Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 7 | 17.12 |
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. |
|---|---|---|---|---|---|---|---|---|
| KKILFJPH_3 | 617357 | 617695 | ykkC | ARO:3003063 | ykkC | 99.11 | 100.00 | AL009126.1 |
| KKILFJPH_3 | 617040 | 617357 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| KKILFJPH_1 | 598545 | 599399 | aadK | ARO:3002627 | aadK | 97.89 | 100.00 | AL009126.1 |
| KKILFJPH_1 | 583150 | 584352 | blt | ARO:3003006 | blt | 98.00 | 100.00 | L32599.1 |
| KKILFJPH_1 | 391337 | 392506 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| KKILFJPH_4 | 325730 | 326650 | mphK | ARO:3004541 | mphK | 93.46 | 100.00 | CP010314.1 |
| KKILFJPH_4 | 312390 | 313829 | lmrB | ARO:3002813 | lmrB | 99.79 | 100.42 | JYFL01000006.1 |
| KKILFJPH_7 | 301703 | 304273 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 100.00 | AL009126.3 |
| KKILFJPH_4 | 13484 | 15118 | vmlR | ARO:3004476 | vmlR | 98.35 | 99.45 | 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. |
|---|---|---|---|---|---|---|---|
| KKILFJPH_1 | 598545 | 599399 | aadK | Streptomycin | 98.36 | 100.00 | M26879 |
| KKILFJPH_2 | 1009627 | 1011006 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 97.97 | 100.00 | X08034 |
| KKILFJPH_4 | 325730 | 326650 | mph(K) | Spiramycin, Telithromycin | 93.60 | 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. |
|---|---|---|---|---|---|---|---|---|
| KKILFJPH_4 | 13484 | 15121 | vmlR | ABC-F type ribosomal protection protein VmlR | INTERNAL_STOP | 98.17 | 99.82 | WP_003234144.1 |
| KKILFJPH_1 | 598548 | 599399 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.89 | 100.00 | WP_003229862.1 |
| KKILFJPH_2 | 1009630 | 1011006 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 97.82 | 100.00 | WP_003242953.1 |
| KKILFJPH_2 | 1007070 | 1007588 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 95.95 | 100.00 | WP_003242546.1 |
| KKILFJPH_4 | 325733 | 326650 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 93.46 | 100.00 | WP_003246254.1 |
| KKILFJPH_1 | 66840 | 69437 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.06 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| KKILFJPH_1 | 157753 | 158394 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| KKILFJPH_2 | 533184 | 534365 | capB | 0.0 | Capsule | Immune modulation | 99.41 | 100.00 | NP_391471 |
| KKILFJPH_2 | 112998 | 113783 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| KKILFJPH_2 | 109161 | 110099 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391077 |
| KKILFJPH_2 | 532720 | 533169 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| KKILFJPH_2 | 531559 | 532701 | capA | 0.0 | Capsule | Immune modulation | 98.78 | 100.00 | NP_391469 |
| KKILFJPH_1 | 20021 | 21784 | dep/capD | 0.0 | Capsule | Immune modulation | 98.64 | 100.00 | NP_389723 |
| KKILFJPH_2 | 102005 | 109141 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.54 | 100.00 | NP_391076 |
| KKILFJPH_2 | 111775 | 112971 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.41 | 100.00 | NP_391079 |
| KKILFJPH_2 | 110127 | 111746 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.15 | 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 |
|---|---|---|---|---|---|---|---|---|
| KKILFJPH_8 | 28006 | 26870 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| KKILFJPH_5 | 4381 | 5250 | pdxS | 1.11e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| KKILFJPH_3 | 305590 | 304814 | CodY | 8.45e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| KKILFJPH_2 | 376482 | 377051 | ClpP | 6.28e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| KKILFJPH_3 | 764630 | 764238 | spxA1 | 6.64e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| KKILFJPH_3 | 764630 | 764238 | spx | 3.96e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| KKILFJPH_6 | 34687 | 34445 | SpoVG | 7.51e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| KKILFJPH_4 | 62839 | 62642 | CspA | 1.82e-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 |
|---|---|---|---|
| KKILFJPH_1 | 0.0 | 1.0 | 0.0 |
| KKILFJPH_2 | 0.0 | 1.0 | 0.0 |
| KKILFJPH_3 | 0.0 | 1.0 | 0.0 |
| KKILFJPH_4 | 0.0 | 1.0 | 0.0 |
| KKILFJPH_5 | 0.0 | 1.0 | 0.0 |
| KKILFJPH_6 | 0.0 | 1.0 | 0.0 |
| KKILFJPH_7 | 0.0 | 1.0 | 0.0 |
| KKILFJPH_8 | 0.0 | 1.0 | 0.0 |
| KKILFJPH_9 | 0.0 | 1.0 | 0.0 |
| KKILFJPH_11 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| KKILFJPH_3 | 647566 | 674391 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490 |
| KKILFJPH_7 | 27677 | 49971 | False | Siphoviridae | VOG0198, VOG8376, VOG8444, VOG0796, VOG10227, VOG0720, VOG4564, VOG4555, VOG4553, VOG1125, VOG0815, VOG4623, VOG0816, VOG5660, VOG0724, VOG0799, VOG0725, VOG4545, VOG4605, VOG4599, VOG5535, VOG4728, VOG0753 |
| KKILFJPH_9 | 3700 | 10495 | False | Unknown | VOG9667, VOG8241, VOG3549, VOG1878, VOG0083, VOG1309, VOG1292, VOG11060 |
| KKILFJPH_9 | 25962 | 48076 | False | Myoviridae | VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG0906, VOG7718, VOG4705 |
Phigaro v2.4.0 (Database: Jan. 2024 release)