Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 5 | 16.40 |
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. |
|---|---|---|---|---|---|---|---|---|
| GKCGLIPO_3 | 1358533 | 1358850 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| GKCGLIPO_3 | 1358195 | 1358533 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| GKCGLIPO_3 | 877432 | 880002 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 100.00 | AL009126.3 |
| GKCGLIPO_2 | 575233 | 576087 | aadK | ARO:3002627 | aadK | 98.94 | 100.00 | AL009126.1 |
| GKCGLIPO_2 | 557968 | 559170 | blt | ARO:3003006 | blt | 99.25 | 100.00 | L32599.1 |
| GKCGLIPO_3 | 545360 | 546988 | vmlR | ARO:3004476 | vmlR | 99.08 | 99.09 | NC_000964.3 |
| GKCGLIPO_3 | 293006 | 293599 | tmrB | ARO:3003059 | tmrB | 100.00 | 100.00 | AL009126.3 |
| GKCGLIPO_3 | 242482 | 243915 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.00 | JYFL01000006.1 |
| GKCGLIPO_3 | 229666 | 230532 | mphK | ARO:3004541 | mphK | 98.61 | 94.12 | 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. |
|---|---|---|---|---|---|---|---|
| GKCGLIPO_2 | 575235 | 576087 | aadK | Streptomycin | 98.94 | 99.77 | M26879 |
| GKCGLIPO_2 | 2125511 | 2126887 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 98.91 | 100.00 | D12567 |
| GKCGLIPO_3 | 229666 | 230586 | 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. |
|---|---|---|---|---|---|---|---|---|
| GKCGLIPO_3 | 545363 | 546988 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 99.08 | 98.90 | WP_003234144.1 |
| GKCGLIPO_2 | 575236 | 576087 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.94 | 100.00 | WP_003229862.1 |
| GKCGLIPO_2 | 2125514 | 2126887 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.91 | 100.00 | WP_063856081.1 |
| GKCGLIPO_3 | 229666 | 230583 | mphK | macrolide 2'-phosphotransferase MphK | INTERNAL_STOP | 98.04 | 100.00 | WP_003246254.1 |
| GKCGLIPO_2 | 2123040 | 2123558 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| GKCGLIPO_3 | 2038499 | 2041087 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.37 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| GKCGLIPO_2 | 1226414 | 1227199 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391080 |
| GKCGLIPO_2 | 1215422 | 1222558 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.99 | 100.00 | NP_391076 |
| GKCGLIPO_2 | 1222578 | 1223516 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.89 | 100.00 | NP_391077 |
| GKCGLIPO_2 | 1633751 | 1634932 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| GKCGLIPO_2 | 1223544 | 1225163 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.57 | 100.00 | NP_391078 |
| GKCGLIPO_2 | 1633287 | 1633736 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| GKCGLIPO_2 | 1225192 | 1226388 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.50 | 100.00 | NP_391079 |
| GKCGLIPO_2 | 188485 | 189126 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.22 | 100.00 | NP_390062 |
| GKCGLIPO_2 | 1632126 | 1633268 | capA | 0.0 | Capsule | Immune modulation | 99.21 | 100.00 | NP_391469 |
| GKCGLIPO_3 | 1984102 | 1985865 | dep/capD | 0.0 | Capsule | Immune modulation | 98.92 | 100.00 | NP_389723 |
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 |
|---|---|---|---|---|---|---|---|---|
| GKCGLIPO_3 | 99766 | 100902 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| GKCGLIPO_1 | 11085 | 11954 | pdxS | 1.86e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| GKCGLIPO_3 | 1668525 | 1669301 | CodY | 1.69e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| GKCGLIPO_2 | 1478629 | 1479198 | ClpP | 1.32e-98 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| GKCGLIPO_3 | 1209373 | 1209765 | spxA1 | 1.33e-69 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| GKCGLIPO_3 | 1209373 | 1209765 | spx | 7.91e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
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 |
|---|---|---|---|
| GKCGLIPO_1 | 0.0 | 1.0 | 0.0 |
| GKCGLIPO_2 | 0.0 | 1.0 | 0.0 |
| GKCGLIPO_3 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| GKCGLIPO_2 | 78559 | 88188 | False | Siphoviridae | VOG0026, VOG0918, VOG4551, VOG0025, VOG10727, VOG7627, VOG0322 |
| GKCGLIPO_2 | 763226 | 787428 | False | Siphoviridae | VOG4574, VOG0136, VOG0753, VOG4728, VOG5535, VOG4599, VOG4605, VOG4545, VOG0725, VOG0799, VOG0724, VOG5660, VOG0816, VOG4623, VOG3480, VOG1329, VOG4555, VOG1300, VOG4564, VOG0720, VOG0720, VOG0796 |
| GKCGLIPO_2 | 1112320 | 1116335 | False | Siphoviridae | VOG0720, VOG5023 |
| GKCGLIPO_3 | 586813 | 592618 | False | Siphoviridae | VOG0275, VOG4602, VOG3304, VOG9667, VOG0650, VOG4552, VOG4603 |
| GKCGLIPO_3 | 603037 | 624667 | False | Siphoviridae | VOG0796, VOG10227, VOG0720, VOG4564, VOG4555, VOG4553, VOG1125, VOG0815, VOG4623, VOG0816, VOG5660, VOG0724, VOG0799, VOG2621, VOG0725, VOG1323, VOG4545, VOG4605, VOG4599, VOG5535, VOG0753, VOG0136 |
| GKCGLIPO_3 | 1302230 | 1328710 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG4282, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG4612, VOG4705 |
Phigaro v2.4.0 (Database: Jan. 2024 release)