safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

Probiotic potential risk score

ARGs	VFs	PGs	PPRS
0	28	29	40.31

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.
NMGINCHK_1	1075847	1076716	rfbA	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681286
NMGINCHK_1	1075254	1075847	STER_RS06030	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226149
NMGINCHK_1	1231976	1233721	STER_RS07045	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681434
NMGINCHK_1	1233723	1235423	STER_RS07050	0.0	Capsule	Immune modulation	100.00	100.00	WP_041827753
NMGINCHK_1	1235441	1236643	STER_RS07055	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681436
NMGINCHK_1	1236643	1237449	STER_RS07060	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681437
NMGINCHK_1	1237449	1238390	STER_RS07065	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681438
NMGINCHK_1	1238387	1239535	STER_RS07070	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681439
NMGINCHK_1	1239654	1240430	STER_RS07075	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681440
NMGINCHK_1	1240776	1241492	STER_RS07085	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681442
NMGINCHK_1	1241493	1242461	STER_RS07090	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681443
NMGINCHK_1	1243453	1244712	STER_RS07100	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681445
NMGINCHK_1	1242479	1243456	STER_RS07095	0.0	Capsule	Immune modulation	99.90	100.00	WP_011681444
NMGINCHK_1	1075254	1075847	STR_RS05880	0.0	Capsule	Immune modulation	99.83	100.00	WP_011226149
NMGINCHK_1	1233723	1235423	STR_RS06890	0.0	Capsule	Immune modulation	99.71	100.00	WP_041827077
NMGINCHK_1	1075254	1075847	STU_RS15260	0.0	Capsule	Immune modulation	99.66	100.00	WP_011226149
NMGINCHK_1	845947	847605	fbp54	0.0	FBPs	Adherence	99.58	100.00	WP_011227179
NMGINCHK_1	43363	44202	cbpD	0.0	Autolysin	Exoenzyme	99.52	100.00	WP_011226733
NMGINCHK_1	1236643	1237449	STR_RS06900	0.0	Capsule	Immune modulation	99.50	100.00	WP_011227429
NMGINCHK_1	1237449	1238390	STR_RS06905	0.0	Capsule	Immune modulation	99.47	100.00	WP_011227430
NMGINCHK_1	1235441	1236643	STR_RS06895	0.0	Capsule	Immune modulation	99.42	100.00	WP_011227428
NMGINCHK_1	1238387	1239535	STR_RS06910	0.0	Capsule	Immune modulation	99.22	100.00	WP_011227431
NMGINCHK_1	953438	954169	STER_RS05315	0.0	Capsule	Immune modulation	98.50	100.00	WP_011681176
NMGINCHK_1	953438	954169	STU_RS14645	0.0	Capsule	Immune modulation	98.50	100.00	WP_011226048
NMGINCHK_1	953438	954169	STR_RS05260	0.0	Capsule	Immune modulation	98.36	100.00	WP_011227248
NMGINCHK_1	1231976	1233721	STR_RS06885	0.0	Capsule	Immune modulation	98.22	100.00	WP_011227426
NMGINCHK_1	954170	955630	STER_RS05320	0.0	Capsule	Immune modulation	97.81	100.00	WP_011681177
NMGINCHK_1	1110618	1111379	srtA	0.0	Sortase A	Exoenzyme	97.77	100.00	-
NMGINCHK_1	954170	955630	STU_RS14650	0.0	Capsule	Immune modulation	97.06	100.21	WP_011226049
NMGINCHK_1	951987	952727	STU_RS14635	0.0	Capsule	Immune modulation	97.03	100.00	WP_011226046
NMGINCHK_1	951987	952727	STER_RS05305	0.0	Capsule	Immune modulation	96.90	100.00	WP_011681174
NMGINCHK_1	1244831	1245682	rfbD	0.0	Capsule	Immune modulation	96.83	100.00	WP_014621820
NMGINCHK_1	951992	952727	STR_RS05250	0.0	Capsule	Immune modulation	96.47	98.13	WP_011227246
NMGINCHK_1	954170	955630	STR_RS05265	0.0	Capsule	Immune modulation	96.23	100.21	WP_041827043
NMGINCHK_1	950566	951931	STER_RS05300	0.0	Capsule	Immune modulation	95.39	99.85	WP_011681173
NMGINCHK_1	952737	953429	STR_RS05255	0.0	Capsule	Immune modulation	95.25	99.86	WP_011227247
NMGINCHK_1	952737	953429	STU_RS14640	0.0	Capsule	Immune modulation	95.25	99.86	WP_011226047
NMGINCHK_1	950564	951931	STU_RS14630	0.0	Capsule	Immune modulation	94.37	100.00	WP_011226045
NMGINCHK_1	1020308	1021086	cshA	0.0	Cell surface hydrophobicity proteins	Adherence	93.19	99.37	-
NMGINCHK_1	952737	953429	STER_RS05310	0.0	Capsule	Immune modulation	89.61	100.00	WP_011681175
