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. |
|---|---|---|---|---|---|---|---|---|
| AGFOBADK_2 | 553206 | 554060 | aadK | ARO:3002627 | aadK | 97.54 | 100.00 | AL009126.1 |
| AGFOBADK_2 | 534038 | 535240 | blt | ARO:3003006 | blt | 99.75 | 100.00 | L32599.1 |
| AGFOBADK_3 | 428138 | 428455 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| AGFOBADK_3 | 427800 | 428138 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| AGFOBADK_4 | 402742 | 404388 | vmlR | ARO:3004476 | vmlR | 98.54 | 100.18 | NC_000964.3 |
| AGFOBADK_2 | 362185 | 363354 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| AGFOBADK_4 | 161704 | 162297 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| AGFOBADK_4 | 111146 | 112585 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| AGFOBADK_4 | 98333 | 99253 | mphK | ARO:3004541 | mphK | 98.37 | 100.00 | CP010314.1 |
| AGFOBADK_5 | 27543 | 30113 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 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. |
|---|---|---|---|---|---|---|---|
| AGFOBADK_1 | 1023551 | 1024927 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 100.00 | 100.00 | X08034 |
| AGFOBADK_2 | 553208 | 554060 | aadK | Streptomycin | 98.12 | 99.77 | M26879 |
| AGFOBADK_4 | 98333 | 99253 | mph(K) | Spiramycin, Telithromycin | 97.94 | 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. |
|---|---|---|---|---|---|---|---|---|
| AGFOBADK_1 | 1023554 | 1024927 | tet(L) | tetracycline efflux MFS transporter Tet(L) | EXACTX | 100.00 | 100.00 | WP_003242953.1 |
| AGFOBADK_4 | 402745 | 404388 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.54 | 100.00 | WP_003234144.1 |
| AGFOBADK_4 | 98333 | 99250 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.37 | 100.00 | WP_003246254.1 |
| AGFOBADK_2 | 553209 | 554060 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.54 | 100.00 | WP_003229862.1 |
| AGFOBADK_1 | 1021080 | 1021598 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| AGFOBADK_2 | 58476 | 61073 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.40 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| AGFOBADK_2 | 163016 | 163657 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 100.00 | 100.00 | NP_390062 |
| AGFOBADK_1 | 527388 | 528569 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| AGFOBADK_1 | 525763 | 526905 | capA | 0.0 | Capsule | Immune modulation | 99.39 | 100.00 | NP_391469 |
| AGFOBADK_1 | 109299 | 110237 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391077 |
| AGFOBADK_1 | 526924 | 527373 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| AGFOBADK_1 | 113135 | 113920 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.24 | 100.00 | NP_391080 |
| AGFOBADK_1 | 111913 | 113109 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.17 | 100.00 | NP_391079 |
| AGFOBADK_2 | 8403 | 10166 | dep/capD | 0.0 | Capsule | Immune modulation | 99.15 | 100.00 | NP_389723 |
| AGFOBADK_1 | 102143 | 109279 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.06 | 100.00 | NP_391076 |
| AGFOBADK_1 | 110265 | 111884 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.52 | 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 |
|---|---|---|---|---|---|---|---|---|
| AGFOBADK_8 | 31930 | 33066 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| AGFOBADK_11 | 11403 | 10534 | pdxS | 1.13e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| AGFOBADK_3 | 738288 | 739064 | CodY | 7.90e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| AGFOBADK_1 | 366044 | 366613 | ClpP | 2.16e-98 | part of proteolytic complex | 80.53 | 97.44 | BAB94595 |
| AGFOBADK_3 | 275586 | 275978 | spxA1 | 2.34e-69 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| AGFOBADK_10 | 34867 | 34625 | SpoVG | 7.53e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| AGFOBADK_4 | 355988 | 356185 | 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 |
|---|---|---|---|
| AGFOBADK_1 | 0.0 | 1.0 | 0.0 |
| AGFOBADK_2 | 0.0 | 1.0 | 0.0 |
| AGFOBADK_3 | 0.0 | 1.0 | 0.0 |
| AGFOBADK_4 | 0.0 | 1.0 | 0.0 |
| AGFOBADK_5 | 0.0 | 1.0 | 0.0 |
| AGFOBADK_6 | 0.0 | 1.0 | 0.0 |
| AGFOBADK_7 | 0.0 | 1.0 | 0.0 |
| AGFOBADK_8 | 0.0 | 1.0 | 0.0 |
| AGFOBADK_9 | 0.0 | 1.0 | 0.0 |
| AGFOBADK_10 | 0.0 | 1.0 | 0.0 |
| AGFOBADK_11 | 0.0 | 1.0 | 0.0 |
| AGFOBADK_12 | 0.0 | 1.0 | 0.0 |
| AGFOBADK_16 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| AGFOBADK_3 | 370417 | 398313 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG3390, VOG4705 |
| AGFOBADK_3 | 942464 | 966055 | False | Siphoviridae | VOG4841, VOG4581, VOG1886, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619, VOG4626, VOG3390, VOG4705, VOG4612, VOG3390, VOG7896 |
| AGFOBADK_6 | 102054 | 107616 | False | Unknown | VOG6211, VOG0322, VOG7476, VOG0025 |
| AGFOBADK_9 | 12973 | 35029 | False | Myoviridae | VOG10227, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4691, VOG4862 |
Phigaro v2.4.0 (Database: Jan. 2024 release)