safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

Probiotic potential risk score

ARGs	VFs	PGs	PPRS
0	26	33	42.01

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.
ACPPJIEM_17	11292	12161	rfbA	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681286
ACPPJIEM_17	10699	11292	STER_RS06030	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226149
ACPPJIEM_17	10699	11292	STR_RS05880	0.0	Capsule	Immune modulation	99.83	100.00	WP_011226149
ACPPJIEM_14	4899	5855	STU_RS16250	0.0	Capsule	Immune modulation	99.79	100.00	WP_011226328
ACPPJIEM_14	5852	7000	STU_RS16255	0.0	Capsule	Immune modulation	99.74	100.00	WP_041828290
ACPPJIEM_17	10699	11292	STU_RS15260	0.0	Capsule	Immune modulation	99.66	100.00	WP_011226149
ACPPJIEM_14	4106	4915	STU_RS16245	0.0	Capsule	Immune modulation	99.63	100.00	WP_002948020
ACPPJIEM_14	2901	4106	STU_RS16240	0.0	Capsule	Immune modulation	99.58	100.00	WP_011226326
ACPPJIEM_27	13299	14957	fbp54	0.0	FBPs	Adherence	99.52	100.00	WP_011227179
ACPPJIEM_14	45	1829	STU_RS16230	0.0	Capsule	Immune modulation	99.50	100.00	WP_011226325
ACPPJIEM_14	1826	2881	STU_RS16235	0.0	Capsule	Immune modulation	99.43	100.00	WP_002948022
ACPPJIEM_18	13261	13953	STU_RS14640	0.0	Capsule	Immune modulation	99.42	100.00	WP_011226047
ACPPJIEM_47	1471	2613	cshA	0.0	Cell surface hydrophobicity proteins	Adherence	99.30	99.83	-
ACPPJIEM_14	9659	10933	STU_RS16265	0.0	Capsule	Immune modulation	98.98	100.00	WP_011226331
ACPPJIEM_18	13261	13953	STR_RS05255	0.0	Capsule	Immune modulation	98.85	100.00	WP_011227247
ACPPJIEM_14	8697	9659	STU_RS16260	0.0	Capsule	Immune modulation	98.75	95.25	WP_011226330
ACPPJIEM_18	13962	14693	STER_RS05315	0.0	Capsule	Immune modulation	98.63	100.00	WP_011681176
ACPPJIEM_10	24966	25727	srtA	0.0	Sortase A	Exoenzyme	98.56	100.00	-
ACPPJIEM_18	13962	14693	STU_RS14645	0.0	Capsule	Immune modulation	98.36	100.00	WP_011226048
ACPPJIEM_18	2512	3927	STER_RS05250	0.0	Capsule	Immune modulation	98.23	100.00	WP_011681165
ACPPJIEM_18	13962	14693	STR_RS05260	0.0	Capsule	Immune modulation	98.22	100.00	WP_011227248
ACPPJIEM_18	14694	16154	STER_RS05320	0.0	Capsule	Immune modulation	97.95	100.00	WP_011681177
ACPPJIEM_14	12034	12885	rfbD	0.0	Capsule	Immune modulation	97.65	100.00	WP_014621820
ACPPJIEM_34	19040	19999	cbpD	0.0	Autolysin	Exoenzyme	97.32	99.90	WP_082302295
ACPPJIEM_18	14694	16154	STU_RS14650	0.0	Capsule	Immune modulation	97.19	100.21	WP_011226049
ACPPJIEM_18	14694	16154	STR_RS05265	0.0	Capsule	Immune modulation	96.37	100.21	WP_041827043
ACPPJIEM_18	11069	12436	STU_RS14630	0.0	Capsule	Immune modulation	95.91	100.00	WP_011226045
ACPPJIEM_18	11071	12436	STER_RS05300	0.0	Capsule	Immune modulation	93.85	99.85	WP_011681173
ACPPJIEM_18	12493	13251	STER_RS05305	0.0	Capsule	Immune modulation	93.54	100.94	WP_011681174
