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. |
|---|---|---|---|---|---|---|---|---|
| NIIKMLNH_1 | 3437996 | 3438313 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| NIIKMLNH_1 | 3437658 | 3437996 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| NIIKMLNH_1 | 2972730 | 2975300 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.42 | 100.00 | AL009126.3 |
| NIIKMLNH_1 | 2660837 | 2662483 | vmlR | ARO:3004476 | vmlR | 98.54 | 100.18 | NC_000964.3 |
| NIIKMLNH_1 | 2382134 | 2382727 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| NIIKMLNH_1 | 2331635 | 2333068 | lmrB | ARO:3002813 | lmrB | 99.58 | 100.00 | JYFL01000006.1 |
| NIIKMLNH_1 | 2318820 | 2319740 | mphK | ARO:3004541 | mphK | 98.68 | 100.00 | CP010314.1 |
| NIIKMLNH_1 | 571093 | 571947 | aadK | ARO:3002627 | aadK | 98.24 | 100.00 | AL009126.1 |
| NIIKMLNH_1 | 552798 | 554000 | blt | ARO:3003006 | blt | 99.50 | 100.00 | L32599.1 |
| NIIKMLNH_1 | 320639 | 321808 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
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. |
|---|---|---|---|---|---|---|---|
| NIIKMLNH_1 | 2318820 | 2319740 | mph(K) | Spiramycin, Telithromycin | 99.02 | 100.00 | NC_000964 |
| NIIKMLNH_1 | 571093 | 571947 | aadK | Streptomycin | 98.83 | 100.00 | 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. |
|---|---|---|---|---|---|---|---|---|
| NIIKMLNH_1 | 2318820 | 2319728 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.68 | 99.02 | WP_003246254.1 |
| NIIKMLNH_1 | 2660840 | 2662483 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.54 | 100.00 | WP_003234144.1 |
| NIIKMLNH_1 | 571096 | 571947 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.24 | 100.00 | WP_003229862.1 |
| NIIKMLNH_1 | 2021082 | 2021600 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 92.49 | 100.00 | WP_003242546.1 |
| NIIKMLNH_1 | 19113 | 21710 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.60 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| NIIKMLNH_1 | 1537204 | 1538385 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| NIIKMLNH_1 | 123115 | 123756 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| NIIKMLNH_1 | 1128637 | 1129422 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| NIIKMLNH_1 | 1124801 | 1125739 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.25 | 100.00 | NP_391077 |
| NIIKMLNH_1 | 1536740 | 1537189 | capC | 0.0 | Capsule | Immune modulation | 99.11 | 100.00 | NP_391470 |
| NIIKMLNH_1 | 4119364 | 4121127 | dep/capD | 0.0 | Capsule | Immune modulation | 99.04 | 100.00 | NP_389723 |
| NIIKMLNH_1 | 1535579 | 1536721 | capA | 0.0 | Capsule | Immune modulation | 98.95 | 100.00 | NP_391469 |
| NIIKMLNH_1 | 1117645 | 1124781 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.50 | 100.00 | NP_391076 |
| NIIKMLNH_1 | 1127415 | 1128611 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.41 | 100.00 | NP_391079 |
| NIIKMLNH_1 | 1125767 | 1127386 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.41 | 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 |
|---|---|---|---|---|---|---|---|---|
| NIIKMLNH_1 | 2184283 | 2185419 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| NIIKMLNH_1 | 2070544 | 2071413 | pdxS | 3.08e-149 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| NIIKMLNH_1 | 3749636 | 3750412 | CodY | 3.36e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| NIIKMLNH_1 | 1379040 | 1379609 | ClpP | 2.49e-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 |
|---|---|---|---|
| NIIKMLNH_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 |
|---|---|---|---|---|---|
| NIIKMLNH_1 | 497436 | 515170 | False | Myoviridae | VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749 |
| NIIKMLNH_1 | 3380531 | 3408105 | 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 |
| NIIKMLNH_1 | 3950164 | 3974622 | False | Siphoviridae | VOG0198, VOG0275, VOG6879, VOG4841, VOG0713, VOG4581, VOG1886, VOG3607, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG1266, VOG9583, VOG0704, VOG4586, VOG0541, VOG5910, VOG0801, VOG4772, VOG4626, VOG3390, VOG4705, VOG4612, VOG3390, VOG7896 |
Phigaro v2.4.0 (Database: Jan. 2024 release)