Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 7 | 17.83 |
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. |
|---|---|---|---|---|---|---|---|---|
| LIAGCGNL_9 | 693874 | 695043 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| LIAGCGNL_9 | 447696 | 448898 | blt | ARO:3003006 | blt | 99.25 | 100.00 | L32599.1 |
| LIAGCGNL_9 | 427793 | 428647 | aadK | ARO:3002627 | aadK | 98.94 | 100.00 | AL009126.1 |
| LIAGCGNL_14 | 424813 | 425130 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| LIAGCGNL_14 | 424475 | 424813 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| LIAGCGNL_19 | 262815 | 265385 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.65 | 100.00 | AL009126.3 |
| LIAGCGNL_23 | 109518 | 110438 | mphK | ARO:3004541 | mphK | 97.71 | 100.00 | CP010314.1 |
| LIAGCGNL_23 | 96186 | 97625 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| LIAGCGNL_23 | 46532 | 47125 | tmrB | ARO:3003059 | tmrB | 97.46 | 100.00 | AL009126.3 |
| LIAGCGNL_21 | 29062 | 30708 | vmlR | ARO:3004476 | vmlR | 98.36 | 100.18 | 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. |
|---|---|---|---|---|---|---|---|
| LIAGCGNL_9 | 427793 | 428647 | aadK | Streptomycin | 98.95 | 100.00 | M26879 |
| LIAGCGNL_1 | 39548 | 40924 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 98.84 | 100.00 | D12567 |
| LIAGCGNL_23 | 109518 | 110438 | mph(K) | Spiramycin, Telithromycin | 98.05 | 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. |
|---|---|---|---|---|---|---|---|---|
| LIAGCGNL_9 | 427793 | 428644 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.94 | 100.00 | WP_003229862.1 |
| LIAGCGNL_1 | 39548 | 40921 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.91 | 100.00 | WP_063856081.1 |
| LIAGCGNL_21 | 29062 | 30705 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.36 | 100.00 | WP_003234144.1 |
| LIAGCGNL_23 | 109521 | 110438 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.71 | 100.00 | WP_003246254.1 |
| LIAGCGNL_1 | 42892 | 43410 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 93.06 | 100.00 | WP_003242546.1 |
| LIAGCGNL_9 | 1004894 | 1007491 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.83 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| LIAGCGNL_1 | 526987 | 528168 | capB | 0.0 | Capsule | Immune modulation | 99.58 | 100.00 | NP_391471 |
| LIAGCGNL_9 | 895123 | 895764 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| LIAGCGNL_1 | 955791 | 956987 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.42 | 100.00 | NP_391079 |
| LIAGCGNL_1 | 954980 | 955765 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| LIAGCGNL_1 | 528183 | 528632 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| LIAGCGNL_9 | 1051618 | 1053381 | dep/capD | 0.0 | Capsule | Immune modulation | 99.04 | 100.00 | NP_389723 |
| LIAGCGNL_1 | 958663 | 959601 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.94 | 100.00 | NP_391077 |
| LIAGCGNL_1 | 528651 | 529793 | capA | 0.0 | Capsule | Immune modulation | 98.78 | 100.00 | NP_391469 |
| LIAGCGNL_1 | 959621 | 966757 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.58 | 100.00 | NP_391076 |
| LIAGCGNL_1 | 957016 | 958635 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.04 | 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 |
|---|---|---|---|---|---|---|---|---|
| LIAGCGNL_26 | 28106 | 26970 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| LIAGCGNL_4 | 11305 | 10436 | pdxS | 1.13e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| LIAGCGNL_14 | 733614 | 734390 | CodY | 7.62e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| LIAGCGNL_1 | 680553 | 679984 | ClpP | 6.43e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| LIAGCGNL_14 | 277870 | 278262 | spxA1 | 5.99e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| LIAGCGNL_14 | 277870 | 278262 | spx | 3.57e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| LIAGCGNL_2 | 20614 | 20856 | SpoVG | 7.52e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| LIAGCGNL_21 | 78614 | 78417 | CspA | 9.59e-32 | 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 |
|---|---|---|---|
| LIAGCGNL_1 | 0.0 | 1.0 | 0.0 |
| LIAGCGNL_2 | 0.0 | 1.0 | 0.0 |
| LIAGCGNL_3 | 0.0 | 1.0 | 0.0 |
| LIAGCGNL_4 | 0.0 | 1.0 | 0.0 |
| LIAGCGNL_5 | 0.0 | 1.0 | 0.0 |
| LIAGCGNL_6 | 0.0 | 1.0 | 0.0 |
| LIAGCGNL_7 | 0.0 | 1.0 | 0.0 |
| LIAGCGNL_9 | 0.0 | 1.0 | 0.0 |
| LIAGCGNL_11 | 1.0 | 0.0 | 1.0 |
| LIAGCGNL_14 | 0.0 | 1.0 | 0.0 |
| LIAGCGNL_19 | 0.0 | 1.0 | 0.0 |
| LIAGCGNL_21 | 0.0 | 1.0 | 0.0 |
| LIAGCGNL_23 | 0.0 | 1.0 | 0.0 |
| LIAGCGNL_24 | 1.0 | 0.0 | 1.0 |
| LIAGCGNL_25 | 0.0 | 1.0 | 0.0 |
| LIAGCGNL_26 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LIAGCGNL_9 | 484244 | 513553 | False | Myoviridae | VOG0189, VOG4693, VOG9667, VOG4673, VOG4662, VOG7145, VOG0796, VOG10227, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4691, VOG4862, VOG7718 |
| LIAGCGNL_14 | 369940 | 395236 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG3390, VOG7895, VOG0753 |
Phigaro v2.4.0 (Database: Jan. 2024 release)