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. |
|---|---|---|---|---|---|---|---|---|
| LENEAMHB_1 | 624584 | 625438 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| LENEAMHB_1 | 606004 | 607206 | blt | ARO:3003006 | blt | 99.00 | 100.00 | L32599.1 |
| LENEAMHB_1 | 432727 | 433896 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| LENEAMHB_2 | 431042 | 431359 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| LENEAMHB_2 | 430704 | 431042 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| LENEAMHB_5 | 276501 | 279071 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| LENEAMHB_6 | 190934 | 192580 | vmlR | ARO:3004476 | vmlR | 98.91 | 100.18 | NC_000964.3 |
| LENEAMHB_7 | 108040 | 108960 | mphK | ARO:3004541 | mphK | 98.69 | 100.00 | CP010314.1 |
| LENEAMHB_7 | 94714 | 96147 | lmrB | ARO:3002813 | lmrB | 99.58 | 100.00 | JYFL01000006.1 |
| LENEAMHB_7 | 44997 | 45590 | tmrB | ARO:3003059 | tmrB | 98.48 | 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. |
|---|---|---|---|---|---|---|---|
| LENEAMHB_7 | 108040 | 108960 | mph(K) | Spiramycin, Telithromycin | 99.35 | 100.00 | NC_000964 |
| LENEAMHB_1 | 624584 | 625438 | aadK | Streptomycin | 98.83 | 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. |
|---|---|---|---|---|---|---|---|---|
| LENEAMHB_6 | 190937 | 192580 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.91 | 100.00 | WP_003234144.1 |
| LENEAMHB_7 | 108043 | 108960 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.69 | 100.00 | WP_003246254.1 |
| LENEAMHB_1 | 624587 | 625438 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| LENEAMHB_4 | 38226 | 38744 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 93.64 | 100.00 | WP_003242546.1 |
| LENEAMHB_1 | 139046 | 141643 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.41 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| LENEAMHB_3 | 172113 | 173294 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| LENEAMHB_1 | 235425 | 236066 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.69 | 100.00 | NP_390062 |
| LENEAMHB_3 | 575275 | 576060 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| LENEAMHB_3 | 576086 | 577282 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.33 | 100.00 | NP_391079 |
| LENEAMHB_1 | 93403 | 95166 | dep/capD | 0.0 | Capsule | Immune modulation | 98.98 | 100.00 | NP_389723 |
| LENEAMHB_3 | 173777 | 174919 | capA | 0.0 | Capsule | Immune modulation | 98.95 | 100.00 | NP_391469 |
| LENEAMHB_3 | 173309 | 173758 | capC | 0.0 | Capsule | Immune modulation | 98.89 | 100.00 | NP_391470 |
| LENEAMHB_3 | 578958 | 579896 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.62 | 100.00 | NP_391077 |
| LENEAMHB_3 | 579916 | 587052 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.53 | 100.00 | NP_391076 |
| LENEAMHB_3 | 577311 | 578930 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 96.97 | 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 |
|---|---|---|---|---|---|---|---|---|
| LENEAMHB_10 | 31768 | 32904 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| LENEAMHB_13 | 11248 | 10379 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| LENEAMHB_2 | 742529 | 743305 | CodY | 7.83e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| LENEAMHB_3 | 315293 | 314724 | ClpP | 4.14e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| LENEAMHB_2 | 275324 | 275716 | spxA1 | 6.15e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| LENEAMHB_2 | 275324 | 275716 | spx | 3.67e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| LENEAMHB_11 | 34759 | 34517 | SpoVG | 7.52e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| LENEAMHB_6 | 144508 | 144705 | 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 |
|---|---|---|---|
| LENEAMHB_1 | 0.0 | 1.0 | 0.0 |
| LENEAMHB_2 | 0.0 | 1.0 | 0.0 |
| LENEAMHB_3 | 0.0 | 1.0 | 0.0 |
| LENEAMHB_4 | 0.0 | 1.0 | 0.0 |
| LENEAMHB_5 | 0.0 | 1.0 | 0.0 |
| LENEAMHB_6 | 0.0 | 1.0 | 0.0 |
| LENEAMHB_7 | 0.0 | 1.0 | 0.0 |
| LENEAMHB_8 | 1.0 | 0.0 | 1.0 |
| LENEAMHB_9 | 1.0 | 0.0 | 1.0 |
| LENEAMHB_10 | 0.0 | 1.0 | 0.0 |
| LENEAMHB_11 | 0.0 | 1.0 | 0.0 |
| LENEAMHB_12 | 1.0 | 0.0 | 1.0 |
| LENEAMHB_13 | 0.0 | 1.0 | 0.0 |
| LENEAMHB_14 | 0.0 | 1.0 | 0.0 |
| LENEAMHB_17 | 0.0 | 1.0 | 0.0 |
| LENEAMHB_18 | 1.0 | 0.0 | 1.0 |
| LENEAMHB_19 | 0.0 | 1.0 | 0.0 |
| LENEAMHB_20 | 1.0 | 0.0 | 1.0 |
| LENEAMHB_21 | 1.0 | 0.0 | 1.0 |
| LENEAMHB_23 | 0.0 | 1.0 | 0.0 |
| LENEAMHB_24 | 0.0 | 1.0 | 0.0 |
| LENEAMHB_25 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LENEAMHB_2 | 375594 | 400829 | False | Myoviridae | VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG4705 |
| LENEAMHB_8 | 70297 | 101446 | False | Myoviridae | VOG0054, VOG3299, VOG4666, VOG9629, VOG4724, VOG2053, VOG0058, VOG8897, VOG4556, VOG4568, VOG0114, VOG0061, VOG0115, VOG0064, VOG0065, VOG0116, VOG0117, VOG0066, VOG0067, VOG0068, VOG7232, VOG4772, VOG11087, VOG2278, VOG4717, VOG4550, VOG4691, VOG10983, VOG0079, VOG0080 |
| LENEAMHB_12 | 3081 | 19577 | False | Myoviridae | VOG0028, VOG0025, VOG0499, VOG0095, VOG7034, VOG0026, VOG5821, VOG0026, VOG0094, VOG7033, VOG0092, VOG7906, VOG0090, VOG7755, VOG7032 |
Phigaro v2.4.0 (Database: Jan. 2024 release)