP_011227430
LPJJPAEB_1	1345206	1345799	STR_RS05880	0.0	Capsule	Immune modulation	91.08	100.00	WP_011226149
LPJJPAEB_1	512927	513900	STER_RS07095	0.0	Capsule	Immune modulation	90.97	99.49	WP_011681444
LPJJPAEB_1	1345206	1345799	STER_RS06030	0.0	Capsule	Immune modulation	90.91	100.00	WP_011226149
LPJJPAEB_1	1345206	1345799	STU_RS15260	0.0	Capsule	Immune modulation	90.91	100.00	WP_011226149
LPJJPAEB_1	1186545	1188005	STER_RS05320	0.0	Capsule	Immune modulation	90.85	99.86	WP_011681177
LPJJPAEB_1	1081414	1083072	fbp54	0.0	FBPs	Adherence	90.78	99.94	WP_011227179
LPJJPAEB_1	1186545	1188005	STU_RS14650	0.0	Capsule	Immune modulation	90.58	100.00	WP_011226049
LPJJPAEB_1	516866	518014	STR_RS06910	0.0	Capsule	Immune modulation	90.17	100.00	WP_011227431
LPJJPAEB_1	516866	518014	STER_RS07070	0.0	Capsule	Immune modulation	89.99	100.00	WP_011681439
LPJJPAEB_1	1186545	1188005	STR_RS05265	0.0	Capsule	Immune modulation	89.90	100.00	WP_041827043
LPJJPAEB_1	1185112	1185804	STU_RS14640	0.0	Capsule	Immune modulation	89.75	100.00	WP_011226047
LPJJPAEB_1	1185112	1185804	STR_RS05255	0.0	Capsule	Immune modulation	89.47	100.00	WP_011227247
LPJJPAEB_1	1185112	1185804	STER_RS05310	0.0	Capsule	Immune modulation	89.32	100.00	WP_011681175
LPJJPAEB_1	429257	430096	cbpD	0.0	Autolysin	Exoenzyme	88.94	99.88	WP_011226733
LPJJPAEB_1	1519444	1520747	eno	0.0	Streptococcal enolase	Exoenzyme	88.24	99.54	WP_000022832
LPJJPAEB_1	522345	524090	STER_RS07045	0.0	Capsule	Immune modulation	86.84	99.89	WP_011681434
LPJJPAEB_1	522345	524090	STR_RS06885	0.0	Capsule	Immune modulation	86.79	99.83	WP_011227426
LPJJPAEB_1	1964702	1965715	plr/gapA	0.0	Streptococcal plasmin receptor/GAPDH	Adherence	85.57	99.90	WP_002986042
LPJJPAEB_1	518952	519758	SGO_RS05020	0.0	Capsule	Immune modulation	85.50	100.00	WP_012000440
LPJJPAEB_1	519758	520981	SGO_RS05025	0.0	Capsule	Immune modulation	84.82	99.92	WP_012000441
LPJJPAEB_1	919642	920403	srtA	0.0	Sortase A	Exoenzyme	83.88	99.87	-
LPJJPAEB_1	1343890	1344936	rfbB	0.0	Capsule	Immune modulation	80.90	100.00	WP_009659423
LPJJPAEB_1	137550	138833	tig/ropA	0.0	Trigger factor	Stress survival	80.76	99.61	WP_000107753
LPJJPAEB_1	1345799	1346668	rfbA	0.0	Capsule	Immune modulation	80.16	99.77	WP_002904719
LPJJPAEB_1	1184432	1185102	STU_RS14635	2.77e-148	Capsule	Immune modulation	81.13	90.28	WP_011226046
LPJJPAEB_1	1184432	1185102	STER_RS05305	1.29e-146	Capsule	Immune modulation	80.98	90.28	WP_011681174
LPJJPAEB_1	1184432	1185102	STR_RS05250	1.31e-136	Capsule	Immune modulation	80.09	89.20	WP_011227246

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
LPJJPAEB_1	916952	915969	ldh(Sp_1220)	0.0	L-lactate dehydrogenase	96.95	100.00	AAK75326
LPJJPAEB_1	928537	929610	MntE	0.0	manganese homeostasis	95.81	99.72	ABF32167
LPJJPAEB_1	1831280	1833583	pfl2(Sp_0459)	0.0	formate acetyltransferase	94.40	99.10	AAK74619
LPJJPAEB_1	1616108	1615140	spr0084	0.0	pathogenitcity related	93.19	98.48	AAK98888
