Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 8 | 17.55 |
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. |
|---|---|---|---|---|---|---|---|---|
| CGEIEKJE_4 | 685279 | 685617 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| CGEIEKJE_4 | 684962 | 685279 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| CGEIEKJE_1 | 258876 | 261446 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 100.00 | AL009126.3 |
| CGEIEKJE_2 | 204515 | 205684 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| CGEIEKJE_8 | 184287 | 185930 | vmlR | ARO:3004476 | vmlR | 98.72 | 100.00 | NC_000964.3 |
| CGEIEKJE_6 | 108152 | 109072 | mphK | ARO:3004541 | mphK | 99.35 | 100.00 | CP010314.1 |
| CGEIEKJE_6 | 94821 | 96260 | lmrB | ARO:3002813 | lmrB | 99.79 | 100.42 | JYFL01000006.1 |
| CGEIEKJE_6 | 45375 | 45968 | tmrB | ARO:3003059 | tmrB | 98.98 | 100.00 | AL009126.3 |
| CGEIEKJE_21 | 2950 | 3804 | aadK | ARO:3002627 | aadK | 98.24 | 100.00 | AL009126.1 |
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. |
|---|---|---|---|---|---|---|---|
| CGEIEKJE_3 | 34535 | 35911 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 99.20 | 100.00 | D12567 |
| CGEIEKJE_6 | 108152 | 109072 | mph(K) | Spiramycin, Telithromycin | 98.91 | 100.00 | NC_000964 |
| CGEIEKJE_21 | 2952 | 3804 | aadK | Streptomycin | 98.71 | 99.77 | 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. |
|---|---|---|---|---|---|---|---|---|
| CGEIEKJE_6 | 108155 | 109072 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 99.35 | 100.00 | WP_003246254.1 |
| CGEIEKJE_3 | 34535 | 35908 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.91 | 100.00 | WP_063856081.1 |
| CGEIEKJE_8 | 184290 | 185930 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.72 | 100.00 | WP_003234144.1 |
| CGEIEKJE_21 | 2953 | 3804 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.24 | 100.00 | WP_003229862.1 |
| CGEIEKJE_3 | 37921 | 38439 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| CGEIEKJE_4 | 1966 | 4563 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.37 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| CGEIEKJE_3 | 519016 | 520197 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| CGEIEKJE_3 | 932590 | 933528 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.68 | 100.00 | NP_391077 |
| CGEIEKJE_3 | 928907 | 929692 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.62 | 100.00 | NP_391080 |
| CGEIEKJE_3 | 520212 | 520661 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| CGEIEKJE_3 | 520680 | 521822 | capA | 0.0 | Capsule | Immune modulation | 99.39 | 100.00 | NP_391469 |
| CGEIEKJE_13 | 89343 | 89984 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.38 | 100.00 | NP_390062 |
| CGEIEKJE_3 | 929718 | 930914 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.00 | 100.00 | NP_391079 |
| CGEIEKJE_3 | 930943 | 932562 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.95 | 100.00 | NP_391078 |
| CGEIEKJE_3 | 933548 | 940684 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.80 | 100.00 | NP_391076 |
| CGEIEKJE_4 | 49737 | 51500 | dep/capD | 0.0 | Capsule | Immune modulation | 98.64 | 100.00 | NP_389723 |
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 |
|---|---|---|---|---|---|---|---|---|
| CGEIEKJE_10 | 31659 | 32795 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| CGEIEKJE_9 | 11312 | 10443 | pdxS | 1.13e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| CGEIEKJE_4 | 375438 | 374662 | CodY | 9.01e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| CGEIEKJE_3 | 667418 | 666849 | ClpP | 6.27e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| CGEIEKJE_4 | 836132 | 835740 | spxA1 | 2.67e-69 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| CGEIEKJE_15 | 34646 | 34404 | SpoVG | 7.49e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| CGEIEKJE_8 | 137529 | 137726 | CspA | 9.28e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| CGEIEKJE_13 | 101947 | 102141 | CspD | 1.41e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
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 |
|---|---|---|---|
| CGEIEKJE_1 | 0.0 | 1.0 | 0.0 |
| CGEIEKJE_2 | 0.0 | 1.0 | 0.0 |
| CGEIEKJE_3 | 0.0 | 1.0 | 0.0 |
| CGEIEKJE_4 | 0.0 | 1.0 | 0.0 |
| CGEIEKJE_5 | 0.0 | 1.0 | 0.0 |
| CGEIEKJE_6 | 0.0 | 1.0 | 0.0 |
| CGEIEKJE_7 | 0.0 | 1.0 | 0.0 |
| CGEIEKJE_8 | 0.0 | 1.0 | 0.0 |
| CGEIEKJE_9 | 0.0 | 1.0 | 0.0 |
| CGEIEKJE_10 | 0.0 | 1.0 | 0.0 |
| CGEIEKJE_12 | 0.0 | 1.0 | 0.0 |
| CGEIEKJE_13 | 0.0 | 1.0 | 0.0 |
| CGEIEKJE_15 | 0.0 | 1.0 | 0.0 |
| CGEIEKJE_16 | 1.0 | 0.0 | 1.0 |
| CGEIEKJE_17 | 0.0 | 1.0 | 0.0 |
| CGEIEKJE_19 | 0.0 | 1.0 | 0.0 |
| CGEIEKJE_20 | 0.0 | 1.0 | 0.0 |
| CGEIEKJE_21 | 0.0 | 1.0 | 0.0 |
| CGEIEKJE_22 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| CGEIEKJE_2 | 9109 | 27422 | False | Myoviridae | VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718 |
| CGEIEKJE_4 | 715129 | 741610 | False | Myoviridae | VOG0753, VOG4705, VOG4612, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
| CGEIEKJE_5 | 175173 | 200507 | False | Myoviridae | VOG4574, VOG0136, VOG0753, VOG4705, VOG3390, VOG7718, VOG4845, VOG4691, VOG4550, VOG0573, VOG1348, VOG1433, VOG1956, VOG6163, VOG4699, VOG1352, VOG1883, VOG1881, VOG1353, VOG4623, VOG4564, VOG4553, VOG4555, VOG0720, VOG10227, VOG0796 |
Phigaro v2.4.0 (Database: Jan. 2024 release)