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. |
|---|---|---|---|---|---|---|---|---|
| CEOCDPLC_10 | 923968 | 924306 | ykkC | ARO:3003063 | ykkC | 98.21 | 100.00 | AL009126.1 |
| CEOCDPLC_10 | 923651 | 923968 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| CEOCDPLC_21 | 453848 | 455050 | blt | ARO:3003006 | blt | 98.00 | 100.00 | L32599.1 |
| CEOCDPLC_21 | 434858 | 435712 | aadK | ARO:3002627 | aadK | 97.18 | 100.00 | AL009126.1 |
| CEOCDPLC_32 | 361476 | 362396 | mphK | ARO:3004541 | mphK | 97.71 | 100.00 | CP010314.1 |
| CEOCDPLC_32 | 348177 | 349610 | lmrB | ARO:3002813 | lmrB | 100.00 | 100.00 | JYFL01000006.1 |
| CEOCDPLC_32 | 298459 | 299052 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| CEOCDPLC_53 | 83533 | 84702 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| CEOCDPLC_32 | 29023 | 30651 | vmlR | ARO:3004476 | vmlR | 95.20 | 99.09 | NC_000964.3 |
| CEOCDPLC_51 | 27415 | 29985 | 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. |
|---|---|---|---|---|---|---|---|
| CEOCDPLC_21 | 434858 | 435712 | aadK | Streptomycin | 98.13 | 100.00 | M26879 |
| CEOCDPLC_32 | 361476 | 362396 | mph(K) | Spiramycin, Telithromycin | 97.07 | 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. |
|---|---|---|---|---|---|---|---|---|
| CEOCDPLC_32 | 361479 | 362396 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.71 | 100.00 | WP_003246254.1 |
| CEOCDPLC_21 | 434858 | 435709 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.18 | 100.00 | WP_003229862.1 |
| CEOCDPLC_32 | 29023 | 30645 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 95.38 | 98.90 | WP_003234144.1 |
| CEOCDPLC_50 | 41775 | 42287 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 91.23 | 98.84 | WP_003242546.1 |
| CEOCDPLC_10 | 244683 | 247280 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.94 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| CEOCDPLC_43 | 168114 | 169295 | capB | 0.0 | Capsule | Immune modulation | 99.41 | 100.00 | NP_391471 |
| CEOCDPLC_43 | 169310 | 169759 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| CEOCDPLC_43 | 169778 | 170920 | capA | 0.0 | Capsule | Immune modulation | 99.30 | 100.00 | NP_391469 |
| CEOCDPLC_52 | 176680 | 177465 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.98 | 100.00 | NP_391080 |
| CEOCDPLC_10 | 23186 | 23827 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 98.75 | 100.00 | NP_390062 |
| CEOCDPLC_52 | 180363 | 181301 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.72 | 100.00 | NP_391077 |
| CEOCDPLC_52 | 177491 | 178687 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.41 | 100.00 | NP_391079 |
| CEOCDPLC_52 | 181321 | 188451 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.32 | 99.99 | NP_391076 |
| CEOCDPLC_10 | 290021 | 291784 | dep/capD | 0.0 | Capsule | Immune modulation | 98.07 | 100.00 | NP_389723 |
| CEOCDPLC_52 | 178716 | 180335 | 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 |
|---|---|---|---|---|---|---|---|---|
| CEOCDPLC_2 | 31784 | 32920 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| CEOCDPLC_7 | 4334 | 5203 | pdxS | 1.11e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| CEOCDPLC_10 | 613109 | 612333 | CodY | 9.86e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| CEOCDPLC_43 | 326935 | 326366 | ClpP | 2.49e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| CEOCDPLC_10 | 1081657 | 1081265 | spxA1 | 7.75e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| CEOCDPLC_10 | 1081657 | 1081265 | spx | 4.62e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| CEOCDPLC_3 | 20589 | 20831 | SpoVG | 7.51e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| CEOCDPLC_32 | 84068 | 83871 | CspA | 1.87e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| CEOCDPLC_1 | 59991 | 60185 | CspB | 8.30e-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. |
|---|---|---|---|---|---|---|
| CEOCDPLC_8 | 51 | 164 | Col440I | 114 / 114 | 95.61 | CP023920.1 |
| CEOCDPLC_9 | 4547 | 4826 | Col440II | 280 / 282 | 83.57 | CP023921.1 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| CEOCDPLC_1 | 0.0 | 1.0 | 0.0 |
| CEOCDPLC_2 | 0.0 | 1.0 | 0.0 |
| CEOCDPLC_3 | 0.0 | 1.0 | 0.0 |
| CEOCDPLC_4 | 0.0 | 1.0 | 0.0 |
| CEOCDPLC_5 | 0.0 | 1.0 | 0.0 |
| CEOCDPLC_6 | 0.0 | 1.0 | 0.0 |
| CEOCDPLC_7 | 0.0 | 1.0 | 0.0 |
| CEOCDPLC_8 | 1.0 | 0.0 | 1.0 |
| CEOCDPLC_9 | 1.0 | 0.0 | 1.0 |
| CEOCDPLC_10 | 0.0 | 1.0 | 0.0 |
| CEOCDPLC_11 | 1.0 | 0.0 | 1.0 |
| CEOCDPLC_13 | 1.0 | 0.0 | 1.0 |
| CEOCDPLC_14 | 1.0 | 0.0 | 1.0 |
| CEOCDPLC_15 | 1.0 | 0.0 | 1.0 |
| CEOCDPLC_16 | 1.0 | 0.0 | 1.0 |
| CEOCDPLC_17 | 1.0 | 0.0 | 1.0 |
| CEOCDPLC_18 | 1.0 | 0.0 | 1.0 |
| CEOCDPLC_19 | 1.0 | 0.0 | 1.0 |
| CEOCDPLC_21 | 0.0 | 1.0 | 0.0 |
| CEOCDPLC_22 | 1.0 | 0.0 | 1.0 |
| CEOCDPLC_32 | 0.0 | 1.0 | 0.0 |
| CEOCDPLC_43 | 0.0 | 1.0 | 0.0 |
| CEOCDPLC_50 | 0.0 | 1.0 | 0.0 |
| CEOCDPLC_51 | 0.0 | 1.0 | 0.0 |
| CEOCDPLC_52 | 0.0 | 1.0 | 0.0 |
| CEOCDPLC_53 | 0.0 | 1.0 | 0.0 |
| CEOCDPLC_54 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| CEOCDPLC_5 | 13381 | 19462 | False | Siphoviridae | VOG0221, VOG7734, VOG0720, VOG4555, VOG4572 |
| CEOCDPLC_10 | 126490 | 131648 | False | Unknown | VOG6211, VOG0322, VOG7476, VOG0025 |
| CEOCDPLC_10 | 955332 | 981446 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
| CEOCDPLC_53 | 252593 | 274322 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG10989, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG5668, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688 |
Phigaro v2.4.0 (Database: Jan. 2024 release)