safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

Probiotic potential risk score

ARGs	VFs	PGs	PPRS
0	35	33	48.10

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.
PNNIAJOG_3	52709	53852	cshA	Cell surface hydrophobicity proteins	Adherence	100.00	100.00	-
PNNIAJOG_55	60320	61189	rfbA	Capsule	Immune modulation	100.00	100.00	WP_011681286
PNNIAJOG_46	231	1646	STER_RS05250	Capsule	Immune modulation	100.00	100.00	WP_011681165
PNNIAJOG_51	705	1685	STER_RS05260	Capsule	Immune modulation	100.00	100.00	WP_011681166
PNNIAJOG_51	1678	2862	STER_RS05265	Capsule	Immune modulation	100.00	100.00	WP_011681167
PNNIAJOG_51	2879	3931	STER_RS05270	Capsule	Immune modulation	100.00	100.00	WP_011681168
PNNIAJOG_51	3946	4854	STER_RS05275	Capsule	Immune modulation	100.00	100.00	WP_011681169
PNNIAJOG_51	4875	5936	STER_RS05280	Capsule	Immune modulation	100.00	100.00	WP_202964935
PNNIAJOG_51	5973	6464	STER_RS05285	Capsule	Immune modulation	100.00	100.00	WP_011681171
PNNIAJOG_51	6476	6952	STER_RS05290	Capsule	Immune modulation	100.00	100.00	WP_011681172
PNNIAJOG_51	9132	9872	STER_RS05305	Capsule	Immune modulation	100.00	100.00	WP_011681174
PNNIAJOG_51	9882	10574	STER_RS05310	Capsule	Immune modulation	100.00	100.00	WP_011681175
PNNIAJOG_51	10583	11314	STER_RS05315	Capsule	Immune modulation	100.00	100.00	WP_011681176
PNNIAJOG_51	11315	12775	STER_RS05320	Capsule	Immune modulation	100.00	100.00	WP_011681177
PNNIAJOG_55	61189	61782	STER_RS06030	Capsule	Immune modulation	100.00	100.00	WP_011226149
PNNIAJOG_2	44248	45993	STER_RS07045	Capsule	Immune modulation	100.00	100.00	WP_011681434
PNNIAJOG_2	42546	44246	STER_RS07050	Capsule	Immune modulation	100.00	100.00	WP_041827753
PNNIAJOG_2	41326	42528	STER_RS07055	Capsule	Immune modulation	100.00	100.00	WP_011681436
PNNIAJOG_2	40520	41326	STER_RS07060	Capsule	Immune modulation	100.00	100.00	WP_011681437
PNNIAJOG_2	39579	40520	STER_RS07065	Capsule	Immune modulation	100.00	100.00	WP_011681438
PNNIAJOG_2	38434	39582	STER_RS07070	Capsule	Immune modulation	100.00	100.00	WP_011681439
PNNIAJOG_2	37539	38315	STER_RS07075	Capsule	Immune modulation	100.00	100.00	WP_011681440
PNNIAJOG_2	36477	37193	STER_RS07085	Capsule	Immune modulation	100.00	100.00	WP_011681442
PNNIAJOG_2	35508	36476	STER_RS07090	Capsule	Immune modulation	100.00	100.00	WP_011681443
PNNIAJOG_2	34513	35490	STER_RS07095	Capsule	Immune modulation	100.00	100.00	WP_011681444
PNNIAJOG_2	33257	34516	STER_RS07100	Capsule	Immune modulation	100.00	100.00	WP_011681445
PNNIAJOG_51	7708	9075	STER_RS05300	Capsule	Immune modulation	99.85	100.00	WP_011681173
PNNIAJOG_55	61189	61782	STR_RS05880	Capsule	Immune modulation	99.83	100.00	WP_011226149
PNNIAJOG_2	42546	44246	STR_RS06890	Capsule	Immune modulation	99.71	100.00	WP_041827077
PNNIAJOG_55	61189	61782	STU_RS15260	Capsule	Immune modulation	99.66	100.00	WP_011226149
PNNIAJOG_19	2393	4051	fbp54	FBPs	Adherence	99.64	100.00	WP_011227179
PNNIAJOG_10	20808	21647	cbpD	Autolysin	Exoenzyme	99.52	100.00	WP_011226733
PNNIAJOG_2	40520	41326	STR_RS06900	Capsule	Immune modulation	99.50	100.00	WP_011227429
