safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

Probiotic potential risk score

ARGs	VFs	PGs	PPRS
0	28	28	39.60

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.
LPIDKOFA_1	1807198	1807890	STU_RS14640	0.0	Capsule	Immune modulation	99.71	100.00	WP_011226047
LPIDKOFA_1	299137	300093	STU_RS16250	0.0	Capsule	Immune modulation	99.48	100.00	WP_011226328
LPIDKOFA_1	1905578	1907236	fbp54	0.0	FBPs	Adherence	99.40	100.00	WP_011227179
LPIDKOFA_1	69176	70045	rfbA	0.0	Capsule	Immune modulation	99.19	100.00	WP_011681286
LPIDKOFA_1	68583	69176	STR_RS05880	0.0	Capsule	Immune modulation	99.16	100.00	WP_011226149
LPIDKOFA_1	1807198	1807890	STR_RS05255	0.0	Capsule	Immune modulation	99.13	100.00	WP_011227247
LPIDKOFA_1	298344	299153	STU_RS16245	0.0	Capsule	Immune modulation	99.01	100.00	WP_002948020
LPIDKOFA_1	68583	69176	STER_RS06030	0.0	Capsule	Immune modulation	98.99	100.00	WP_011226149
LPIDKOFA_1	68583	69176	STU_RS15260	0.0	Capsule	Immune modulation	98.99	100.00	WP_011226149
LPIDKOFA_1	1806458	1807189	STER_RS05315	0.0	Capsule	Immune modulation	98.91	100.00	WP_011681176
LPIDKOFA_1	300090	301238	STU_RS16255	0.0	Capsule	Immune modulation	98.78	100.00	WP_041828290
LPIDKOFA_1	297139	298344	STU_RS16240	0.0	Capsule	Immune modulation	98.76	100.00	WP_011226326
LPIDKOFA_1	294271	296055	STU_RS16230	0.0	Capsule	Immune modulation	98.66	100.00	WP_011226325
LPIDKOFA_1	1806458	1807189	STU_RS14645	0.0	Capsule	Immune modulation	98.63	100.00	WP_011226048
LPIDKOFA_1	103984	104745	srtA	0.0	Sortase A	Exoenzyme	98.56	100.00	-
LPIDKOFA_1	1806458	1807189	STR_RS05260	0.0	Capsule	Immune modulation	98.50	100.00	WP_011227248
LPIDKOFA_1	11124	11912	cshA	0.0	Cell surface hydrophobicity proteins	Adherence	98.36	99.75	-
LPIDKOFA_1	881189	882028	cbpD	0.0	Autolysin	Exoenzyme	98.33	100.00	WP_011226733
LPIDKOFA_1	1804997	1806457	STER_RS05320	0.0	Capsule	Immune modulation	97.74	100.00	WP_011681177
LPIDKOFA_1	306280	307131	rfbD	0.0	Capsule	Immune modulation	97.30	100.00	WP_014621820
LPIDKOFA_1	1810311	1811307	STU_RS14625*	0.0	Capsule	Immune modulation	96.79	100.00	-
LPIDKOFA_1	1804997	1806457	STU_RS14650	0.0	Capsule	Immune modulation	96.44	100.21	WP_011226049
LPIDKOFA_1	1816263	1817707	STR_RS05265	0.0	Capsule	Immune modulation	96.43	99.93	WP_041827043
LPIDKOFA_1	1006828	1011723	SAG_RS09105	0.0	Agglutinin receptor	Adherence	95.81	99.96	WP_000167699
LPIDKOFA_1	1006780	1011723	SSU98_0978	0.0	Agglutinin receptor	Adherence	95.65	99.78	YP_001200536
LPIDKOFA_1	1006780	1011723	SSU05_0965	0.0	Agglutinin receptor	Adherence	95.63	99.78	YP_001198331
LPIDKOFA_1	1808715	1810078	STER_RS05300	0.0	Capsule	Immune modulation	95.45	99.71	WP_011681173
LPIDKOFA_1	296052	297119	STU_RS16235	0.0	Capsule	Immune modulation	95.27	101.14	WP_002948022
LPIDKOFA_1	1808715	1810082	STU_RS14630	0.0	Capsule	Immune modulation	94.15	100.00	WP_011226045
LPIDKOFA_1	1807900	1808658	STER_RS05305	0.0	Capsule	Immune modulation	93.81	100.94	WP_011681174
LPIDKOFA_1	1807900	1808658	STU_RS14635	0.0	Capsule	Immune modulation	93.41	100.94	WP_011226046
LPIDKOFA_1	1807900	1808653	STR_RS05250	0.0	Capsule	Immune modulation	93.10	99.07	WP_011227246
LPIDKOFA_1	1807198	1807890	STER_RS05310	0.0	Capsule	Immune modulation	89.61	100.00	WP_011681175
LPIDKOFA_1	303903	305177	STU_RS16265	0.0	Capsule	Immune modulation	89.42	99.92	WP_011226331
LPIDKOFA_1	1519543	1520846	eno	0.0	Streptococcal enolase	Exoenzyme	87.94	99.54	WP_000022832
LPIDKOFA_1	603016	604026	plr/gapA	0.0	Streptococcal plasmin receptor/GAPDH	Adherence	86.86	99.90	WP_002986042
LPIDKOFA_1	987101	988384	tig/ropA	0.0	Trigger factor	Stress survival	80.73	99.77	WP_000107753
LPIDKOFA_1	67107	68153	rfbB	0.0	Capsule	Immune modulation	80.61	100.00	WP_009659423
LPIDKOFA_1	1811316	1811765	STU_RS14620	6.73e-179	Capsule	Immune modulation	92.22	100.00	WP_011226042
LPIDKOFA_1	1821095	1821678	SPD_RS01775	5.46e-145	Capsule	Immune modulation	82.91	96.20	WP_001819836
LPIDKOFA_1	1811765	1812072	STU_RS14615	1.17e-146	Capsule	Immune modulation	97.73	63.37	WP_011226041

