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.
PNEMOBHH_1	1048065	1048855	cshA	0.0	Cell surface hydrophobicity proteins	Adherence	100.00	100.00	-
PNEMOBHH_1	1305589	1306440	rfbD	0.0	Capsule	Immune modulation	100.00	100.00	WP_014621820
PNEMOBHH_1	963149	963907	STU_RS14545	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226028
PNEMOBHH_1	963894	965012	STU_RS14550	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226029
PNEMOBHH_1	965123	965746	STU_RS14555	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226030
PNEMOBHH_1	965887	967062	STU_RS14560	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226032
PNEMOBHH_1	967069	968469	STU_RS14565	0.0	Capsule	Immune modulation	100.00	100.00	WP_179970486
PNEMOBHH_1	968965	969957	STU_RS14570	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226034
PNEMOBHH_1	969982	970707	STU_RS14575	0.0	Capsule	Immune modulation	100.00	100.00	WP_041828375
PNEMOBHH_1	971804	972445	STU_RS14590	0.0	Capsule	Immune modulation	100.00	100.00	WP_041828240
PNEMOBHH_1	974456	974935	STU_RS14610	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226040
PNEMOBHH_1	975038	975523	STU_RS14615	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226041
PNEMOBHH_1	975523	975972	STU_RS14620	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226042
PNEMOBHH_1	975981	976977	STU_RS14625*	0.0	Capsule	Immune modulation	100.00	100.00	-
PNEMOBHH_1	977206	978573	STU_RS14630	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226045
PNEMOBHH_1	978630	979370	STU_RS14635	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226046
PNEMOBHH_1	979380	980072	STU_RS14640	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226047
PNEMOBHH_1	980081	980812	STU_RS14645	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226048
PNEMOBHH_1	980813	982267	STU_RS14650	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226049
PNEMOBHH_1	1092884	1093477	STU_RS15260	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226149
PNEMOBHH_1	1295138	1296922	STU_RS16230	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226325
PNEMOBHH_1	1296919	1297974	STU_RS16235	0.0	Capsule	Immune modulation	100.00	100.00	WP_002948022
PNEMOBHH_1	1297994	1299199	STU_RS16240	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226326
PNEMOBHH_1	1299199	1300008	STU_RS16245	0.0	Capsule	Immune modulation	100.00	100.00	WP_002948020
PNEMOBHH_1	1299992	1300948	STU_RS16250	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226328
PNEMOBHH_1	1300945	1302093	STU_RS16255	0.0	Capsule	Immune modulation	100.00	100.00	WP_041828290
PNEMOBHH_1	1302202	1303212	STU_RS16260	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226330
PNEMOBHH_1	1303212	1304486	STU_RS16265	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226331
PNEMOBHH_1	857068	858726	fbp54	0.0	FBPs	Adherence	99.94	100.00	WP_011227179
PNEMOBHH_1	1128243	1129004	srtA	0.0	Sortase A	Exoenzyme	99.87	100.00	-
PNEMOBHH_1	1092884	1093477	STR_RS05880	0.0	Capsule	Immune modulation	99.83	100.00	WP_011226149
PNEMOBHH_1	1092884	1093477	STER_RS06030	0.0	Capsule	Immune modulation	99.66	100.00	WP_011226149
PNEMOBHH_1	43821	44660	cbpD	0.0	Autolysin	Exoenzyme	99.64	100.00	WP_011226733
PNEMOBHH_1	1093477	1094346	rfbA	0.0	Capsule	Immune modulation	99.54	100.00	WP_011681286
PNEMOBHH_1	979380	980072	STR_RS05255	0.0	Capsule	Immune modulation	99.42	100.00	WP_011227247
PNEMOBHH_1	980081	980812	STR_RS05260	0.0	Capsule	Immune modulation	98.77	100.00	WP_011227248
PNEMOBHH_1	978630	979370	STER_RS05305	0.0	Capsule	Immune modulation	98.25	100.00	WP_011681174
PNEMOBHH_1	980081	980812	STER_RS05315	0.0	Capsule	Immune modulation	98.09	100.00	WP_011681176
PNEMOBHH_1	978635	979370	STR_RS05250	0.0	Capsule	Immune modulation	97.96	98.13	WP_011227246
PNEMOBHH_1	980813	982267	STR_RS05265	0.0	Capsule	Immune modulation	97.94	100.00	WP_041827043
