Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 7 | 17.83 |
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. |
|---|---|---|---|---|---|---|---|---|
| PJDHMHBC_7 | 568578 | 569432 | aadK | ARO:3002627 | aadK | 98.24 | 100.00 | AL009126.1 |
| PJDHMHBC_7 | 549789 | 550991 | blt | ARO:3003006 | blt | 99.75 | 100.00 | L32599.1 |
| PJDHMHBC_6 | 425762 | 426079 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| PJDHMHBC_6 | 425424 | 425762 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| PJDHMHBC_8 | 401721 | 403367 | vmlR | ARO:3004476 | vmlR | 98.91 | 100.18 | NC_000964.3 |
| PJDHMHBC_7 | 357539 | 358708 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| PJDHMHBC_8 | 155706 | 156299 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| PJDHMHBC_8 | 105150 | 106589 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.42 | JYFL01000006.1 |
| PJDHMHBC_8 | 92337 | 93257 | mphK | ARO:3004541 | mphK | 97.39 | 100.00 | CP010314.1 |
| PJDHMHBC_9 | 27474 | 30044 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 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. |
|---|---|---|---|---|---|---|---|
| PJDHMHBC_5 | 34673 | 36049 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 99.13 | 100.00 | D12567 |
| PJDHMHBC_7 | 568580 | 569432 | aadK | Streptomycin | 98.59 | 99.77 | M26879 |
| PJDHMHBC_8 | 92337 | 93257 | mph(K) | Spiramycin, Telithromycin | 96.96 | 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. |
|---|---|---|---|---|---|---|---|---|
| PJDHMHBC_5 | 34673 | 36046 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.91 | 100.00 | WP_063856081.1 |
| PJDHMHBC_8 | 401724 | 403367 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.91 | 100.00 | WP_003234144.1 |
| PJDHMHBC_7 | 568581 | 569432 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.24 | 100.00 | WP_003229862.1 |
| PJDHMHBC_8 | 92337 | 93254 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.39 | 100.00 | WP_003246254.1 |
| PJDHMHBC_5 | 38061 | 38579 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| PJDHMHBC_7 | 59543 | 62140 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.71 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| PJDHMHBC_7 | 9494 | 11257 | dep/capD | 0.0 | Capsule | Immune modulation | 99.89 | 100.00 | NP_389723 |
| PJDHMHBC_7 | 154690 | 155331 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.84 | 100.00 | NP_390062 |
| PJDHMHBC_5 | 535210 | 536391 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| PJDHMHBC_5 | 941377 | 942162 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.62 | 100.00 | NP_391080 |
| PJDHMHBC_5 | 536406 | 536855 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| PJDHMHBC_5 | 536874 | 538016 | capA | 0.0 | Capsule | Immune modulation | 99.30 | 100.00 | NP_391469 |
| PJDHMHBC_5 | 946018 | 953154 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.17 | 100.00 | NP_391076 |
| PJDHMHBC_5 | 942188 | 943384 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.91 | 100.00 | NP_391079 |
| PJDHMHBC_5 | 943413 | 945032 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.52 | 100.00 | NP_391078 |
| PJDHMHBC_5 | 945060 | 945998 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.30 | 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 |
|---|---|---|---|---|---|---|---|---|
| PJDHMHBC_11 | 31799 | 32935 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| PJDHMHBC_13 | 11332 | 10463 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| PJDHMHBC_6 | 737479 | 738255 | CodY | 8.31e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PJDHMHBC_5 | 690897 | 690328 | ClpP | 6.34e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| PJDHMHBC_6 | 276740 | 277132 | spxA1 | 6.53e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| PJDHMHBC_6 | 276740 | 277132 | spx | 3.90e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| PJDHMHBC_12 | 20641 | 20883 | SpoVG | 7.53e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| PJDHMHBC_8 | 353742 | 353939 | CspA | 1.87e-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 |
|---|---|---|---|
| PJDHMHBC_1 | 0.0 | 1.0 | 0.0 |
| PJDHMHBC_2 | 0.0 | 1.0 | 0.0 |
| PJDHMHBC_3 | 0.0 | 1.0 | 0.0 |
| PJDHMHBC_5 | 0.0 | 1.0 | 0.0 |
| PJDHMHBC_6 | 0.0 | 1.0 | 0.0 |
| PJDHMHBC_7 | 0.0 | 1.0 | 0.0 |
| PJDHMHBC_8 | 0.0 | 1.0 | 0.0 |
| PJDHMHBC_9 | 0.0 | 1.0 | 0.0 |
| PJDHMHBC_10 | 1.0 | 0.0 | 1.0 |
| PJDHMHBC_11 | 0.0 | 1.0 | 0.0 |
| PJDHMHBC_12 | 0.0 | 1.0 | 0.0 |
| PJDHMHBC_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 |
|---|---|---|---|---|---|
| PJDHMHBC_6 | 369602 | 395964 | False | Myoviridae | VOG4602, VOG9667, VOG10599, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG4612, VOG4705 |
| PJDHMHBC_10 | 56266 | 79446 | False | Siphoviridae | VOG0221, VOG4581, VOG4544, VOG4556, VOG4568, VOG4553, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG5852, VOG6163, VOG4605, VOG4599, VOG9244, VOG10944 |
Phigaro v2.4.0 (Database: Jan. 2024 release)