Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 7 | 17.12 |
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. |
|---|---|---|---|---|---|---|---|---|
| EFAHGJHA_8 | 673753 | 674922 | bmr | ARO:3003007 | bmr | 98.71 | 100.00 | M33768.1 |
| EFAHGJHA_8 | 477662 | 478864 | blt | ARO:3003006 | blt | 99.75 | 100.00 | L32599.1 |
| EFAHGJHA_1 | 458670 | 458987 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| EFAHGJHA_1 | 458332 | 458670 | ykkC | ARO:3003063 | ykkC | 99.11 | 100.00 | AL009126.1 |
| EFAHGJHA_8 | 448342 | 449196 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| EFAHGJHA_12 | 110046 | 110966 | mphK | ARO:3004541 | mphK | 98.35 | 100.00 | CP010314.1 |
| EFAHGJHA_12 | 96726 | 98159 | lmrB | ARO:3002813 | lmrB | 98.74 | 100.00 | JYFL01000006.1 |
| EFAHGJHA_12 | 47021 | 47614 | tmrB | ARO:3003059 | tmrB | 96.95 | 100.00 | AL009126.3 |
| EFAHGJHA_11 | 29376 | 31022 | vmlR | ARO:3004476 | vmlR | 98.18 | 100.18 | NC_000964.3 |
| EFAHGJHA_10 | 27465 | 30035 | 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. |
|---|---|---|---|---|---|---|---|
| EFAHGJHA_12 | 110046 | 110966 | mph(K) | Spiramycin, Telithromycin | 98.37 | 100.00 | NC_000964 |
| EFAHGJHA_8 | 448342 | 449196 | aadK | Streptomycin | 98.25 | 100.00 | M26879 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| EFAHGJHA_8 | 448342 | 449193 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| EFAHGJHA_12 | 110058 | 110966 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.35 | 99.02 | WP_003246254.1 |
| EFAHGJHA_11 | 29376 | 31019 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.18 | 100.00 | WP_003234144.1 |
| EFAHGJHA_9 | 39690 | 40208 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 94.22 | 100.00 | WP_003242546.1 |
| EFAHGJHA_1 | 1117999 | 1120596 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.17 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| EFAHGJHA_1 | 1212914 | 1213555 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.69 | 100.00 | NP_390062 |
| EFAHGJHA_9 | 528492 | 529673 | capB | 0.0 | Capsule | Immune modulation | 99.32 | 100.00 | NP_391471 |
| EFAHGJHA_9 | 935703 | 936488 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.98 | 100.00 | NP_391080 |
| EFAHGJHA_1 | 1072447 | 1074210 | dep/capD | 0.0 | Capsule | Immune modulation | 98.92 | 100.00 | NP_389723 |
| EFAHGJHA_9 | 529688 | 530137 | capC | 0.0 | Capsule | Immune modulation | 98.89 | 100.00 | NP_391470 |
| EFAHGJHA_9 | 530156 | 531298 | capA | 0.0 | Capsule | Immune modulation | 98.78 | 100.00 | NP_391469 |
| EFAHGJHA_9 | 939387 | 940325 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.40 | 100.00 | NP_391077 |
| EFAHGJHA_9 | 940345 | 947481 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.46 | 99.99 | NP_391076 |
| EFAHGJHA_9 | 937740 | 939359 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 96.79 | 100.00 | NP_391078 |
| EFAHGJHA_9 | 936515 | 937711 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 96.66 | 100.00 | NP_391079 |
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 |
|---|---|---|---|---|---|---|---|---|
| EFAHGJHA_13 | 31841 | 32977 | tufA | 0.0 | elongation factor Tu | 85.22 | 95.69 | AHM69299 |
| EFAHGJHA_15 | 11338 | 10469 | pdxS | 2.54e-152 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 84.14 | 98.31 | ACE61268 |
| EFAHGJHA_1 | 769388 | 770164 | CodY | 1.12e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| EFAHGJHA_9 | 671792 | 671223 | ClpP | 6.31e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| EFAHGJHA_1 | 271726 | 272118 | spxA1 | 5.53e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| EFAHGJHA_1 | 271726 | 272118 | spx | 8.86e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| EFAHGJHA_14 | 34783 | 34541 | SpoVG | 7.53e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| EFAHGJHA_11 | 78079 | 77882 | CspA | 9.58e-32 | 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 |
|---|---|---|---|
| EFAHGJHA_1 | 0.0 | 1.0 | 0.0 |
| EFAHGJHA_2 | 0.0 | 1.0 | 0.0 |
| EFAHGJHA_3 | 0.0 | 1.0 | 0.0 |
| EFAHGJHA_4 | 0.0 | 1.0 | 0.0 |
| EFAHGJHA_8 | 0.0 | 1.0 | 0.0 |
| EFAHGJHA_9 | 0.0 | 1.0 | 0.0 |
| EFAHGJHA_10 | 0.0 | 1.0 | 0.0 |
| EFAHGJHA_11 | 0.0 | 1.0 | 0.0 |
| EFAHGJHA_12 | 0.0 | 1.0 | 0.0 |
| EFAHGJHA_13 | 0.0 | 1.0 | 0.0 |
| EFAHGJHA_14 | 0.0 | 1.0 | 0.0 |
| EFAHGJHA_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 |
|---|---|---|---|---|---|
| EFAHGJHA_1 | 402290 | 428459 | 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)