Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 8 | 17.55 |
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. |
|---|---|---|---|---|---|---|---|---|
| ADFONCBC_2 | 454893 | 455210 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| ADFONCBC_2 | 454555 | 454893 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| ADFONCBC_4 | 365523 | 366692 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| ADFONCBC_3 | 346326 | 347246 | mphK | ARO:3004541 | mphK | 97.71 | 100.00 | CP010314.1 |
| ADFONCBC_3 | 332994 | 334433 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| ADFONCBC_3 | 283366 | 283959 | tmrB | ARO:3003059 | tmrB | 100.00 | 100.00 | AL009126.3 |
| ADFONCBC_7 | 258732 | 261302 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.53 | 100.00 | AL009126.3 |
| ADFONCBC_4 | 139146 | 140348 | blt | ARO:3003006 | blt | 99.50 | 100.00 | L32599.1 |
| ADFONCBC_4 | 122447 | 123301 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| ADFONCBC_3 | 29103 | 30746 | 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. |
|---|---|---|---|---|---|---|---|
| ADFONCBC_4 | 122447 | 123301 | aadK | Streptomycin | 98.83 | 100.00 | M26879 |
| ADFONCBC_3 | 346326 | 347246 | 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. |
|---|---|---|---|---|---|---|---|---|
| ADFONCBC_3 | 29103 | 30743 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 99.09 | 100.00 | WP_003234144.1 |
| ADFONCBC_4 | 122447 | 123298 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| ADFONCBC_3 | 346329 | 347246 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.71 | 100.00 | WP_003246254.1 |
| ADFONCBC_1 | 1028834 | 1029352 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 94.80 | 100.00 | WP_003242546.1 |
| ADFONCBC_6 | 174423 | 177020 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| ADFONCBC_6 | 288300 | 288941 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.69 | 100.00 | NP_390062 |
| ADFONCBC_1 | 536267 | 537448 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| ADFONCBC_1 | 112869 | 113654 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| ADFONCBC_1 | 111647 | 112843 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.33 | 100.00 | NP_391079 |
| ADFONCBC_6 | 128654 | 130417 | dep/capD | 0.0 | Capsule | Immune modulation | 98.98 | 100.00 | NP_389723 |
| ADFONCBC_1 | 534642 | 535784 | capA | 0.0 | Capsule | Immune modulation | 98.69 | 100.00 | NP_391469 |
| ADFONCBC_1 | 535803 | 536252 | capC | 0.0 | Capsule | Immune modulation | 98.67 | 100.00 | NP_391470 |
| ADFONCBC_1 | 109033 | 109971 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.40 | 100.00 | NP_391077 |
| ADFONCBC_1 | 101877 | 109013 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.36 | 100.00 | NP_391076 |
| ADFONCBC_1 | 109999 | 111618 | 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 |
|---|---|---|---|---|---|---|---|---|
| ADFONCBC_10 | 31733 | 32869 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| ADFONCBC_11 | 4359 | 5228 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| ADFONCBC_2 | 763662 | 764438 | CodY | 7.07e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| ADFONCBC_1 | 377691 | 378260 | ClpP | 6.43e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| ADFONCBC_2 | 277328 | 277720 | spxA1 | 5.56e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| ADFONCBC_2 | 277328 | 277720 | spx | 3.31e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| ADFONCBC_9 | 20607 | 20849 | SpoVG | 7.51e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| ADFONCBC_3 | 74539 | 74342 | CspA | 1.91e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| ADFONCBC_6 | 300173 | 300367 | CspD | 9.00e-28 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| ADFONCBC_6 | 300173 | 300370 | CspB | 1.87e-27 | cold shock protein | 80.30 | 100.00 | 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 |
|---|---|---|---|
| ADFONCBC_1 | 0.0 | 1.0 | 0.0 |
| ADFONCBC_2 | 0.0 | 1.0 | 0.0 |
| ADFONCBC_3 | 0.0 | 1.0 | 0.0 |
| ADFONCBC_4 | 0.0 | 1.0 | 0.0 |
| ADFONCBC_5 | 0.0 | 1.0 | 0.0 |
| ADFONCBC_6 | 0.0 | 1.0 | 0.0 |
| ADFONCBC_7 | 0.0 | 1.0 | 0.0 |
| ADFONCBC_8 | 0.0 | 1.0 | 0.0 |
| ADFONCBC_9 | 0.0 | 1.0 | 0.0 |
| ADFONCBC_10 | 0.0 | 1.0 | 0.0 |
| ADFONCBC_11 | 0.0 | 1.0 | 0.0 |
| ADFONCBC_12 | 0.0 | 1.0 | 0.0 |
| ADFONCBC_14 | 0.0 | 1.0 | 0.0 |
| ADFONCBC_15 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| ADFONCBC_2 | 397458 | 424739 | 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 |
| ADFONCBC_4 | 176252 | 194020 | False | Myoviridae | VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG0906, VOG7718 |
| ADFONCBC_5 | 152407 | 174138 | False | Siphoviridae | VOG4841, VOG4581, VOG1886, VOG0202, VOG4556, VOG4573, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619, VOG4626, VOG4612, VOG6243, VOG4705, VOG0641 |
| ADFONCBC_5 | 344896 | 377772 | False | Siphoviridae | VOG7438, VOG1047, VOG0021, VOG1565, VOG0026, VOG4609, VOG0327, VOG4548, VOG0198, VOG4556, VOG4581, VOG1886, VOG3607, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619, VOG4626, VOG4612, VOG6243, VOG4705, VOG0641, VOG4574 |
Phigaro v2.4.0 (Database: Jan. 2024 release)