safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

Probiotic potential risk score

ARGs	VFs	PGs	PPRS
0	26	28	38.21

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.
KLJLNCCH_1	1573369	1574208	cbpD	0.0	Autolysin	Exoenzyme	100.00	100.00	WP_011226733
KLJLNCCH_1	11013	12068	STU_RS16235	0.0	Capsule	Immune modulation	100.00	100.00	WP_002948022
KLJLNCCH_1	13293	14102	STU_RS16245	0.0	Capsule	Immune modulation	100.00	100.00	WP_002948020
KLJLNCCH_1	9232	11016	STU_RS16230	0.0	Capsule	Immune modulation	99.94	100.00	WP_011226325
KLJLNCCH_1	12088	13293	STU_RS16240	0.0	Capsule	Immune modulation	99.83	100.00	WP_011226326
KLJLNCCH_1	14086	15042	STU_RS16250	0.0	Capsule	Immune modulation	99.79	100.00	WP_011226328
KLJLNCCH_1	346546	347139	STR_RS05880	0.0	Capsule	Immune modulation	99.66	100.00	WP_011226149
KLJLNCCH_1	15039	16187	STU_RS16255	0.0	Capsule	Immune modulation	99.65	100.00	WP_041828290
KLJLNCCH_1	346546	347139	STER_RS06030	0.0	Capsule	Immune modulation	99.50	100.00	WP_011226149
KLJLNCCH_1	1637952	1638551	STR_RS05245	0.0	Capsule	Immune modulation	99.50	100.00	WP_196767671
KLJLNCCH_1	346546	347139	STU_RS15260	0.0	Capsule	Immune modulation	99.50	100.00	WP_011226149
KLJLNCCH_1	673799	675457	fbp54	0.0	FBPs	Adherence	99.46	100.00	WP_011227179
KLJLNCCH_1	1698532	1699900	STR_RS05265	0.0	Capsule	Immune modulation	99.12	94.09	WP_041827043
KLJLNCCH_1	391174	391964	cshA	0.0	Cell surface hydrophobicity proteins	Adherence	99.11	100.00	-
KLJLNCCH_1	345677	346546	rfbA	0.0	Capsule	Immune modulation	99.08	100.00	WP_011681286
KLJLNCCH_1	1638702	1639437	STER_RS05305	0.0	Capsule	Immune modulation	99.05	99.33	WP_011681174
KLJLNCCH_1	311017	311778	srtA	0.0	Sortase A	Exoenzyme	98.95	100.00	-
KLJLNCCH_1	1638688	1639437	STR_RS05250	0.0	Capsule	Immune modulation	98.93	100.00	WP_011227246
KLJLNCCH_1	1640148	1640757	STR_RS05260	0.0	Capsule	Immune modulation	98.85	83.33	WP_011227248
KLJLNCCH_1	18846	20120	STU_RS16265	0.0	Capsule	Immune modulation	98.82	100.00	WP_011226331
KLJLNCCH_1	17884	18846	STU_RS16260	0.0	Capsule	Immune modulation	98.75	95.25	WP_011226330
KLJLNCCH_1	1640148	1640757	STU_RS14645	0.0	Capsule	Immune modulation	98.69	83.33	WP_011226048
KLJLNCCH_1	1638702	1639437	STU_RS14635	0.0	Capsule	Immune modulation	98.37	99.33	WP_011226046
KLJLNCCH_1	1698532	1699900	STU_RS14650	0.0	Capsule	Immune modulation	98.25	94.09	WP_011226049
KLJLNCCH_1	1636828	1637787	STR_RS05240	0.0	Capsule	Immune modulation	98.23	100.00	WP_041827042
KLJLNCCH_1	1640148	1640757	STER_RS05315	0.0	Capsule	Immune modulation	98.20	83.33	WP_011681176
KLJLNCCH_1	1639447	1640139	STR_RS05255	0.0	Capsule	Immune modulation	97.69	100.00	WP_011227247
KLJLNCCH_1	1639447	1640139	STU_RS14640	0.0	Capsule	Immune modulation	97.69	100.00	WP_011226047
KLJLNCCH_1	1698532	1699900	STER_RS05320	0.0	Capsule	Immune modulation	96.87	93.91	WP_011681177
KLJLNCCH_1	21221	22072	rfbD	0.0	Capsule	Immune modulation	96.24	100.00	WP_014621820
KLJLNCCH_1	1639447	1640139	STER_RS05310	0.0	Capsule	Immune modulation	90.91	100.00	WP_011681175
KLJLNCCH_1	477400	478703	eno	0.0	Streptococcal enolase	Exoenzyme	88.10	99.46	WP_000022832
KLJLNCCH_1	1613427	1614437	plr/gapA	0.0	Streptococcal plasmin receptor/GAPDH	Adherence	86.82	99.51	WP_002986042
KLJLNCCH_1	1143770	1145053	tig/ropA	0.0	Trigger factor	Stress survival	80.58	99.77	WP_000107753
