Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 4 | 16.88 |
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. |
|---|---|---|---|---|---|---|---|---|
| PFCDCFGI_1 | 3823835 | 3824755 | mphK | ARO:3004541 | mphK | 98.69 | 100.00 | CP010314.1 |
| PFCDCFGI_1 | 3810509 | 3811942 | lmrB | ARO:3002813 | lmrB | 100.00 | 100.00 | JYFL01000006.1 |
| PFCDCFGI_1 | 3760844 | 3761437 | tmrB | ARO:3003059 | tmrB | 99.49 | 100.00 | AL009126.3 |
| PFCDCFGI_1 | 3487116 | 3488762 | vmlR | ARO:3004476 | vmlR | 98.91 | 100.18 | NC_000964.3 |
| PFCDCFGI_1 | 3182383 | 3184953 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 100.00 | AL009126.3 |
| PFCDCFGI_1 | 2704756 | 2705094 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| PFCDCFGI_1 | 2704439 | 2704756 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| PFCDCFGI_1 | 1804536 | 1805705 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| PFCDCFGI_1 | 1577722 | 1578924 | blt | ARO:3003006 | blt | 99.25 | 100.00 | L32599.1 |
| PFCDCFGI_1 | 1560971 | 1561825 | aadK | ARO:3002627 | aadK | 98.59 | 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. |
|---|---|---|---|---|---|---|---|
| PFCDCFGI_1 | 26420 | 27796 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 98.84 | 100.00 | D12567 |
| PFCDCFGI_1 | 1560971 | 1561825 | aadK | Streptomycin | 98.83 | 100.00 | M26879 |
| PFCDCFGI_1 | 3823835 | 3824755 | mph(K) | Spiramycin, Telithromycin | 98.26 | 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. |
|---|---|---|---|---|---|---|---|---|
| PFCDCFGI_1 | 26420 | 27793 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.91 | 100.00 | WP_063856081.1 |
| PFCDCFGI_1 | 3487116 | 3488759 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.91 | 100.00 | WP_003234144.1 |
| PFCDCFGI_1 | 3823838 | 3824755 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.69 | 100.00 | WP_003246254.1 |
| PFCDCFGI_1 | 1560971 | 1561822 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| PFCDCFGI_1 | 29793 | 30311 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| PFCDCFGI_1 | 2119949 | 2122537 | rphC | rifamycin-inactivating phosphotransferase RphC | INTERNAL_STOP | 80.14 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| PFCDCFGI_1 | 522502 | 523683 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| PFCDCFGI_1 | 523698 | 524147 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| PFCDCFGI_1 | 1003754 | 1004539 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| PFCDCFGI_1 | 1008395 | 1015531 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.31 | 100.00 | NP_391076 |
| PFCDCFGI_1 | 524166 | 525308 | capA | 0.0 | Capsule | Immune modulation | 99.21 | 100.00 | NP_391469 |
| PFCDCFGI_1 | 1004565 | 1005761 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.08 | 100.00 | NP_391079 |
| PFCDCFGI_1 | 2170238 | 2172001 | dep/capD | 0.0 | Capsule | Immune modulation | 98.92 | 100.00 | NP_389723 |
| PFCDCFGI_1 | 2004915 | 2005556 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 98.91 | 100.00 | NP_390062 |
| PFCDCFGI_1 | 1007437 | 1008375 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.30 | 100.00 | NP_391077 |
| PFCDCFGI_1 | 1005790 | 1007409 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.41 | 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 |
|---|---|---|---|---|---|---|---|---|
| PFCDCFGI_1 | 3958748 | 3957612 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| PFCDCFGI_1 | 4072563 | 4071694 | pdxS | 3.04e-149 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| PFCDCFGI_1 | 2393423 | 2392647 | CodY | 3.32e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PFCDCFGI_1 | 678392 | 677823 | ClpP | 2.46e-98 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
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 |
|---|---|---|---|
| PFCDCFGI_1 | 0.0 | 1.0 | 0.0 |
| PFCDCFGI_2 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PFCDCFGI_1 | 768572 | 775427 | False | Siphoviridae | VOG0275, VOG1563, VOG9667, VOG9667, VOG7581, VOG4566, VOG0189, VOG6587 |
| PFCDCFGI_1 | 775783 | 803412 | False | Siphoviridae | VOG1336, VOG0245, VOG5836, VOG0397, VOG0102, VOG0044, VOG0198, VOG0275, VOG4841, VOG0713, VOG4581, VOG1886, VOG3607, VOG4556, VOG4568, VOG4553, VOG10223, VOG0204, VOG9583, VOG0704, VOG4586, VOG0541, VOG5910, VOG0801, VOG4772, VOG4626, VOG4612, VOG6243, VOG4705 |
| PFCDCFGI_1 | 914616 | 937352 | False | Siphoviridae | VOG4841, VOG4581, VOG4544, VOG4556, VOG4573, VOG4553, VOG0204, VOG4589, VOG0207, VOG4586, VOG5852, VOG6163, VOG0801, VOG3462, VOG4619, VOG4856, VOG0804, VOG4705, VOG5221 |
| PFCDCFGI_1 | 1604011 | 1633908 | False | Myoviridae | VOG4600, VOG1309, VOG11060, VOG0189, VOG4693, VOG9587, VOG4673, VOG0796, VOG10227, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4691, VOG4862 |
| PFCDCFGI_1 | 2734581 | 2762067 | False | Myoviridae | VOG0753, VOG4705, VOG4612, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
Phigaro v2.4.0 (Database: Jan. 2024 release)