LPJJPAEB_1	767581	766100	SPD_0310	0.0	UPF0371 protein SPD_0310	92.71	100.00	ABJ54480
LPJJPAEB_1	948080	950326	metE	0.0	methionine biosynthesis enzymes	92.66	100.00	AAK74738
LPJJPAEB_1	24334	25305	prsA2	0.0	ribose-phosphate pyrophosphokinase	91.67	100.00	ABF36968
LPJJPAEB_1	1373218	1371488	ptsI	0.0	phosphoenolpyruvate-protein phosphotransferase	89.95	100.00	AAK34199
LPJJPAEB_1	498526	500514	uvrB	0.0	excinuclease ABC, B subunit	89.59	100.00	AE014259_2
LPJJPAEB_1	1699051	1697900	potA	0.0	ABC transporter ATP-binding protein-spermidine/putrescine transport	89.58	99.74	AAL00050
LPJJPAEB_1	2173700	2172222	IMPDH	0.0	inosine-5'-monophosphate dehydrogenase	87.83	100.00	ADE32434
LPJJPAEB_1	1520747	1519446	Eno	0.0	enolase	86.44	99.77	ABP90468
LPJJPAEB_1	2157920	2156028	gidA	0.0	tRNA uridine 5-carboxymethylaminomethyl modification enzyme	85.58	98.90	ABP91129
LPJJPAEB_1	58864	59955	recA	0.0	DNA recombination and repair	84.91	95.36	AAL00560
LPJJPAEB_1	953244	951535	PGM	0.0	phosphoglucomutase	84.76	99.65	ACH87041
LPJJPAEB_1	2016372	2017382	pdh	0.0	pyruvate dehydrogenase	82.79	99.70	ABP91006
LPJJPAEB_1	1096999	1095638	mnmE	0.0	central tRNA-modifying GTPase	82.46	99.56	ABP90420
LPJJPAEB_1	1535157	1534267	bglB	2.37e-176	putative phospho--glucosidase	87.20	99.66	AAK33487
LPJJPAEB_1	996235	995285	SP_0676	3.23e-169	transcription facot	81.39	98.45	AAK74821
LPJJPAEB_1	950516	951373	metF	9.48e-168	methionine biosynthesis enzymes	87.06	99.31	AAK74739
LPJJPAEB_1	1222549	1221845	covR	9.75e-126	responder protein	85.53	100.00	AAK71319
LPJJPAEB_1	843726	844397	rr01	2.10e-125	response regulator	84.38	99.56	CAB54566
LPJJPAEB_1	957909	958580	ciaR	9.76e-124	two component system response regulator	85.71	99.12	AIK75708
LPJJPAEB_1	957909	958577	CiaR	1.21e-123	two-component response regulator	87.00	99.55	AAK74935
LPJJPAEB_1	296611	297297	CovR	1.84e-119	serves to repress GAS virulence factor-encoding genes	82.10	100.00	ACE75886
LPJJPAEB_1	1222549	1221845	walR	2.21e-119	DNA-binding response regulator	82.13	100.00	ANC99504
LPJJPAEB_1	61216	61611	SpxA2	2.15e-74	transcriptional regulator	91.67	100.00	ERL21461
LPJJPAEB_1	1108456	1108857	SpxA1	1.39e-68	transcriptional regulator	82.09	100.00	ERL19273
LPJJPAEB_1	118188	118601	GrpE	1.70e-66	protein grpE	81.88	80.59	ABP89267
LPJJPAEB_1	139000	139491	RopE (M5005_Spy_1611)	1.06e-71	probable DNA-directed RNA polymerase subunit delta	82.93	85.86	AAK34603
LPJJPAEB_1	1831280	1833580	PFL (B9H01_RS01125)	0.0	formate C-acetyltransferase	83.22	98.08	MYN69560
LPJJPAEB_1	2054348	2053329	ilvC (SPD_0406)	0.0	ketol-acid reductoisomerase (NADP(+))	85.88	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
LPJJPAEB_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
LPJJPAEB_1	1265161	1271333	False	Unknown	VOG3303, VOG3300, VOG8184, VOG8294, VOG0054, VOG11077, VOG8337, VOG3622, VOG0743, VOG6422