Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 4 | 16.12 |
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. |
|---|---|---|---|---|---|---|---|---|
| PMCCGKEK_1 | 3977298 | 3978467 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| PMCCGKEK_1 | 3745102 | 3746304 | blt | ARO:3003006 | blt | 99.50 | 100.00 | L32599.1 |
| PMCCGKEK_1 | 3727154 | 3728008 | aadK | ARO:3002627 | aadK | 98.24 | 100.00 | AL009126.1 |
| PMCCGKEK_1 | 1973712 | 1974632 | mphK | ARO:3004541 | mphK | 98.68 | 100.00 | CP010314.1 |
| PMCCGKEK_1 | 1960384 | 1961817 | lmrB | ARO:3002813 | lmrB | 99.58 | 100.00 | JYFL01000006.1 |
| PMCCGKEK_1 | 1910724 | 1911317 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| PMCCGKEK_1 | 1630966 | 1632612 | vmlR | ARO:3004476 | vmlR | 98.54 | 100.18 | NC_000964.3 |
| PMCCGKEK_1 | 1318143 | 1320713 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.42 | 100.00 | AL009126.3 |
| PMCCGKEK_1 | 855443 | 855781 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| PMCCGKEK_1 | 855126 | 855443 | ykkD | ARO:3003064 | ykkD | 99.05 | 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. |
|---|---|---|---|---|---|---|---|
| PMCCGKEK_1 | 1973712 | 1974632 | mph(K) | Spiramycin, Telithromycin | 99.02 | 100.00 | NC_000964 |
| PMCCGKEK_1 | 3727154 | 3728008 | 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. |
|---|---|---|---|---|---|---|---|---|
| PMCCGKEK_1 | 1973724 | 1974632 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.68 | 99.02 | WP_003246254.1 |
| PMCCGKEK_1 | 1630966 | 1632609 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.54 | 100.00 | WP_003234144.1 |
| PMCCGKEK_1 | 3727154 | 3728005 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.24 | 100.00 | WP_003229862.1 |
| PMCCGKEK_1 | 2277473 | 2277991 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 92.49 | 100.00 | WP_003242546.1 |
| PMCCGKEK_1 | 125781 | 128378 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.60 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| PMCCGKEK_1 | 2760695 | 2761876 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| PMCCGKEK_1 | 23734 | 24375 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| PMCCGKEK_1 | 3169663 | 3170448 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| PMCCGKEK_1 | 3173346 | 3174284 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.25 | 100.00 | NP_391077 |
| PMCCGKEK_1 | 2761891 | 2762340 | capC | 0.0 | Capsule | Immune modulation | 99.11 | 100.00 | NP_391470 |
| PMCCGKEK_1 | 172303 | 174066 | dep/capD | 0.0 | Capsule | Immune modulation | 99.04 | 100.00 | NP_389723 |
| PMCCGKEK_1 | 2762359 | 2763501 | capA | 0.0 | Capsule | Immune modulation | 98.95 | 100.00 | NP_391469 |
| PMCCGKEK_1 | 3174304 | 3181440 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.50 | 100.00 | NP_391076 |
| PMCCGKEK_1 | 3170474 | 3171670 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.41 | 100.00 | NP_391079 |
| PMCCGKEK_1 | 3171699 | 3173318 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.41 | 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 |
|---|---|---|---|---|---|---|---|---|
| PMCCGKEK_1 | 2114787 | 2113651 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| PMCCGKEK_1 | 2228527 | 2227658 | pdxS | 3.08e-149 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| PMCCGKEK_1 | 543801 | 543025 | CodY | 5.41e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PMCCGKEK_1 | 2920044 | 2919475 | ClpP | 2.50e-98 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
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 |
|---|---|---|---|
| PMCCGKEK_1 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PMCCGKEK_1 | 318810 | 343269 | False | Siphoviridae | VOG0641, VOG7896, VOG3390, VOG4612, VOG4705, VOG3390, VOG4626, VOG4772, VOG0801, VOG5910, VOG0541, VOG4586, VOG0704, VOG9583, VOG1266, VOG0204, VOG5361, VOG4553, VOG4568, VOG4556, VOG3607, VOG1886, VOG4581, VOG0713, VOG4841, VOG6879, VOG0275 |
| PMCCGKEK_1 | 885334 | 912908 | False | Myoviridae | VOG0753, VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
| PMCCGKEK_1 | 3783933 | 3801667 | False | Myoviridae | VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718 |
Phigaro v2.4.0 (Database: Jan. 2024 release)