Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 11 | 4 | 16.76 |
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. |
|---|---|---|---|---|---|---|---|---|
| CBMICMCF_1 | 2414130 | 2414984 | aadK | ARO:3002627 | aadK | 97.54 | 100.00 | AL009126.1 |
| CBMICMCF_1 | 2395372 | 2396574 | blt | ARO:3003006 | blt | 100.00 | 100.00 | L32599.1 |
| CBMICMCF_1 | 2222645 | 2223814 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| CBMICMCF_1 | 1199374 | 1199691 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| CBMICMCF_1 | 1199036 | 1199374 | ykkC | ARO:3003063 | ykkC | 99.11 | 100.00 | AL009126.1 |
| CBMICMCF_1 | 721644 | 724214 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| CBMICMCF_1 | 213155 | 213805 | Limosilactobacillus reuteri cat-TC | ARO:3002671 | Lreu_cat-TC | 98.54 | 90.76 | U75299.1 |
| CBMICMCF_1 | 123359 | 124792 | lmrB | ARO:3002813 | lmrB | 98.95 | 100.00 | JYFL01000006.1 |
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. |
|---|---|---|---|---|---|---|---|
| CBMICMCF_1 | 213155 | 213805 | cat(pC194) | Chloramphenicol | 99.85 | 100.00 | NC_002013 |
| CBMICMCF_1 | 3899980 | 3901356 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 98.77 | 100.00 | D12567 |
| CBMICMCF_1 | 2414132 | 2414984 | aadK | Streptomycin | 98.48 | 99.77 | M26879 |
| CBMICMCF_1 | 97092 | 98011 | 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. |
|---|---|---|---|---|---|---|---|---|
| CBMICMCF_1 | 213158 | 213805 | catA | type A-9 chloramphenicol O-acetyltransferase | BLASTX | 99.54 | 100.00 | WP_001010387.1 |
| CBMICMCF_1 | 3899983 | 3901356 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.69 | 100.00 | WP_063856081.1 |
| CBMICMCF_1 | 420933 | 422573 | vmlR | ABC-F type ribosomal protection protein VmlR | INTERNAL_STOP | 97.62 | 100.00 | WP_003234144.1 |
| CBMICMCF_1 | 2414133 | 2414984 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.54 | 100.00 | WP_003229862.1 |
| CBMICMCF_1 | 3897488 | 3898006 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| CBMICMCF_1 | 2974062 | 2975000 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.68 | 100.00 | NP_391077 |
| CBMICMCF_1 | 3395590 | 3396771 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| CBMICMCF_1 | 3393965 | 3395107 | capA | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391469 |
| CBMICMCF_1 | 3395126 | 3395575 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| CBMICMCF_1 | 2977887 | 2978672 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| CBMICMCF_1 | 1740056 | 1741819 | dep/capD | 0.0 | Capsule | Immune modulation | 99.15 | 100.00 | NP_389723 |
| CBMICMCF_1 | 2966906 | 2974042 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.78 | 100.00 | NP_391076 |
| CBMICMCF_1 | 2976665 | 2977861 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.58 | 100.00 | NP_391079 |
| CBMICMCF_1 | 2019479 | 2020120 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 97.82 | 100.00 | NP_390062 |
| CBMICMCF_1 | 2975028 | 2976647 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.78 | 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. |
|---|---|---|---|---|---|---|---|---|
| CBMICMCF_2 | 1484 | 1776 | virulence_ecoli | iss | Increased serum survival | 98.98 | 100.00 | CP001509 |
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 |
|---|---|---|---|---|---|---|---|---|
| CBMICMCF_1 | 4059046 | 4060182 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| CBMICMCF_1 | 3945187 | 3946056 | pdxS | 5.34e-149 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.45 | 98.31 | ACE61268 |
| CBMICMCF_1 | 1525642 | 1526412 | CodY | 6.99e-122 | nutrient-responsive regulator | 80.16 | 99.23 | ACJ80679 |
| CBMICMCF_1 | 3240661 | 3241230 | ClpP | 2.47e-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 |
|---|---|---|---|
| CBMICMCF_1 | 0.0 | 1.0 | 0.0 |
| CBMICMCF_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 |
|---|---|---|---|---|---|
| CBMICMCF_1 | 1143962 | 1170731 | 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, VOG4705, VOG0753, VOG0136 |
| CBMICMCF_1 | 1968302 | 1987891 | False | Unknown | VOG4705, VOG5008, VOG8610, VOG0275, VOG9312, VOG4910, VOG3389, VOG5042, VOG9712, VOG4660, VOG4579 |
Phigaro v2.4.0 (Database: Jan. 2024 release)