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. |
|---|---|---|---|---|---|---|---|---|
| LDCDBPCC_1 | 3923383 | 3924303 | mphK | ARO:3004541 | mphK | 98.04 | 100.00 | CP010314.1 |
| LDCDBPCC_1 | 3910050 | 3911483 | lmrB | ARO:3002813 | lmrB | 100.00 | 100.00 | JYFL01000006.1 |
| LDCDBPCC_1 | 3860325 | 3860918 | tmrB | ARO:3003059 | tmrB | 97.46 | 100.00 | AL009126.3 |
| LDCDBPCC_1 | 3600529 | 3602157 | vmlR | ARO:3004476 | vmlR | 95.38 | 99.09 | NC_000964.3 |
| LDCDBPCC_1 | 3302671 | 3305241 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| LDCDBPCC_1 | 2846348 | 2846686 | ykkC | ARO:3003063 | ykkC | 99.11 | 100.00 | AL009126.1 |
| LDCDBPCC_1 | 2846031 | 2846348 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| LDCDBPCC_1 | 1874601 | 1875770 | bmr | ARO:3003007 | bmr | 99.23 | 100.00 | M33768.1 |
| LDCDBPCC_1 | 1690479 | 1691681 | blt | ARO:3003006 | blt | 98.50 | 100.00 | L32599.1 |
| LDCDBPCC_1 | 1671528 | 1672382 | aadK | ARO:3002627 | aadK | 97.54 | 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. |
|---|---|---|---|---|---|---|---|
| LDCDBPCC_1 | 1671528 | 1672382 | aadK | Streptomycin | 98.25 | 100.00 | M26879 |
| LDCDBPCC_1 | 3923383 | 3924303 | mph(K) | Spiramycin, Telithromycin | 97.39 | 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. |
|---|---|---|---|---|---|---|---|---|
| LDCDBPCC_1 | 3923386 | 3924303 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.04 | 100.00 | WP_003246254.1 |
| LDCDBPCC_1 | 1671528 | 1672379 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.54 | 100.00 | WP_003229862.1 |
| LDCDBPCC_1 | 3600529 | 3602151 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 95.38 | 98.90 | WP_003234144.1 |
| LDCDBPCC_1 | 194665 | 195183 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.75 | 100.00 | WP_003242546.1 |
| LDCDBPCC_1 | 2165475 | 2168072 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.29 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| LDCDBPCC_1 | 694443 | 695625 | capB | 0.0 | Capsule | Immune modulation | 99.41 | 100.00 | NP_391471 |
| LDCDBPCC_1 | 695640 | 696089 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| LDCDBPCC_1 | 696108 | 697250 | capA | 0.0 | Capsule | Immune modulation | 99.04 | 100.00 | NP_391469 |
| LDCDBPCC_1 | 1118972 | 1119757 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.98 | 100.00 | NP_391080 |
| LDCDBPCC_1 | 2074741 | 2075382 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 98.75 | 100.00 | NP_390062 |
| LDCDBPCC_1 | 1122655 | 1123593 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.72 | 100.00 | NP_391077 |
| LDCDBPCC_1 | 1119783 | 1120979 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.50 | 100.00 | NP_391079 |
| LDCDBPCC_1 | 1123613 | 1130743 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.32 | 99.99 | NP_391076 |
| LDCDBPCC_1 | 2211253 | 2213016 | dep/capD | 0.0 | Capsule | Immune modulation | 98.02 | 100.00 | NP_389723 |
| LDCDBPCC_1 | 1121008 | 1122627 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.59 | 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 |
|---|---|---|---|---|---|---|---|---|
| LDCDBPCC_1 | 27922 | 26786 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| LDCDBPCC_1 | 141634 | 140765 | pdxS | 2.98e-149 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| LDCDBPCC_1 | 2537053 | 2536277 | CodY | 3.26e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| LDCDBPCC_1 | 852125 | 851556 | ClpP | 2.41e-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 |
|---|---|---|---|
| LDCDBPCC_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 |
|---|---|---|---|---|---|
| LDCDBPCC_1 | 2876520 | 2902656 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
Phigaro v2.4.0 (Database: Jan. 2024 release)