PNNIAJOG_2	39579	40520	STR_RS06905	Capsule	Immune modulation	99.47	100.00	WP_011227430
PNNIAJOG_2	41326	42528	STR_RS06895	Capsule	Immune modulation	99.42	100.00	WP_011227428
PNNIAJOG_2	38434	39582	STR_RS06910	Capsule	Immune modulation	99.22	100.00	WP_011227431
PNNIAJOG_51	9137	9872	STR_RS05250	Capsule	Immune modulation	98.50	98.13	WP_011227246
PNNIAJOG_51	9132	9872	STU_RS14635	Capsule	Immune modulation	98.25	100.00	WP_011226046
PNNIAJOG_51	10583	11314	STR_RS05260	Capsule	Immune modulation	98.22	100.00	WP_011227248
PNNIAJOG_2	44248	45993	STR_RS06885	Capsule	Immune modulation	98.22	100.00	WP_011227426
PNNIAJOG_51	10583	11314	STU_RS14645	Capsule	Immune modulation	98.09	100.00	WP_011226048
PNNIAJOG_55	25659	26420	srtA	Sortase A	Exoenzyme	97.64	100.00	-
PNNIAJOG_51	11315	12775	STU_RS14650	Capsule	Immune modulation	97.47	100.21	WP_011226049
PNNIAJOG_51	11315	12775	STR_RS05265	Capsule	Immune modulation	96.92	100.21	WP_041827043
PNNIAJOG_2	32287	33138	rfbD	Capsule	Immune modulation	96.83	100.00	WP_014621820
PNNIAJOG_51	7712	9075	STU_RS14630	Capsule	Immune modulation	94.94	99.71	WP_011226045
PNNIAJOG_51	9882	10574	STU_RS14640	Capsule	Immune modulation	89.90	100.00	WP_011226047
PNNIAJOG_51	9882	10574	STR_RS05255	Capsule	Immune modulation	89.61	100.00	WP_011227247
PNNIAJOG_22	46460	47763	eno	Streptococcal enolase	Exoenzyme	88.10	99.46	WP_000022832
PNNIAJOG_24	14294	15304	plr/gapA	Streptococcal plasmin receptor/GAPDH	Adherence	86.54	99.41	WP_002986042
PNNIAJOG_2	40520	41326	SGO_RS05020	Capsule	Immune modulation	82.90	100.00	WP_012000440
PNNIAJOG_11	2215	3498	tig/ropA	Trigger factor	Stress survival	80.73	99.77	WP_000107753
PNNIAJOG_55	62211	63257	rfbB	Capsule	Immune modulation	80.61	100.00	WP_009659423
PNNIAJOG_2	41326	42063	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
PNNIAJOG_55	22972	21989	ldh(Sp_1220)	0.0	L-lactate dehydrogenase	94.82	100.00	AAK75326
PNNIAJOG_9	27677	28750	MntE	0.0	manganese homeostasis	94.41	99.72	ABF32167
PNNIAJOG_33	63435	61132	pfl2(Sp_0459)	0.0	formate acetyltransferase	92.97	99.22	AAK74619
PNNIAJOG_3	37294	36326	spr0084	0.0	pathogenitcity related	92.88	98.48	AAK98888
PNNIAJOG_61	14002	12521	SPD_0310	0.0	UPF0371 protein SPD_0310	92.51	100.00	ABJ54480
PNNIAJOG_41	11490	9244	metE	0.0	methionine biosynthesis enzymes	91.99	100.00	AAK74738
PNNIAJOG_10	2016	1018	recA	0.0	DNA recombination and repair	91.29	85.82	AAL00560
PNNIAJOG_10	38131	37160	prsA2	0.0	ribose-phosphate pyrophosphokinase	90.12	100.00	ABF36968
PNNIAJOG_67	44935	46086	potA	0.0	ABC transporter ATP-binding protein-spermidine/putrescine transport	89.32	99.74	AAL00050
PNNIAJOG_2	19248	21236	uvrB	0.0	excinuclease ABC, B subunit	89.14	100.00	AE014259_2
PNNIAJOG_55	39171	40901	ptsI	0.0	phosphoenolpyruvate-protein phosphotransferase	87.87	100.00	AAK34199
PNNIAJOG_68	47264	45786	IMPDH	0.0	inosine-5'-monophosphate dehydrogenase	87.63	100.00	ADE32434
PNNIAJOG_22	46460	47761	Eno	0.0	enolase	86.21	99.77	ABP90468
PNNIAJOG_68	32529	30637	gidA	0.0	tRNA uridine 5-carboxymethylaminomethyl modification enzyme	85.74	98.90	ABP91129
PNNIAJOG_41	6319	8028	PGM	0.0	phosphoglucomutase	84.06	99.65	ACH87041
