Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 2 | 15 | 33 | 36.30 |
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. |
|---|---|---|---|---|---|---|---|
| LHJCHJAH_15 | 174073 | 175536 | msr(D) | Erythromycin, Azithromycin, Telithromycin, Quinupristin, Pristinamycin IA, Virginiamycin S | 100.00 | 100.00 | AF274302 |
| LHJCHJAH_15 | 172736 | 173953 | mef(A) | Erythromycin, Azithromycin | 99.92 | 100.00 | U83667 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| LHJCHJAH_15 | 172736 | 173950 | mef(A) | macrolide efflux MFS transporter Mef(A) | EXACTX | 100.00 | 100.00 | WP_000417519.1 |
| LHJCHJAH_15 | 174073 | 175533 | msr(D) | ABC-F type ribosomal protection protein Msr(D) | EXACTX | 100.00 | 100.00 | WP_000420313.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| LHJCHJAH_8 | 42871 | 44331 | STER_RS05320 | 0.0 | Capsule | Immune modulation | 97.26 | 100.00 | WP_011681177 |
| LHJCHJAH_8 | 42871 | 44331 | STU_RS14650 | 0.0 | Capsule | Immune modulation | 96.92 | 100.21 | WP_011226049 |
| LHJCHJAH_8 | 42871 | 44331 | STR_RS05265 | 0.0 | Capsule | Immune modulation | 96.37 | 100.21 | WP_041827043 |
| LHJCHJAH_6 | 340703 | 341554 | rfbD | 0.0 | Capsule | Immune modulation | 94.84 | 100.00 | WP_014621820 |
| LHJCHJAH_8 | 39266 | 40631 | STER_RS05300 | 0.0 | Capsule | Immune modulation | 94.66 | 99.85 | WP_011681173 |
| LHJCHJAH_10 | 124349 | 124942 | STR_RS05880 | 0.0 | Capsule | Immune modulation | 94.61 | 100.00 | WP_011226149 |
| LHJCHJAH_10 | 124349 | 124942 | STER_RS06030 | 0.0 | Capsule | Immune modulation | 94.44 | 100.00 | WP_011226149 |
| LHJCHJAH_10 | 124349 | 124942 | STU_RS15260 | 0.0 | Capsule | Immune modulation | 94.44 | 100.00 | WP_011226149 |
| LHJCHJAH_8 | 40688 | 41428 | STER_RS05305 | 0.0 | Capsule | Immune modulation | 94.06 | 100.00 | WP_011681174 |
| LHJCHJAH_8 | 39264 | 40631 | STU_RS14630 | 0.0 | Capsule | Immune modulation | 93.93 | 100.00 | WP_011226045 |
| LHJCHJAH_8 | 42139 | 42870 | STER_RS05315 | 0.0 | Capsule | Immune modulation | 93.85 | 100.00 | WP_011681176 |
| LHJCHJAH_8 | 42139 | 42870 | STU_RS14645 | 0.0 | Capsule | Immune modulation | 93.72 | 100.00 | WP_011226048 |
| LHJCHJAH_8 | 40688 | 41428 | STU_RS14635 | 0.0 | Capsule | Immune modulation | 93.66 | 100.00 | WP_011226046 |
| LHJCHJAH_8 | 42139 | 42870 | STR_RS05260 | 0.0 | Capsule | Immune modulation | 93.17 | 100.00 | WP_011227248 |
| LHJCHJAH_8 | 40693 | 41428 | STR_RS05250 | 0.0 | Capsule | Immune modulation | 93.07 | 98.13 | WP_011227246 |
| LHJCHJAH_10 | 124942 | 125811 | rfbA | 0.0 | Capsule | Immune modulation | 91.26 | 100.00 | WP_011681286 |
| LHJCHJAH_18 | 19230 | 20069 | cbpD | 0.0 | Autolysin | Exoenzyme | 91.07 | 100.00 | WP_011226733 |
| LHJCHJAH_1 | 65840 | 67498 | fbp54 | 0.0 | FBPs | Adherence | 90.36 | 99.94 | WP_011227179 |
