Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 9 | 18.03 |
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. |
|---|---|---|---|---|---|---|---|---|
| LNKONGDC_3 | 237287 | 238141 | aadK | ARO:3002627 | aadK | 98.24 | 100.00 | AL009126.1 |
| LNKONGDC_3 | 218502 | 219704 | blt | ARO:3003006 | blt | 100.00 | 100.00 | L32599.1 |
| LNKONGDC_10 | 166821 | 167159 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| LNKONGDC_10 | 166504 | 166821 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| LNKONGDC_2 | 110683 | 111603 | mphK | ARO:3004541 | mphK | 99.35 | 100.00 | CP010314.1 |
| LNKONGDC_2 | 97350 | 98789 | lmrB | ARO:3002813 | lmrB | 99.79 | 100.42 | JYFL01000006.1 |
| LNKONGDC_2 | 47641 | 48234 | tmrB | ARO:3003059 | tmrB | 99.49 | 100.00 | AL009126.3 |
| LNKONGDC_6 | 29027 | 30673 | vmlR | ARO:3004476 | vmlR | 98.91 | 100.18 | NC_000964.3 |
| LNKONGDC_4 | 27340 | 29910 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 100.00 | 100.00 | AL009126.3 |
| LNKONGDC_3 | 20384 | 21553 | bmr | ARO:3003007 | bmr | 99.74 | 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. |
|---|---|---|---|---|---|---|---|
| LNKONGDC_2 | 110683 | 111603 | mph(K) | Spiramycin, Telithromycin | 99.02 | 100.00 | NC_000964 |
| LNKONGDC_3 | 237289 | 238141 | aadK | Streptomycin | 98.83 | 99.77 | 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. |
|---|---|---|---|---|---|---|---|---|
| LNKONGDC_2 | 110686 | 111603 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 99.35 | 100.00 | WP_003246254.1 |
| LNKONGDC_6 | 29027 | 30670 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.91 | 100.00 | WP_003234144.1 |
| LNKONGDC_3 | 237290 | 238141 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.24 | 100.00 | WP_003229862.1 |
| LNKONGDC_7 | 71439 | 71957 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 91.33 | 100.00 | WP_003242546.1 |
| LNKONGDC_9 | 419309 | 421906 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| LNKONGDC_9 | 517647 | 518288 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.84 | 100.00 | NP_390062 |
| LNKONGDC_1 | 459288 | 466424 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.68 | 100.00 | NP_391076 |
| LNKONGDC_8 | 2854 | 3303 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| LNKONGDC_8 | 3318 | 4499 | capB | 0.0 | Capsule | Immune modulation | 99.49 | 100.00 | NP_391471 |
| LNKONGDC_1 | 454647 | 455432 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| LNKONGDC_8 | 1693 | 2835 | capA | 0.0 | Capsule | Immune modulation | 99.39 | 100.00 | NP_391469 |
| LNKONGDC_9 | 365454 | 367217 | dep/capD | 0.0 | Capsule | Immune modulation | 99.38 | 100.00 | NP_389723 |
| LNKONGDC_1 | 455458 | 456654 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.08 | 100.00 | NP_391079 |
| LNKONGDC_1 | 458330 | 459268 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.30 | 100.00 | NP_391077 |
| LNKONGDC_1 | 456683 | 458302 | 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 |
|---|---|---|---|---|---|---|---|---|
| LNKONGDC_12 | 27987 | 26851 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| LNKONGDC_16 | 11174 | 10305 | pdxS | 1.11e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| LNKONGDC_9 | 144372 | 145148 | CodY | 5.75e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| LNKONGDC_1 | 151023 | 150454 | ClpP | 3.42e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| LNKONGDC_10 | 334580 | 334188 | spxA1 | 3.89e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| LNKONGDC_10 | 334580 | 334188 | spx | 2.32e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| LNKONGDC_5 | 34692 | 34450 | SpoVG | 7.50e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| LNKONGDC_6 | 78819 | 78622 | CspA | 9.66e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| LNKONGDC_9 | 530248 | 530442 | CspD | 4.36e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| LNKONGDC_10 | 579325 | 579519 | CspB | 5.60e-27 | 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. |
|---|---|---|---|---|---|---|
| LNKONGDC_89 | 1971 | 2250 | Col440II | 280 / 282 | 84.29 | CP023921.1 |
| LNKONGDC_89 | 1238 | 1340 | Col440I | 104 / 114 | 83.65 | CP023920.1 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| LNKONGDC_1 | 0.0 | 1.0 | 0.0 |
| LNKONGDC_2 | 0.0 | 1.0 | 0.0 |
| LNKONGDC_3 | 0.0 | 1.0 | 0.0 |
| LNKONGDC_4 | 0.0 | 1.0 | 0.0 |
| LNKONGDC_5 | 0.0 | 1.0 | 0.0 |
| LNKONGDC_6 | 0.0 | 1.0 | 0.0 |
| LNKONGDC_7 | 0.0 | 1.0 | 0.0 |
| LNKONGDC_8 | 0.0 | 1.0 | 0.0 |
| LNKONGDC_9 | 0.0 | 1.0 | 0.0 |
| LNKONGDC_10 | 0.0 | 1.0 | 0.0 |
| LNKONGDC_11 | 0.0 | 1.0 | 0.0 |
| LNKONGDC_12 | 0.0 | 1.0 | 0.0 |
| LNKONGDC_13 | 1.0 | 0.0 | 1.0 |
| LNKONGDC_15 | 0.0 | 1.0 | 0.0 |
| LNKONGDC_16 | 0.0 | 1.0 | 0.0 |
| LNKONGDC_21 | 1.0 | 0.0 | 1.0 |
| LNKONGDC_49 | 1.0 | 0.0 | 1.0 |
| LNKONGDC_89 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LNKONGDC_1 | 166656 | 187915 | False | Siphoviridae | VOG8287, VOG0275, VOG5023, VOG3699, VOG2613, VOG0692, VOG9317, VOG4319, VOG11074, VOG0801, VOG4619, VOG4626, VOG4612, VOG6243, VOG4705, VOG5221, VOG4574, VOG0602 |
| LNKONGDC_10 | 196647 | 224089 | False | Myoviridae | VOG0753, VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG2752, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
Phigaro v2.4.0 (Database: Jan. 2024 release)