Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 8 | 18.25 |
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. |
|---|---|---|---|---|---|---|---|---|
| CFKGPEMK_3 | 1641865 | 1642203 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| CFKGPEMK_3 | 1641548 | 1641865 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| CFKGPEMK_3 | 660664 | 661833 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| CFKGPEMK_3 | 464422 | 465624 | blt | ARO:3003006 | blt | 99.00 | 100.00 | L32599.1 |
| CFKGPEMK_3 | 447672 | 448529 | aadK | ARO:3002627 | aadK | 97.18 | 100.35 | AL009126.1 |
| CFKGPEMK_1 | 209881 | 211527 | vmlR | ARO:3004476 | vmlR | 98.18 | 100.18 | NC_000964.3 |
| CFKGPEMK_5 | 124860 | 127430 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| CFKGPEMK_7 | 109247 | 110167 | mphK | ARO:3004541 | mphK | 99.01 | 100.00 | CP010314.1 |
| CFKGPEMK_7 | 95913 | 97352 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| CFKGPEMK_7 | 46263 | 46856 | 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. |
|---|---|---|---|---|---|---|---|
| CFKGPEMK_7 | 109247 | 110167 | mph(K) | Spiramycin, Telithromycin | 99.02 | 100.00 | NC_000964 |
| CFKGPEMK_10 | 37522 | 38898 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 98.47 | 100.00 | D12567 |
| CFKGPEMK_3 | 447672 | 448523 | aadK | Streptomycin | 98.24 | 99.65 | 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. |
|---|---|---|---|---|---|---|---|---|
| CFKGPEMK_7 | 109259 | 110167 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 99.01 | 99.02 | WP_003246254.1 |
| CFKGPEMK_10 | 37522 | 38895 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.25 | 100.00 | WP_063856081.1 |
| CFKGPEMK_1 | 209884 | 211527 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.18 | 100.00 | WP_003234144.1 |
| CFKGPEMK_3 | 447672 | 448523 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.18 | 100.00 | WP_003229862.1 |
| CFKGPEMK_10 | 40872 | 41390 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 93.06 | 100.00 | WP_003242546.1 |
| CFKGPEMK_3 | 953280 | 955874 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.15 | 99.88 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| CFKGPEMK_3 | 858692 | 859333 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.84 | 100.00 | NP_390062 |
| CFKGPEMK_20 | 2171 | 3352 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| CFKGPEMK_4 | 58792 | 59577 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| CFKGPEMK_4 | 59603 | 60799 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.17 | 100.00 | NP_391079 |
| CFKGPEMK_4 | 62475 | 63413 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.15 | 100.00 | NP_391077 |
| CFKGPEMK_20 | 1707 | 2156 | capC | 0.0 | Capsule | Immune modulation | 98.89 | 100.00 | NP_391470 |
| CFKGPEMK_3 | 1003603 | 1005366 | dep/capD | 0.0 | Capsule | Immune modulation | 98.81 | 100.00 | NP_389723 |
| CFKGPEMK_20 | 546 | 1688 | capA | 0.0 | Capsule | Immune modulation | 98.78 | 100.00 | NP_391469 |
| CFKGPEMK_4 | 60828 | 62447 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.39 | 100.00 | NP_391078 |
| CFKGPEMK_4 | 63433 | 70569 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.39 | 100.00 | NP_391076 |
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 |
|---|---|---|---|---|---|---|---|---|
| CFKGPEMK_12 | 31668 | 32804 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| CFKGPEMK_14 | 4400 | 5269 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| CFKGPEMK_3 | 1331206 | 1330430 | CodY | 1.63e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| CFKGPEMK_9 | 151378 | 150809 | ClpP | 2.08e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| CFKGPEMK_3 | 1792022 | 1791630 | spxA1 | 1.28e-69 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| CFKGPEMK_3 | 1792022 | 1791630 | spx | 7.63e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| CFKGPEMK_11 | 20679 | 20921 | SpoVG | 7.51e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| CFKGPEMK_1 | 156009 | 156206 | CspA | 1.04e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| CFKGPEMK_2 | 33146 | 32952 | CspB | 5.75e-28 | cold shock protein | 83.08 | 98.48 | CAD00094 |
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 |
|---|---|---|---|
| CFKGPEMK_1 | 0.0 | 1.0 | 0.0 |
| CFKGPEMK_2 | 0.0 | 1.0 | 0.0 |
| CFKGPEMK_3 | 0.0 | 1.0 | 0.0 |
| CFKGPEMK_4 | 0.0 | 1.0 | 0.0 |
| CFKGPEMK_5 | 0.0 | 1.0 | 0.0 |
| CFKGPEMK_6 | 0.0 | 1.0 | 0.0 |
| CFKGPEMK_7 | 0.0 | 1.0 | 0.0 |
| CFKGPEMK_9 | 0.0 | 1.0 | 0.0 |
| CFKGPEMK_10 | 0.0 | 1.0 | 0.0 |
| CFKGPEMK_11 | 0.0 | 1.0 | 0.0 |
| CFKGPEMK_12 | 0.0 | 1.0 | 0.0 |
| CFKGPEMK_13 | 0.0 | 1.0 | 0.0 |
| CFKGPEMK_14 | 0.0 | 1.0 | 0.0 |
| CFKGPEMK_17 | 0.0 | 1.0 | 0.0 |
| CFKGPEMK_18 | 1.0 | 0.0 | 1.0 |
| CFKGPEMK_19 | 0.0 | 1.0 | 0.0 |
| CFKGPEMK_20 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| CFKGPEMK_3 | 1671753 | 1698114 | False | Myoviridae | VOG0753, VOG4705, VOG4612, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4843, VOG0189, VOG3490, VOG9667 |
| CFKGPEMK_4 | 160018 | 165043 | False | Unknown | VOG8241, VOG4552, VOG1878, VOG8233, VOG0186 |
| CFKGPEMK_4 | 170222 | 191273 | False | Siphoviridae | VOG0044, VOG7007, VOG0198, VOG7983, VOG0796, VOG10227, VOG0691, VOG0692, VOG9317, VOG4572, VOG2621, VOG0695, VOG0696, VOG0697, VOG0698, VOG10044, VOG0701, VOG9745, VOG4605, VOG4599, VOG5535 |
Phigaro v2.4.0 (Database: Jan. 2024 release)