Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 11 | 10 | 4 | 15.39 |
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. |
|---|---|---|---|---|---|---|---|---|
| ICPCCDEL_1 | 2956419 | 2957852 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.00 | JYFL01000006.1 |
| ICPCCDEL_1 | 2362238 | 2364808 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| ICPCCDEL_1 | 1883370 | 1883708 | ykkC | ARO:3003063 | ykkC | 99.11 | 100.00 | AL009126.1 |
| ICPCCDEL_1 | 1883053 | 1883370 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| ICPCCDEL_1 | 922328 | 923497 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| ICPCCDEL_1 | 721527 | 722729 | blt | ARO:3003006 | blt | 100.00 | 100.00 | L32599.1 |
| ICPCCDEL_1 | 700587 | 701441 | aadK | ARO:3002627 | aadK | 97.89 | 100.00 | AL009126.1 |
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. |
|---|---|---|---|---|---|---|---|
| ICPCCDEL_1 | 3311659 | 3313035 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 99.35 | 100.00 | X08034 |
| ICPCCDEL_1 | 700587 | 701439 | aadK | Streptomycin | 98.59 | 99.77 | M26879 |
| ICPCCDEL_1 | 2983202 | 2984121 | mph(K) | Spiramycin, Telithromycin | 97.61 | 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. |
|---|---|---|---|---|---|---|---|---|
| ICPCCDEL_1 | 3311659 | 3313032 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 99.13 | 100.00 | WP_003242953.1 |
| ICPCCDEL_1 | 700587 | 701438 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.89 | 100.00 | WP_003229862.1 |
| ICPCCDEL_1 | 2657107 | 2658747 | vmlR | ABC-F type ribosomal protection protein VmlR | INTERNAL_STOP | 97.62 | 100.00 | WP_003234144.1 |
| ICPCCDEL_1 | 3314950 | 3315468 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 93.64 | 100.00 | WP_003242546.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| ICPCCDEL_1 | 3824450 | 3825592 | capA | 0.0 | Capsule | Immune modulation | 99.74 | 100.00 | NP_391469 |
| ICPCCDEL_1 | 3822786 | 3823967 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| ICPCCDEL_1 | 3823982 | 3824431 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| ICPCCDEL_1 | 68642 | 69427 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| ICPCCDEL_1 | 1303086 | 1304849 | dep/capD | 0.0 | Capsule | Immune modulation | 99.26 | 100.00 | NP_389723 |
| ICPCCDEL_1 | 73283 | 80419 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.95 | 100.00 | NP_391076 |
| ICPCCDEL_1 | 69453 | 70649 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.83 | 100.00 | NP_391079 |
| ICPCCDEL_1 | 72325 | 73263 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.62 | 100.00 | NP_391077 |
| ICPCCDEL_1 | 70678 | 72297 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.90 | 100.00 | NP_391078 |
| ICPCCDEL_1 | 1166038 | 1166679 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 97.82 | 100.00 | NP_390062 |
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 |
|---|---|---|---|---|---|---|---|---|
| ICPCCDEL_1 | 3152152 | 3151016 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| ICPCCDEL_1 | 3266233 | 3265364 | pdxS | 5.48e-149 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.45 | 98.31 | ACE61268 |
| ICPCCDEL_1 | 1564947 | 1564171 | CodY | 3.42e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| ICPCCDEL_1 | 3978391 | 3977822 | ClpP | 2.53e-98 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
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 |
|---|---|---|---|
| ICPCCDEL_1 | 0.0 | 1.0 | 0.0 |
| ICPCCDEL_2 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| ICPCCDEL_1 | 333648 | 366453 | False | Siphoviridae | VOG11060, VOG9600, VOG0025, VOG1884, VOG0198, VOG0376, VOG2545, VOG2533, VOG4841, VOG4581, VOG1886, VOG0202, VOG4556, VOG4573, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG4705, VOG5008, VOG0641 |
| ICPCCDEL_1 | 503774 | 508312 | False | Siphoviridae | VOG9576, VOG9667, VOG9667, VOG0806, VOG4322, VOG4552, VOG4603 |
| ICPCCDEL_1 | 516621 | 542627 | False | Myoviridae | VOG10640, VOG0796, VOG10227, VOG0720, VOG4555, VOG4553, VOG4564, VOG4623, VOG1353, VOG1881, VOG1883, VOG1352, VOG4699, VOG6163, VOG1956, VOG1433, VOG1348, VOG0573, VOG4550, VOG4691, VOG4845, VOG7718, VOG3390, VOG4705, VOG0641, VOG4707, VOG0944, VOG5532 |
| ICPCCDEL_1 | 1116678 | 1125098 | False | Siphoviridae | VOG0221, VOG5023, VOG0720, VOG4555, VOG4553, VOG4713 |
| ICPCCDEL_1 | 1416122 | 1439188 | False | Siphoviridae | VOG4574, VOG0641, VOG4705, VOG3390, VOG4612, VOG4660, VOG4619, VOG0801, VOG6163, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5361, VOG4553, VOG4573, VOG4556, VOG2935, VOG1886, VOG4581, VOG4841 |
| ICPCCDEL_1 | 1913705 | 1936470 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861 |
| ICPCCDEL_1 | 4185276 | 4208110 | False | Siphoviridae | VOG4841, VOG4581, VOG4544, VOG4556, VOG4573, VOG4553, VOG0204, VOG4589, VOG0207, VOG4586, VOG5852, VOG6163, VOG0801, VOG3462, VOG4619, VOG4856, VOG0804, VOG4705, VOG5221, VOG0136 |
Phigaro v2.4.0 (Database: Jan. 2024 release)