Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 8 | 18.25 |
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. |
|---|---|---|---|---|---|---|---|---|
| NDAKLFID_1 | 1013836 | 1014690 | aadK | ARO:3002627 | aadK | 98.24 | 100.00 | AL009126.1 |
| NDAKLFID_1 | 984705 | 985907 | blt | ARO:3003006 | blt | 99.00 | 100.00 | L32599.1 |
| NDAKLFID_1 | 782296 | 783465 | bmr | ARO:3003007 | bmr | 99.23 | 100.00 | M33768.1 |
| NDAKLFID_14 | 428393 | 428710 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| NDAKLFID_14 | 428055 | 428393 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| NDAKLFID_16 | 194299 | 195942 | vmlR | ARO:3004476 | vmlR | 98.90 | 100.00 | NC_000964.3 |
| NDAKLFID_17 | 108356 | 109276 | mphK | ARO:3004541 | mphK | 100.00 | 100.00 | CP010314.1 |
| NDAKLFID_17 | 95023 | 96462 | lmrB | ARO:3002813 | lmrB | 99.79 | 100.42 | JYFL01000006.1 |
| NDAKLFID_17 | 45316 | 45909 | tmrB | ARO:3003059 | tmrB | 96.95 | 100.00 | AL009126.3 |
| NDAKLFID_15 | 27381 | 29951 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 100.00 | 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. |
|---|---|---|---|---|---|---|---|
| NDAKLFID_17 | 108356 | 109276 | mph(K) | Spiramycin, Telithromycin | 99.78 | 100.00 | NC_000964 |
| NDAKLFID_1 | 1013838 | 1014690 | aadK | Streptomycin | 98.59 | 99.77 | M26879 |
| NDAKLFID_12 | 40441 | 41817 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 98.33 | 100.00 | D12567 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| NDAKLFID_17 | 108359 | 109276 | mphK | macrolide 2'-phosphotransferase MphK | EXACTX | 100.00 | 100.00 | WP_003246254.1 |
| NDAKLFID_16 | 194302 | 195942 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.90 | 100.00 | WP_003234144.1 |
| NDAKLFID_1 | 1013839 | 1014690 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.24 | 100.00 | WP_003229862.1 |
| NDAKLFID_12 | 40441 | 41814 | tet(L) | tetracycline efflux MFS transporter Tet(L) | INTERNAL_STOP | 98.03 | 100.00 | WP_063856081.1 |
| NDAKLFID_12 | 43822 | 44340 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 91.91 | 100.00 | WP_003242546.1 |
| NDAKLFID_1 | 478577 | 481174 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| NDAKLFID_1 | 583111 | 583752 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.84 | 100.00 | NP_390062 |
| NDAKLFID_12 | 535354 | 536535 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| NDAKLFID_12 | 948480 | 949265 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.62 | 100.00 | NP_391080 |
| NDAKLFID_12 | 537018 | 538160 | capA | 0.0 | Capsule | Immune modulation | 99.47 | 100.00 | NP_391469 |
| NDAKLFID_12 | 536550 | 536999 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| NDAKLFID_12 | 952163 | 953101 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.25 | 100.00 | NP_391077 |
| NDAKLFID_12 | 949291 | 950487 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.25 | 100.00 | NP_391079 |
| NDAKLFID_1 | 428437 | 430200 | dep/capD | 0.0 | Capsule | Immune modulation | 99.15 | 100.00 | NP_389723 |
| NDAKLFID_12 | 953121 | 960257 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.77 | 100.00 | NP_391076 |
| NDAKLFID_12 | 950516 | 952135 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.03 | 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 |
|---|---|---|---|---|---|---|---|---|
| NDAKLFID_18 | 28140 | 27004 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| NDAKLFID_20 | 4391 | 5260 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| NDAKLFID_1 | 92672 | 93448 | CodY | 1.18e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| NDAKLFID_12 | 697884 | 697315 | ClpP | 6.39e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| NDAKLFID_14 | 276407 | 276799 | spxA1 | 4.15e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| NDAKLFID_14 | 276407 | 276799 | spx | 2.47e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| NDAKLFID_19 | 34757 | 34515 | SpoVG | 7.52e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| NDAKLFID_16 | 141404 | 141601 | CspA | 9.72e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| NDAKLFID_14 | 33244 | 33050 | CspB | 5.98e-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. |
|---|---|---|---|---|---|---|
| No hit found | ||||||
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| NDAKLFID_1 | 0.0 | 1.0 | 0.0 |
| NDAKLFID_2 | 1.0 | 0.0 | 1.0 |
| NDAKLFID_3 | 0.0 | 1.0 | 0.0 |
| NDAKLFID_4 | 1.0 | 0.0 | 1.0 |
| NDAKLFID_6 | 1.0 | 0.0 | 1.0 |
| NDAKLFID_7 | 1.0 | 0.0 | 1.0 |
| NDAKLFID_8 | 1.0 | 0.0 | 1.0 |
| NDAKLFID_12 | 0.0 | 1.0 | 0.0 |
| NDAKLFID_14 | 0.0 | 1.0 | 0.0 |
| NDAKLFID_15 | 0.0 | 1.0 | 0.0 |
| NDAKLFID_16 | 0.0 | 1.0 | 0.0 |
| NDAKLFID_17 | 0.0 | 1.0 | 0.0 |
| NDAKLFID_18 | 0.0 | 1.0 | 0.0 |
| NDAKLFID_19 | 0.0 | 1.0 | 0.0 |
| NDAKLFID_20 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| NDAKLFID_14 | 370741 | 397372 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718 |
Phigaro v2.4.0 (Database: Jan. 2024 release)