Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 7 | 17.83 |
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. |
|---|---|---|---|---|---|---|---|---|
| NGIDKDEO_10 | 1793002 | 1793856 | aadK | ARO:3002627 | aadK | 97.54 | 100.00 | AL009126.1 |
| NGIDKDEO_10 | 1763478 | 1764680 | blt | ARO:3003006 | blt | 99.00 | 100.00 | L32599.1 |
| NGIDKDEO_10 | 1533200 | 1534369 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| NGIDKDEO_10 | 549659 | 549976 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| NGIDKDEO_10 | 549321 | 549659 | ykkC | ARO:3003063 | ykkC | 98.21 | 100.00 | AL009126.1 |
| NGIDKDEO_12 | 353708 | 354628 | mphK | ARO:3004541 | mphK | 96.73 | 100.00 | CP010314.1 |
| NGIDKDEO_12 | 340376 | 341815 | lmrB | ARO:3002813 | lmrB | 99.79 | 100.42 | JYFL01000006.1 |
| NGIDKDEO_12 | 290667 | 291260 | tmrB | ARO:3003059 | tmrB | 97.97 | 100.00 | AL009126.3 |
| NGIDKDEO_13 | 266722 | 269292 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.53 | 100.00 | AL009126.3 |
| NGIDKDEO_12 | 29096 | 30742 | vmlR | ARO:3004476 | vmlR | 98.54 | 100.18 | NC_000964.3 |
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. |
|---|---|---|---|---|---|---|---|
| NGIDKDEO_11 | 999293 | 1000669 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 99.42 | 100.00 | D12567 |
| NGIDKDEO_10 | 1793002 | 1793856 | aadK | Streptomycin | 98.48 | 100.00 | M26879 |
| NGIDKDEO_12 | 353708 | 354628 | mph(K) | Spiramycin, Telithromycin | 96.85 | 99.89 | 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. |
|---|---|---|---|---|---|---|---|---|
| NGIDKDEO_11 | 999296 | 1000669 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 99.34 | 100.00 | WP_063856081.1 |
| NGIDKDEO_12 | 29096 | 30739 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.54 | 100.00 | WP_003234144.1 |
| NGIDKDEO_10 | 1793005 | 1793856 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.54 | 100.00 | WP_003229862.1 |
| NGIDKDEO_12 | 353711 | 354628 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 96.73 | 100.00 | WP_003246254.1 |
| NGIDKDEO_11 | 996765 | 997283 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 92.49 | 100.00 | WP_003242546.1 |
| NGIDKDEO_10 | 1227688 | 1230285 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.94 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| NGIDKDEO_11 | 109408 | 110346 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.89 | 100.00 | NP_391077 |
| NGIDKDEO_11 | 520978 | 522159 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| NGIDKDEO_11 | 110374 | 111993 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.69 | 100.00 | NP_391078 |
| NGIDKDEO_10 | 1329613 | 1330254 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| NGIDKDEO_11 | 113244 | 114029 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| NGIDKDEO_11 | 519353 | 520495 | capA | 0.0 | Capsule | Immune modulation | 99.30 | 100.00 | NP_391469 |
| NGIDKDEO_11 | 102252 | 109388 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.27 | 100.00 | NP_391076 |
| NGIDKDEO_11 | 520514 | 520963 | capC | 0.0 | Capsule | Immune modulation | 99.11 | 100.00 | NP_391470 |
| NGIDKDEO_10 | 1181849 | 1183612 | dep/capD | 0.0 | Capsule | Immune modulation | 98.92 | 100.00 | NP_389723 |
| NGIDKDEO_11 | 112022 | 113218 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.91 | 100.00 | NP_391079 |
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 |
|---|---|---|---|---|---|---|---|---|
| NGIDKDEO_14 | 28050 | 26914 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| NGIDKDEO_16 | 11297 | 10428 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| NGIDKDEO_10 | 863073 | 863849 | CodY | 1.81e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| NGIDKDEO_11 | 367042 | 367611 | ClpP | 6.25e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| NGIDKDEO_10 | 276440 | 276832 | spxA1 | 1.42e-69 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| NGIDKDEO_10 | 276440 | 276832 | spx | 8.48e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| NGIDKDEO_15 | 34705 | 34463 | SpoVG | 7.51e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| NGIDKDEO_12 | 86043 | 85846 | CspA | 1.96e-31 | 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 |
|---|---|---|---|
| NGIDKDEO_10 | 0.0 | 1.0 | 0.0 |
| NGIDKDEO_11 | 0.0 | 1.0 | 0.0 |
| NGIDKDEO_12 | 0.0 | 1.0 | 0.0 |
| NGIDKDEO_13 | 0.0 | 1.0 | 0.0 |
| NGIDKDEO_14 | 0.0 | 1.0 | 0.0 |
| NGIDKDEO_15 | 0.0 | 1.0 | 0.0 |
| NGIDKDEO_16 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| NGIDKDEO_10 | 313573 | 324929 | False | Siphoviridae | VOG6013, VOG5526, VOG0026, VOG8598, VOG8506, VOG4551, VOG0025, VOG0189, VOG3490 |
| NGIDKDEO_10 | 492472 | 519473 | 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 |
| NGIDKDEO_10 | 1709425 | 1739251 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG10227, VOG0796, VOG4673, VOG3449, VOG4693, VOG0189 |
Phigaro v2.4.0 (Database: Jan. 2024 release)