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. |
|---|---|---|---|---|---|---|---|---|
| GPIDLDNF_2 | 541570 | 542772 | blt | ARO:3003006 | blt | 99.50 | 100.00 | L32599.1 |
| GPIDLDNF_3 | 506563 | 506901 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| GPIDLDNF_3 | 506246 | 506563 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| GPIDLDNF_2 | 353372 | 354541 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| GPIDLDNF_5 | 191628 | 193274 | vmlR | ARO:3004476 | vmlR | 98.91 | 100.18 | NC_000964.3 |
| GPIDLDNF_6 | 109584 | 110504 | mphK | ARO:3004541 | mphK | 98.68 | 100.00 | CP010314.1 |
| GPIDLDNF_6 | 96250 | 97689 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| GPIDLDNF_6 | 46600 | 47193 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| GPIDLDNF_4 | 27187 | 29757 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.65 | 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. |
|---|---|---|---|---|---|---|---|
| GPIDLDNF_6 | 109584 | 110504 | mph(K) | Spiramycin, Telithromycin | 99.02 | 100.00 | NC_000964 |
| GPIDLDNF_2 | 560093 | 560964 | aadK | Streptomycin | 96.90 | 100.00 | 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. |
|---|---|---|---|---|---|---|---|---|
| GPIDLDNF_5 | 191631 | 193274 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.91 | 100.00 | WP_003234144.1 |
| GPIDLDNF_6 | 109596 | 110504 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.68 | 99.02 | WP_003246254.1 |
| GPIDLDNF_2 | 560096 | 560806 | aadK | aminoglycoside 6-adenylyltransferase AadK | PARTIALX | 98.31 | 83.45 | WP_003229862.1 |
| GPIDLDNF_1 | 1063770 | 1064288 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 92.49 | 100.00 | WP_003242546.1 |
| GPIDLDNF_2 | 54798 | 57395 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.71 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| GPIDLDNF_2 | 152635 | 153276 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.84 | 100.00 | NP_390062 |
| GPIDLDNF_1 | 109059 | 109997 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.68 | 100.00 | NP_391077 |
| GPIDLDNF_1 | 575715 | 576896 | capB | 0.0 | Capsule | Immune modulation | 99.58 | 100.00 | NP_391471 |
| GPIDLDNF_1 | 112895 | 113680 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| GPIDLDNF_2 | 9027 | 10790 | dep/capD | 0.0 | Capsule | Immune modulation | 98.98 | 100.00 | NP_389723 |
| GPIDLDNF_1 | 111673 | 112869 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.91 | 100.00 | NP_391079 |
| GPIDLDNF_1 | 575251 | 575700 | capC | 0.0 | Capsule | Immune modulation | 98.89 | 100.00 | NP_391470 |
| GPIDLDNF_1 | 101903 | 109039 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.80 | 100.00 | NP_391076 |
| GPIDLDNF_1 | 574090 | 575232 | capA | 0.0 | Capsule | Immune modulation | 98.69 | 100.00 | NP_391469 |
| GPIDLDNF_1 | 110025 | 111644 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.53 | 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 |
|---|---|---|---|---|---|---|---|---|
| GPIDLDNF_9 | 27970 | 26834 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| GPIDLDNF_12 | 11114 | 10245 | pdxS | 1.10e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| GPIDLDNF_3 | 195161 | 194385 | CodY | 7.62e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| GPIDLDNF_1 | 413477 | 414046 | ClpP | 6.65e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| GPIDLDNF_3 | 664815 | 664423 | spxA1 | 5.99e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| GPIDLDNF_3 | 664815 | 664423 | spx | 3.57e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| GPIDLDNF_10 | 20497 | 20739 | SpoVG | 7.48e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| GPIDLDNF_5 | 145302 | 145499 | CspA | 9.60e-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. |
|---|---|---|---|---|---|---|
| GPIDLDNF_14 | 11592 | 12746 | rep31 | 1159 / 1155 | 86.54 | DQ489739 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| GPIDLDNF_1 | 0.0 | 1.0 | 0.0 |
| GPIDLDNF_2 | 0.0 | 1.0 | 0.0 |
| GPIDLDNF_3 | 0.0 | 1.0 | 0.0 |
| GPIDLDNF_4 | 0.0 | 1.0 | 0.0 |
| GPIDLDNF_5 | 0.0 | 1.0 | 0.0 |
| GPIDLDNF_6 | 0.0 | 1.0 | 0.0 |
| GPIDLDNF_7 | 0.0 | 1.0 | 0.0 |
| GPIDLDNF_8 | 0.0 | 1.0 | 0.0 |
| GPIDLDNF_9 | 0.0 | 1.0 | 0.0 |
| GPIDLDNF_10 | 0.0 | 1.0 | 0.0 |
| GPIDLDNF_11 | 1.0 | 0.0 | 1.0 |
| GPIDLDNF_12 | 0.0 | 1.0 | 0.0 |
| GPIDLDNF_13 | 0.0 | 1.0 | 0.0 |
| GPIDLDNF_14 | 1.0 | 0.0 | 1.0 |
| GPIDLDNF_15 | 0.0 | 1.0 | 0.0 |
| GPIDLDNF_16 | 0.0 | 1.0 | 0.0 |
| GPIDLDNF_17 | 1.0 | 0.0 | 1.0 |
| GPIDLDNF_18 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| GPIDLDNF_1 | 277765 | 300479 | False | Siphoviridae | VOG4707, VOG0641, VOG4705, VOG3390, VOG4612, VOG4705, VOG3390, VOG4626, VOG4772, VOG0801, VOG4545, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG0204, VOG10223, VOG4553, VOG4568, VOG4556, VOG3607, VOG1886, VOG4581, VOG0713, VOG4841 |
| GPIDLDNF_1 | 310358 | 314700 | False | Siphoviridae | VOG9667, VOG1563, VOG0275 |
| GPIDLDNF_3 | 536740 | 562758 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
| GPIDLDNF_11 | 2108 | 19154 | False | Siphoviridae | VOG0198, VOG1517, VOG7407, VOG0720, VOG4564, VOG4555, VOG4711, VOG3438, VOG4623, VOG1266, VOG5660, VOG1278, VOG1269, VOG1270, VOG5793, VOG3653, VOG3654 |
Phigaro v2.4.0 (Database: Jan. 2024 release)