Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 9 | 18.71 |
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. |
|---|---|---|---|---|---|---|---|---|
| JFCPBKDH_1 | 614936 | 615274 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| JFCPBKDH_1 | 614619 | 614936 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| JFCPBKDH_35 | 277988 | 280558 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.65 | 100.00 | AL009126.3 |
| JFCPBKDH_12 | 207142 | 208311 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| JFCPBKDH_36 | 182991 | 184634 | vmlR | ARO:3004476 | vmlR | 98.54 | 100.00 | NC_000964.3 |
| JFCPBKDH_37 | 162251 | 162844 | tmrB | ARO:3003059 | tmrB | 100.00 | 100.00 | AL009126.3 |
| JFCPBKDH_37 | 111770 | 113209 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| JFCPBKDH_37 | 98956 | 99876 | mphK | ARO:3004541 | mphK | 97.71 | 100.00 | CP010314.1 |
| JFCPBKDH_33 | 34786 | 35640 | aadK | ARO:3002627 | aadK | 98.24 | 100.00 | AL009126.1 |
| JFCPBKDH_33 | 16125 | 17327 | blt | ARO:3003006 | blt | 99.25 | 100.00 | L32599.1 |
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. |
|---|---|---|---|---|---|---|---|
| JFCPBKDH_32 | 469219 | 470595 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 98.84 | 100.00 | X08034 |
| JFCPBKDH_33 | 34788 | 35640 | aadK | Streptomycin | 98.71 | 99.77 | M26879 |
| JFCPBKDH_37 | 98956 | 99876 | mph(K) | Spiramycin, Telithromycin | 97.72 | 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. |
|---|---|---|---|---|---|---|---|---|
| JFCPBKDH_32 | 469222 | 470595 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.69 | 100.00 | WP_003242953.1 |
| JFCPBKDH_36 | 182994 | 184634 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.54 | 100.00 | WP_003234144.1 |
| JFCPBKDH_33 | 34789 | 35640 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.24 | 100.00 | WP_003229862.1 |
| JFCPBKDH_37 | 98956 | 99873 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.71 | 100.00 | WP_003246254.1 |
| JFCPBKDH_32 | 466745 | 467263 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| JFCPBKDH_12 | 503270 | 505867 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.60 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| JFCPBKDH_23 | 411235 | 412173 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.68 | 100.00 | NP_391077 |
| JFCPBKDH_23 | 14248 | 15429 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| JFCPBKDH_12 | 409079 | 409720 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| JFCPBKDH_23 | 409588 | 411207 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.26 | 100.00 | NP_391078 |
| JFCPBKDH_23 | 407552 | 408337 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.24 | 100.00 | NP_391080 |
| JFCPBKDH_23 | 15912 | 17054 | capA | 0.0 | Capsule | Immune modulation | 98.95 | 100.00 | NP_391469 |
| JFCPBKDH_23 | 408363 | 409559 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.91 | 100.00 | NP_391079 |
| JFCPBKDH_12 | 551045 | 552808 | dep/capD | 0.0 | Capsule | Immune modulation | 98.87 | 100.00 | NP_389723 |
| JFCPBKDH_23 | 412193 | 419329 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.82 | 100.00 | NP_391076 |
| JFCPBKDH_23 | 15444 | 15893 | capC | 0.0 | Capsule | Immune modulation | 98.67 | 100.00 | NP_391470 |
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 |
|---|---|---|---|---|---|---|---|---|
| JFCPBKDH_3 | 27922 | 26786 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| JFCPBKDH_11 | 4231 | 5100 | pdxS | 4.51e-152 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| JFCPBKDH_1 | 304991 | 304215 | CodY | 5.32e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| JFCPBKDH_23 | 156827 | 156258 | ClpP | 3.13e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| JFCPBKDH_34 | 274764 | 275156 | spxA1 | 2.45e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| JFCPBKDH_34 | 274764 | 275156 | spx | 1.46e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| JFCPBKDH_5 | 14314 | 14072 | SpoVG | 4.72e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| JFCPBKDH_36 | 136264 | 136461 | CspA | 9.22e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| JFCPBKDH_12 | 397154 | 396960 | CspD | 3.41e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| JFCPBKDH_34 | 31521 | 31327 | CspB | 3.53e-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 |
|---|---|---|---|
| JFCPBKDH_1 | 0.0 | 1.0 | 0.0 |
| JFCPBKDH_2 | 0.0 | 1.0 | 0.0 |
| JFCPBKDH_3 | 0.0 | 1.0 | 0.0 |
| JFCPBKDH_4 | 0.0 | 1.0 | 0.0 |
| JFCPBKDH_5 | 0.0 | 1.0 | 0.0 |
| JFCPBKDH_6 | 0.0 | 1.0 | 0.0 |
| JFCPBKDH_7 | 0.0 | 1.0 | 0.0 |
| JFCPBKDH_8 | 0.0 | 1.0 | 0.0 |
| JFCPBKDH_9 | 0.0 | 1.0 | 0.0 |
| JFCPBKDH_10 | 0.0 | 1.0 | 0.0 |
| JFCPBKDH_11 | 0.0 | 1.0 | 0.0 |
| JFCPBKDH_12 | 0.0 | 1.0 | 0.0 |
| JFCPBKDH_13 | 0.0 | 1.0 | 0.0 |
| JFCPBKDH_14 | 0.0 | 1.0 | 0.0 |
| JFCPBKDH_15 | 0.0 | 1.0 | 0.0 |
| JFCPBKDH_23 | 0.0 | 1.0 | 0.0 |
| JFCPBKDH_32 | 0.0 | 1.0 | 0.0 |
| JFCPBKDH_33 | 0.0 | 1.0 | 0.0 |
| JFCPBKDH_34 | 0.0 | 1.0 | 0.0 |
| JFCPBKDH_35 | 0.0 | 1.0 | 0.0 |
| JFCPBKDH_36 | 0.0 | 1.0 | 0.0 |
| JFCPBKDH_37 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| JFCPBKDH_1 | 81331 | 98589 | False | Siphoviridae | VOG3390, VOG4705, VOG5008, VOG8610, VOG7930, VOG0275, VOG9312, VOG4910, VOG3389, VOG5042 |
| JFCPBKDH_1 | 645073 | 652168 | False | Myoviridae | VOG4705, VOG4612, VOG4862, VOG4691, VOG4550, VOG3894 |
| JFCPBKDH_12 | 6111 | 30359 | False | Myoviridae | VOG7060, VOG0796, VOG9315, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718 |
| JFCPBKDH_34 | 369279 | 379200 | False | Siphoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685 |
| JFCPBKDH_35 | 7527 | 34240 | False | Myoviridae | VOG0198, VOG0796, VOG10227, VOG0720, VOG4555, VOG4553, VOG0815, VOG4564, VOG4623, VOG1353, VOG1881, VOG1883, VOG1352, VOG4699, VOG6163, VOG1956, VOG1433, VOG1348, VOG0573, VOG4550, VOG4691, VOG4845, VOG7718, VOG3390, VOG4705, VOG5008, VOG0753, VOG0136, VOG4574, VOG2703, VOG9093 |
Phigaro v2.4.0 (Database: Jan. 2024 release)