NMGINCHK_1	608362	609665	eno	0.0	Streptococcal enolase	Exoenzyme	88.10	99.46	WP_000022832
NMGINCHK_1	1540602	1541612	plr/gapA	0.0	Streptococcal plasmin receptor/GAPDH	Adherence	86.54	99.41	WP_002986042
NMGINCHK_1	1236643	1237449	SGO_RS05020	0.0	Capsule	Immune modulation	82.90	100.00	WP_012000440
NMGINCHK_1	143673	144956	tig/ropA	0.0	Trigger factor	Stress survival	80.73	99.77	WP_000107753
NMGINCHK_1	1073779	1074825	rfbB	0.0	Capsule	Immune modulation	80.61	100.00	WP_009659423
NMGINCHK_1	941033	941616	SPD_RS01775	1.02e-146	Capsule	Immune modulation	83.11	96.04	WP_001819836
NMGINCHK_1	1235906	1236643	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
NMGINCHK_1	712769	713842	MntE	0.0	manganese homeostasis	94.41	99.72	ABF32167
NMGINCHK_1	1114066	1115049	ldh(Sp_1220)	0.0	L-lactate dehydrogenase	94.21	100.00	AAK75326
NMGINCHK_1	525474	526442	spr0084	0.0	pathogenitcity related	93.19	98.48	AAK98888
NMGINCHK_1	1417161	1419464	pfl2(Sp_0459)	0.0	formate acetyltransferase	92.97	99.22	AAK74619
NMGINCHK_1	1194157	1195638	SPD_0310	0.0	UPF0371 protein SPD_0310	92.71	100.00	ABJ54480
NMGINCHK_1	733054	735300	metE	0.0	methionine biosynthesis enzymes	91.99	100.00	AAK74738
NMGINCHK_1	78536	79534	recA	0.0	DNA recombination and repair	91.29	85.82	AAL00560
NMGINCHK_1	26840	27811	prsA2	0.0	ribose-phosphate pyrophosphokinase	90.12	100.00	ABF36968
NMGINCHK_1	1294608	1293457	potA	0.0	ABC transporter ATP-binding protein-spermidine/putrescine transport	89.32	99.74	AAL00050
NMGINCHK_1	1258719	1256731	uvrB	0.0	excinuclease ABC, B subunit	88.84	100.00	AE014259_2
NMGINCHK_1	1097867	1096137	ptsI	0.0	phosphoenolpyruvate-protein phosphotransferase	88.04	100.00	AAK34199
NMGINCHK_1	1725877	1724399	IMPDH	0.0	inosine-5'-monophosphate dehydrogenase	87.63	100.00	ADE32434
NMGINCHK_1	608362	609663	Eno	0.0	enolase	86.21	99.77	ABP90468
NMGINCHK_1	1711139	1709247	gidA	0.0	tRNA uridine 5-carboxymethylaminomethyl modification enzyme	85.74	98.90	ABP91129
NMGINCHK_1	738225	736516	PGM	0.0	phosphoglucomutase	84.06	99.65	ACH87041
NMGINCHK_1	1578509	1579519	pdh	0.0	pyruvate dehydrogenase	82.79	99.70	ABP91006
NMGINCHK_1	872582	871221	mnmE	0.0	central tRNA-modifying GTPase	82.24	99.56	ABP90420
NMGINCHK_1	1628827	1626935	PepO	0.0	endopeptidase	80.03	100.00	ABF32980
NMGINCHK_1	593927	594817	bglB	1.25e-178	putative phospho--glucosidase	88.89	99.66	AAK33487
NMGINCHK_1	792783	791848	SP_0676	6.92e-168	transcription facot	81.73	96.89	AAK74821
NMGINCHK_1	735492	736349	metF	1.43e-164	methionine biosynthesis enzymes	86.36	99.31	AAK74739
NMGINCHK_1	992676	991972	covR	4.10e-131	responder protein	85.53	100.00	AAK71319
NMGINCHK_1	1166053	1165382	rr01	2.82e-124	response regulator	83.93	99.56	CAB54566
NMGINCHK_1	992676	991972	walR	1.73e-121	DNA-binding response regulator	82.13	100.00	ANC99504
NMGINCHK_1	742179	742847	CiaR	4.23e-119	two-component response regulator	84.75	99.55	AAK74935
NMGINCHK_1	310078	310764	CovR	9.43e-118	serves to repress GAS virulence factor-encoding genes	80.79	100.00	ACE75886
NMGINCHK_1	742179	742850	ciaR	8.35e-117	two component system response regulator	82.59	99.12	AIK75708
NMGINCHK_1	79810	80184	SpxA2	1.08e-69	transcriptional regulator	91.20	94.70	ERL21461
NMGINCHK_1	884047	884448	SpxA1	3.53e-66	transcriptional regulator	80.60	100.00	ERL19273
NMGINCHK_1	145114	145614	RopE (M5005_Spy_1611)	4.61e-75	probable DNA-directed RNA polymerase subunit delta	81.44	87.43	AAK34603
NMGINCHK_1	1417161	1419458	PFL (B9H01_RS01125)	0.0	formate C-acetyltransferase	82.94	98.08	MYN69560
NMGINCHK_1	1614373	1613354	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.
NMGINCHK_2	96	1046	rep37	954 / 948	87.21	AF177168

PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)

PlasmidHunter

Query ID	Prediction	Chromosome	Plasmid
NMGINCHK_1	0.0	1.0	0.0
NMGINCHK_2	1.0	0.0	1.0
NMGINCHK_3	1.0	0.0	1.0
NMGINCHK_4	1.0	0.0	1.0
NMGINCHK_5	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