Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 9 | 18.03 |
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. |
|---|---|---|---|---|---|---|---|---|
| LLCHGBIK_1 | 416698 | 417036 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| LLCHGBIK_1 | 416381 | 416698 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| LLCHGBIK_2 | 346621 | 347541 | mphK | ARO:3004541 | mphK | 97.71 | 100.00 | CP010314.1 |
| LLCHGBIK_2 | 333289 | 334728 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| LLCHGBIK_2 | 283661 | 284254 | tmrB | ARO:3003059 | tmrB | 100.00 | 100.00 | AL009126.3 |
| LLCHGBIK_4 | 255833 | 256687 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| LLCHGBIK_4 | 238786 | 239988 | blt | ARO:3003006 | blt | 99.50 | 100.00 | L32599.1 |
| LLCHGBIK_2 | 29398 | 31041 | vmlR | ARO:3004476 | vmlR | 99.09 | 100.00 | NC_000964.3 |
| LLCHGBIK_6 | 27425 | 29995 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.53 | 100.00 | AL009126.3 |
| LLCHGBIK_4 | 12442 | 13611 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
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. |
|---|---|---|---|---|---|---|---|
| LLCHGBIK_4 | 255833 | 256687 | aadK | Streptomycin | 98.83 | 100.00 | M26879 |
| LLCHGBIK_2 | 346621 | 347541 | 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. |
|---|---|---|---|---|---|---|---|---|
| LLCHGBIK_2 | 29398 | 31038 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 99.09 | 100.00 | WP_003234144.1 |
| LLCHGBIK_4 | 255836 | 256687 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| LLCHGBIK_2 | 346624 | 347541 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.71 | 100.00 | WP_003246254.1 |
| LLCHGBIK_3 | 375925 | 376443 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 94.80 | 100.00 | WP_003242546.1 |
| LLCHGBIK_17 | 16566 | 19163 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.29 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| LLCHGBIK_10 | 94816 | 95457 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.69 | 100.00 | NP_390062 |
| LLCHGBIK_9 | 46893 | 48074 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| LLCHGBIK_12 | 23540 | 24325 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| LLCHGBIK_12 | 22318 | 23514 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.33 | 100.00 | NP_391079 |
| LLCHGBIK_17 | 63169 | 64932 | dep/capD | 0.0 | Capsule | Immune modulation | 98.98 | 100.00 | NP_389723 |
| LLCHGBIK_9 | 45268 | 46410 | capA | 0.0 | Capsule | Immune modulation | 98.69 | 100.00 | NP_391469 |
| LLCHGBIK_9 | 46429 | 46878 | capC | 0.0 | Capsule | Immune modulation | 98.67 | 100.00 | NP_391470 |
| LLCHGBIK_12 | 19704 | 20642 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.40 | 100.00 | NP_391077 |
| LLCHGBIK_12 | 12548 | 19684 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.36 | 100.00 | NP_391076 |
| LLCHGBIK_12 | 20670 | 22289 | 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 |
|---|---|---|---|---|---|---|---|---|
| LLCHGBIK_20 | 31733 | 32869 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| LLCHGBIK_25 | 11262 | 10393 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| LLCHGBIK_1 | 107935 | 107159 | CodY | 4.36e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| LLCHGBIK_5 | 191528 | 192097 | ClpP | 1.82e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| LLCHGBIK_16 | 32780 | 33172 | spxA1 | 4.84e-71 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| LLCHGBIK_16 | 32780 | 33172 | spx | 2.89e-69 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| LLCHGBIK_19 | 34765 | 34523 | SpoVG | 7.51e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| LLCHGBIK_2 | 74834 | 74637 | CspA | 1.91e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| LLCHGBIK_10 | 106689 | 106883 | CspD | 4.03e-28 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| LLCHGBIK_18 | 31694 | 31500 | CspB | 6.40e-28 | 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 |
|---|---|---|---|
| LLCHGBIK_1 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_2 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_3 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_4 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_5 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_6 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_7 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_8 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_9 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_10 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_11 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_12 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_13 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_14 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_15 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_16 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_17 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_18 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_19 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_20 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_21 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_22 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_23 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_24 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_25 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_26 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_27 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_28 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_30 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_31 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_32 | 1.0 | 0.0 | 1.0 |
| LLCHGBIK_34 | 0.0 | 1.0 | 0.0 |
| LLCHGBIK_36 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LLCHGBIK_1 | 446852 | 474133 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
| LLCHGBIK_4 | 185114 | 202882 | False | Myoviridae | VOG4705, VOG7718, VOG0906, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749 |
| LLCHGBIK_7 | 144299 | 177175 | False | Siphoviridae | VOG7438, VOG1047, VOG0021, VOG1565, VOG0026, VOG4609, VOG0327, VOG4548, VOG0198, VOG4556, VOG4581, VOG1886, VOG3607, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619, VOG4626, VOG4612, VOG6243, VOG4705, VOG0641, VOG4574 |
| LLCHGBIK_24 | 5421 | 21954 | False | Siphoviridae | VOG4841, VOG4581, VOG1886, VOG0202, VOG4556, VOG4573, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801 |
Phigaro v2.4.0 (Database: Jan. 2024 release)