safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

Probiotic potential risk score

ARGs	VFs	PGs	PPRS
0	29	30	41.73

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.
LIDOAIMJ_1	1538408	1539124	STER_RS07085	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681442
LIDOAIMJ_1	1539125	1540093	STER_RS07090	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681443
LIDOAIMJ_1	1529608	1531353	STER_RS07045	0.0	Capsule	Immune modulation	99.94	100.00	WP_011681434
LIDOAIMJ_1	1531355	1533055	STER_RS07050	0.0	Capsule	Immune modulation	99.94	100.00	WP_041827753
LIDOAIMJ_1	1536019	1537167	STER_RS07070	0.0	Capsule	Immune modulation	99.91	100.00	WP_011681439
LIDOAIMJ_1	1535081	1536022	STER_RS07065	0.0	Capsule	Immune modulation	99.89	100.00	WP_011681438
LIDOAIMJ_1	1537286	1538062	STER_RS07075	0.0	Capsule	Immune modulation	99.87	100.00	WP_011681440
LIDOAIMJ_1	1533073	1534275	STER_RS07055	0.0	Capsule	Immune modulation	99.83	100.00	WP_011681436
LIDOAIMJ_1	1531355	1533055	STR_RS06890	0.0	Capsule	Immune modulation	99.77	100.00	WP_041827077
LIDOAIMJ_1	1534275	1535081	STER_RS07060	0.0	Capsule	Immune modulation	99.63	100.00	WP_011681437
LIDOAIMJ_1	1533073	1534275	STR_RS06895	0.0	Capsule	Immune modulation	99.58	100.00	WP_011227428
LIDOAIMJ_1	43761	44600	cbpD	0.0	Autolysin	Exoenzyme	99.41	100.00	WP_011226733
LIDOAIMJ_1	1071048	1072706	fbp54	0.0	FBPs	Adherence	99.40	100.00	WP_011227179
LIDOAIMJ_1	1540111	1541088	STER_RS07095	0.0	Capsule	Immune modulation	99.39	100.00	WP_011681444
LIDOAIMJ_1	1535081	1536022	STR_RS06905	0.0	Capsule	Immune modulation	99.36	100.00	WP_011227430
LIDOAIMJ_1	1536019	1537167	STR_RS06910	0.0	Capsule	Immune modulation	99.30	100.00	WP_011227431
LIDOAIMJ_1	1292001	1292594	STR_RS05880	0.0	Capsule	Immune modulation	99.16	100.00	WP_011226149
LIDOAIMJ_1	1534275	1535081	STR_RS06900	0.0	Capsule	Immune modulation	99.13	100.00	WP_011227429
LIDOAIMJ_1	1292594	1293463	rfbA	0.0	Capsule	Immune modulation	99.08	100.00	WP_011681286
LIDOAIMJ_1	1292001	1292594	STER_RS06030	0.0	Capsule	Immune modulation	98.99	100.00	WP_011226149
LIDOAIMJ_1	1292001	1292594	STU_RS15260	0.0	Capsule	Immune modulation	98.99	100.00	WP_011226149
LIDOAIMJ_1	1327351	1328112	srtA	0.0	Sortase A	Exoenzyme	98.56	100.00	-
LIDOAIMJ_1	1542462	1543313	rfbD	0.0	Capsule	Immune modulation	98.47	100.00	WP_014621820
LIDOAIMJ_1	1234541	1235329	cshA	0.0	Cell surface hydrophobicity proteins	Adherence	98.36	99.75	-
LIDOAIMJ_1	1529608	1531353	STR_RS06885	0.0	Capsule	Immune modulation	98.28	100.00	WP_011227426
LIDOAIMJ_1	1167855	1168586	STER_RS05315	0.0	Capsule	Immune modulation	97.40	100.00	WP_011681176
LIDOAIMJ_1	1168587	1170047	STER_RS05320	0.0	Capsule	Immune modulation	97.40	100.00	WP_011681177
LIDOAIMJ_1	1167855	1168586	STU_RS14645	0.0	Capsule	Immune modulation	97.40	100.00	WP_011226048
LIDOAIMJ_1	1167855	1168586	STR_RS05260	0.0	Capsule	Immune modulation	97.27	100.00	WP_011227248
