Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 7 | 17.83 |
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. |
|---|---|---|---|---|---|---|---|---|
| FCGKHCPH_1 | 1640104 | 1640442 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| FCGKHCPH_1 | 1639787 | 1640104 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| FCGKHCPH_1 | 658903 | 660072 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| FCGKHCPH_1 | 462661 | 463863 | blt | ARO:3003006 | blt | 99.00 | 100.00 | L32599.1 |
| FCGKHCPH_1 | 445911 | 446768 | aadK | ARO:3002627 | aadK | 97.18 | 100.35 | AL009126.1 |
| FCGKHCPH_6 | 209740 | 211386 | vmlR | ARO:3004476 | vmlR | 98.18 | 100.18 | NC_000964.3 |
| FCGKHCPH_5 | 124887 | 127457 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| FCGKHCPH_4 | 109286 | 110206 | mphK | ARO:3004541 | mphK | 99.01 | 100.00 | CP010314.1 |
| FCGKHCPH_4 | 95952 | 97391 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| FCGKHCPH_4 | 46302 | 46895 | tmrB | ARO:3003059 | tmrB | 98.48 | 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. |
|---|---|---|---|---|---|---|---|
| FCGKHCPH_4 | 109286 | 110206 | mph(K) | Spiramycin, Telithromycin | 99.02 | 100.00 | NC_000964 |
| FCGKHCPH_2 | 37443 | 38819 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 98.47 | 100.00 | D12567 |
| FCGKHCPH_1 | 445911 | 446762 | aadK | Streptomycin | 98.24 | 99.65 | 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. |
|---|---|---|---|---|---|---|---|---|
| FCGKHCPH_4 | 109298 | 110206 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 99.01 | 99.02 | WP_003246254.1 |
| FCGKHCPH_2 | 37443 | 38816 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.25 | 100.00 | WP_063856081.1 |
| FCGKHCPH_6 | 209743 | 211386 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.18 | 100.00 | WP_003234144.1 |
| FCGKHCPH_1 | 445911 | 446762 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.18 | 100.00 | WP_003229862.1 |
| FCGKHCPH_2 | 40793 | 41311 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 93.06 | 100.00 | WP_003242546.1 |
| FCGKHCPH_1 | 951519 | 954113 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.15 | 99.88 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| FCGKHCPH_1 | 856931 | 857572 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.84 | 100.00 | NP_390062 |
| FCGKHCPH_2 | 536259 | 537440 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| FCGKHCPH_2 | 946916 | 947701 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| FCGKHCPH_2 | 947727 | 948923 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.17 | 100.00 | NP_391079 |
| FCGKHCPH_2 | 950599 | 951537 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.15 | 100.00 | NP_391077 |
| FCGKHCPH_2 | 537455 | 537904 | capC | 0.0 | Capsule | Immune modulation | 98.89 | 100.00 | NP_391470 |
| FCGKHCPH_1 | 1001842 | 1003605 | dep/capD | 0.0 | Capsule | Immune modulation | 98.81 | 100.00 | NP_389723 |
| FCGKHCPH_2 | 537923 | 539065 | capA | 0.0 | Capsule | Immune modulation | 98.78 | 100.00 | NP_391469 |
| FCGKHCPH_2 | 948952 | 950571 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.39 | 100.00 | NP_391078 |
| FCGKHCPH_2 | 951557 | 958693 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.39 | 100.00 | NP_391076 |
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 |
|---|---|---|---|---|---|---|---|---|
| FCGKHCPH_7 | 28140 | 27004 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| FCGKHCPH_15 | 11190 | 10321 | pdxS | 1.11e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| FCGKHCPH_1 | 1329445 | 1328669 | CodY | 1.68e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| FCGKHCPH_2 | 693372 | 692803 | ClpP | 5.92e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| FCGKHCPH_1 | 1790261 | 1789869 | spxA1 | 1.32e-69 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| FCGKHCPH_1 | 1790261 | 1789869 | spx | 7.86e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| FCGKHCPH_12 | 34621 | 34379 | SpoVG | 7.51e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| FCGKHCPH_6 | 155868 | 156065 | CspA | 1.04e-31 | 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. |
|---|---|---|---|---|---|---|
| No hit found | ||||||
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| FCGKHCPH_1 | 0.0 | 1.0 | 0.0 |
| FCGKHCPH_2 | 0.0 | 1.0 | 0.0 |
| FCGKHCPH_3 | 0.0 | 1.0 | 0.0 |
| FCGKHCPH_4 | 0.0 | 1.0 | 0.0 |
| FCGKHCPH_5 | 0.0 | 1.0 | 0.0 |
| FCGKHCPH_6 | 0.0 | 1.0 | 0.0 |
| FCGKHCPH_7 | 0.0 | 1.0 | 0.0 |
| FCGKHCPH_8 | 0.0 | 1.0 | 0.0 |
| FCGKHCPH_9 | 0.0 | 1.0 | 0.0 |
| FCGKHCPH_11 | 0.0 | 1.0 | 0.0 |
| FCGKHCPH_12 | 0.0 | 1.0 | 0.0 |
| FCGKHCPH_15 | 0.0 | 1.0 | 0.0 |
| FCGKHCPH_16 | 0.0 | 1.0 | 0.0 |
| FCGKHCPH_18 | 1.0 | 0.0 | 1.0 |
| FCGKHCPH_19 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| FCGKHCPH_1 | 1669992 | 1696353 | False | Myoviridae | VOG0753, VOG4705, VOG4612, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4843, VOG0189, VOG3490, VOG9667 |
| FCGKHCPH_16 | 4776 | 25827 | False | Siphoviridae | VOG0753, VOG5535, VOG4599, VOG4605, VOG9745, VOG0701, VOG10044, VOG0698, VOG0697, VOG0696, VOG0695, VOG2621, VOG4572, VOG9317, VOG0692, VOG0691, VOG10227, VOG0796, VOG7983, VOG0198, VOG7007 |
| FCGKHCPH_16 | 31006 | 35838 | False | Unknown | VOG4566, VOG0186, VOG8233, VOG1878 |
Phigaro v2.4.0 (Database: Jan. 2024 release)