safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

Probiotic potential risk score

ARGs	VFs	PGs	PPRS
0	34	33	47.38

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.
HAHPEENI_12	26707	27558	rfbD	0.0	Capsule	Immune modulation	100.00	100.00	WP_014621820
HAHPEENI_80	65295	66056	srtA	0.0	Sortase A	Exoenzyme	100.00	100.00	-
HAHPEENI_38	4629	5552	STR_RS05205	0.0	Capsule	Immune modulation	100.00	100.00	WP_011227237
HAHPEENI_38	5512	6462	STR_RS05210	0.0	Capsule	Immune modulation	100.00	100.00	WP_011227238
HAHPEENI_38	6487	7569	STR_RS05215	0.0	Capsule	Immune modulation	100.00	100.00	WP_011227239
HAHPEENI_38	7659	8633	STR_RS05220	0.0	Capsule	Immune modulation	100.00	100.00	WP_011227240
HAHPEENI_38	8639	9118	STR_RS05225	0.0	Capsule	Immune modulation	100.00	100.00	WP_041827041
HAHPEENI_38	9311	10429	STR_RS05230	0.0	Capsule	Immune modulation	100.00	100.00	WP_148148887
HAHPEENI_38	12120	12719	STR_RS05245	0.0	Capsule	Immune modulation	100.00	100.00	WP_196767671
HAHPEENI_38	12856	13605	STR_RS05250	0.0	Capsule	Immune modulation	100.00	100.00	WP_011227246
HAHPEENI_38	14316	15047	STR_RS05260	0.0	Capsule	Immune modulation	100.00	100.00	WP_011227248
HAHPEENI_80	29938	30531	STR_RS05880	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226149
HAHPEENI_12	14229	15974	STR_RS06885	0.0	Capsule	Immune modulation	100.00	100.00	WP_011227426
HAHPEENI_12	15976	17676	STR_RS06890	0.0	Capsule	Immune modulation	100.00	100.00	WP_041827077
HAHPEENI_12	18896	19702	STR_RS06900	0.0	Capsule	Immune modulation	100.00	100.00	WP_011227429
HAHPEENI_12	19702	20643	STR_RS06905	0.0	Capsule	Immune modulation	100.00	100.00	WP_011227430
HAHPEENI_12	20640	21788	STR_RS06910	0.0	Capsule	Immune modulation	100.00	100.00	WP_011227431
HAHPEENI_51	5371	7029	fbp54	0.0	FBPs	Adherence	99.94	100.00	WP_011227179
HAHPEENI_38	448	1506	waaB	0.0	Capsule	Immune modulation	99.91	100.00	WP_157822584
HAHPEENI_38	10997	11956	STR_RS05240	0.0	Capsule	Immune modulation	99.90	100.00	WP_041827042
HAHPEENI_38	3200	4621	STR_RS05200	0.0	Capsule	Immune modulation	99.86	100.00	WP_011227236
HAHPEENI_38	13615	14307	STR_RS05255	0.0	Capsule	Immune modulation	99.86	100.00	WP_011227247
HAHPEENI_80	29938	30531	STER_RS06030	0.0	Capsule	Immune modulation	99.83	100.00	WP_011226149
HAHPEENI_12	17694	18896	STR_RS06895	0.0	Capsule	Immune modulation	99.83	100.00	WP_011227428
HAHPEENI_80	29938	30531	STU_RS15260	0.0	Capsule	Immune modulation	99.83	100.00	WP_011226149
HAHPEENI_12	15976	17676	STER_RS07050	0.0	Capsule	Immune modulation	99.71	100.00	WP_041827753
HAHPEENI_12	17694	18896	STER_RS07055	0.0	Capsule	Immune modulation	99.58	100.00	WP_011681436
HAHPEENI_38	13615	14307	STU_RS14640	0.0	Capsule	Immune modulation	99.57	100.00	WP_011226047
HAHPEENI_12	18896	19702	STER_RS07060	0.0	Capsule	Immune modulation	99.50	100.00	WP_011681437
HAHPEENI_12	19702	20643	STER_RS07065	0.0	Capsule	Immune modulation	99.47	100.00	WP_011681438
HAHPEENI_26	50786	51754	cbpD	0.0	Autolysin	Exoenzyme	99.38	100.00	WP_082302295
HAHPEENI_23	14292	15082	cshA	0.0	Cell surface hydrophobicity proteins	Adherence	99.37	100.00	-
HAHPEENI_12	20640	21788	STER_RS07070	0.0	Capsule	Immune modulation	99.22	100.00	WP_011681439
HAHPEENI_80	30531	31400	rfbA	0.0	Capsule	Immune modulation	99.19	100.00	WP_011681286
HAHPEENI_38	15048	16490	STR_RS05265	0.0	Capsule	Immune modulation	99.11	99.93	WP_041827043
HAHPEENI_38	14316	15047	STU_RS14645	0.0	Capsule	Immune modulation	98.77	100.00	WP_011226048
HAHPEENI_38	12870	13605	STER_RS05305	0.0	Capsule	Immune modulation	98.50	99.33	WP_011681174
HAHPEENI_38	14316	15047	STER_RS05315	0.0	Capsule	Immune modulation	98.22	100.00	WP_011681176
HAHPEENI_12	14229	15974	STER_RS07045	0.0	Capsule	Immune modulation	98.22	100.00	WP_011681434
HAHPEENI_38	12870	13605	STU_RS14635	0.0	Capsule	Immune modulation	97.96	99.33	WP_011226046
HAHPEENI_12	25327	26586	STER_RS07100	0.0	Capsule	Immune modulation	97.70	100.00	WP_011681445
HAHPEENI_38	15048	16490	STU_RS14650	0.0	Capsule	Immune modulation	97.18	99.93	WP_011226049
HAHPEENI_38	15048	16490	STER_RS05320	0.0	Capsule	Immune modulation	96.17	99.73	WP_011681177
HAHPEENI_38	13615	14307	STER_RS05310	0.0	Capsule	Immune modulation	89.75	100.00	WP_011681175