PNEMOBHH_1	980813	982267	STER_RS05320	0.0	Capsule	Immune modulation	97.47	99.79	WP_011681177
PNEMOBHH_1	977210	978573	STER_RS05300	0.0	Capsule	Immune modulation	94.94	99.71	WP_011681173
PNEMOBHH_1	979380	980072	STER_RS05310	0.0	Capsule	Immune modulation	89.90	100.00	WP_011681175
PNEMOBHH_1	600778	602081	eno	0.0	Streptococcal enolase	Exoenzyme	88.09	99.54	WP_000022832
PNEMOBHH_1	1592201	1593211	plr/gapA	0.0	Streptococcal plasmin receptor/GAPDH	Adherence	86.92	99.51	WP_002986042
PNEMOBHH_1	1091408	1092454	rfbB	0.0	Capsule	Immune modulation	80.71	100.00	WP_009659423
PNEMOBHH_1	149218	150501	tig/ropA	0.0	Trigger factor	Stress survival	80.58	99.77	WP_000107753
PNEMOBHH_1	970775	971113	STU_RS19955	1.31e-175	Capsule	Immune modulation	100.00	100.00	WP_148148905

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
PNEMOBHH_1	1131691	1132674	ldh(Sp_1220)	0.0	L-lactate dehydrogenase	94.82	100.00	AAK75326
PNEMOBHH_1	710268	711341	MntE	0.0	manganese homeostasis	94.41	99.72	ABF32167
PNEMOBHH_1	1469630	1471933	pfl2(Sp_0459)	0.0	formate acetyltransferase	92.97	99.22	AAK74619
PNEMOBHH_1	518542	519510	spr0084	0.0	pathogenitcity related	92.88	98.48	AAK98888
PNEMOBHH_1	730791	733037	metE	0.0	methionine biosynthesis enzymes	91.99	100.00	AAK74738
PNEMOBHH_1	1210446	1211927	SPD_0310	0.0	UPF0371 protein SPD_0310	91.90	100.00	ABJ54480
PNEMOBHH_1	64696	65688	recA	0.0	DNA recombination and repair	91.24	85.31	AAL00560
PNEMOBHH_1	27337	28308	prsA2	0.0	ribose-phosphate pyrophosphokinase	90.12	100.00	ABF36968
PNEMOBHH_1	1355889	1354738	potA	0.0	ABC transporter ATP-binding protein-spermidine/putrescine transport	89.06	99.74	AAL00050
PNEMOBHH_1	1321422	1319440	uvrB	0.0	excinuclease ABC, B subunit	88.96	99.70	AE014259_2
PNEMOBHH_1	1115497	1113767	ptsI	0.0	phosphoenolpyruvate-protein phosphotransferase	87.87	100.00	AAK34199
PNEMOBHH_1	1784707	1783229	IMPDH	0.0	inosine-5'-monophosphate dehydrogenase	87.22	100.00	ADE32434
PNEMOBHH_1	600778	602079	Eno	0.0	enolase	86.21	99.77	ABP90468
PNEMOBHH_1	1769971	1768079	gidA	0.0	tRNA uridine 5-carboxymethylaminomethyl modification enzyme	85.89	98.90	ABP91129
PNEMOBHH_1	735962	734253	PGM	0.0	phosphoglucomutase	83.89	99.65	ACH87041
PNEMOBHH_1	1635147	1636157	pdh	0.0	pyruvate dehydrogenase	83.09	99.70	ABP91006
PNEMOBHH_1	884295	882934	mnmE	0.0	central tRNA-modifying GTPase	82.02	99.56	ABP90420
PNEMOBHH_1	1687164	1685272	PepO	0.0	endopeptidase	80.03	100.00	ABF32980
PNEMOBHH_1	586348	587238	bglB	1.29e-178	putative phospho--glucosidase	88.89	99.66	AAK33487
PNEMOBHH_1	795360	794425	SP_0676	7.16e-168	transcription facot	81.73	96.89	AAK74821
PNEMOBHH_1	733229	734086	metF	8.38e-165	methionine biosynthesis enzymes	86.36	99.31	AAK74739
PNEMOBHH_1	1020391	1019687	covR	6.56e-131	responder protein	85.53	100.00	AAK71319
PNEMOBHH_1	1184876	1184205	rr01	1.16e-125	response regulator	84.38	99.56	CAB54566
PNEMOBHH_1	1020391	1019687	walR	3.10e-121	DNA-binding response regulator	81.70	100.00	ANC99504
PNEMOBHH_1	308104	308790	CovR	9.76e-118	serves to repress GAS virulence factor-encoding genes	80.79	100.00	ACE75886
PNEMOBHH_1	739916	740584	CiaR	6.89e-117	two-component response regulator	83.86	99.55	AAK74935
PNEMOBHH_1	739916	740587	ciaR	6.85e-115	two component system response regulator	81.70	99.12	AIK75708
PNEMOBHH_1	65985	66380	SpxA2	3.59e-74	transcriptional regulator	90.91	100.00	ERL21461
PNEMOBHH_1	895652	896053	SpxA1	3.65e-66	transcriptional regulator	80.60	100.00	ERL19273
PNEMOBHH_1	150659	151159	RopE (M5005_Spy_1611)	9.58e-75	probable DNA-directed RNA polymerase subunit delta	80.84	87.43	AAK34603
PNEMOBHH_1	1469630	1471927	PFL (B9H01_RS01125)	0.0	formate C-acetyltransferase	82.94	98.08	MYN69560
PNEMOBHH_1	1672703	1671684	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
PNEMOBHH_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