Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 8 | 17.55 |
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. |
|---|---|---|---|---|---|---|---|---|
| JHDLBKHM_40 | 495997 | 496335 | ykkC | ARO:3003063 | ykkC | 98.21 | 100.00 | AL009126.1 |
| JHDLBKHM_40 | 495680 | 495997 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| JHDLBKHM_42 | 383325 | 384494 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| JHDLBKHM_92 | 259855 | 262425 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.65 | 100.00 | AL009126.3 |
| JHDLBKHM_69 | 238083 | 239711 | vmlR | ARO:3004476 | vmlR | 98.89 | 99.09 | NC_000964.3 |
| JHDLBKHM_68 | 160105 | 160698 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| JHDLBKHM_42 | 160022 | 161224 | blt | ARO:3003006 | blt | 99.75 | 100.00 | L32599.1 |
| JHDLBKHM_42 | 130851 | 131705 | aadK | ARO:3002627 | aadK | 98.94 | 100.00 | AL009126.1 |
| JHDLBKHM_68 | 109705 | 111144 | lmrB | ARO:3002813 | lmrB | 99.58 | 100.42 | JYFL01000006.1 |
| JHDLBKHM_68 | 96890 | 97810 | mphK | ARO:3004541 | mphK | 96.08 | 100.00 | CP010314.1 |
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. |
|---|---|---|---|---|---|---|---|
| JHDLBKHM_42 | 130851 | 131705 | aadK | Streptomycin | 98.83 | 100.00 | M26879 |
| JHDLBKHM_68 | 96890 | 97810 | mph(K) | Spiramycin, Telithromycin | 96.42 | 99.89 | 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. |
|---|---|---|---|---|---|---|---|---|
| JHDLBKHM_42 | 130851 | 131702 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.94 | 100.00 | WP_003229862.1 |
| JHDLBKHM_69 | 238086 | 239711 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.89 | 98.90 | WP_003234144.1 |
| JHDLBKHM_68 | 96890 | 97807 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 96.08 | 100.00 | WP_003246254.1 |
| JHDLBKHM_80 | 29182 | 29700 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.75 | 100.00 | WP_003242546.1 |
| JHDLBKHM_44 | 163584 | 166181 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| JHDLBKHM_55 | 158013 | 159194 | capB | 0.0 | Capsule | Immune modulation | 99.83 | 100.00 | NP_391471 |
| JHDLBKHM_57 | 62492 | 63430 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.68 | 100.00 | NP_391077 |
| JHDLBKHM_44 | 62283 | 62924 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| JHDLBKHM_55 | 159209 | 159658 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| JHDLBKHM_57 | 58809 | 59594 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.24 | 100.00 | NP_391080 |
| JHDLBKHM_55 | 159677 | 160819 | capA | 0.0 | Capsule | Immune modulation | 99.21 | 100.00 | NP_391469 |
| JHDLBKHM_57 | 63450 | 70586 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.86 | 100.00 | NP_391076 |
| JHDLBKHM_57 | 59620 | 60816 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.83 | 100.00 | NP_391079 |
| JHDLBKHM_44 | 216921 | 218684 | dep/capD | 0.0 | Capsule | Immune modulation | 98.58 | 100.00 | NP_389723 |
| JHDLBKHM_57 | 60845 | 62464 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.52 | 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 |
|---|---|---|---|---|---|---|---|---|
| JHDLBKHM_103 | 31748 | 32884 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| JHDLBKHM_127 | 11267 | 10398 | pdxS | 1.11e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| JHDLBKHM_40 | 185264 | 184488 | CodY | 7.48e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| JHDLBKHM_55 | 309679 | 309110 | ClpP | 1.91e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| JHDLBKHM_40 | 645075 | 644683 | spxA1 | 5.88e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| JHDLBKHM_40 | 645075 | 644683 | spx | 3.51e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| JHDLBKHM_106 | 20624 | 20866 | SpoVG | 7.51e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| JHDLBKHM_69 | 179407 | 179604 | CspA | 1.16e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| JHDLBKHM_44 | 50321 | 50127 | CspD | 2.14e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
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 |
|---|---|---|---|
| JHDLBKHM_39 | 0.0 | 1.0 | 0.0 |
| JHDLBKHM_40 | 0.0 | 1.0 | 0.0 |
| JHDLBKHM_41 | 0.0 | 1.0 | 0.0 |
| JHDLBKHM_42 | 0.0 | 1.0 | 0.0 |
| JHDLBKHM_43 | 0.0 | 1.0 | 0.0 |
| JHDLBKHM_44 | 0.0 | 1.0 | 0.0 |
| JHDLBKHM_55 | 0.0 | 1.0 | 0.0 |
| JHDLBKHM_56 | 0.0 | 1.0 | 0.0 |
| JHDLBKHM_57 | 0.0 | 1.0 | 0.0 |
| JHDLBKHM_68 | 0.0 | 1.0 | 0.0 |
| JHDLBKHM_69 | 0.0 | 1.0 | 0.0 |
| JHDLBKHM_79 | 0.0 | 1.0 | 0.0 |
| JHDLBKHM_80 | 0.0 | 1.0 | 0.0 |
| JHDLBKHM_91 | 0.0 | 1.0 | 0.0 |
| JHDLBKHM_92 | 0.0 | 1.0 | 0.0 |
| JHDLBKHM_103 | 0.0 | 1.0 | 0.0 |
| JHDLBKHM_104 | 0.0 | 1.0 | 0.0 |
| JHDLBKHM_105 | 0.0 | 1.0 | 0.0 |
| JHDLBKHM_106 | 0.0 | 1.0 | 0.0 |
| JHDLBKHM_116 | 0.0 | 1.0 | 0.0 |
| JHDLBKHM_127 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| JHDLBKHM_40 | 525880 | 552365 | 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 |
| JHDLBKHM_41 | 99113 | 124839 | False | Siphoviridae | VOG0198, VOG4581, VOG1886, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG4705, VOG5008, VOG0641 |
| JHDLBKHM_42 | 188207 | 207434 | False | Myoviridae | VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG10095, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718 |
| JHDLBKHM_116 | 5753 | 31906 | False | Myoviridae | VOG0136, VOG0753, VOG4705, VOG7718, VOG0906, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG9315 |
| JHDLBKHM_116 | 41696 | 50779 | False | Unknown | VOG10041, VOG0025, VOG9600, VOG11060, VOG1292, VOG1309, VOG0083, VOG1878, VOG3549, VOG8241, VOG9667 |
Phigaro v2.4.0 (Database: Jan. 2024 release)