ACPPJIEM_18	12493	13251	STU_RS14635	0.0	Capsule	Immune modulation	93.15	100.94	WP_011226046
ACPPJIEM_18	12498	13251	STR_RS05250	0.0	Capsule	Immune modulation	92.84	99.07	WP_011227246
ACPPJIEM_18	13261	13953	STER_RS05310	0.0	Capsule	Immune modulation	89.32	100.00	WP_011681175
ACPPJIEM_3	35660	36963	eno	0.0	Streptococcal enolase	Exoenzyme	88.02	99.54	WP_000022832
ACPPJIEM_28	14245	15255	plr/gapA	0.0	Streptococcal plasmin receptor/GAPDH	Adherence	87.46	99.80	WP_002986042
ACPPJIEM_67	2325	3608	tig/ropA	0.0	Trigger factor	Stress survival	80.73	99.77	WP_000107753
ACPPJIEM_17	9224	10270	rfbB	0.0	Capsule	Immune modulation	80.61	100.00	WP_009659423
ACPPJIEM_18	109	692	SPD_RS01775	1.65e-153	Capsule	Immune modulation	83.59	96.20	WP_001819836

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
ACPPJIEM_9	28013	29086	MntE	0.0	manganese homeostasis	94.97	99.72	ABF32167
ACPPJIEM_10	22279	21296	ldh(Sp_1220)	0.0	L-lactate dehydrogenase	94.82	100.00	AAK75326
ACPPJIEM_22	5311	7614	pfl2(Sp_0459)	0.0	formate acetyltransferase	92.97	99.22	AAK74619
ACPPJIEM_84	12332	13300	spr0084	0.0	pathogenitcity related	92.88	98.48	AAK98888
ACPPJIEM_26	6128	8374	metE	0.0	methionine biosynthesis enzymes	91.86	100.00	AAK74738
ACPPJIEM_2	57313	58794	SPD_0310	0.0	UPF0371 protein SPD_0310	91.30	100.00	ABJ54480
ACPPJIEM_30	1992	1000	recA	0.0	DNA recombination and repair	91.24	85.31	AAL00560
ACPPJIEM_24	4261	5232	prsA2	0.0	ribose-phosphate pyrophosphokinase	90.12	100.00	ABF36968
ACPPJIEM_1	36568	35417	potA	0.0	ABC transporter ATP-binding protein-spermidine/putrescine transport	89.32	99.74	AAL00050
ACPPJIEM_14	24657	22669	uvrB	0.0	excinuclease ABC, B subunit	88.84	100.00	AE014259_2
ACPPJIEM_10	38607	40337	ptsI	0.0	phosphoenolpyruvate-protein phosphotransferase	88.04	100.00	AAK34199
ACPPJIEM_4	29221	27743	IMPDH	0.0	inosine-5'-monophosphate dehydrogenase	87.42	100.00	ADE32434
ACPPJIEM_3	35660	36961	Eno	0.0	enolase	86.21	99.77	ABP90468
ACPPJIEM_4	14032	12140	gidA	0.0	tRNA uridine 5-carboxymethylaminomethyl modification enzyme	86.05	98.90	ABP91129
ACPPJIEM_26	11299	9590	PGM	0.0	phosphoglucomutase	83.89	99.65	ACH87041
ACPPJIEM_45	20088	21098	pdh	0.0	pyruvate dehydrogenase	82.79	99.70	ABP91006
ACPPJIEM_56	42759	44120	mnmE	0.0	central tRNA-modifying GTPase	81.80	99.56	ABP90420
ACPPJIEM_45	70405	68513	PepO	0.0	endopeptidase	80.19	100.00	ABF32980
ACPPJIEM_3	21221	22111	bglB	1.65e-179	putative phospho--glucosidase	88.55	99.66	AAK33487
ACPPJIEM_39	4802	5740	SP_0676	1.01e-169	transcription facot	81.15	97.20	AAK74821
ACPPJIEM_26	8566	9423	metF	1.39e-166	methionine biosynthesis enzymes	86.36	99.31	AAK74739
ACPPJIEM_6	24391	23687	covR	4.92e-132	responder protein	85.11	100.00	AAK71319
ACPPJIEM_2	29216	28545	rr01	9.48e-126	response regulator	83.93	99.56	CAB54566
ACPPJIEM_26	15254	15922	CiaR	8.01e-125	two-component response regulator	86.10	99.55	AAK74935
