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. |
|---|---|---|---|---|---|---|---|---|
| APDHJNMF_2 | 678903 | 680072 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| APDHJNMF_11 | 534104 | 534442 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| APDHJNMF_11 | 533787 | 534104 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| APDHJNMF_2 | 505601 | 506803 | blt | ARO:3003006 | blt | 99.25 | 100.00 | L32599.1 |
| APDHJNMF_2 | 488987 | 489841 | aadK | ARO:3002627 | aadK | 97.54 | 100.00 | AL009126.1 |
| APDHJNMF_14 | 183844 | 185487 | vmlR | ARO:3004476 | vmlR | 98.35 | 100.00 | NC_000964.3 |
| APDHJNMF_15 | 116868 | 117461 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| APDHJNMF_15 | 66393 | 67832 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.42 | JYFL01000006.1 |
| APDHJNMF_15 | 53579 | 54499 | mphK | ARO:3004541 | mphK | 97.71 | 100.00 | CP010314.1 |
| APDHJNMF_13 | 27474 | 30044 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.65 | 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. |
|---|---|---|---|---|---|---|---|
| APDHJNMF_1 | 34613 | 35989 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 99.27 | 100.00 | D12567 |
| APDHJNMF_2 | 488987 | 489839 | aadK | Streptomycin | 98.48 | 99.77 | M26879 |
| APDHJNMF_15 | 53579 | 54499 | mph(K) | Spiramycin, Telithromycin | 97.61 | 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. |
|---|---|---|---|---|---|---|---|---|
| APDHJNMF_1 | 34613 | 35986 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.91 | 100.00 | WP_063856081.1 |
| APDHJNMF_14 | 183847 | 185487 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.35 | 100.00 | WP_003234144.1 |
| APDHJNMF_15 | 53579 | 54496 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.71 | 100.00 | WP_003246254.1 |
| APDHJNMF_2 | 488987 | 489838 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.54 | 100.00 | WP_003229862.1 |
| APDHJNMF_1 | 37988 | 38506 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 89.60 | 100.00 | WP_003242546.1 |
| APDHJNMF_16 | 62834 | 65431 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.60 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| APDHJNMF_2 | 876732 | 877373 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.69 | 100.00 | NP_390062 |
| APDHJNMF_1 | 515399 | 516580 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| APDHJNMF_1 | 934219 | 935004 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| APDHJNMF_1 | 935030 | 936226 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.33 | 100.00 | NP_391079 |
| APDHJNMF_16 | 8516 | 10279 | dep/capD | 0.0 | Capsule | Immune modulation | 98.98 | 100.00 | NP_389723 |
| APDHJNMF_1 | 517063 | 518205 | capA | 0.0 | Capsule | Immune modulation | 98.95 | 100.00 | NP_391469 |
| APDHJNMF_1 | 516595 | 517044 | capC | 0.0 | Capsule | Immune modulation | 98.67 | 100.00 | NP_391470 |
| APDHJNMF_1 | 938860 | 945994 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.42 | 99.97 | NP_391076 |
| APDHJNMF_1 | 937902 | 938840 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.40 | 100.00 | NP_391077 |
| APDHJNMF_1 | 936255 | 937874 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.41 | 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 |
|---|---|---|---|---|---|---|---|---|
| APDHJNMF_4 | 31881 | 33017 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| APDHJNMF_7 | 11332 | 10463 | pdxS | 2.59e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.45 | 98.31 | ACE61268 |
| APDHJNMF_11 | 223929 | 223153 | CodY | 5.04e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| APDHJNMF_1 | 677864 | 677295 | ClpP | 6.30e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| APDHJNMF_12 | 273489 | 273881 | spxA1 | 2.45e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| APDHJNMF_12 | 273489 | 273881 | spx | 1.46e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| APDHJNMF_5 | 34770 | 34528 | SpoVG | 7.54e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| APDHJNMF_14 | 141711 | 141908 | CspA | 9.27e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| APDHJNMF_12 | 31159 | 30965 | CspB | 3.52e-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 |
|---|---|---|---|
| APDHJNMF_1 | 0.0 | 1.0 | 0.0 |
| APDHJNMF_2 | 0.0 | 1.0 | 0.0 |
| APDHJNMF_3 | 1.0 | 0.0 | 1.0 |
| APDHJNMF_4 | 0.0 | 1.0 | 0.0 |
| APDHJNMF_5 | 0.0 | 1.0 | 0.0 |
| APDHJNMF_6 | 0.0 | 1.0 | 0.0 |
| APDHJNMF_7 | 0.0 | 1.0 | 0.0 |
| APDHJNMF_8 | 0.0 | 1.0 | 0.0 |
| APDHJNMF_9 | 0.0 | 1.0 | 0.0 |
| APDHJNMF_10 | 0.0 | 1.0 | 0.0 |
| APDHJNMF_11 | 0.0 | 1.0 | 0.0 |
| APDHJNMF_12 | 0.0 | 1.0 | 0.0 |
| APDHJNMF_13 | 0.0 | 1.0 | 0.0 |
| APDHJNMF_14 | 0.0 | 1.0 | 0.0 |
| APDHJNMF_15 | 0.0 | 1.0 | 0.0 |
| APDHJNMF_16 | 0.0 | 1.0 | 0.0 |
| APDHJNMF_17 | 0.0 | 1.0 | 0.0 |
| APDHJNMF_18 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| APDHJNMF_3 | 29964 | 41892 | False | Siphoviridae | VOG6211, VOG0322, VOG7476, VOG0025, VOG4551, VOG0918 |
| APDHJNMF_6 | 15460 | 45309 | False | Myoviridae | VOG4600, VOG1309, VOG11060, VOG0189, VOG4693, VOG4673, VOG0796, VOG9315, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718 |
| APDHJNMF_11 | 565218 | 571765 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894 |
| APDHJNMF_12 | 369098 | 377301 | False | Unknown | VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773 |
| APDHJNMF_17 | 18764 | 46014 | False | Siphoviridae | VOG7134, VOG9867, VOG6036, VOG5495, VOG9219, VOG9713, VOG6940, VOG5534, VOG7718, VOG4705, VOG8610, VOG7930, VOG0275, VOG9312, VOG4910, VOG3389, VOG5042, VOG9712, VOG7900, VOG4707 |
Phigaro v2.4.0 (Database: Jan. 2024 release)