HAHPEENI_25	107056	108359	eno	0.0	Streptococcal enolase	Exoenzyme	88.09	99.54	WP_000022832
HAHPEENI_48	375	1385	plr/gapA	0.0	Streptococcal plasmin receptor/GAPDH	Adherence	86.92	99.51	WP_002986042
HAHPEENI_12	18896	19702	SGO_RS05020	0.0	Capsule	Immune modulation	82.90	100.00	WP_012000440
HAHPEENI_45	62939	64222	tig/ropA	0.0	Trigger factor	Stress survival	80.65	99.77	WP_000107753
HAHPEENI_80	28463	29509	rfbB	0.0	Capsule	Immune modulation	80.61	100.00	WP_009659423
HAHPEENI_12	24632	25330	STER_RS07095	5.34e-154	Capsule	Immune modulation	81.15	70.35	WP_011681444
HAHPEENI_38	10705	10941	STR_RS05235*	1.06e-120	Capsule	Immune modulation	100.00	100.00	-
HAHPEENI_12	23812	24278	STER_RS07085	0.0	Capsule	Immune modulation	94.02	65.13	WP_011681442
HAHPEENI_12	18159	18896	SGO_RS05025	0.0	Capsule	Immune modulation	85.09	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
HAHPEENI_80	68743	69726	ldh(Sp_1220)	0.0	L-lactate dehydrogenase	94.82	100.00	AAK75326
HAHPEENI_44	58950	60023	MntE	0.0	manganese homeostasis	94.41	99.72	ABF32167
HAHPEENI_25	24821	25789	spr0084	0.0	pathogenitcity related	93.19	98.48	AAK98888
HAHPEENI_52	155161	157464	pfl2(Sp_0459)	0.0	formate acetyltransferase	92.97	99.22	AAK74619
HAHPEENI_39	5585	7831	metE	0.0	methionine biosynthesis enzymes	91.99	100.00	AAK74738
HAHPEENI_30	38075	36594	SPD_0310	0.0	UPF0371 protein SPD_0310	91.90	100.00	ABJ54480
HAHPEENI_29	1922	930	recA	0.0	DNA recombination and repair	91.24	85.31	AAL00560
HAHPEENI_33	15302	14331	prsA2	0.0	ribose-phosphate pyrophosphokinase	90.12	100.00	ABF36968
HAHPEENI_52	41330	40179	potA	0.0	ABC transporter ATP-binding protein-spermidine/putrescine transport	89.06	99.74	AAL00050
HAHPEENI_52	6857	4875	uvrB	0.0	excinuclease ABC, B subunit	88.96	99.70	AE014259_2
HAHPEENI_80	52549	50819	ptsI	0.0	phosphoenolpyruvate-protein phosphotransferase	87.87	100.00	AAK34199
HAHPEENI_41	63082	61604	IMPDH	0.0	inosine-5'-monophosphate dehydrogenase	87.63	100.00	ADE32434
HAHPEENI_25	107056	108357	Eno	0.0	enolase	86.21	99.77	ABP90468
HAHPEENI_41	48346	46454	gidA	0.0	tRNA uridine 5-carboxymethylaminomethyl modification enzyme	85.74	98.90	ABP91129
HAHPEENI_39	10756	9047	PGM	0.0	phosphoglucomutase	83.89	99.65	ACH87041
HAHPEENI_70	18873	19883	pdh	0.0	pyruvate dehydrogenase	83.09	99.70	ABP91006
HAHPEENI_34	7431	6070	mnmE	0.0	central tRNA-modifying GTPase	82.24	99.56	ABP90420
HAHPEENI_70	69204	67312	PepO	0.0	endopeptidase	80.03	100.00	ABF32980
HAHPEENI_25	92626	93516	bglB	2.48e-179	putative phospho--glucosidase	88.55	99.66	AAK33487
HAHPEENI_16	47040	47975	SP_0676	1.90e-169	transcription facot	81.73	96.89	AAK74821
HAHPEENI_39	8023	8880	metF	7.64e-167	methionine biosynthesis enzymes	86.36	99.31	AAK74739
HAHPEENI_23	42781	43485	covR	1.26e-131	responder protein	84.68	100.00	AAK71319
HAHPEENI_46	29860	29189	rr01	5.07e-127	response regulator	84.38	99.56	CAB54566
HAHPEENI_23	42781	43485	walR	9.06e-122	DNA-binding response regulator	80.85	100.00	ANC99504
HAHPEENI_63	10111	9425	CovR	1.70e-119	serves to repress GAS virulence factor-encoding genes	80.79	100.00	ACE75886
HAHPEENI_39	14709	15359	CiaR	1.23e-118	two-component response regulator	86.17	96.88	AAK74935
HAHPEENI_39	14709	15359	ciaR	6.34e-116	two component system response regulator	83.87	96.02	AIK75708
HAHPEENI_29	633	238	SpxA2	4.31e-76	transcriptional regulator	90.91	100.00	ERL21461
HAHPEENI_34	18789	19190	SpxA1	1.05e-67	transcriptional regulator	80.60	100.00	ERL19273
HAHPEENI_8	13397	13684	spr0479	3.36e-49	essential gene	86.46	98.97	AAK99283
HAHPEENI_26	9898	9644	spr1327	1.05e-45	essential gene	95.29	100.00	AAL00131
HAHPEENI_41	14702	14965	spr0175	6.33e-42	pathogenitcity related	82.95	100.00	AAK98979
HAHPEENI_41	15529	15795	spr0177	1.11e-33	essential gene	84.27	88.12	AAK98981
HAHPEENI_45	62781	62281	RopE (M5005_Spy_1611)	3.53e-76	probable DNA-directed RNA polymerase subunit delta	80.84	87.43	AAK34603
HAHPEENI_52	155161	157458	PFL (B9H01_RS01125)	0.0	formate C-acetyltransferase	82.94	98.08	MYN69560
HAHPEENI_70	54743	53724	ilvC (SPD_0406)	0.0	ketol-acid reductoisomerase (NADP(+))	96.18	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.
HAHPEENI_56	1541	2212	rep35	672 / 672	100.00	AF295100

