Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 8 | 17.55 |
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. |
|---|---|---|---|---|---|---|---|---|
| JCMNHDLE_2 | 428935 | 429252 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| JCMNHDLE_2 | 428597 | 428935 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| JCMNHDLE_4 | 366303 | 367472 | bmr | ARO:3003007 | bmr | 99.23 | 100.00 | M33768.1 |
| JCMNHDLE_3 | 343486 | 344406 | mphK | ARO:3004541 | mphK | 98.69 | 100.00 | CP010314.1 |
| JCMNHDLE_3 | 330158 | 331591 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.00 | JYFL01000006.1 |
| JCMNHDLE_3 | 280440 | 281033 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| JCMNHDLE_4 | 142488 | 143690 | blt | ARO:3003006 | blt | 98.75 | 100.00 | L32599.1 |
| JCMNHDLE_4 | 123698 | 124552 | aadK | ARO:3002627 | aadK | 97.54 | 100.00 | AL009126.1 |
| JCMNHDLE_3 | 28977 | 30620 | vmlR | ARO:3004476 | vmlR | 98.54 | 100.00 | NC_000964.3 |
| JCMNHDLE_7 | 27386 | 29956 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 100.00 | AL009126.3 |
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. |
|---|---|---|---|---|---|---|---|
| JCMNHDLE_1 | 34611 | 35987 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 99.42 | 100.00 | D12567 |
| JCMNHDLE_3 | 343486 | 344406 | mph(K) | Spiramycin, Telithromycin | 99.13 | 100.00 | NC_000964 |
| JCMNHDLE_4 | 123698 | 124550 | aadK | Streptomycin | 98.12 | 99.77 | M26879 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| JCMNHDLE_1 | 34611 | 35984 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 99.34 | 100.00 | WP_063856081.1 |
| JCMNHDLE_3 | 343489 | 344406 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.69 | 100.00 | WP_003246254.1 |
| JCMNHDLE_3 | 28977 | 30617 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.54 | 100.00 | WP_003234144.1 |
| JCMNHDLE_4 | 123698 | 124549 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.54 | 100.00 | WP_003229862.1 |
| JCMNHDLE_1 | 37997 | 38515 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| JCMNHDLE_1 | 519100 | 520281 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| JCMNHDLE_1 | 938498 | 945634 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.62 | 100.00 | NP_391076 |
| JCMNHDLE_5 | 62326 | 62967 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| JCMNHDLE_1 | 933857 | 934642 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| JCMNHDLE_1 | 937540 | 938478 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.25 | 100.00 | NP_391077 |
| JCMNHDLE_1 | 934668 | 935864 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.17 | 100.00 | NP_391079 |
| JCMNHDLE_5 | 206771 | 208534 | dep/capD | 0.0 | Capsule | Immune modulation | 99.15 | 100.00 | NP_389723 |
| JCMNHDLE_1 | 935893 | 937512 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.07 | 100.00 | NP_391078 |
| JCMNHDLE_1 | 520764 | 521906 | capA | 0.0 | Capsule | Immune modulation | 98.95 | 100.00 | NP_391469 |
| JCMNHDLE_1 | 520296 | 520745 | capC | 0.0 | Capsule | Immune modulation | 98.67 | 100.00 | NP_391470 |
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 |
|---|---|---|---|---|---|---|---|---|
| JCMNHDLE_10 | 13681 | 12545 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| JCMNHDLE_12 | 11216 | 10347 | pdxS | 1.11e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| JCMNHDLE_2 | 738748 | 739524 | CodY | 7.49e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| JCMNHDLE_1 | 681642 | 681073 | ClpP | 6.30e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| JCMNHDLE_2 | 276391 | 276783 | spxA1 | 5.89e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| JCMNHDLE_2 | 276391 | 276783 | spx | 3.51e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| JCMNHDLE_9 | 20595 | 20837 | SpoVG | 7.52e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| JCMNHDLE_3 | 80177 | 79980 | CspA | 1.91e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| JCMNHDLE_5 | 50363 | 50169 | CspD | 2.07e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
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 |
|---|---|---|---|
| JCMNHDLE_1 | 0.0 | 1.0 | 0.0 |
| JCMNHDLE_2 | 0.0 | 1.0 | 0.0 |
| JCMNHDLE_3 | 0.0 | 1.0 | 0.0 |
| JCMNHDLE_4 | 0.0 | 1.0 | 0.0 |
| JCMNHDLE_5 | 0.0 | 1.0 | 0.0 |
| JCMNHDLE_6 | 0.0 | 1.0 | 0.0 |
| JCMNHDLE_7 | 0.0 | 1.0 | 0.0 |
| JCMNHDLE_8 | 0.0 | 1.0 | 0.0 |
| JCMNHDLE_9 | 0.0 | 1.0 | 0.0 |
| JCMNHDLE_10 | 0.0 | 1.0 | 0.0 |
| JCMNHDLE_11 | 0.0 | 1.0 | 0.0 |
| JCMNHDLE_12 | 0.0 | 1.0 | 0.0 |
| JCMNHDLE_13 | 1.0 | 0.0 | 1.0 |
| JCMNHDLE_14 | 0.0 | 1.0 | 0.0 |
| JCMNHDLE_15 | 1.0 | 0.0 | 1.0 |
| JCMNHDLE_16 | 1.0 | 0.0 | 1.0 |
| JCMNHDLE_17 | 1.0 | 0.0 | 1.0 |
| JCMNHDLE_18 | 1.0 | 0.0 | 1.0 |
| JCMNHDLE_20 | 0.0 | 1.0 | 0.0 |
| JCMNHDLE_22 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| JCMNHDLE_2 | 371217 | 399113 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG3390, VOG4705 |
| JCMNHDLE_4 | 162261 | 194260 | False | Myoviridae | VOG4600, VOG1309, VOG11060, VOG0189, VOG4693, VOG0143, VOG4673, VOG4662, VOG0796, VOG10227, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4691, VOG4862 |
Phigaro v2.4.0 (Database: Jan. 2024 release)