Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 11 | 10 | 7 | 16.43 |
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. |
|---|---|---|---|---|---|---|---|---|
| PJAFHMCM_7 | 637417 | 638586 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| PJAFHMCM_7 | 467388 | 468590 | blt | ARO:3003006 | blt | 99.00 | 100.00 | L32599.1 |
| PJAFHMCM_7 | 438516 | 439370 | aadK | ARO:3002627 | aadK | 99.30 | 100.00 | AL009126.1 |
| PJAFHMCM_6 | 427636 | 427953 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| PJAFHMCM_6 | 427298 | 427636 | ykkC | ARO:3003063 | ykkC | 98.21 | 100.00 | AL009126.1 |
| PJAFHMCM_8 | 355078 | 355998 | mphK | ARO:3004541 | mphK | 98.69 | 100.00 | CP010314.1 |
| PJAFHMCM_8 | 341743 | 343182 | lmrB | ARO:3002813 | lmrB | 99.58 | 100.42 | JYFL01000006.1 |
| PJAFHMCM_8 | 292029 | 292622 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| PJAFHMCM_9 | 267173 | 269743 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| PJAFHMCM_8 | 28766 | 30412 | vmlR | ARO:3004476 | vmlR | 98.54 | 100.18 | 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. |
|---|---|---|---|---|---|---|---|
| PJAFHMCM_7 | 438516 | 439370 | aadK | Streptomycin | 99.18 | 100.00 | M26879 |
| PJAFHMCM_8 | 355078 | 355998 | mph(K) | Spiramycin, Telithromycin | 99.02 | 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. |
|---|---|---|---|---|---|---|---|---|
| PJAFHMCM_7 | 438516 | 439367 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 99.30 | 100.00 | WP_003229862.1 |
| PJAFHMCM_8 | 355081 | 355998 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.69 | 100.00 | WP_003246254.1 |
| PJAFHMCM_8 | 28766 | 30409 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.54 | 100.00 | WP_003234144.1 |
| PJAFHMCM_7 | 931200 | 933797 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.29 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| PJAFHMCM_5 | 523215 | 523664 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| PJAFHMCM_5 | 523679 | 524860 | capB | 0.0 | Capsule | Immune modulation | 99.49 | 100.00 | NP_391471 |
| PJAFHMCM_5 | 113478 | 114263 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| PJAFHMCM_7 | 837333 | 837974 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.22 | 100.00 | NP_390062 |
| PJAFHMCM_5 | 522054 | 523196 | capA | 0.0 | Capsule | Immune modulation | 99.21 | 100.00 | NP_391469 |
| PJAFHMCM_5 | 112256 | 113452 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.00 | 100.00 | NP_391079 |
| PJAFHMCM_5 | 102486 | 109622 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.92 | 100.00 | NP_391076 |
| PJAFHMCM_5 | 110608 | 112227 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.64 | 100.00 | NP_391078 |
| PJAFHMCM_7 | 981650 | 983413 | dep/capD | 0.0 | Capsule | Immune modulation | 98.58 | 100.00 | NP_389723 |
| PJAFHMCM_5 | 109642 | 110580 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.08 | 100.00 | NP_391077 |
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 |
|---|---|---|---|---|---|---|---|---|
| PJAFHMCM_10 | 31745 | 32881 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| PJAFHMCM_12 | 11198 | 10329 | pdxS | 1.11e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| PJAFHMCM_6 | 737665 | 738441 | CodY | 8.40e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PJAFHMCM_5 | 366965 | 367534 | ClpP | 6.38e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| PJAFHMCM_6 | 276398 | 276790 | spxA1 | 6.60e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| PJAFHMCM_6 | 276398 | 276790 | spx | 3.94e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| PJAFHMCM_11 | 20557 | 20799 | SpoVG | 7.50e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| PJAFHMCM_8 | 85684 | 85487 | CspA | 1.93e-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. |
|---|---|---|---|---|---|---|
| PJAFHMCM_1 | 256 | 449 | Col(SD853) | 194 / 194 | 99.48 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| PJAFHMCM_1 | 1.0 | 0.0 | 1.0 |
| PJAFHMCM_5 | 0.0 | 1.0 | 0.0 |
| PJAFHMCM_6 | 0.0 | 1.0 | 0.0 |
| PJAFHMCM_7 | 0.0 | 1.0 | 0.0 |
| PJAFHMCM_8 | 0.0 | 1.0 | 0.0 |
| PJAFHMCM_9 | 0.0 | 1.0 | 0.0 |
| PJAFHMCM_10 | 0.0 | 1.0 | 0.0 |
| PJAFHMCM_11 | 0.0 | 1.0 | 0.0 |
| PJAFHMCM_12 | 0.0 | 1.0 | 0.0 |
| PJAFHMCM_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 |
|---|---|---|---|---|---|
| PJAFHMCM_6 | 369935 | 397430 | 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 |
Phigaro v2.4.0 (Database: Jan. 2024 release)