Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 11 | 9 | 18.60 |
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. |
|---|---|---|---|---|---|---|---|---|
| PHDEBCGH_335 | 349949 | 350869 | mphK | ARO:3004541 | mphK | 96.08 | 100.00 | CP010314.1 |
| PHDEBCGH_335 | 336653 | 338086 | lmrB | ARO:3002813 | lmrB | 99.58 | 100.00 | JYFL01000006.1 |
| PHDEBCGH_335 | 286988 | 287581 | tmrB | ARO:3003059 | tmrB | 97.46 | 100.00 | AL009126.3 |
| PHDEBCGH_368 | 263394 | 265964 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.53 | 100.00 | AL009126.3 |
| PHDEBCGH_220 | 250191 | 251360 | bmr | ARO:3003007 | bmr | 99.23 | 100.00 | M33768.1 |
| PHDEBCGH_220 | 87931 | 89133 | blt | ARO:3003006 | blt | 98.75 | 100.00 | L32599.1 |
| PHDEBCGH_379 | 64256 | 64573 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| PHDEBCGH_379 | 63918 | 64256 | ykkC | ARO:3003063 | ykkC | 98.21 | 100.00 | AL009126.1 |
| PHDEBCGH_220 | 60696 | 61550 | aadK | ARO:3002627 | aadK | 97.89 | 100.00 | AL009126.1 |
| PHDEBCGH_335 | 28569 | 30197 | vmlR | ARO:3004476 | vmlR | 95.19 | 99.09 | 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. |
|---|---|---|---|---|---|---|---|
| PHDEBCGH_220 | 60696 | 61550 | aadK | Streptomycin | 98.25 | 100.00 | M26879 |
| PHDEBCGH_335 | 349949 | 350869 | mph(K) | Spiramycin, Telithromycin | 96.31 | 100.00 | 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. |
|---|---|---|---|---|---|---|---|---|
| PHDEBCGH_220 | 60696 | 61547 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.89 | 100.00 | WP_003229862.1 |
| PHDEBCGH_335 | 349952 | 350869 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 96.08 | 100.00 | WP_003246254.1 |
| PHDEBCGH_335 | 28569 | 30191 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 95.19 | 98.90 | WP_003234144.1 |
| PHDEBCGH_313 | 480542 | 481060 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 91.33 | 100.00 | WP_003242546.1 |
| PHDEBCGH_324 | 494953 | 497550 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| PHDEBCGH_109 | 9516 | 9965 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| PHDEBCGH_109 | 8320 | 9501 | capB | 0.0 | Capsule | Immune modulation | 99.49 | 100.00 | NP_391471 |
| PHDEBCGH_109 | 9984 | 11126 | capA | 0.0 | Capsule | Immune modulation | 99.12 | 100.00 | NP_391469 |
| PHDEBCGH_220 | 450101 | 450742 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 98.91 | 100.00 | NP_390062 |
| PHDEBCGH_109 | 459576 | 460361 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.86 | 100.00 | NP_391080 |
| PHDEBCGH_109 | 463259 | 464197 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.83 | 100.00 | NP_391077 |
| PHDEBCGH_109 | 464217 | 471353 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.44 | 100.00 | NP_391076 |
| PHDEBCGH_109 | 460387 | 461583 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.33 | 100.00 | NP_391079 |
| PHDEBCGH_262 | 1 | 377 | flgB | 0.0 | Flagella | Motility | 97.88 | 77.10 | WP_011546417 |
| PHDEBCGH_324 | 449773 | 451536 | dep/capD | 0.0 | Capsule | Immune modulation | 97.73 | 100.00 | NP_389723 |
| PHDEBCGH_109 | 461612 | 463231 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.59 | 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 |
|---|---|---|---|---|---|---|---|---|
| PHDEBCGH_11 | 31784 | 32920 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| PHDEBCGH_53 | 4356 | 5225 | pdxS | 6.88e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.45 | 98.31 | ACE61268 |
| PHDEBCGH_324 | 150913 | 151689 | CodY | 4.07e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PHDEBCGH_109 | 163312 | 162743 | ClpP | 3.45e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| PHDEBCGH_357 | 273728 | 274120 | spxA1 | 2.29e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| PHDEBCGH_357 | 273728 | 274120 | spx | 1.37e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| PHDEBCGH_22 | 20605 | 20847 | SpoVG | 7.51e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| PHDEBCGH_335 | 79727 | 79530 | CspA | 1.92e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| PHDEBCGH_220 | 438137 | 437943 | CspD | 3.34e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| PHDEBCGH_357 | 31260 | 31066 | CspB | 3.30e-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 |
|---|---|---|---|
| PHDEBCGH_11 | 0.0 | 1.0 | 0.0 |
| PHDEBCGH_22 | 0.0 | 1.0 | 0.0 |
| PHDEBCGH_31 | 0.0 | 1.0 | 0.0 |
| PHDEBCGH_42 | 0.0 | 1.0 | 0.0 |
| PHDEBCGH_53 | 0.0 | 1.0 | 0.0 |
| PHDEBCGH_97 | 1.0 | 0.0 | 1.0 |
| PHDEBCGH_108 | 1.0 | 0.0 | 1.0 |
| PHDEBCGH_109 | 0.0 | 1.0 | 0.0 |
| PHDEBCGH_120 | 0.0 | 1.0 | 0.0 |
| PHDEBCGH_220 | 0.0 | 1.0 | 0.0 |
| PHDEBCGH_313 | 0.0 | 1.0 | 0.0 |
| PHDEBCGH_324 | 0.0 | 1.0 | 0.0 |
| PHDEBCGH_335 | 0.0 | 1.0 | 0.0 |
| PHDEBCGH_346 | 0.0 | 1.0 | 0.0 |
| PHDEBCGH_357 | 0.0 | 1.0 | 0.0 |
| PHDEBCGH_368 | 0.0 | 1.0 | 0.0 |
| PHDEBCGH_379 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PHDEBCGH_109 | 370438 | 395237 | False | Siphoviridae | VOG0198, VOG0275, VOG0531, VOG4841, VOG4581, VOG4544, VOG4556, VOG4568, VOG4553, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG6163, VOG0801, VOG4619, VOG4626, VOG4612, VOG3390, VOG4705, VOG0641, VOG4707 |
| PHDEBCGH_379 | 6894 | 34433 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4843, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG4612, VOG4705 |
Phigaro v2.4.0 (Database: Jan. 2024 release)