safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

Probiotic potential risk score

ARGs	VFs	PGs	PPRS
0	37	29	47.01

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.
BEIGJADO_1	43663	44502	cbpD	0.0	Autolysin	Exoenzyme	100.00	100.00	WP_011226733
BEIGJADO_1	1322288	1323139	rfbD	0.0	Capsule	Immune modulation	100.00	100.00	WP_014621820
BEIGJADO_1	1133211	1133972	srtA	0.0	Sortase A	Exoenzyme	100.00	100.00	-
BEIGJADO_1	1097854	1098447	STR_RS05880	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226149
BEIGJADO_1	1309810	1311555	STR_RS06885	0.0	Capsule	Immune modulation	100.00	100.00	WP_011227426
BEIGJADO_1	1311557	1313257	STR_RS06890	0.0	Capsule	Immune modulation	100.00	100.00	WP_041827077
BEIGJADO_1	1314477	1315283	STR_RS06900	0.0	Capsule	Immune modulation	100.00	100.00	WP_011227429
BEIGJADO_1	1315283	1316224	STR_RS06905	0.0	Capsule	Immune modulation	100.00	100.00	WP_011227430
BEIGJADO_1	1316221	1317369	STR_RS06910	0.0	Capsule	Immune modulation	100.00	100.00	WP_011227431
BEIGJADO_1	969032	970150	STU_RS14550	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226029
BEIGJADO_1	970261	970884	STU_RS14555	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226030
BEIGJADO_1	972207	973607	STU_RS14565	0.0	Capsule	Immune modulation	100.00	100.00	WP_179970486
BEIGJADO_1	974103	975095	STU_RS14570	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226034
BEIGJADO_1	975120	975845	STU_RS14575	0.0	Capsule	Immune modulation	100.00	100.00	WP_041828375
BEIGJADO_1	979593	980072	STU_RS14610	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226040
BEIGJADO_1	980175	980660	STU_RS14615	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226041
BEIGJADO_1	980660	981109	STU_RS14620	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226042
BEIGJADO_1	981118	982114	STU_RS14625*	0.0	Capsule	Immune modulation	100.00	100.00	-
BEIGJADO_1	982343	983710	STU_RS14630	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226045
BEIGJADO_1	984517	985209	STU_RS14640	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226047
BEIGJADO_1	985950	987404	STU_RS14650	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226049
BEIGJADO_1	862361	864019	fbp54	0.0	FBPs	Adherence	99.94	100.00	WP_011227179
BEIGJADO_1	1313275	1314477	STR_RS06895	0.0	Capsule	Immune modulation	99.92	100.00	WP_011227428
BEIGJADO_1	971025	972200	STU_RS14560	0.0	Capsule	Immune modulation	99.92	100.00	WP_011226032
BEIGJADO_1	983767	984507	STU_RS14635	0.0	Capsule	Immune modulation	99.86	100.00	WP_011226046
BEIGJADO_1	976942	977582	STU_RS14590	0.0	Capsule	Immune modulation	99.84	99.84	WP_041828240
BEIGJADO_1	1097854	1098447	STER_RS06030	0.0	Capsule	Immune modulation	99.83	100.00	WP_011226149
BEIGJADO_1	1097854	1098447	STU_RS15260	0.0	Capsule	Immune modulation	99.83	100.00	WP_011226149
BEIGJADO_1	985218	985949	STU_RS14645	0.0	Capsule	Immune modulation	99.73	100.00	WP_011226048
