Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 8 | 18.25 |
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. |
|---|---|---|---|---|---|---|---|---|
| CFHKNLOA_21 | 596088 | 596942 | aadK | ARO:3002627 | aadK | 98.24 | 100.00 | AL009126.1 |
| CFHKNLOA_21 | 566957 | 568159 | blt | ARO:3003006 | blt | 99.00 | 100.00 | L32599.1 |
| CFHKNLOA_21 | 364548 | 365717 | bmr | ARO:3003007 | bmr | 99.23 | 100.00 | M33768.1 |
| CFHKNLOA_3 | 266666 | 269236 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 100.00 | 100.00 | AL009126.3 |
| CFHKNLOA_18 | 221331 | 221669 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| CFHKNLOA_18 | 221014 | 221331 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| CFHKNLOA_16 | 195194 | 196837 | vmlR | ARO:3004476 | vmlR | 98.90 | 100.00 | NC_000964.3 |
| CFHKNLOA_1 | 153627 | 154220 | tmrB | ARO:3003059 | tmrB | 96.95 | 100.00 | AL009126.3 |
| CFHKNLOA_1 | 103074 | 104513 | lmrB | ARO:3002813 | lmrB | 99.79 | 100.42 | JYFL01000006.1 |
| CFHKNLOA_1 | 90260 | 91180 | mphK | ARO:3004541 | mphK | 100.00 | 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. |
|---|---|---|---|---|---|---|---|
| CFHKNLOA_1 | 90260 | 91180 | mph(K) | Spiramycin, Telithromycin | 99.78 | 100.00 | NC_000964 |
| CFHKNLOA_21 | 596090 | 596942 | aadK | Streptomycin | 98.59 | 99.77 | M26879 |
| CFHKNLOA_22 | 40538 | 41914 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 98.40 | 100.00 | D12567 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| CFHKNLOA_1 | 90260 | 91177 | mphK | macrolide 2'-phosphotransferase MphK | EXACTX | 100.00 | 100.00 | WP_003246254.1 |
| CFHKNLOA_16 | 195197 | 196837 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.90 | 100.00 | WP_003234144.1 |
| CFHKNLOA_22 | 40538 | 41911 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.25 | 100.00 | WP_063856081.1 |
| CFHKNLOA_21 | 596091 | 596942 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.24 | 100.00 | WP_003229862.1 |
| CFHKNLOA_22 | 43919 | 44437 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 91.91 | 100.00 | WP_003242546.1 |
| CFHKNLOA_21 | 60829 | 63426 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.94 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| CFHKNLOA_21 | 165363 | 166004 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.84 | 100.00 | NP_390062 |
| CFHKNLOA_22 | 535396 | 536577 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| CFHKNLOA_22 | 948521 | 949306 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.62 | 100.00 | NP_391080 |
| CFHKNLOA_22 | 537060 | 538202 | capA | 0.0 | Capsule | Immune modulation | 99.47 | 100.00 | NP_391469 |
| CFHKNLOA_22 | 536592 | 537041 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| CFHKNLOA_22 | 952204 | 953142 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.25 | 100.00 | NP_391077 |
| CFHKNLOA_22 | 949332 | 950528 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.25 | 100.00 | NP_391079 |
| CFHKNLOA_21 | 10689 | 12452 | dep/capD | 0.0 | Capsule | Immune modulation | 99.15 | 100.00 | NP_389723 |
| CFHKNLOA_22 | 953162 | 960298 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.77 | 100.00 | NP_391076 |
| CFHKNLOA_22 | 950557 | 952176 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.03 | 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 |
|---|---|---|---|---|---|---|---|---|
| CFHKNLOA_6 | 31890 | 33026 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| CFHKNLOA_20 | 16020 | 15151 | pdxS | 1.48e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| CFHKNLOA_19 | 92843 | 93619 | CodY | 3.30e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| CFHKNLOA_22 | 697926 | 697357 | ClpP | 6.39e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| CFHKNLOA_18 | 373136 | 372744 | spxA1 | 4.15e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| CFHKNLOA_18 | 373136 | 372744 | spx | 2.48e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| CFHKNLOA_12 | 23266 | 23508 | SpoVG | 7.89e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| CFHKNLOA_16 | 142299 | 142496 | CspA | 9.76e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| CFHKNLOA_18 | 616299 | 616493 | CspB | 5.99e-27 | cold shock protein | 83.08 | 98.48 | CAD00094 |
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 |
|---|---|---|---|
| CFHKNLOA_1 | 0.0 | 1.0 | 0.0 |
| CFHKNLOA_2 | 0.0 | 1.0 | 0.0 |
| CFHKNLOA_3 | 0.0 | 1.0 | 0.0 |
| CFHKNLOA_4 | 1.0 | 0.0 | 1.0 |
| CFHKNLOA_6 | 0.0 | 1.0 | 0.0 |
| CFHKNLOA_8 | 1.0 | 0.0 | 1.0 |
| CFHKNLOA_12 | 0.0 | 1.0 | 0.0 |
| CFHKNLOA_13 | 1.0 | 0.0 | 1.0 |
| CFHKNLOA_14 | 1.0 | 0.0 | 1.0 |
| CFHKNLOA_15 | 0.0 | 1.0 | 0.0 |
| CFHKNLOA_16 | 0.0 | 1.0 | 0.0 |
| CFHKNLOA_17 | 1.0 | 0.0 | 1.0 |
| CFHKNLOA_18 | 0.0 | 1.0 | 0.0 |
| CFHKNLOA_19 | 0.0 | 1.0 | 0.0 |
| CFHKNLOA_20 | 0.0 | 1.0 | 0.0 |
| CFHKNLOA_21 | 0.0 | 1.0 | 0.0 |
| CFHKNLOA_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 |
|---|---|---|---|---|---|
| CFHKNLOA_18 | 251469 | 278802 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
Phigaro v2.4.0 (Database: Jan. 2024 release)