KLJLNCCH_1	347568	348614	rfbB	0.0	Capsule	Immune modulation	80.33	100.00	WP_009659423
KLJLNCCH_1	1678593	1679176	SPD_RS01775	1.01e-146	Capsule	Immune modulation	83.08	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
KLJLNCCH_1	308330	307347	ldh(Sp_1220)	0.0	L-lactate dehydrogenase	94.82	100.00	AAK75326
KLJLNCCH_1	1581005	1582078	MntE	0.0	manganese homeostasis	94.41	99.72	ABF32167
KLJLNCCH_1	177203	179506	pfl2(Sp_0459)	0.0	formate acetyltransferase	92.97	99.22	AAK74619
KLJLNCCH_1	559898	558930	spr0084	0.0	pathogenitcity related	92.88	98.48	AAK98888
KLJLNCCH_1	718272	719753	SPD_0310	0.0	UPF0371 protein SPD_0310	92.11	100.00	ABJ54480
KLJLNCCH_1	1499588	1497342	metE	0.0	methionine biosynthesis enzymes	91.72	100.00	AAK74738
KLJLNCCH_1	1553707	1552709	recA	0.0	DNA recombination and repair	91.29	85.82	AAL00560
KLJLNCCH_1	1610042	1609071	prsA2	0.0	ribose-phosphate pyrophosphokinase	90.12	100.00	ABF36968
KLJLNCCH_1	63279	62128	potA	0.0	ABC transporter ATP-binding protein-spermidine/putrescine transport	89.06	99.74	AAL00050
KLJLNCCH_1	35279	33291	uvrB	0.0	excinuclease ABC, B subunit	88.84	100.00	AE014259_2
KLJLNCCH_1	324526	326256	ptsI	0.0	phosphoenolpyruvate-protein phosphotransferase	87.69	100.00	AAK34199
KLJLNCCH_1	1114040	1112562	IMPDH	0.0	inosine-5'-monophosphate dehydrogenase	87.42	100.00	ADE32434
KLJLNCCH_1	478703	477402	Eno	0.0	enolase	86.21	99.77	ABP90468
KLJLNCCH_1	1098844	1096952	gidA	0.0	tRNA uridine 5-carboxymethylaminomethyl modification enzyme	86.05	98.90	ABP91129
KLJLNCCH_1	1494417	1496126	PGM	0.0	phosphoglucomutase	83.89	99.65	ACH87041
KLJLNCCH_1	1026319	1025309	pdh	0.0	pyruvate dehydrogenase	83.38	99.70	ABP91006
KLJLNCCH_1	649277	650638	mnmE	0.0	central tRNA-modifying GTPase	82.24	99.56	ABP90420
KLJLNCCH_1	493142	492252	bglB	5.97e-178	putative phospho--glucosidase	88.55	99.66	AAK33487
KLJLNCCH_1	1372386	1373321	SP_0676	6.79e-168	transcription facot	81.73	96.89	AAK74821
KLJLNCCH_1	1497150	1496293	metF	7.06e-164	methionine biosynthesis enzymes	86.01	99.31	AAK74739
KLJLNCCH_1	423628	424332	covR	9.80e-131	responder protein	85.11	100.00	AAK71319
KLJLNCCH_1	693686	693015	rr01	9.43e-123	response regulator	83.04	99.56	CAB54566
KLJLNCCH_1	423628	424332	walR	4.91e-121	DNA-binding response regulator	81.28	100.00	ANC99504
KLJLNCCH_1	1490463	1489795	CiaR	6.41e-120	two-component response regulator	85.65	99.55	AAK74935
KLJLNCCH_1	1490463	1489792	ciaR	7.81e-118	two component system response regulator	83.48	99.12	AIK75708
KLJLNCCH_1	868526	869212	CovR	9.25e-118	serves to repress GAS virulence factor-encoding genes	80.79	100.00	ACE75886
KLJLNCCH_1	1552433	1552059	SpxA2	1.06e-69	transcriptional regulator	91.20	94.70	ERL21461
KLJLNCCH_1	637918	637517	SpxA1	3.46e-66	transcriptional regulator	80.60	100.00	ERL19273
KLJLNCCH_1	1145211	1145711	RopE (M5005_Spy_1611)	4.52e-75	probable DNA-directed RNA polymerase subunit delta	81.44	87.43	AAK34603
KLJLNCCH_1	177203	179500	PFL (B9H01_RS01125)	0.0	formate C-acetyltransferase	82.81	98.08	MYN69560
KLJLNCCH_1	988774	989793	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.
KLJLNCCH_1	1681170	1681991	rep37	824 / 948	94.90	AF177168

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

PlasmidHunter

Query ID	Prediction	Chromosome	Plasmid
KLJLNCCH_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
KLJLNCCH_1	777576	780987	False	Unknown	VOG3526, VOG2352, VOG0189