| LHJCHJAH_8 | 41438 | 42130 | STR_RS05255 | 0.0 | Capsule | Immune modulation | 88.47 | 99.86 | WP_011227247 |
| LHJCHJAH_8 | 41438 | 42130 | STU_RS14640 | 0.0 | Capsule | Immune modulation | 88.47 | 99.86 | WP_011226047 |
| LHJCHJAH_6 | 14437 | 15447 | plr/gapA | 0.0 | Streptococcal plasmin receptor/GAPDH | Adherence | 88.45 | 99.80 | WP_002986042 |
| LHJCHJAH_15 | 151896 | 153199 | eno | 0.0 | Streptococcal enolase | Exoenzyme | 88.40 | 99.54 | WP_000022832 |
| LHJCHJAH_8 | 41438 | 42130 | STER_RS05310 | 0.0 | Capsule | Immune modulation | 88.18 | 99.86 | WP_011681175 |
| LHJCHJAH_1 | 222984 | 223745 | srtA | 0.0 | Sortase A | Exoenzyme | 83.90 | 99.74 | - |
| LHJCHJAH_10 | 123038 | 124084 | rfbB | 0.0 | Capsule | Immune modulation | 81.57 | 100.00 | WP_009659423 |
| LHJCHJAH_4 | 2743 | 4026 | tig/ropA | 0.0 | Trigger factor | Stress survival | 80.93 | 99.53 | WP_000107753 |
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 |
|---|---|---|---|---|---|---|---|---|
| LHJCHJAH_1 | 226434 | 227408 | ldh(Sp_1220) | 0.0 | L-lactate dehydrogenase | 95.69 | 99.09 | AAK75326 |
| LHJCHJAH_1 | 214851 | 213778 | MntE | 0.0 | manganese homeostasis | 95.53 | 99.72 | ABF32167 |
| LHJCHJAH_6 | 140591 | 138285 | pfl2(Sp_0459) | 0.0 | formate acetyltransferase | 94.54 | 99.22 | AAK74619 |
| LHJCHJAH_6 | 574876 | 573395 | SPD_0310 | 0.0 | UPF0371 protein SPD_0310 | 93.12 | 100.00 | ABJ54480 |
| LHJCHJAH_15 | 56882 | 57850 | spr0084 | 0.0 | pathogenitcity related | 92.88 | 98.48 | AAK98888 |
| LHJCHJAH_1 | 186800 | 184554 | metE | 0.0 | methionine biosynthesis enzymes | 92.39 | 100.00 | AAK74738 |
| LHJCHJAH_18 | 4807 | 5778 | prsA2 | 0.0 | ribose-phosphate pyrophosphokinase | 91.67 | 100.00 | ABF36968 |
| LHJCHJAH_6 | 298917 | 300065 | potA | 0.0 | ABC transporter ATP-binding protein-spermidine/putrescine transport | 90.08 | 99.48 | AAL00050 |
| LHJCHJAH_11 | 9719 | 11449 | ptsI | 0.0 | phosphoenolpyruvate-protein phosphotransferase | 89.95 | 100.00 | AAK34199 |
| LHJCHJAH_6 | 327268 | 329256 | uvrB | 0.0 | excinuclease ABC, B subunit | 89.59 | 100.00 | AE014259_2 |
| LHJCHJAH_2 | 26055 | 27533 | IMPDH | 0.0 | inosine-5'-monophosphate dehydrogenase | 87.63 | 100.00 | ADE32434 |
| LHJCHJAH_15 | 151896 | 153197 | Eno | 0.0 | enolase | 86.44 | 99.77 | ABP90468 |
| LHJCHJAH_2 | 41390 | 43282 | gidA | 0.0 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme | 85.42 | 98.90 | ABP91129 |
| LHJCHJAH_1 | 181633 | 183342 | PGM | 0.0 | phosphoglucomutase | 84.94 | 99.65 | ACH87041 |
| LHJCHJAH_18 | 40284 | 41375 | recA | 0.0 | DNA recombination and repair | 84.64 | 95.36 | AAL00560 |
| LHJCHJAH_2 | 158658 | 157648 | pdh | 0.0 | pyruvate dehydrogenase | 83.09 | 99.70 | ABP91006 |
| LHJCHJAH_1 | 52068 | 53429 | mnmE | 0.0 | central tRNA-modifying GTPase | 82.24 | 99.56 | ABP90420 |