PNNIAJOG_4	40149	39139	pdh	0.0	pyruvate dehydrogenase	83.09	99.70	ABP91006
PNNIAJOG_41	44774	43413	mnmE	0.0	central tRNA-modifying GTPase	82.24	99.56	ABP90420
PNNIAJOG_17	16716	18608	PepO	0.0	endopeptidase	80.19	100.00	ABF32980
PNNIAJOG_22	32024	32914	bglB	3.48e-179	putative phospho--glucosidase	88.55	99.66	AAK33487
PNNIAJOG_5	7381	6443	SP_0676	2.05e-169	transcription facot	81.47	97.20	AAK74821
PNNIAJOG_41	9052	8195	metF	9.04e-166	methionine biosynthesis enzymes	86.36	99.31	AAK74739
PNNIAJOG_51	49598	48894	covR	2.07e-132	responder protein	85.53	100.00	AAK71319
PNNIAJOG_61	38609	39280	rr01	1.08e-125	response regulator	83.93	99.56	CAB54566
PNNIAJOG_51	49598	48894	walR	8.72e-123	DNA-binding response regulator	82.13	100.00	ANC99504
PNNIAJOG_15	16745	17431	CovR	1.84e-119	serves to repress GAS virulence factor-encoding genes	80.79	100.00	ACE75886
PNNIAJOG_41	2364	1696	CiaR	1.20e-118	two-component response regulator	84.31	99.55	AAK74935
PNNIAJOG_41	2364	1693	ciaR	1.18e-116	two component system response regulator	82.14	99.12	AIK75708
PNNIAJOG_10	742	368	SpxA2	2.56e-71	transcriptional regulator	91.20	94.70	ERL21461
PNNIAJOG_41	56137	56538	SpxA1	2.23e-67	transcriptional regulator	80.60	100.00	ERL19273
PNNIAJOG_13	13496	13783	spr0479	2.98e-49	essential gene	86.46	98.97	AAK99283
PNNIAJOG_12	33675	33929	spr1327	4.16e-45	essential gene	94.12	100.00	AAL00131
PNNIAJOG_21	1215	952	spr0175	6.41e-43	pathogenitcity related	84.09	100.00	AAK98979
PNNIAJOG_21	388	122	spr0177	1.40e-34	essential gene	84.27	88.12	AAK98981
PNNIAJOG_11	3656	4156	RopE (M5005_Spy_1611)	3.46e-76	probable DNA-directed RNA polymerase subunit delta	81.44	87.43	AAK34603
PNNIAJOG_33	63435	61138	PFL (B9H01_RS01125)	0.0	formate C-acetyltransferase	82.94	98.08	MYN69560
PNNIAJOG_4	4288	5307	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
PNNIAJOG_1	0.0	1.0	0.0
PNNIAJOG_2	0.0	1.0	0.0
PNNIAJOG_3	0.0	1.0	0.0
PNNIAJOG_4	0.0	1.0	0.0
PNNIAJOG_5	0.0	1.0	0.0
PNNIAJOG_6	0.0	1.0	0.0
PNNIAJOG_7	0.0	1.0	0.0
PNNIAJOG_8	0.0	1.0	0.0
PNNIAJOG_9	0.0	1.0	0.0
PNNIAJOG_10	0.0	1.0	0.0
PNNIAJOG_11	0.0	1.0	0.0
PNNIAJOG_12	0.0	1.0	0.0
PNNIAJOG_13	0.0	1.0	0.0
PNNIAJOG_14	0.0	1.0	0.0
PNNIAJOG_15	0.0	1.0	0.0
PNNIAJOG_16	0.0	1.0	0.0
PNNIAJOG_17	0.0	1.0	0.0
PNNIAJOG_18	0.0	1.0	0.0
PNNIAJOG_19	0.0	1.0	0.0
PNNIAJOG_20	0.0	1.0	0.0
PNNIAJOG_21	0.0	1.0	0.0
PNNIAJOG_22	0.0	1.0	0.0
PNNIAJOG_23	0.0	1.0	0.0
PNNIAJOG_24	0.0	1.0	0.0
PNNIAJOG_25	0.0	1.0	0.0
PNNIAJOG_26	0.0	1.0	0.0
PNNIAJOG_27	0.0	1.0	0.0
PNNIAJOG_28	0.0	1.0	0.0
PNNIAJOG_29	0.0	1.0	0.0
PNNIAJOG_30	0.0	1.0	0.0
PNNIAJOG_31	0.0	1.0	0.0
PNNIAJOG_32	0.0	1.0	0.0
PNNIAJOG_33	0.0	1.0	0.0
PNNIAJOG_34	0.0	1.0	0.0
PNNIAJOG_35	0.0	1.0	0.0
PNNIAJOG_36	1.0	0.0	1.0
PNNIAJOG_37	1.0	0.0	1.0
PNNIAJOG_38	0.0	1.0	0.0
PNNIAJOG_39	0.0	1.0	0.0
PNNIAJOG_40	0.0	1.0	0.0
PNNIAJOG_41	0.0	1.0	0.0
PNNIAJOG_42	1.0	0.0	1.0
PNNIAJOG_43	1.0	0.0	1.0
PNNIAJOG_44	0.0	1.0	0.0
PNNIAJOG_45	0.0	1.0	0.0
PNNIAJOG_46	1.0	0.0	1.0
PNNIAJOG_47	0.0	1.0	0.0
PNNIAJOG_51	0.0	1.0	0.0
PNNIAJOG_55	0.0	1.0	0.0
PNNIAJOG_61	0.0	1.0	0.0
PNNIAJOG_67	0.0	1.0	0.0
PNNIAJOG_68	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