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. |
|---|---|---|---|---|---|---|---|---|
| HGOMGNOE_1 | 1496968 | 1497285 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| HGOMGNOE_1 | 1496630 | 1496968 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| HGOMGNOE_12 | 544778 | 545632 | aadK | ARO:3002627 | aadK | 98.24 | 100.00 | AL009126.1 |
| HGOMGNOE_12 | 526025 | 527227 | blt | ARO:3003006 | blt | 99.00 | 100.00 | L32599.1 |
| HGOMGNOE_12 | 352758 | 353927 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| HGOMGNOE_23 | 265981 | 268551 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| HGOMGNOE_31 | 109850 | 110770 | mphK | ARO:3004541 | mphK | 98.68 | 100.00 | CP010314.1 |
| HGOMGNOE_31 | 96518 | 97957 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| HGOMGNOE_31 | 46806 | 47399 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| HGOMGNOE_30 | 29062 | 30708 | vmlR | ARO:3004476 | vmlR | 99.45 | 100.18 | 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. |
|---|---|---|---|---|---|---|---|
| HGOMGNOE_1 | 34462 | 35838 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 99.27 | 100.00 | D12567 |
| HGOMGNOE_12 | 544780 | 545632 | aadK | Streptomycin | 99.18 | 99.77 | M26879 |
| HGOMGNOE_31 | 109850 | 110770 | mph(K) | Spiramycin, Telithromycin | 99.13 | 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. |
|---|---|---|---|---|---|---|---|---|
| HGOMGNOE_30 | 29062 | 30705 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 99.45 | 100.00 | WP_003234144.1 |
| HGOMGNOE_1 | 34462 | 35835 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.91 | 100.00 | WP_063856081.1 |
| HGOMGNOE_31 | 109862 | 110770 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.68 | 99.02 | WP_003246254.1 |
| HGOMGNOE_12 | 544781 | 545632 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.24 | 100.00 | WP_003229862.1 |
| HGOMGNOE_1 | 37830 | 38348 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 91.91 | 100.00 | WP_003242546.1 |
| HGOMGNOE_12 | 58863 | 61460 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.71 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| HGOMGNOE_12 | 155438 | 156079 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.69 | 100.00 | NP_390062 |
| HGOMGNOE_1 | 527858 | 529039 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| HGOMGNOE_1 | 942685 | 943470 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| HGOMGNOE_1 | 529054 | 529503 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| HGOMGNOE_1 | 946368 | 947306 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.25 | 100.00 | NP_391077 |
| HGOMGNOE_12 | 8270 | 10033 | dep/capD | 0.0 | Capsule | Immune modulation | 99.15 | 100.00 | NP_389723 |
| HGOMGNOE_1 | 943496 | 944692 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.00 | 100.00 | NP_391079 |
| HGOMGNOE_1 | 529522 | 530664 | capA | 0.0 | Capsule | Immune modulation | 98.95 | 100.00 | NP_391469 |
| HGOMGNOE_1 | 947326 | 954459 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.54 | 99.99 | NP_391076 |
| HGOMGNOE_1 | 944721 | 946340 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.16 | 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 |
|---|---|---|---|---|---|---|---|---|
| HGOMGNOE_33 | 31638 | 32774 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| HGOMGNOE_2 | 4264 | 5133 | pdxS | 1.10e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| HGOMGNOE_1 | 1838058 | 1838834 | CodY | 1.65e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| HGOMGNOE_1 | 671589 | 671020 | ClpP | 1.22e-98 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| HGOMGNOE_1 | 1336515 | 1336907 | spxA1 | 1.29e-69 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| HGOMGNOE_1 | 1336515 | 1336907 | spx | 7.72e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| HGOMGNOE_34 | 20479 | 20721 | SpoVG | 7.48e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| HGOMGNOE_30 | 84466 | 84269 | CspA | 9.99e-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 |
|---|---|---|---|
| HGOMGNOE_1 | 0.0 | 1.0 | 0.0 |
| HGOMGNOE_2 | 0.0 | 1.0 | 0.0 |
| HGOMGNOE_3 | 0.0 | 1.0 | 0.0 |
| HGOMGNOE_4 | 0.0 | 1.0 | 0.0 |
| HGOMGNOE_5 | 0.0 | 1.0 | 0.0 |
| HGOMGNOE_8 | 0.0 | 1.0 | 0.0 |
| HGOMGNOE_12 | 0.0 | 1.0 | 0.0 |
| HGOMGNOE_23 | 0.0 | 1.0 | 0.0 |
| HGOMGNOE_30 | 0.0 | 1.0 | 0.0 |
| HGOMGNOE_31 | 0.0 | 1.0 | 0.0 |
| HGOMGNOE_32 | 0.0 | 1.0 | 0.0 |
| HGOMGNOE_33 | 0.0 | 1.0 | 0.0 |
| HGOMGNOE_34 | 0.0 | 1.0 | 0.0 |
| HGOMGNOE_35 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| HGOMGNOE_1 | 1440831 | 1466826 | 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 |
| HGOMGNOE_12 | 711652 | 740299 | False | Siphoviridae | VOG5353, VOG7531, VOG0705, VOG6116, VOG0602, VOG4824, VOG5221, VOG4705, VOG4612, VOG4660, VOG4619, VOG0801, VOG6163, VOG0725, VOG0799, VOG5589, VOG4564, VOG5504, VOG3676, VOG4555, VOG5012, VOG5023, VOG0275, VOG3699, VOG0274 |
| HGOMGNOE_12 | 756685 | 774029 | False | Siphoviridae | VOG1093, VOG6398, VOG5543, VOG0422, VOG0026, VOG7784, VOG10937, VOG5753, VOG6546, VOG0052, VOG1563, VOG11003, VOG2215, VOG4551, VOG0025, VOG0943, VOG0189, VOG5086, VOG6168, VOG1227 |
Phigaro v2.4.0 (Database: Jan. 2024 release)