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
LPIDKOFA_1	1006807	1011720	B9H01_RS04765	0.0	glucan-binding protein	97.13	99.70	AUS90958
LPIDKOFA_1	1640134	1641207	MntE	0.0	manganese homeostasis	94.97	99.72	ABF32167
LPIDKOFA_1	107432	108415	ldh(Sp_1220)	0.0	L-lactate dehydrogenase	94.82	100.00	AAK75326
LPIDKOFA_1	465717	468020	pfl2(Sp_0459)	0.0	formate acetyltransferase	92.32	99.22	AAK74619
LPIDKOFA_1	188883	190364	SPD_0310	0.0	UPF0371 protein SPD_0310	92.31	100.00	ABJ54480
LPIDKOFA_1	1437529	1438497	spr0084	0.0	pathogenitcity related	92.26	98.48	AAK98888
LPIDKOFA_1	1660662	1662908	metE	0.0	methionine biosynthesis enzymes	91.72	100.00	AAK74738
LPIDKOFA_1	864560	865531	prsA2	0.0	ribose-phosphate pyrophosphokinase	90.12	100.00	ABF36968
LPIDKOFA_1	350504	349353	potA	0.0	ABC transporter ATP-binding protein-spermidine/putrescine transport	89.32	99.74	AAL00050
LPIDKOFA_1	320488	318500	uvrB	0.0	excinuclease ABC, B subunit	89.14	100.00	AE014259_2
LPIDKOFA_1	91244	89514	ptsI	0.0	phosphoenolpyruvate-protein phosphotransferase	87.87	100.00	AAK34199
LPIDKOFA_1	826347	824869	IMPDH	0.0	inosine-5'-monophosphate dehydrogenase	87.63	100.00	ADE32434
LPIDKOFA_1	1519543	1520844	Eno	0.0	enolase	85.98	99.77	ABP90468
LPIDKOFA_1	811150	809258	gidA	0.0	tRNA uridine 5-carboxymethylaminomethyl modification enzyme	85.58	98.90	ABP91129
LPIDKOFA_1	1665833	1664124	PGM	0.0	phosphoglucomutase	84.06	99.65	ACH87041
LPIDKOFA_1	648818	649828	pdh	0.0	pyruvate dehydrogenase	83.09	99.70	ABP91006
LPIDKOFA_1	1892188	1893549	mnmE	0.0	central tRNA-modifying GTPase	81.80	99.56	ABP90420
LPIDKOFA_1	699117	697225	PepO	0.0	endopeptidase	80.51	100.00	ABF32980
LPIDKOFA_1	1505111	1506001	bglB	1.43e-178	putative phospho--glucosidase	88.89	99.66	AAK33487
LPIDKOFA_1	1969373	1970311	SP_0676	2.53e-167	transcription facot	81.15	97.20	AAK74821
LPIDKOFA_1	1663100	1663957	metF	5.78e-165	methionine biosynthesis enzymes	86.36	99.31	AAK74739
LPIDKOFA_1	1768249	1768953	covR	4.70e-131	responder protein	85.53	100.00	AAK71319
LPIDKOFA_1	1669787	1670455	CiaR	6.30e-124	two-component response regulator	87.44	99.55	AAK74935
LPIDKOFA_1	156729	156058	rr01	3.04e-123	response regulator	83.48	99.56	CAB54566
LPIDKOFA_1	1669787	1670458	ciaR	6.77e-122	two component system response regulator	85.27	99.12	AIK75708
LPIDKOFA_1	1768249	1768953	walR	1.98e-121	DNA-binding response regulator	82.13	100.00	ANC99504
LPIDKOFA_1	1208347	1209033	CovR	3.32e-118	serves to repress GAS virulence factor-encoding genes	81.22	100.00	ACE75886
LPIDKOFA_1	913665	914060	SpxA2	3.98e-74	transcriptional regulator	90.91	100.00	ERL21461
LPIDKOFA_1	988542	989015	RopE (M5005_Spy_1611)	4.08e-69	probable DNA-directed RNA polymerase subunit delta	81.01	82.72	AAK34603
LPIDKOFA_1	465741	468014	PFL (B9H01_RS01125)	0.0	formate C-acetyltransferase	83.03	97.06	MYN69560
LPIDKOFA_1	684680	683661	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
LPIDKOFA_1	0.0	1.0	0.0
LPIDKOFA_2	1.0	0.0	1.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Prophage

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
LPIDKOFA_1	208561	214295	True	Unknown	VOG0944, VOG0944, VOG5532, VOG1837, VOG6628, VOG0249, VOG8916, VOG8916, VOG0944