BEIGJADO_1	1311557	1313257	STER_RS07050	0.0	Capsule	Immune modulation	99.71	100.00	WP_041827753
BEIGJADO_1	1313275	1314477	STER_RS07055	0.0	Capsule	Immune modulation	99.50	100.00	WP_011681436
BEIGJADO_1	1314477	1315283	STER_RS07060	0.0	Capsule	Immune modulation	99.50	100.00	WP_011681437
BEIGJADO_1	1315283	1316224	STER_RS07065	0.0	Capsule	Immune modulation	99.47	100.00	WP_011681438
BEIGJADO_1	984517	985209	STR_RS05255	0.0	Capsule	Immune modulation	99.42	100.00	WP_011227247
BEIGJADO_1	1051799	1052589	cshA	0.0	Cell surface hydrophobicity proteins	Adherence	99.37	100.00	-
BEIGJADO_1	968282	969045	STU_RS14545	0.0	Capsule	Immune modulation	99.35	100.53	WP_011226028
BEIGJADO_1	1316221	1317369	STER_RS07070	0.0	Capsule	Immune modulation	99.22	100.00	WP_011681439
BEIGJADO_1	1098447	1099316	rfbA	0.0	Capsule	Immune modulation	99.19	100.00	WP_011681286
BEIGJADO_1	985218	985949	STR_RS05260	0.0	Capsule	Immune modulation	98.50	100.00	WP_011227248
BEIGJADO_1	983767	984507	STER_RS05305	0.0	Capsule	Immune modulation	98.38	100.00	WP_011681174
BEIGJADO_1	1309810	1311555	STER_RS07045	0.0	Capsule	Immune modulation	98.22	100.00	WP_011681434
BEIGJADO_1	983772	984507	STR_RS05250	0.0	Capsule	Immune modulation	98.10	98.13	WP_011227246
BEIGJADO_1	985950	987404	STR_RS05265	0.0	Capsule	Immune modulation	97.94	100.00	WP_041827043
BEIGJADO_1	985218	985949	STER_RS05315	0.0	Capsule	Immune modulation	97.81	100.00	WP_011681176
BEIGJADO_1	1320908	1322167	STER_RS07100	0.0	Capsule	Immune modulation	97.70	100.00	WP_011681445
BEIGJADO_1	985950	987404	STER_RS05320	0.0	Capsule	Immune modulation	97.47	99.79	WP_011681177
BEIGJADO_1	982347	983710	STER_RS05300	0.0	Capsule	Immune modulation	94.94	99.71	WP_011681173
BEIGJADO_1	984517	985209	STER_RS05310	0.0	Capsule	Immune modulation	89.90	100.00	WP_011681175
BEIGJADO_1	604411	605714	eno	0.0	Streptococcal enolase	Exoenzyme	88.09	99.54	WP_000022832
BEIGJADO_1	1603994	1605004	plr/gapA	0.0	Streptococcal plasmin receptor/GAPDH	Adherence	86.92	99.51	WP_002986042
BEIGJADO_1	1314477	1315283	SGO_RS05020	0.0	Capsule	Immune modulation	82.90	100.00	WP_012000440
BEIGJADO_1	149039	150322	tig/ropA	0.0	Trigger factor	Stress survival	80.65	99.77	WP_000107753
BEIGJADO_1	1096379	1097425	rfbB	0.0	Capsule	Immune modulation	80.61	100.00	WP_009659423
BEIGJADO_1	975913	976251	STU_RS19955	1.32e-175	Capsule	Immune modulation	100.00	100.00	WP_148148905
BEIGJADO_1	1320213	1320911	STER_RS07095	2.94e-152	Capsule	Immune modulation	81.15	70.35	WP_011681444
BEIGJADO_1	1319393	1319859	STER_RS07085	0.0	Capsule	Immune modulation	94.02	65.13	WP_011681442
BEIGJADO_1	1313740	1314477	SGO_RS05025	0.0	Capsule	Immune modulation	85.23	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
BEIGJADO_1	1136659	1137642	ldh(Sp_1220)	0.0	L-lactate dehydrogenase	94.82	100.00	AAK75326
BEIGJADO_1	716248	717321	MntE	0.0	manganese homeostasis	94.41	99.72	ABF32167
BEIGJADO_1	522174	523142	spr0084	0.0	pathogenitcity related	93.19	98.48	AAK98888
