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. |
|---|---|---|---|---|---|---|---|---|
| NNLABGEN_2 | 731964 | 733133 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| NNLABGEN_2 | 488623 | 489477 | aadK | ARO:3002627 | aadK | 98.24 | 100.00 | AL009126.1 |
| NNLABGEN_4 | 426212 | 426529 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| NNLABGEN_4 | 425874 | 426212 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| NNLABGEN_3 | 258877 | 261447 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 100.00 | AL009126.3 |
| NNLABGEN_5 | 184292 | 185935 | vmlR | ARO:3004476 | vmlR | 98.72 | 100.00 | NC_000964.3 |
| NNLABGEN_10 | 164777 | 165370 | tmrB | ARO:3003059 | tmrB | 98.98 | 100.00 | AL009126.3 |
| NNLABGEN_10 | 114485 | 115924 | lmrB | ARO:3002813 | lmrB | 99.79 | 100.42 | JYFL01000006.1 |
| NNLABGEN_10 | 101673 | 102593 | mphK | ARO:3004541 | mphK | 99.35 | 100.00 | CP010314.1 |
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. |
|---|---|---|---|---|---|---|---|
| NNLABGEN_1 | 34637 | 36013 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 99.20 | 100.00 | D12567 |
| NNLABGEN_10 | 101673 | 102593 | mph(K) | Spiramycin, Telithromycin | 98.91 | 100.00 | NC_000964 |
| NNLABGEN_2 | 488623 | 489475 | aadK | Streptomycin | 98.71 | 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. |
|---|---|---|---|---|---|---|---|---|
| NNLABGEN_10 | 101673 | 102590 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 99.35 | 100.00 | WP_003246254.1 |
| NNLABGEN_1 | 34637 | 36010 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.91 | 100.00 | WP_063856081.1 |
| NNLABGEN_5 | 184295 | 185935 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.72 | 100.00 | WP_003234144.1 |
| NNLABGEN_2 | 488623 | 489474 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.24 | 100.00 | WP_003229862.1 |
| NNLABGEN_1 | 38023 | 38541 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| NNLABGEN_2 | 1031351 | 1033948 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.37 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| NNLABGEN_1 | 519266 | 520447 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| NNLABGEN_1 | 932840 | 933778 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.68 | 100.00 | NP_391077 |
| NNLABGEN_1 | 929157 | 929942 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.62 | 100.00 | NP_391080 |
| NNLABGEN_1 | 520462 | 520911 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| NNLABGEN_1 | 520930 | 522072 | capA | 0.0 | Capsule | Immune modulation | 99.39 | 100.00 | NP_391469 |
| NNLABGEN_2 | 934737 | 935378 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.38 | 100.00 | NP_390062 |
| NNLABGEN_1 | 929968 | 931164 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.00 | 100.00 | NP_391079 |
| NNLABGEN_1 | 931193 | 932812 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.95 | 100.00 | NP_391078 |
| NNLABGEN_1 | 933798 | 940934 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.80 | 100.00 | NP_391076 |
| NNLABGEN_2 | 1079122 | 1080885 | dep/capD | 0.0 | Capsule | Immune modulation | 98.64 | 100.00 | NP_389723 |
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 |
|---|---|---|---|---|---|---|---|---|
| NNLABGEN_7 | 27941 | 26805 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| NNLABGEN_9 | 11182 | 10313 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| NNLABGEN_4 | 736053 | 736829 | CodY | 8.40e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| NNLABGEN_1 | 667668 | 667099 | ClpP | 6.27e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| NNLABGEN_4 | 275359 | 275751 | spxA1 | 2.49e-69 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| NNLABGEN_11 | 34787 | 34545 | SpoVG | 7.52e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| NNLABGEN_5 | 137534 | 137731 | CspA | 9.29e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
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 |
|---|---|---|---|
| NNLABGEN_1 | 0.0 | 1.0 | 0.0 |
| NNLABGEN_2 | 0.0 | 1.0 | 0.0 |
| NNLABGEN_3 | 0.0 | 1.0 | 0.0 |
| NNLABGEN_4 | 0.0 | 1.0 | 0.0 |
| NNLABGEN_5 | 0.0 | 1.0 | 0.0 |
| NNLABGEN_6 | 0.0 | 1.0 | 0.0 |
| NNLABGEN_7 | 0.0 | 1.0 | 0.0 |
| NNLABGEN_9 | 0.0 | 1.0 | 0.0 |
| NNLABGEN_10 | 0.0 | 1.0 | 0.0 |
| NNLABGEN_11 | 0.0 | 1.0 | 0.0 |
| NNLABGEN_12 | 0.0 | 1.0 | 0.0 |
| NNLABGEN_14 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| NNLABGEN_2 | 283978 | 309312 | False | Myoviridae | VOG0796, VOG10227, VOG0720, VOG4555, VOG4553, VOG4564, VOG4623, VOG1353, VOG1881, VOG1883, VOG1352, VOG4699, VOG6163, VOG1956, VOG1433, VOG1348, VOG0573, VOG4550, VOG4691, VOG4845, VOG7718, VOG3390, VOG4705, VOG0753, VOG0136, VOG4574 |
| NNLABGEN_2 | 532198 | 554871 | False | Myoviridae | VOG9315, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718 |
| NNLABGEN_4 | 369881 | 396362 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG4612, VOG4705 |
Phigaro v2.4.0 (Database: Jan. 2024 release)