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

PlasmidHunter

Query ID	Prediction	Chromosome	Plasmid
HAHPEENI_2	0.0	1.0	0.0
HAHPEENI_5	0.0	1.0	0.0
HAHPEENI_8	0.0	1.0	0.0
HAHPEENI_12	0.0	1.0	0.0
HAHPEENI_13	0.0	1.0	0.0
HAHPEENI_16	0.0	1.0	0.0
HAHPEENI_20	0.0	1.0	0.0
HAHPEENI_23	0.0	1.0	0.0
HAHPEENI_24	0.0	1.0	0.0
HAHPEENI_25	0.0	1.0	0.0
HAHPEENI_26	0.0	1.0	0.0
HAHPEENI_29	0.0	1.0	0.0
HAHPEENI_30	0.0	1.0	0.0
HAHPEENI_33	0.0	1.0	0.0
HAHPEENI_34	0.0	1.0	0.0
HAHPEENI_35	0.0	1.0	0.0
HAHPEENI_36	0.0	1.0	0.0
HAHPEENI_37	0.0	1.0	0.0
HAHPEENI_38	0.0	1.0	0.0
HAHPEENI_39	0.0	1.0	0.0
HAHPEENI_40	0.0	1.0	0.0
HAHPEENI_41	0.0	1.0	0.0
HAHPEENI_42	0.0	1.0	0.0
HAHPEENI_43	0.0	1.0	0.0
HAHPEENI_44	0.0	1.0	0.0
HAHPEENI_45	0.0	1.0	0.0
HAHPEENI_46	0.0	1.0	0.0
HAHPEENI_47	0.0	1.0	0.0
HAHPEENI_48	0.0	1.0	0.0
HAHPEENI_49	0.0	1.0	0.0
HAHPEENI_51	0.0	1.0	0.0
HAHPEENI_52	0.0	1.0	0.0
HAHPEENI_53	0.0	1.0	0.0
HAHPEENI_54	0.0	1.0	0.0
HAHPEENI_55	1.0	0.0	1.0
HAHPEENI_56	1.0	0.0	1.0
HAHPEENI_57	1.0	0.0	1.0
HAHPEENI_59	0.0	1.0	0.0
HAHPEENI_61	0.0	1.0	0.0
HAHPEENI_62	0.0	1.0	0.0
HAHPEENI_63	0.0	1.0	0.0
HAHPEENI_64	0.0	1.0	0.0
HAHPEENI_65	1.0	0.0	1.0
HAHPEENI_66	0.0	1.0	0.0
HAHPEENI_67	0.0	1.0	0.0
HAHPEENI_70	0.0	1.0	0.0
HAHPEENI_72	0.0	1.0	0.0
HAHPEENI_74	0.0	1.0	0.0
HAHPEENI_75	0.0	1.0	0.0
HAHPEENI_79	0.0	1.0	0.0
HAHPEENI_80	0.0	1.0	0.0
HAHPEENI_81	1.0	0.0	1.0
HAHPEENI_83	0.0	1.0	0.0
HAHPEENI_85	0.0	1.0	0.0
HAHPEENI_86	0.0	1.0	0.0
HAHPEENI_87	0.0	1.0	0.0
HAHPEENI_91	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