| LHJCHJAH_15 | 137486 | 138376 | bglB | 2.46e-178 | putative phospho--glucosidase | 87.88 | 99.66 | AAK33487 |
| LHJCHJAH_1 | 140662 | 141612 | SP_0676 | 3.18e-170 | transcription facot | 81.39 | 98.45 | AAK74821 |
| LHJCHJAH_1 | 184364 | 183507 | metF | 3.63e-170 | methionine biosynthesis enzymes | 88.11 | 99.31 | AAK74739 |
| LHJCHJAH_8 | 90836 | 90132 | covR | 1.45e-126 | responder protein | 85.11 | 100.00 | AAK71319 |
| LHJCHJAH_6 | 637801 | 638472 | rr01 | 1.47e-126 | response regulator | 84.82 | 99.56 | CAB54566 |
| LHJCHJAH_1 | 177665 | 176994 | ciaR | 1.08e-124 | two component system response regulator | 85.71 | 99.12 | AIK75708 |
| LHJCHJAH_1 | 177665 | 176997 | CiaR | 1.35e-124 | two-component response regulator | 87.00 | 99.55 | AAK74935 |
| LHJCHJAH_8 | 90836 | 90132 | walR | 2.66e-120 | DNA-binding response regulator | 81.70 | 100.00 | ANC99504 |
| LHJCHJAH_4 | 159807 | 160493 | CovR | 4.70e-120 | serves to repress GAS virulence factor-encoding genes | 81.66 | 100.00 | ACE75886 |
| LHJCHJAH_18 | 41549 | 41944 | SpxA2 | 4.17e-76 | transcriptional regulator | 91.67 | 100.00 | ERL21461 |
| LHJCHJAH_1 | 40598 | 40197 | SpxA1 | 2.68e-69 | transcriptional regulator | 82.09 | 100.00 | ERL19273 |
| LHJCHJAH_16 | 50136 | 50549 | GrpE | 4.09e-68 | protein grpE | 81.88 | 80.59 | ABP89267 |
| LHJCHJAH_4 | 183013 | 183300 | spr0479 | 9.07e-48 | essential gene | 84.38 | 98.97 | AAK99283 |
| LHJCHJAH_15 | 16802 | 17056 | spr1327 | 9.00e-45 | essential gene | 92.94 | 100.00 | AAL00131 |
| LHJCHJAH_2 | 72381 | 72118 | spr0175 | 9.69e-43 | pathogenitcity related | 85.23 | 100.00 | AAK98979 |
| LHJCHJAH_2 | 71555 | 71289 | spr0177 | 1.35e-41 | essential gene | 83.15 | 88.12 | AAK98981 |
| LHJCHJAH_4 | 4193 | 4684 | RopE (M5005_Spy_1611) | 1.04e-72 | probable DNA-directed RNA polymerase subunit delta | 82.93 | 85.86 | AAK34603 |
| LHJCHJAH_6 | 140591 | 138291 | PFL (B9H01_RS01125) | 0.0 | formate C-acetyltransferase | 83.36 | 98.08 | MYN69560 |
| LHJCHJAH_2 | 121946 | 122965 | ilvC (SPD_0406) | 0.0 | ketol-acid reductoisomerase (NADP(+)) | 97.35 | 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 |
|---|---|---|---|
| LHJCHJAH_1 | 0.0 | 1.0 | 0.0 |
| LHJCHJAH_2 | 0.0 | 1.0 | 0.0 |
| LHJCHJAH_3 | 0.0 | 1.0 | 0.0 |
| LHJCHJAH_4 | 0.0 | 1.0 | 0.0 |
| LHJCHJAH_5 | 0.0 | 1.0 | 0.0 |
| LHJCHJAH_6 | 0.0 | 1.0 | 0.0 |
| LHJCHJAH_7 | 0.0 | 1.0 | 0.0 |
| LHJCHJAH_8 | 0.0 | 1.0 | 0.0 |
| LHJCHJAH_10 | 0.0 | 1.0 | 0.0 |
| LHJCHJAH_11 | 0.0 | 1.0 | 0.0 |
| LHJCHJAH_12 | 0.0 | 1.0 | 0.0 |
| LHJCHJAH_14 | 0.0 | 1.0 | 0.0 |
| LHJCHJAH_15 | 0.0 | 1.0 | 0.0 |
| LHJCHJAH_16 | 0.0 | 1.0 | 0.0 |
| LHJCHJAH_17 | 0.0 | 1.0 | 0.0 |
| LHJCHJAH_18 | 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 | |||||
Phigaro v2.4.0 (Database: Jan. 2024 release)