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. |
|---|---|---|---|---|---|---|---|---|
| CFDGDPAD_1 | 432157 | 432474 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| CFDGDPAD_1 | 431819 | 432157 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| CFDGDPAD_3 | 374017 | 375186 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| CFDGDPAD_6 | 185875 | 187518 | vmlR | ARO:3004476 | vmlR | 99.63 | 100.00 | NC_000964.3 |
| CFDGDPAD_7 | 96094 | 96687 | tmrB | ARO:3003059 | tmrB | 97.97 | 100.00 | AL009126.3 |
| CFDGDPAD_4 | 57899 | 58687 | aadK | ARO:3002627 | aadK | 97.71 | 92.25 | AL009126.1 |
| CFDGDPAD_7 | 45572 | 47011 | lmrB | ARO:3002813 | lmrB | 99.58 | 100.42 | JYFL01000006.1 |
| CFDGDPAD_4 | 39190 | 40392 | blt | ARO:3003006 | blt | 100.00 | 100.00 | L32599.1 |
| CFDGDPAD_7 | 32757 | 33677 | mphK | ARO:3004541 | mphK | 98.37 | 100.00 | CP010314.1 |
| CFDGDPAD_5 | 27373 | 29943 | 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. |
|---|---|---|---|---|---|---|---|
| CFDGDPAD_4 | 57901 | 58754 | aadK | Streptomycin | 98.71 | 99.77 | M26879 |
| CFDGDPAD_7 | 32757 | 33677 | mph(K) | Spiramycin, Telithromycin | 97.72 | 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. |
|---|---|---|---|---|---|---|---|---|
| CFDGDPAD_6 | 185878 | 187518 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 99.63 | 100.00 | WP_003234144.1 |
| CFDGDPAD_7 | 32757 | 33674 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.37 | 100.00 | WP_003246254.1 |
| CFDGDPAD_4 | 57902 | 58693 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.11 | 92.96 | WP_003229862.1 |
| CFDGDPAD_2 | 38458 | 38976 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.75 | 100.00 | WP_003242546.1 |
| CFDGDPAD_3 | 58755 | 61352 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| CFDGDPAD_2 | 964892 | 965830 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391077 |
| CFDGDPAD_2 | 540960 | 542141 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| CFDGDPAD_2 | 542156 | 542605 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| CFDGDPAD_2 | 961209 | 961994 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| CFDGDPAD_3 | 8317 | 10080 | dep/capD | 0.0 | Capsule | Immune modulation | 99.43 | 100.00 | NP_389723 |
| CFDGDPAD_2 | 963245 | 964864 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.38 | 100.00 | NP_391078 |
| CFDGDPAD_2 | 965850 | 972986 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.33 | 100.00 | NP_391076 |
| CFDGDPAD_2 | 962020 | 963216 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.25 | 100.00 | NP_391079 |
| CFDGDPAD_2 | 542624 | 543766 | capA | 0.0 | Capsule | Immune modulation | 99.21 | 100.00 | NP_391469 |
| CFDGDPAD_3 | 171015 | 171656 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.06 | 100.00 | NP_390062 |
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 |
|---|---|---|---|---|---|---|---|---|
| CFDGDPAD_9 | 28139 | 27003 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| CFDGDPAD_11 | 4422 | 5291 | pdxS | 1.13e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| CFDGDPAD_1 | 742010 | 742786 | CodY | 9.45e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| CFDGDPAD_2 | 700757 | 700188 | ClpP | 6.46e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| CFDGDPAD_1 | 276408 | 276800 | spxA1 | 7.42e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| CFDGDPAD_1 | 276408 | 276800 | spx | 4.43e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| CFDGDPAD_10 | 20642 | 20884 | SpoVG | 7.53e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| CFDGDPAD_6 | 137864 | 138061 | CspA | 9.35e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| CFDGDPAD_3 | 183620 | 183814 | CspD | 3.27e-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. |
|---|---|---|---|---|---|---|
| CFDGDPAD_16 | 2467 | 2660 | Col(SD853) | 194 / 194 | 98.97 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| CFDGDPAD_1 | 0.0 | 1.0 | 0.0 |
| CFDGDPAD_2 | 0.0 | 1.0 | 0.0 |
| CFDGDPAD_3 | 0.0 | 1.0 | 0.0 |
| CFDGDPAD_4 | 0.0 | 1.0 | 0.0 |
| CFDGDPAD_5 | 0.0 | 1.0 | 0.0 |
| CFDGDPAD_6 | 0.0 | 1.0 | 0.0 |
| CFDGDPAD_7 | 0.0 | 1.0 | 0.0 |
| CFDGDPAD_8 | 0.0 | 1.0 | 0.0 |
| CFDGDPAD_9 | 0.0 | 1.0 | 0.0 |
| CFDGDPAD_10 | 0.0 | 1.0 | 0.0 |
| CFDGDPAD_11 | 0.0 | 1.0 | 0.0 |
| CFDGDPAD_12 | 0.0 | 1.0 | 0.0 |
| CFDGDPAD_13 | 0.0 | 1.0 | 0.0 |
| CFDGDPAD_14 | 0.0 | 1.0 | 0.0 |
| CFDGDPAD_15 | 0.0 | 1.0 | 0.0 |
| CFDGDPAD_16 | 1.0 | 0.0 | 1.0 |
| CFDGDPAD_19 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| CFDGDPAD_1 | 374775 | 401970 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG4705 |
| CFDGDPAD_1 | 946531 | 962614 | False | Siphoviridae | VOG4574, VOG4358, VOG9712, VOG5042, VOG3389, VOG4910, VOG6163, VOG9312 |
| CFDGDPAD_5 | 272402 | 296285 | False | Myoviridae | VOG2703, VOG4574, VOG0136, VOG0753, VOG5008, VOG4705, VOG3390, VOG7718, VOG4845, VOG4691, VOG4550, VOG0573, VOG1348, VOG1433, VOG1956, VOG6163, VOG4699, VOG1352, VOG1883, VOG1881, VOG1353, VOG4623, VOG4564, VOG4553, VOG4555, VOG0720 |
Phigaro v2.4.0 (Database: Jan. 2024 release)