Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 10 | 10 | 2 | 14.28 |
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. |
|---|---|---|---|---|---|---|---|---|
| NLLPAPJA_1 | 3481387 | 3482589 | blt | ARO:3003006 | blt | 98.50 | 100.00 | L32599.1 |
| NLLPAPJA_1 | 1319528 | 1320382 | aadK | ARO:3002627 | aadK | 98.24 | 100.00 | AL009126.1 |
| NLLPAPJA_1 | 1151258 | 1152691 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.00 | JYFL01000006.1 |
| NLLPAPJA_1 | 1138447 | 1139367 | mphK | ARO:3004541 | mphK | 98.69 | 100.00 | CP010314.1 |
| NLLPAPJA_1 | 1053979 | 1055148 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| NLLPAPJA_1 | 682078 | 682671 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| NLLPAPJA_1 | 233027 | 234673 | vmlR | ARO:3004476 | vmlR | 98.54 | 100.18 | NC_000964.3 |
| NLLPAPJA_1 | 93199 | 93537 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| NLLPAPJA_1 | 92882 | 93199 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
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. |
|---|---|---|---|---|---|---|---|
| NLLPAPJA_1 | 1138447 | 1139367 | mph(K) | Spiramycin, Telithromycin | 99.24 | 100.00 | NC_000964 |
| NLLPAPJA_1 | 1319530 | 1320382 | aadK | Streptomycin | 98.59 | 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. |
|---|---|---|---|---|---|---|---|---|
| NLLPAPJA_1 | 1138447 | 1139364 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.69 | 100.00 | WP_003246254.1 |
| NLLPAPJA_1 | 233030 | 234673 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.54 | 100.00 | WP_003234144.1 |
| NLLPAPJA_1 | 1319531 | 1320382 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.24 | 100.00 | WP_003229862.1 |
| NLLPAPJA_1 | 2346837 | 2347355 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 91.33 | 100.00 | WP_003242546.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| NLLPAPJA_1 | 2356994 | 2357635 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.69 | 100.00 | NP_390062 |
| NLLPAPJA_1 | 1380604 | 1381389 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.62 | 100.00 | NP_391080 |
| NLLPAPJA_1 | 1462880 | 1463949 | capB | 0.0 | Capsule | Immune modulation | 99.53 | 90.52 | NP_391471 |
| NLLPAPJA_1 | 1384287 | 1385225 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391077 |
| NLLPAPJA_1 | 1464432 | 1465574 | capA | 0.0 | Capsule | Immune modulation | 99.12 | 100.00 | NP_391469 |
| NLLPAPJA_1 | 2555710 | 2557473 | dep/capD | 0.0 | Capsule | Immune modulation | 99.09 | 100.00 | NP_389723 |
| NLLPAPJA_1 | 1381415 | 1382611 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.08 | 100.00 | NP_391079 |
| NLLPAPJA_1 | 1385245 | 1392381 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.77 | 100.00 | NP_391076 |
| NLLPAPJA_1 | 1463964 | 1464413 | capC | 0.0 | Capsule | Immune modulation | 98.44 | 100.00 | NP_391470 |
| NLLPAPJA_1 | 1382640 | 1384259 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 96.79 | 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 |
|---|---|---|---|---|---|---|---|---|
| NLLPAPJA_1 | 3093756 | 3094625 | pdxS | 2.67e-149 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| NLLPAPJA_1 | 3018179 | 3018955 | CodY | 2.91e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
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 |
|---|---|---|---|
| NLLPAPJA_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 |
|---|---|---|---|---|---|
| NLLPAPJA_1 | 562071 | 567118 | False | Siphoviridae | VOG4553, VOG4573, VOG4556, VOG4544, VOG4581 |
| NLLPAPJA_1 | 578725 | 585625 | False | Myoviridae | VOG0052, VOG4567, VOG0020, VOG5357, VOG1298, VOG4724, VOG4561 |
| NLLPAPJA_1 | 737039 | 756033 | False | Siphoviridae | VOG0705, VOG6116, VOG8440, VOG0602, VOG4574, VOG0753, VOG4705, VOG4626, VOG4619, VOG0801, VOG6163, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5601 |
| NLLPAPJA_1 | 1422701 | 1443248 | False | Myoviridae | VOG0348, VOG0382, VOG0384, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890 |
| NLLPAPJA_1 | 2658044 | 2659991 | False | Siphoviridae | VOG0539, VOG0704, VOG4586, VOG0541 |
Phigaro v2.4.0 (Database: Jan. 2024 release)