Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 7 | 17.12 |
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. |
|---|---|---|---|---|---|---|---|---|
| KCLPBONO_4 | 1758140 | 1758994 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| KCLPBONO_4 | 1741047 | 1742249 | blt | ARO:3003006 | blt | 99.50 | 100.00 | L32599.1 |
| KCLPBONO_4 | 1509097 | 1510266 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| KCLPBONO_4 | 577661 | 577978 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| KCLPBONO_4 | 577323 | 577661 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| KCLPBONO_3 | 346285 | 347205 | mphK | ARO:3004541 | mphK | 97.71 | 100.00 | CP010314.1 |
| KCLPBONO_3 | 332952 | 334391 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.42 | JYFL01000006.1 |
| KCLPBONO_3 | 283322 | 283915 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| KCLPBONO_10 | 125772 | 128342 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| KCLPBONO_3 | 29036 | 30679 | vmlR | ARO:3004476 | vmlR | 99.09 | 100.00 | NC_000964.3 |
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. |
|---|---|---|---|---|---|---|---|
| KCLPBONO_4 | 1758140 | 1758994 | aadK | Streptomycin | 98.83 | 100.00 | M26879 |
| KCLPBONO_3 | 346285 | 347205 | mph(K) | Spiramycin, Telithromycin | 97.72 | 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. |
|---|---|---|---|---|---|---|---|---|
| KCLPBONO_3 | 29036 | 30676 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 99.09 | 100.00 | WP_003234144.1 |
| KCLPBONO_4 | 1758143 | 1758994 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| KCLPBONO_3 | 346288 | 347205 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.71 | 100.00 | WP_003246254.1 |
| KCLPBONO_2 | 930492 | 931010 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 94.80 | 100.00 | WP_003242546.1 |
| KCLPBONO_4 | 1171025 | 1173622 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.41 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| KCLPBONO_4 | 1296349 | 1296990 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.69 | 100.00 | NP_390062 |
| KCLPBONO_2 | 433129 | 434310 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| KCLPBONO_6 | 112967 | 113752 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| KCLPBONO_6 | 111745 | 112941 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.17 | 100.00 | NP_391079 |
| KCLPBONO_4 | 1124006 | 1125769 | dep/capD | 0.0 | Capsule | Immune modulation | 99.04 | 100.00 | NP_389723 |
| KCLPBONO_2 | 431504 | 432646 | capA | 0.0 | Capsule | Immune modulation | 98.69 | 100.00 | NP_391469 |
| KCLPBONO_2 | 432665 | 433114 | capC | 0.0 | Capsule | Immune modulation | 98.67 | 100.00 | NP_391470 |
| KCLPBONO_6 | 109131 | 110069 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.62 | 100.00 | NP_391077 |
| KCLPBONO_6 | 101975 | 109111 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.53 | 100.00 | NP_391076 |
| KCLPBONO_6 | 110097 | 111716 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.53 | 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 |
|---|---|---|---|---|---|---|---|---|
| KCLPBONO_9 | 31659 | 32795 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| KCLPBONO_13 | 4495 | 5364 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| KCLPBONO_4 | 886423 | 887199 | CodY | 1.78e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| KCLPBONO_2 | 267735 | 268304 | ClpP | 5.84e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| KCLPBONO_4 | 277085 | 277477 | spxA1 | 1.40e-69 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| KCLPBONO_4 | 277085 | 277477 | spx | 8.34e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| KCLPBONO_7 | 20501 | 20743 | SpoVG | 7.48e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| KCLPBONO_3 | 74414 | 74217 | CspA | 1.91e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
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 |
|---|---|---|---|
| KCLPBONO_1 | 0.0 | 1.0 | 0.0 |
| KCLPBONO_2 | 0.0 | 1.0 | 0.0 |
| KCLPBONO_3 | 0.0 | 1.0 | 0.0 |
| KCLPBONO_4 | 0.0 | 1.0 | 0.0 |
| KCLPBONO_6 | 0.0 | 1.0 | 0.0 |
| KCLPBONO_7 | 0.0 | 1.0 | 0.0 |
| KCLPBONO_8 | 0.0 | 1.0 | 0.0 |
| KCLPBONO_9 | 0.0 | 1.0 | 0.0 |
| KCLPBONO_10 | 0.0 | 1.0 | 0.0 |
| KCLPBONO_13 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| KCLPBONO_1 | 11722 | 19914 | False | Siphoviridae | VOG0275, VOG4602, VOG9667, VOG9667, VOG0650, VOG4552, VOG4603, VOG8233, VOG0186 |
| KCLPBONO_1 | 21628 | 43924 | False | Siphoviridae | VOG1985, VOG0198, VOG0713, VOG4841, VOG4581, VOG1886, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619 |
| KCLPBONO_2 | 1 | 23450 | False | Siphoviridae | VOG4612, VOG4626, VOG4619, VOG0801, VOG6163, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5361, VOG4553, VOG4568, VOG4556, VOG3644, VOG1886, VOG4581, VOG4556, VOG4841, VOG0198, VOG1884, VOG0025, VOG9600 |
| KCLPBONO_2 | 230905 | 258676 | False | Siphoviridae | VOG0705, VOG7531, VOG7508, VOG0602, VOG4666, VOG5221, VOG4705, VOG3390, VOG4612, VOG4626, VOG4619, VOG0801, VOG4545, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5601, VOG4553, VOG4573, VOG4556, VOG4544, VOG4581, VOG4841, VOG1655 |
| KCLPBONO_4 | 314013 | 325369 | False | Siphoviridae | VOG6013, VOG5526, VOG0026, VOG8598, VOG8506, VOG4551, VOG0025, VOG0189, VOG3490 |
| KCLPBONO_4 | 520226 | 547507 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG4705 |
| KCLPBONO_4 | 1687375 | 1705143 | False | Myoviridae | VOG4705, VOG7718, VOG0906, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749 |
Phigaro v2.4.0 (Database: Jan. 2024 release)