LIDOAIMJ_1	1167154	1167846	STU_RS14640	0.0	Capsule	Immune modulation	97.26	100.00	WP_011226047
LIDOAIMJ_1	1167154	1167846	STR_RS05255	0.0	Capsule	Immune modulation	96.97	100.00	WP_011227247
LIDOAIMJ_1	1168587	1170047	STU_RS14650	0.0	Capsule	Immune modulation	96.78	100.21	WP_011226049
LIDOAIMJ_1	1541085	1542343	STER_RS07100	0.0	Capsule	Immune modulation	96.43	99.92	WP_011681445
LIDOAIMJ_1	1168587	1170047	STR_RS05265	0.0	Capsule	Immune modulation	96.10	100.21	WP_041827043
LIDOAIMJ_1	1166404	1167144	STU_RS14635	0.0	Capsule	Immune modulation	96.09	100.00	WP_011226046
LIDOAIMJ_1	1166404	1167144	STER_RS05305	0.0	Capsule	Immune modulation	95.95	100.00	WP_011681174
LIDOAIMJ_1	163100	167995	SAG_RS09105	0.0	Agglutinin receptor	Adherence	95.81	99.96	WP_000167699
LIDOAIMJ_1	163052	167995	SSU98_0978	0.0	Agglutinin receptor	Adherence	95.73	99.78	YP_001200536
LIDOAIMJ_1	163052	167995	SSU05_0965	0.0	Agglutinin receptor	Adherence	95.71	99.78	YP_001198331
LIDOAIMJ_1	1166409	1167144	STR_RS05250	0.0	Capsule	Immune modulation	95.65	98.13	WP_011227246
LIDOAIMJ_1	1164982	1166347	STER_RS05300	0.0	Capsule	Immune modulation	95.24	99.85	WP_011681173
LIDOAIMJ_1	1164980	1166347	STU_RS14630	0.0	Capsule	Immune modulation	94.30	100.00	WP_011226045
LIDOAIMJ_1	1167154	1167846	STER_RS05310	0.0	Capsule	Immune modulation	90.77	100.00	WP_011681175
LIDOAIMJ_1	726278	727581	eno	0.0	Streptococcal enolase	Exoenzyme	87.94	99.54	WP_000022832
LIDOAIMJ_1	1882749	1883759	plr/gapA	0.0	Streptococcal plasmin receptor/GAPDH	Adherence	86.74	99.41	WP_002986042
LIDOAIMJ_1	1534275	1535081	SGO_RS05020	0.0	Capsule	Immune modulation	83.27	100.00	WP_012000440
LIDOAIMJ_1	143372	144655	tig/ropA	0.0	Trigger factor	Stress survival	80.73	99.77	WP_000107753
LIDOAIMJ_1	1290525	1291571	rfbB	0.0	Capsule	Immune modulation	80.61	100.00	WP_009659423
LIDOAIMJ_1	1155489	1156072	SPD_RS01775	2.69e-143	Capsule	Immune modulation	82.73	96.20	WP_001819836
LIDOAIMJ_1	1533538	1534275	SGO_RS05025	0.0	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
LIDOAIMJ_1	163079	167992	B9H01_RS04765	0.0	glucan-binding protein	97.19	99.70	AUS90958
LIDOAIMJ_1	885720	886793	MntE	0.0	manganese homeostasis	94.97	99.72	ABF32167
LIDOAIMJ_1	1330799	1331782	ldh(Sp_1220)	0.0	L-lactate dehydrogenase	94.82	100.00	AAK75326
LIDOAIMJ_1	644272	645240	spr0084	0.0	pathogenitcity related	93.19	98.48	AAK98888
LIDOAIMJ_1	1718281	1720584	pfl2(Sp_0459)	0.0	formate acetyltransferase	92.32	99.22	AAK74619
LIDOAIMJ_1	1422483	1423964	SPD_0310	0.0	UPF0371 protein SPD_0310	91.90	100.00	ABJ54480
LIDOAIMJ_1	906247	908493	metE	0.0	methionine biosynthesis enzymes	91.72	100.00	AAK74738
LIDOAIMJ_1	72609	73607	recA	0.0	DNA recombination and repair	91.29	85.82	AAL00560
LIDOAIMJ_1	27133	28104	prsA2	0.0	ribose-phosphate pyrophosphokinase	90.12	100.00	ABF36968
