Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 8 | 17.55 |
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. |
|---|---|---|---|---|---|---|---|---|
| NFIBKKDF_2 | 591023 | 591361 | ykkC | ARO:3003063 | ykkC | 99.11 | 100.00 | AL009126.1 |
| NFIBKKDF_2 | 590706 | 591023 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| NFIBKKDF_4 | 426146 | 427792 | vmlR | ARO:3004476 | vmlR | 98.54 | 100.18 | NC_000964.3 |
| NFIBKKDF_3 | 383406 | 384575 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| NFIBKKDF_5 | 274668 | 277238 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 100.00 | AL009126.3 |
| NFIBKKDF_3 | 210157 | 211359 | blt | ARO:3003006 | blt | 98.50 | 100.00 | L32599.1 |
| NFIBKKDF_3 | 191919 | 192782 | aadK | ARO:3002627 | aadK | 97.89 | 101.06 | AL009126.1 |
| NFIBKKDF_4 | 152134 | 152727 | tmrB | ARO:3003059 | tmrB | 97.97 | 100.00 | AL009126.3 |
| NFIBKKDF_4 | 101614 | 103053 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| NFIBKKDF_4 | 88801 | 89721 | mphK | ARO:3004541 | mphK | 99.34 | 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. |
|---|---|---|---|---|---|---|---|
| NFIBKKDF_4 | 88801 | 89721 | mph(K) | Spiramycin, Telithromycin | 99.24 | 100.00 | NC_000964 |
| NFIBKKDF_3 | 191919 | 192771 | aadK | Streptomycin | 98.12 | 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. |
|---|---|---|---|---|---|---|---|---|
| NFIBKKDF_4 | 88801 | 89709 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 99.34 | 99.02 | WP_003246254.1 |
| NFIBKKDF_4 | 426149 | 427792 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.54 | 100.00 | WP_003234144.1 |
| NFIBKKDF_3 | 191919 | 192770 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.89 | 100.00 | WP_003229862.1 |
| NFIBKKDF_1 | 38294 | 38812 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| NFIBKKDF_3 | 673176 | 675773 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.06 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| NFIBKKDF_3 | 728298 | 730061 | dep/capD | 0.0 | Capsule | Immune modulation | 99.94 | 100.00 | NP_389723 |
| NFIBKKDF_1 | 522918 | 524099 | capB | 0.0 | Capsule | Immune modulation | 99.58 | 100.00 | NP_391471 |
| NFIBKKDF_3 | 581965 | 582606 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| NFIBKKDF_1 | 945147 | 945932 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| NFIBKKDF_1 | 945958 | 947154 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.33 | 100.00 | NP_391079 |
| NFIBKKDF_1 | 948830 | 949768 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.15 | 100.00 | NP_391077 |
| NFIBKKDF_1 | 524582 | 525724 | capA | 0.0 | Capsule | Immune modulation | 99.04 | 100.00 | NP_391469 |
| NFIBKKDF_1 | 524114 | 524563 | capC | 0.0 | Capsule | Immune modulation | 98.67 | 100.00 | NP_391470 |
| NFIBKKDF_1 | 949788 | 956924 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.40 | 100.00 | NP_391076 |
| NFIBKKDF_1 | 947183 | 948802 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 96.97 | 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 |
|---|---|---|---|---|---|---|---|---|
| NFIBKKDF_7 | 28226 | 27090 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| NFIBKKDF_10 | 4391 | 5260 | pdxS | 1.13e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| NFIBKKDF_2 | 279572 | 278796 | CodY | 8.25e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| NFIBKKDF_1 | 682527 | 681958 | ClpP | 6.37e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| NFIBKKDF_2 | 740764 | 740372 | spxA1 | 6.48e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| NFIBKKDF_2 | 740764 | 740372 | spx | 3.87e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| NFIBKKDF_8 | 34886 | 34644 | SpoVG | 7.90e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| NFIBKKDF_4 | 379805 | 380002 | CspA | 1.97e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| NFIBKKDF_3 | 570006 | 569812 | CspD | 4.55e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
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 |
|---|---|---|---|
| NFIBKKDF_1 | 0.0 | 1.0 | 0.0 |
| NFIBKKDF_2 | 0.0 | 1.0 | 0.0 |
| NFIBKKDF_3 | 0.0 | 1.0 | 0.0 |
| NFIBKKDF_4 | 0.0 | 1.0 | 0.0 |
| NFIBKKDF_5 | 0.0 | 1.0 | 0.0 |
| NFIBKKDF_6 | 0.0 | 1.0 | 0.0 |
| NFIBKKDF_7 | 0.0 | 1.0 | 0.0 |
| NFIBKKDF_8 | 0.0 | 1.0 | 0.0 |
| NFIBKKDF_9 | 0.0 | 1.0 | 0.0 |
| NFIBKKDF_10 | 0.0 | 1.0 | 0.0 |
| NFIBKKDF_11 | 0.0 | 1.0 | 0.0 |
| NFIBKKDF_12 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| NFIBKKDF_2 | 619782 | 647248 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
| NFIBKKDF_9 | 13384 | 37775 | False | Myoviridae | VOG6282, VOG0796, VOG0720, VOG4555, VOG4553, VOG0815, VOG4564, VOG4623, VOG1353, VOG1881, VOG1883, VOG1352, VOG4699, VOG1350, VOG6163, VOG1956, VOG1433, VOG1348, VOG0573, VOG4550, VOG4691, VOG4845, VOG7718, VOG3390, VOG4705, VOG0753, VOG0136, VOG4574 |
Phigaro v2.4.0 (Database: Jan. 2024 release)