ACPPJIEM_26	15254	15925	ciaR	1.08e-122	two component system response regulator	83.93	99.12	AIK75708
ACPPJIEM_6	24391	23687	walR	2.09e-122	DNA-binding response regulator	81.70	100.00	ANC99504
ACPPJIEM_23	83939	84625	CovR	5.06e-119	serves to repress GAS virulence factor-encoding genes	80.79	100.00	ACE75886
ACPPJIEM_30	703	308	SpxA2	2.87e-76	transcriptional regulator	90.91	100.00	ERL21461
ACPPJIEM_56	31399	30998	SpxA1	1.36e-67	transcriptional regulator	80.60	100.00	ERL19273
ACPPJIEM_11	13636	13923	spr0479	3.01e-49	essential gene	86.46	98.97	AAK99283
ACPPJIEM_34	60881	61135	spr1327	1.24e-45	essential gene	95.29	100.00	AAL00131
ACPPJIEM_15	15501	15764	spr0175	1.29e-42	pathogenitcity related	84.09	100.00	AAK98979
ACPPJIEM_15	16328	16594	spr0177	2.81e-34	essential gene	84.27	88.12	AAK98981
ACPPJIEM_67	3766	4266	RopE (M5005_Spy_1611)	1.22e-76	probable DNA-directed RNA polymerase subunit delta	82.04	87.43	AAK34603
ACPPJIEM_22	5311	7608	PFL (B9H01_RS01125)	0.0	formate C-acetyltransferase	82.94	98.08	MYN69560
ACPPJIEM_45	55949	54930	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
ACPPJIEM_1	0.0	1.0	0.0
ACPPJIEM_2	0.0	1.0	0.0
ACPPJIEM_3	0.0	1.0	0.0
ACPPJIEM_4	0.0	1.0	0.0
ACPPJIEM_5	0.0	1.0	0.0
ACPPJIEM_6	0.0	1.0	0.0
ACPPJIEM_7	0.0	1.0	0.0
ACPPJIEM_8	0.0	1.0	0.0
ACPPJIEM_9	0.0	1.0	0.0
ACPPJIEM_10	0.0	1.0	0.0
ACPPJIEM_11	0.0	1.0	0.0
ACPPJIEM_12	0.0	1.0	0.0
ACPPJIEM_13	0.0	1.0	0.0
ACPPJIEM_14	0.0	1.0	0.0
ACPPJIEM_15	0.0	1.0	0.0
ACPPJIEM_16	0.0	1.0	0.0
ACPPJIEM_17	0.0	1.0	0.0
ACPPJIEM_18	0.0	1.0	0.0
ACPPJIEM_19	0.0	1.0	0.0
ACPPJIEM_20	0.0	1.0	0.0
ACPPJIEM_21	0.0	1.0	0.0
ACPPJIEM_22	0.0	1.0	0.0
ACPPJIEM_23	0.0	1.0	0.0
ACPPJIEM_24	0.0	1.0	0.0
ACPPJIEM_25	0.0	1.0	0.0
ACPPJIEM_26	0.0	1.0	0.0
ACPPJIEM_27	0.0	1.0	0.0
ACPPJIEM_28	0.0	1.0	0.0
ACPPJIEM_29	0.0	1.0	0.0
ACPPJIEM_30	0.0	1.0	0.0
ACPPJIEM_31	0.0	1.0	0.0
ACPPJIEM_32	0.0	1.0	0.0
ACPPJIEM_33	0.0	1.0	0.0
ACPPJIEM_34	0.0	1.0	0.0
ACPPJIEM_35	0.0	1.0	0.0
ACPPJIEM_36	0.0	1.0	0.0
ACPPJIEM_37	0.0	1.0	0.0
ACPPJIEM_38	0.0	1.0	0.0
ACPPJIEM_39	0.0	1.0	0.0
ACPPJIEM_40	0.0	1.0	0.0
ACPPJIEM_41	0.0	1.0	0.0
ACPPJIEM_42	0.0	1.0	0.0
ACPPJIEM_43	0.0	1.0	0.0
ACPPJIEM_44	1.0	0.0	1.0
ACPPJIEM_45	0.0	1.0	0.0
ACPPJIEM_46	0.0	1.0	0.0
ACPPJIEM_47	1.0	0.0	1.0
ACPPJIEM_48	1.0	0.0	1.0
ACPPJIEM_49	0.0	1.0	0.0
ACPPJIEM_50	0.0	1.0	0.0
ACPPJIEM_51	0.0	1.0	0.0
ACPPJIEM_52	0.0	1.0	0.0
ACPPJIEM_53	1.0	0.0	1.0
ACPPJIEM_54	0.0	1.0	0.0
ACPPJIEM_55	0.0	1.0	0.0
ACPPJIEM_56	0.0	1.0	0.0
ACPPJIEM_58	1.0	0.0	1.0
ACPPJIEM_59	0.0	1.0	0.0
ACPPJIEM_60	0.0	1.0	0.0
ACPPJIEM_61	0.0	1.0	0.0
ACPPJIEM_63	0.0	1.0	0.0
ACPPJIEM_64	0.0	1.0	0.0
ACPPJIEM_66	0.0	1.0	0.0
ACPPJIEM_67	0.0	1.0	0.0
ACPPJIEM_68	0.0	1.0	0.0
ACPPJIEM_69	0.0	1.0	0.0
ACPPJIEM_70	0.0	1.0	0.0
ACPPJIEM_71	1.0	0.0	1.0
ACPPJIEM_78	0.0	1.0	0.0
ACPPJIEM_84	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