Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 7 | 17.12 |
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. |
|---|---|---|---|---|---|---|---|---|
| DKNCIDDN_7 | 210197 | 211051 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| DKNCIDDN_5 | 210092 | 211012 | mphK | ARO:3004541 | mphK | 97.71 | 100.00 | CP010314.1 |
| DKNCIDDN_5 | 196759 | 198198 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| DKNCIDDN_7 | 193104 | 194306 | blt | ARO:3003006 | blt | 99.50 | 100.00 | L32599.1 |
| DKNCIDDN_5 | 147129 | 147722 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| DKNCIDDN_15 | 105954 | 106271 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| DKNCIDDN_15 | 105616 | 105954 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| DKNCIDDN_11 | 88458 | 90101 | vmlR | ARO:3004476 | vmlR | 99.09 | 100.00 | NC_000964.3 |
| DKNCIDDN_2 | 65501 | 66670 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| DKNCIDDN_3 | 20969 | 23539 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 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. |
|---|---|---|---|---|---|---|---|
| DKNCIDDN_7 | 210197 | 211051 | aadK | Streptomycin | 98.83 | 100.00 | M26879 |
| DKNCIDDN_5 | 210092 | 211012 | 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. |
|---|---|---|---|---|---|---|---|---|
| DKNCIDDN_11 | 88458 | 90098 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 99.09 | 100.00 | WP_003234144.1 |
| DKNCIDDN_7 | 210200 | 211051 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| DKNCIDDN_5 | 210095 | 211012 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.71 | 100.00 | WP_003246254.1 |
| DKNCIDDN_6 | 38296 | 38814 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 94.80 | 100.00 | WP_003242546.1 |
| DKNCIDDN_15 | 699358 | 701955 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.41 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| DKNCIDDN_14 | 185395 | 186576 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| DKNCIDDN_10 | 86760 | 87401 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| DKNCIDDN_7 | 803312 | 804097 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| DKNCIDDN_7 | 802090 | 803286 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.17 | 100.00 | NP_391079 |
| DKNCIDDN_15 | 652339 | 654102 | dep/capD | 0.0 | Capsule | Immune modulation | 99.04 | 100.00 | NP_389723 |
| DKNCIDDN_14 | 187059 | 188201 | capA | 0.0 | Capsule | Immune modulation | 98.69 | 100.00 | NP_391469 |
| DKNCIDDN_14 | 186591 | 187040 | capC | 0.0 | Capsule | Immune modulation | 98.67 | 100.00 | NP_391470 |
| DKNCIDDN_7 | 799476 | 800414 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.62 | 100.00 | NP_391077 |
| DKNCIDDN_7 | 792320 | 799456 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.53 | 100.00 | NP_391076 |
| DKNCIDDN_7 | 800442 | 802061 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.53 | 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 |
|---|---|---|---|---|---|---|---|---|
| DKNCIDDN_12 | 85988 | 84852 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| DKNCIDDN_6 | 87758 | 88627 | pdxS | 1.29e-150 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| DKNCIDDN_15 | 414728 | 415504 | CodY | 5.70e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| DKNCIDDN_7 | 1068121 | 1068690 | ClpP | 7.08e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| DKNCIDDN_3 | 332628 | 333020 | spxA1 | 2.52e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| DKNCIDDN_3 | 332628 | 333020 | spx | 1.50e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| DKNCIDDN_6 | 124551 | 124793 | SpoVG | 2.37e-38 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| DKNCIDDN_10 | 98633 | 98827 | CspD | 5.86e-28 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| DKNCIDDN_10 | 98633 | 98830 | CspB | 1.22e-27 | cold shock protein | 80.30 | 100.00 | 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 |
|---|---|---|---|
| DKNCIDDN_1 | 0.0 | 1.0 | 0.0 |
| DKNCIDDN_2 | 0.0 | 1.0 | 0.0 |
| DKNCIDDN_3 | 0.0 | 1.0 | 0.0 |
| DKNCIDDN_4 | 0.0 | 1.0 | 0.0 |
| DKNCIDDN_5 | 0.0 | 1.0 | 0.0 |
| DKNCIDDN_6 | 0.0 | 1.0 | 0.0 |
| DKNCIDDN_7 | 0.0 | 1.0 | 0.0 |
| DKNCIDDN_8 | 0.0 | 1.0 | 0.0 |
| DKNCIDDN_9 | 0.0 | 1.0 | 0.0 |
| DKNCIDDN_10 | 0.0 | 1.0 | 0.0 |
| DKNCIDDN_11 | 0.0 | 1.0 | 0.0 |
| DKNCIDDN_12 | 0.0 | 1.0 | 0.0 |
| DKNCIDDN_13 | 0.0 | 1.0 | 0.0 |
| DKNCIDDN_14 | 0.0 | 1.0 | 0.0 |
| DKNCIDDN_15 | 0.0 | 1.0 | 0.0 |
| DKNCIDDN_16 | 0.0 | 1.0 | 0.0 |
| DKNCIDDN_17 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| DKNCIDDN_7 | 143491 | 166644 | False | Myoviridae | VOG4705, VOG7718, VOG0906, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG10227 |
| DKNCIDDN_7 | 169055 | 172150 | False | Unknown | VOG4693, VOG0189, VOG11060 |
| DKNCIDDN_7 | 511816 | 533547 | False | Siphoviridae | VOG4574, VOG0641, VOG4705, VOG6243, VOG4612, VOG4626, VOG4619, VOG0801, VOG6163, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5361, VOG4553, VOG4573, VOG4556, VOG0202, VOG1886, VOG4581, VOG4841 |
| DKNCIDDN_11 | 3150 | 25734 | False | Myoviridae | 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 |
| DKNCIDDN_12 | 6781 | 30930 | False | Myoviridae | VOG7895, VOG7718, VOG0906, VOG4862, VOG4691, VOG10120, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG1581, VOG0749, VOG4685, VOG4688, VOG4773 |
| DKNCIDDN_12 | 41516 | 49589 | False | Siphoviridae | VOG0025, VOG3709, VOG11060, VOG1292, VOG1309, VOG0083, VOG1878, VOG3549, VOG8241 |
| DKNCIDDN_15 | 48519 | 75800 | 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 |
Phigaro v2.4.0 (Database: Jan. 2024 release)