BEIGJADO_1	1484472	1486775	pfl2(Sp_0459)	0.0	formate acetyltransferase	92.97	99.22	AAK74619
BEIGJADO_1	1223522	1225003	SPD_0310	0.0	UPF0371 protein SPD_0310	92.11	100.00	ABJ54480
BEIGJADO_1	736772	739018	metE	0.0	methionine biosynthesis enzymes	91.99	100.00	AAK74738
BEIGJADO_1	63294	64286	recA	0.0	DNA recombination and repair	91.24	85.31	AAL00560
BEIGJADO_1	27181	28152	prsA2	0.0	ribose-phosphate pyrophosphokinase	90.12	100.00	ABF36968
BEIGJADO_1	1370642	1369491	potA	0.0	ABC transporter ATP-binding protein-spermidine/putrescine transport	89.06	99.74	AAL00050
BEIGJADO_1	1336169	1334187	uvrB	0.0	excinuclease ABC, B subunit	88.96	99.70	AE014259_2
BEIGJADO_1	1120465	1118735	ptsI	0.0	phosphoenolpyruvate-protein phosphotransferase	87.87	100.00	AAK34199
BEIGJADO_1	1793567	1792089	IMPDH	0.0	inosine-5'-monophosphate dehydrogenase	87.63	100.00	ADE32434
BEIGJADO_1	604411	605712	Eno	0.0	enolase	86.21	99.77	ABP90468
BEIGJADO_1	1778831	1776939	gidA	0.0	tRNA uridine 5-carboxymethylaminomethyl modification enzyme	85.89	98.90	ABP91129
BEIGJADO_1	741943	740234	PGM	0.0	phosphoglucomutase	83.89	99.65	ACH87041
BEIGJADO_1	1645688	1646698	pdh	0.0	pyruvate dehydrogenase	83.09	99.70	ABP91006
BEIGJADO_1	889440	888079	mnmE	0.0	central tRNA-modifying GTPase	82.24	99.56	ABP90420
BEIGJADO_1	1696025	1694133	PepO	0.0	endopeptidase	80.03	100.00	ABF32980
BEIGJADO_1	589981	590871	bglB	2.84e-178	putative phospho--glucosidase	88.55	99.66	AAK33487
BEIGJADO_1	801342	800407	SP_0676	7.19e-168	transcription facot	81.73	96.89	AAK74821
BEIGJADO_1	739210	740067	metF	8.42e-165	methionine biosynthesis enzymes	86.36	99.31	AAK74739
BEIGJADO_1	1024100	1023396	covR	3.41e-130	responder protein	84.68	100.00	AAK71319
BEIGJADO_1	1189841	1189170	rr01	1.17e-125	response regulator	84.38	99.56	CAB54566
BEIGJADO_1	1024100	1023396	walR	2.45e-120	DNA-binding response regulator	80.85	100.00	ANC99504
BEIGJADO_1	309223	309909	CovR	9.80e-118	serves to repress GAS virulence factor-encoding genes	80.79	100.00	ACE75886
BEIGJADO_1	745896	746546	CiaR	1.35e-116	two-component response regulator	86.17	96.88	AAK74935
BEIGJADO_1	745896	746546	ciaR	6.94e-114	two component system response regulator	83.87	96.02	AIK75708
BEIGJADO_1	64583	64978	SpxA2	3.61e-74	transcriptional regulator	90.91	100.00	ERL21461
BEIGJADO_1	900798	901199	SpxA1	3.66e-66	transcriptional regulator	80.60	100.00	ERL19273
BEIGJADO_1	150480	150980	RopE (M5005_Spy_1611)	9.62e-75	probable DNA-directed RNA polymerase subunit delta	80.84	87.43	AAK34603
BEIGJADO_1	1484472	1486769	PFL (B9H01_RS01125)	0.0	formate C-acetyltransferase	82.94	98.08	MYN69560
BEIGJADO_1	1681564	1680545	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.
No hit found

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

PlasmidHunter

Query ID	Prediction	Chromosome	Plasmid
BEIGJADO_1	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