LIDOAIMJ_1	1592978	1591827	potA	0.0	ABC transporter ATP-binding protein-spermidine/putrescine transport	89.32	99.74	AAL00050
LIDOAIMJ_1	1556812	1554824	uvrB	0.0	excinuclease ABC, B subunit	89.14	100.00	AE014259_2
LIDOAIMJ_1	1314612	1312882	ptsI	0.0	phosphoenolpyruvate-protein phosphotransferase	87.87	100.00	AAK34199
LIDOAIMJ_1	2091193	2089715	IMPDH	0.0	inosine-5'-monophosphate dehydrogenase	87.83	100.00	ADE32434
LIDOAIMJ_1	726278	727579	Eno	0.0	enolase	85.98	99.77	ABP90468
LIDOAIMJ_1	2075995	2074103	gidA	0.0	tRNA uridine 5-carboxymethylaminomethyl modification enzyme	85.42	98.90	ABP91129
LIDOAIMJ_1	911418	909709	PGM	0.0	phosphoglucomutase	84.06	99.65	ACH87041
LIDOAIMJ_1	1927140	1928150	pdh	0.0	pyruvate dehydrogenase	83.09	99.70	ABP91006
LIDOAIMJ_1	1086095	1084734	mnmE	0.0	central tRNA-modifying GTPase	81.80	99.56	ABP90420
LIDOAIMJ_1	1977446	1975554	PepO	0.0	endopeptidase	80.03	100.00	ABF32980
LIDOAIMJ_1	711846	712736	bglB	1.51e-178	putative phospho--glucosidase	88.89	99.66	AAK33487
LIDOAIMJ_1	1011542	1010604	SP_0676	2.67e-167	transcription facot	81.15	97.20	AAK74821
LIDOAIMJ_1	908685	909542	metF	6.11e-165	methionine biosynthesis enzymes	86.36	99.31	AAK74739
LIDOAIMJ_1	1206854	1206150	covR	4.97e-131	responder protein	85.53	100.00	AAK71319
LIDOAIMJ_1	1379751	1379080	rr01	4.34e-126	response regulator	84.82	99.56	CAB54566
LIDOAIMJ_1	915372	916040	CiaR	6.66e-124	two-component response regulator	87.44	99.55	AAK74935
LIDOAIMJ_1	915372	916043	ciaR	7.15e-122	two component system response regulator	85.27	99.12	AIK75708
LIDOAIMJ_1	1206854	1206150	walR	2.09e-121	DNA-binding response regulator	82.13	100.00	ANC99504
LIDOAIMJ_1	366020	366706	CovR	3.51e-118	serves to repress GAS virulence factor-encoding genes	81.22	100.00	ACE75886
LIDOAIMJ_1	73883	74278	SpxA2	4.20e-74	transcriptional regulator	90.91	100.00	ERL21461
LIDOAIMJ_1	144813	145313	RopE (M5005_Spy_1611)	4.02e-75	probable DNA-directed RNA polymerase subunit delta	82.04	87.43	AAK34603
LIDOAIMJ_1	1718305	1720578	PFL (B9H01_RS01125)	0.0	formate C-acetyltransferase	83.03	97.06	MYN69560
LIDOAIMJ_1	621476	622666	AUS90997 (B9H01_RS07385)	0.0	site-specific integrase	88.67	99.50	AUS90997
LIDOAIMJ_1	1963009	1961990	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
LIDOAIMJ_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
LIDOAIMJ_1	728953	767549	False	Siphoviridae	VOG7656, VOG4602, VOG0743, VOG3622, VOG1564, VOG9469, VOG3478, VOG8482, VOG0651, VOG4566, VOG0189, VOG3430, VOG0283, VOG0685, VOG0226, VOG4693, VOG0655, VOG3468, VOG0656, VOG0152, VOG0044, VOG0152, VOG6495, VOG0657, VOG0044, VOG0658, VOG0198, VOG0796, VOG4544, VOG0720, VOG4564, VOG4555, VOG3434, VOG1887, VOG3435, VOG4713, VOG0723, VOG5660, VOG0724, VOG0799, VOG0725, VOG0800, VOG4605, VOG4599, VOG0647, VOG4782, VOG3298, VOG3424, VOG0054, VOG4649, VOG3299, VOG3300
LIDOAIMJ_1	1442560	1448008	True	Unknown	VOG0944, VOG5532, VOG1837, VOG6628, VOG0249, VOG8916, VOG0944