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. |
|---|---|---|---|---|---|---|---|---|
| EFPMHGIB_2 | 708319 | 709488 | bmr | ARO:3003007 | bmr | 99.23 | 100.00 | M33768.1 |
| EFPMHGIB_1 | 515945 | 516283 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| EFPMHGIB_1 | 515628 | 515945 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| EFPMHGIB_2 | 480262 | 481464 | blt | ARO:3003006 | blt | 99.50 | 100.00 | L32599.1 |
| EFPMHGIB_2 | 461433 | 462287 | aadK | ARO:3002627 | aadK | 98.24 | 100.00 | AL009126.1 |
| EFPMHGIB_6 | 193130 | 194773 | vmlR | ARO:3004476 | vmlR | 98.54 | 100.00 | NC_000964.3 |
| EFPMHGIB_8 | 108152 | 109072 | mphK | ARO:3004541 | mphK | 99.02 | 100.00 | CP010314.1 |
| EFPMHGIB_8 | 94816 | 96255 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.42 | JYFL01000006.1 |
| EFPMHGIB_8 | 45137 | 45730 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| EFPMHGIB_5 | 27377 | 29947 | 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. |
|---|---|---|---|---|---|---|---|
| EFPMHGIB_2 | 461433 | 462285 | aadK | Streptomycin | 98.71 | 99.77 | M26879 |
| EFPMHGIB_4 | 39209 | 40585 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 98.62 | 100.00 | D12567 |
| EFPMHGIB_8 | 108152 | 109072 | mph(K) | Spiramycin, Telithromycin | 98.05 | 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. |
|---|---|---|---|---|---|---|---|---|
| EFPMHGIB_8 | 108155 | 109072 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 99.02 | 100.00 | WP_003246254.1 |
| EFPMHGIB_4 | 39209 | 40582 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.69 | 100.00 | WP_063856081.1 |
| EFPMHGIB_6 | 193133 | 194773 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.54 | 100.00 | WP_003234144.1 |
| EFPMHGIB_2 | 461433 | 462284 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.24 | 100.00 | WP_003229862.1 |
| EFPMHGIB_4 | 42588 | 43106 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.75 | 100.00 | WP_003242546.1 |
| EFPMHGIB_2 | 1011083 | 1013134 | rphC | rifamycin-inactivating phosphotransferase RphC | PARTIALX | 80.12 | 79.03 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| EFPMHGIB_2 | 908015 | 908656 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 100.00 | 100.00 | NP_390062 |
| EFPMHGIB_3 | 527625 | 528806 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| EFPMHGIB_3 | 113251 | 114036 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.62 | 100.00 | NP_391080 |
| EFPMHGIB_3 | 109415 | 110353 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.57 | 100.00 | NP_391077 |
| EFPMHGIB_3 | 526000 | 527142 | capA | 0.0 | Capsule | Immune modulation | 99.39 | 100.00 | NP_391469 |
| EFPMHGIB_3 | 102261 | 109395 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.34 | 99.97 | NP_391076 |
| EFPMHGIB_3 | 527161 | 527610 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| EFPMHGIB_2 | 1061452 | 1063215 | dep/capD | 0.0 | Capsule | Immune modulation | 99.15 | 100.00 | NP_389723 |
| EFPMHGIB_3 | 112029 | 113225 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.08 | 100.00 | NP_391079 |
| EFPMHGIB_3 | 110381 | 112000 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.84 | 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 |
|---|---|---|---|---|---|---|---|---|
| EFPMHGIB_15 | 32005 | 33141 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| EFPMHGIB_13 | 4383 | 5252 | pdxS | 2.58e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.45 | 98.31 | ACE61268 |
| EFPMHGIB_1 | 205755 | 204979 | CodY | 7.66e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| EFPMHGIB_3 | 366265 | 366834 | ClpP | 3.27e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| EFPMHGIB_1 | 668507 | 668115 | spxA1 | 2.27e-69 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| EFPMHGIB_10 | 20742 | 20984 | SpoVG | 7.54e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| EFPMHGIB_6 | 143630 | 143827 | CspA | 9.67e-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 |
|---|---|---|---|
| EFPMHGIB_1 | 0.0 | 1.0 | 0.0 |
| EFPMHGIB_2 | 0.0 | 1.0 | 0.0 |
| EFPMHGIB_3 | 0.0 | 1.0 | 0.0 |
| EFPMHGIB_4 | 0.0 | 1.0 | 0.0 |
| EFPMHGIB_5 | 0.0 | 1.0 | 0.0 |
| EFPMHGIB_6 | 0.0 | 1.0 | 0.0 |
| EFPMHGIB_7 | 0.0 | 1.0 | 0.0 |
| EFPMHGIB_8 | 0.0 | 1.0 | 0.0 |
| EFPMHGIB_10 | 0.0 | 1.0 | 0.0 |
| EFPMHGIB_12 | 0.0 | 1.0 | 0.0 |
| EFPMHGIB_13 | 0.0 | 1.0 | 0.0 |
| EFPMHGIB_14 | 0.0 | 1.0 | 0.0 |
| EFPMHGIB_15 | 0.0 | 1.0 | 0.0 |
| EFPMHGIB_16 | 0.0 | 1.0 | 0.0 |
| EFPMHGIB_17 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| EFPMHGIB_1 | 545770 | 573676 | False | Myoviridae | VOG0753, VOG4705, VOG3390, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
| EFPMHGIB_2 | 501449 | 531298 | False | Myoviridae | VOG4600, VOG1309, VOG11060, VOG0189, VOG4693, VOG4673, VOG0796, VOG9315, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718 |
Phigaro v2.4.0 (Database: Jan. 2024 release)