Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 8 | 10 | 8 | 15.10 |
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. |
|---|---|---|---|---|---|---|---|---|
| NNGJICEO_4 | 598628 | 599215 | tmrB | ARO:3003059 | tmrB | 95.94 | 98.98 | AL009126.3 |
| NNGJICEO_2 | 439101 | 439418 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| NNGJICEO_2 | 438763 | 439101 | ykkC | ARO:3003063 | ykkC | 99.11 | 100.00 | AL009126.1 |
| NNGJICEO_3 | 345104 | 346273 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| NNGJICEO_4 | 341375 | 343000 | vmlR | ARO:3004476 | vmlR | 96.49 | 98.90 | NC_000964.3 |
| NNGJICEO_1 | 39181 | 40035 | aadK | ARO:3002627 | aadK | 90.14 | 100.00 | AL009126.1 |
| NNGJICEO_4 | 29774 | 32344 | 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. |
|---|---|---|---|---|---|---|---|
| NNGJICEO_1 | 39181 | 40035 | aadK | Streptomycin | 89.84 | 99.88 | 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. |
|---|---|---|---|---|---|---|---|---|
| NNGJICEO_4 | 341375 | 342997 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 96.49 | 98.90 | WP_003234144.1 |
| NNGJICEO_6 | 192621 | 193139 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 91.91 | 100.00 | WP_003242546.1 |
| NNGJICEO_1 | 39184 | 40035 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 90.14 | 100.00 | WP_003229862.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| NNGJICEO_13 | 107193 | 108131 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.68 | 100.00 | NP_391077 |
| NNGJICEO_13 | 572407 | 573588 | capB | 0.0 | Capsule | Immune modulation | 99.58 | 100.00 | NP_391471 |
| NNGJICEO_13 | 111029 | 111814 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| NNGJICEO_3 | 128936 | 129577 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.22 | 100.00 | NP_390062 |
| NNGJICEO_2 | 971891 | 973654 | dep/capD | 0.0 | Capsule | Immune modulation | 99.09 | 100.00 | NP_389723 |
| NNGJICEO_13 | 109807 | 111003 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.00 | 100.00 | NP_391079 |
| NNGJICEO_13 | 108159 | 109778 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.89 | 100.00 | NP_391078 |
| NNGJICEO_13 | 570782 | 571924 | capA | 0.0 | Capsule | Immune modulation | 98.69 | 100.00 | NP_391469 |
| NNGJICEO_13 | 571943 | 572392 | capC | 0.0 | Capsule | Immune modulation | 98.67 | 100.00 | NP_391470 |
| NNGJICEO_13 | 100037 | 107173 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.60 | 100.00 | NP_391076 |
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 |
|---|---|---|---|---|---|---|---|---|
| NNGJICEO_5 | 48392 | 49528 | tufA | 0.0 | elongation factor Tu | 85.22 | 95.69 | AHM69299 |
| NNGJICEO_6 | 238717 | 239586 | pdxS | 2.30e-150 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| NNGJICEO_2 | 758181 | 758957 | CodY | 6.90e-124 | nutrient-responsive regulator | 80.69 | 100.00 | ACJ80679 |
| NNGJICEO_13 | 420246 | 420815 | ClpP | 5.25e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| NNGJICEO_2 | 289475 | 289867 | spxA1 | 6.34e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| NNGJICEO_2 | 289475 | 289867 | spx | 3.78e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| NNGJICEO_6 | 275576 | 275818 | SpoVG | 5.76e-38 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| NNGJICEO_4 | 380059 | 379862 | CspA | 3.24e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| NNGJICEO_3 | 140805 | 140999 | CspD | 3.19e-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. |
|---|---|---|---|---|---|---|
| NNGJICEO_9 | 3065 | 3229 | Col(SD853) | 165 / 194 | 86.06 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| NNGJICEO_1 | 0.0 | 1.0 | 0.0 |
| NNGJICEO_2 | 0.0 | 1.0 | 0.0 |
| NNGJICEO_3 | 0.0 | 1.0 | 0.0 |
| NNGJICEO_4 | 0.0 | 1.0 | 0.0 |
| NNGJICEO_5 | 0.0 | 1.0 | 0.0 |
| NNGJICEO_6 | 0.0 | 1.0 | 0.0 |
| NNGJICEO_7 | 1.0 | 0.0 | 1.0 |
| NNGJICEO_8 | 1.0 | 0.0 | 1.0 |
| NNGJICEO_9 | 1.0 | 0.0 | 1.0 |
| NNGJICEO_10 | 1.0 | 0.0 | 1.0 |
| NNGJICEO_11 | 1.0 | 0.0 | 1.0 |
| NNGJICEO_13 | 0.0 | 1.0 | 0.0 |
| NNGJICEO_14 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| NNGJICEO_1 | 3215 | 34363 | False | Myoviridae | VOG7718, VOG4862, VOG4691, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG10227, VOG0796, VOG4673, VOG6054, VOG2505, VOG9667, VOG4693, VOG0189 |
| NNGJICEO_1 | 180563 | 213041 | False | Siphoviridae | VOG4574, VOG0641, VOG4705, VOG6243, VOG4612, VOG4358, VOG4619, VOG0801, VOG6163, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5361, VOG4553, VOG4568, VOG4556, VOG2935, VOG4544, VOG4581, VOG4556, VOG8909, VOG0198, VOG4548, VOG0327, VOG4609, VOG0026, VOG1565, VOG0021, VOG1047, VOG7438 |
| NNGJICEO_1 | 260698 | 287348 | False | Myoviridae | VOG0221, VOG6116, 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, VOG0796, VOG4681 |
| NNGJICEO_1 | 296207 | 300830 | False | Siphoviridae | VOG1878, VOG4552, VOG4322, VOG0806, VOG9667, VOG9667 |
| NNGJICEO_2 | 384114 | 409524 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4843, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG3390, VOG7895, VOG0753 |
| NNGJICEO_13 | 207588 | 212322 | False | Unknown | VOG6965, VOG0198, VOG1884, VOG0025, VOG0737 |
Phigaro v2.4.0 (Database: Jan. 2024 release)