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. |
|---|---|---|---|---|---|---|---|---|
| LCAHIECF_5 | 590578 | 591780 | blt | ARO:3003006 | blt | 99.00 | 100.00 | L32599.1 |
| LCAHIECF_6 | 441486 | 442340 | aadK | ARO:3002627 | aadK | 98.24 | 100.00 | AL009126.1 |
| LCAHIECF_5 | 408428 | 409597 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| LCAHIECF_1 | 212281 | 213924 | vmlR | ARO:3004476 | vmlR | 98.54 | 100.00 | NC_000964.3 |
| LCAHIECF_7 | 162486 | 163079 | tmrB | ARO:3003059 | tmrB | 97.46 | 100.00 | AL009126.3 |
| LCAHIECF_7 | 111936 | 113375 | lmrB | ARO:3002813 | lmrB | 99.58 | 100.42 | JYFL01000006.1 |
| LCAHIECF_2 | 107913 | 108251 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| LCAHIECF_2 | 107596 | 107913 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| LCAHIECF_7 | 99750 | 100670 | mphK | ARO:3004541 | mphK | 99.67 | 100.00 | CP010314.1 |
| LCAHIECF_9 | 27319 | 29889 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 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. |
|---|---|---|---|---|---|---|---|
| LCAHIECF_7 | 99750 | 100670 | mph(K) | Spiramycin, Telithromycin | 99.57 | 100.00 | NC_000964 |
| LCAHIECF_6 | 441486 | 442340 | aadK | Streptomycin | 98.71 | 100.00 | 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. |
|---|---|---|---|---|---|---|---|---|
| LCAHIECF_7 | 99750 | 100667 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 99.67 | 100.00 | WP_003246254.1 |
| LCAHIECF_1 | 212284 | 213924 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.54 | 100.00 | WP_003234144.1 |
| LCAHIECF_6 | 441486 | 442337 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.24 | 100.00 | WP_003229862.1 |
| LCAHIECF_1 | 7294 | 7812 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 89.60 | 100.00 | WP_003242546.1 |
| LCAHIECF_5 | 64577 | 67174 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| LCAHIECF_3 | 390560 | 391345 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.87 | 100.00 | NP_391080 |
| LCAHIECF_8 | 25468 | 25917 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| LCAHIECF_5 | 209077 | 209718 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| LCAHIECF_8 | 25932 | 27113 | capB | 0.0 | Capsule | Immune modulation | 99.41 | 100.00 | NP_391471 |
| LCAHIECF_8 | 24307 | 25449 | capA | 0.0 | Capsule | Immune modulation | 98.86 | 100.00 | NP_391469 |
| LCAHIECF_3 | 394243 | 395181 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.83 | 100.00 | NP_391077 |
| LCAHIECF_3 | 391371 | 392567 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.83 | 100.00 | NP_391079 |
| LCAHIECF_5 | 10125 | 11888 | dep/capD | 0.0 | Capsule | Immune modulation | 98.36 | 100.00 | NP_389723 |
| LCAHIECF_3 | 395201 | 402337 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.36 | 100.00 | NP_391076 |
| LCAHIECF_3 | 392596 | 394215 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.96 | 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 |
|---|---|---|---|---|---|---|---|---|
| LCAHIECF_15 | 27918 | 26782 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| LCAHIECF_16 | 4285 | 5154 | pdxS | 1.10e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| LCAHIECF_4 | 278673 | 277897 | CodY | 3.92e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| LCAHIECF_3 | 115561 | 114992 | ClpP | 2.70e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| LCAHIECF_2 | 257854 | 257462 | spxA1 | 3.09e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| LCAHIECF_2 | 257854 | 257462 | spx | 1.85e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| LCAHIECF_11 | 34765 | 34523 | SpoVG | 7.48e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| LCAHIECF_1 | 166015 | 166212 | CspA | 3.70e-32 | cold shock protein | 92.42 | 100.00 | CAA62903 |
| LCAHIECF_10 | 31246 | 31440 | CspB | 6.13e-28 | cold shock protein | 83.08 | 98.48 | CAD00094 |
| LCAHIECF_5 | 221680 | 221874 | CspD | 1.55e-27 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| LCAHIECF_1 | 166015 | 166209 | CspR | 1.84e-26 | cold shock protein | 80.00 | 98.48 | AAO82613 |
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 |
|---|---|---|---|
| LCAHIECF_1 | 0.0 | 1.0 | 0.0 |
| LCAHIECF_2 | 0.0 | 1.0 | 0.0 |
| LCAHIECF_3 | 0.0 | 1.0 | 0.0 |
| LCAHIECF_4 | 0.0 | 1.0 | 0.0 |
| LCAHIECF_5 | 0.0 | 1.0 | 0.0 |
| LCAHIECF_6 | 0.0 | 1.0 | 0.0 |
| LCAHIECF_7 | 0.0 | 1.0 | 0.0 |
| LCAHIECF_8 | 0.0 | 1.0 | 0.0 |
| LCAHIECF_9 | 0.0 | 1.0 | 0.0 |
| LCAHIECF_10 | 0.0 | 1.0 | 0.0 |
| LCAHIECF_11 | 0.0 | 1.0 | 0.0 |
| LCAHIECF_12 | 0.0 | 1.0 | 0.0 |
| LCAHIECF_13 | 0.0 | 1.0 | 0.0 |
| LCAHIECF_14 | 0.0 | 1.0 | 0.0 |
| LCAHIECF_15 | 0.0 | 1.0 | 0.0 |
| LCAHIECF_16 | 0.0 | 1.0 | 0.0 |
| LCAHIECF_19 | 1.0 | 0.0 | 1.0 |
| LCAHIECF_20 | 0.0 | 1.0 | 0.0 |
| LCAHIECF_21 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LCAHIECF_2 | 137510 | 163687 | False | Myoviridae | VOG0136, VOG0753, VOG4705, VOG3390, VOG5384, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
Phigaro v2.4.0 (Database: Jan. 2024 release)