Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 11 | 10 | 4 | 15.39 |
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. |
|---|---|---|---|---|---|---|---|---|
| KHOMDLFI_1 | 2515858 | 2516712 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| KHOMDLFI_1 | 2497382 | 2498584 | blt | ARO:3003006 | blt | 99.25 | 100.00 | L32599.1 |
| KHOMDLFI_1 | 1365241 | 1365558 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| KHOMDLFI_1 | 1364903 | 1365241 | ykkC | ARO:3003063 | ykkC | 98.21 | 100.00 | AL009126.1 |
| KHOMDLFI_1 | 891122 | 893692 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.65 | 100.00 | AL009126.3 |
| KHOMDLFI_1 | 603139 | 604785 | vmlR | ARO:3004476 | vmlR | 98.91 | 100.18 | NC_000964.3 |
| KHOMDLFI_1 | 334000 | 334593 | tmrB | ARO:3003059 | tmrB | 99.49 | 100.00 | AL009126.3 |
| KHOMDLFI_1 | 284900 | 286333 | lmrB | ARO:3002813 | lmrB | 99.79 | 100.00 | JYFL01000006.1 |
| KHOMDLFI_1 | 272085 | 273005 | mphK | ARO:3004541 | mphK | 98.68 | 100.00 | CP010314.1 |
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. |
|---|---|---|---|---|---|---|---|
| KHOMDLFI_1 | 2515858 | 2516712 | aadK | Streptomycin | 98.83 | 100.00 | M26879 |
| KHOMDLFI_1 | 272085 | 273005 | mph(K) | Spiramycin, Telithromycin | 98.05 | 100.00 | NC_000964 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| KHOMDLFI_1 | 603142 | 604785 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.91 | 100.00 | WP_003234144.1 |
| KHOMDLFI_1 | 272085 | 272993 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.68 | 99.02 | WP_003246254.1 |
| KHOMDLFI_1 | 2515861 | 2516712 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| KHOMDLFI_1 | 3980468 | 3980986 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 91.91 | 100.00 | WP_003242546.1 |
| KHOMDLFI_1 | 1978329 | 1980926 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.48 | 100.00 | WP_087347987.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| KHOMDLFI_1 | 3512542 | 3512991 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| KHOMDLFI_1 | 3513006 | 3514187 | capB | 0.0 | Capsule | Immune modulation | 99.49 | 100.00 | NP_391471 |
| KHOMDLFI_1 | 3511381 | 3512523 | capA | 0.0 | Capsule | Immune modulation | 99.39 | 100.00 | NP_391469 |
| KHOMDLFI_1 | 3057945 | 3058730 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| KHOMDLFI_1 | 3054109 | 3055047 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.15 | 100.00 | NP_391077 |
| KHOMDLFI_1 | 3056723 | 3057919 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.00 | 100.00 | NP_391079 |
| KHOMDLFI_1 | 1925467 | 1927230 | dep/capD | 0.0 | Capsule | Immune modulation | 98.98 | 100.00 | NP_389723 |
| KHOMDLFI_1 | 2101727 | 2102368 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 98.91 | 100.00 | NP_390062 |
| KHOMDLFI_1 | 3046953 | 3054089 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.63 | 100.00 | NP_391076 |
| KHOMDLFI_1 | 3055075 | 3056694 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.04 | 100.00 | NP_391078 |
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 |
|---|---|---|---|---|---|---|---|---|
| KHOMDLFI_1 | 133860 | 134996 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| KHOMDLFI_1 | 18600 | 19469 | pdxS | 2.98e-149 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| KHOMDLFI_1 | 1674231 | 1675007 | CodY | 3.25e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| KHOMDLFI_1 | 3361766 | 3362335 | ClpP | 2.41e-98 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
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 |
|---|---|---|---|
| KHOMDLFI_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 |
|---|---|---|---|---|---|
| KHOMDLFI_1 | 1306447 | 1335440 | False | Myoviridae | VOG0101, VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG4705 |
| KHOMDLFI_1 | 1799631 | 1831008 | False | Siphoviridae | VOG4552, VOG0650, VOG0535, VOG1936, VOG1227, VOG4606, VOG2752, VOG5607, VOG0044, VOG0198, VOG0531, VOG4841, VOG7403, VOG4581, VOG4544, VOG2935, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619, VOG4626, VOG4612, VOG6243, VOG4705, VOG5221, VOG0136 |
| KHOMDLFI_1 | 3236452 | 3274964 | True | Siphoviridae | VOG0641, VOG4705, VOG6243, VOG4612, VOG4626, VOG4772, VOG0801, VOG5910, VOG0541, VOG4586, VOG0704, VOG9583, VOG0204, VOG10223, VOG4553, VOG4568, VOG4556, VOG3607, VOG1886, VOG4581, VOG0713, VOG4841, VOG0275, VOG0198, VOG0044, VOG0102, VOG0397, VOG5836, VOG0245, VOG1336, VOG6587, VOG0189, VOG4566, VOG7581, VOG9667, VOG9667, VOG1563, VOG0275, VOG0275 |
Phigaro v2.4.0 (Database: Jan. 2024 release)