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. |
|---|---|---|---|---|---|---|---|---|
| CLFMJCJL_23 | 279765 | 280619 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| CLFMJCJL_23 | 262668 | 263870 | blt | ARO:3003006 | blt | 99.25 | 100.00 | L32599.1 |
| CLFMJCJL_3 | 107613 | 109052 | lmrB | ARO:3002813 | lmrB | 99.79 | 100.42 | JYFL01000006.1 |
| CLFMJCJL_3 | 94801 | 95721 | mphK | ARO:3004541 | mphK | 99.35 | 100.00 | CP010314.1 |
| CLFMJCJL_23 | 84009 | 85178 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| CLFMJCJL_11 | 62687 | 64333 | vmlR | ARO:3004476 | vmlR | 97.45 | 100.18 | NC_000964.3 |
| CLFMJCJL_56 | 46663 | 47256 | tmrB | ARO:3003059 | tmrB | 97.97 | 100.00 | AL009126.3 |
| CLFMJCJL_18 | 18460 | 18798 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| CLFMJCJL_18 | 18143 | 18460 | ykkD | ARO:3003064 | ykkD | 99.05 | 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. |
|---|---|---|---|---|---|---|---|
| CLFMJCJL_3 | 94801 | 95721 | mph(K) | Spiramycin, Telithromycin | 99.02 | 100.00 | NC_000964 |
| CLFMJCJL_12 | 272520 | 273896 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 98.84 | 100.00 | D12567 |
| CLFMJCJL_23 | 279765 | 280619 | aadK | Streptomycin | 98.83 | 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. |
|---|---|---|---|---|---|---|---|---|
| CLFMJCJL_3 | 94801 | 95718 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 99.35 | 100.00 | WP_003246254.1 |
| CLFMJCJL_12 | 272523 | 273896 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.91 | 100.00 | WP_063856081.1 |
| CLFMJCJL_23 | 279768 | 280619 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| CLFMJCJL_11 | 62690 | 64333 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 97.45 | 100.00 | WP_003234144.1 |
| CLFMJCJL_12 | 269999 | 270517 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| CLFMJCJL_34 | 172997 | 175585 | rphC | rifamycin-inactivating phosphotransferase RphC | INTERNAL_STOP | 80.14 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| CLFMJCJL_67 | 57422 | 64558 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.72 | 100.00 | NP_391076 |
| CLFMJCJL_5 | 17986 | 18435 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| CLFMJCJL_5 | 16790 | 17971 | capB | 0.0 | Capsule | Immune modulation | 99.49 | 100.00 | NP_391471 |
| CLFMJCJL_67 | 52781 | 53566 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| CLFMJCJL_5 | 18454 | 19596 | capA | 0.0 | Capsule | Immune modulation | 99.30 | 100.00 | NP_391469 |
| CLFMJCJL_34 | 122413 | 124176 | dep/capD | 0.0 | Capsule | Immune modulation | 98.92 | 100.00 | NP_389723 |
| CLFMJCJL_34 | 286793 | 287434 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 98.91 | 100.00 | NP_390062 |
| CLFMJCJL_67 | 56464 | 57402 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.72 | 100.00 | NP_391077 |
| CLFMJCJL_67 | 53592 | 54788 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.66 | 100.00 | NP_391079 |
| CLFMJCJL_67 | 54817 | 56436 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.10 | 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 |
|---|---|---|---|---|---|---|---|---|
| CLFMJCJL_9 | 31850 | 32986 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| CLFMJCJL_40 | 4250 | 5119 | pdxS | 1.13e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| CLFMJCJL_86 | 196990 | 197766 | CodY | 2.33e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| CLFMJCJL_5 | 172929 | 172360 | ClpP | 1.32e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| CLFMJCJL_19 | 29016 | 28624 | spxA1 | 2.45e-71 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| CLFMJCJL_19 | 29016 | 28624 | spx | 1.46e-69 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| CLFMJCJL_6 | 34666 | 34424 | SpoVG | 7.49e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| CLFMJCJL_11 | 19463 | 19660 | CspA | 4.04e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| CLFMJCJL_34 | 298663 | 298857 | CspD | 2.48e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| CLFMJCJL_29 | 30936 | 30742 | CspB | 3.95e-28 | cold shock protein | 83.08 | 98.48 | CAD00094 |
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 |
|---|---|---|---|
| CLFMJCJL_1 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_2 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_3 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_4 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_5 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_6 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_7 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_8 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_9 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_10 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_11 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_12 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_13 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_15 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_16 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_17 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_18 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_19 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_20 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_21 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_22 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_23 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_24 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_25 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_27 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_28 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_29 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_30 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_31 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_32 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_33 | 1.0 | 0.0 | 1.0 |
| CLFMJCJL_34 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_35 | 1.0 | 0.0 | 1.0 |
| CLFMJCJL_36 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_38 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_39 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_40 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_42 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_43 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_45 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_49 | 1.0 | 0.0 | 1.0 |
| CLFMJCJL_51 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_52 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_53 | 1.0 | 0.0 | 1.0 |
| CLFMJCJL_54 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_55 | 1.0 | 0.0 | 1.0 |
| CLFMJCJL_56 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_60 | 1.0 | 0.0 | 1.0 |
| CLFMJCJL_61 | 1.0 | 0.0 | 1.0 |
| CLFMJCJL_63 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_67 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_70 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_78 | 0.0 | 1.0 | 0.0 |
| CLFMJCJL_86 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| CLFMJCJL_10 | 4856 | 8100 | False | Siphoviridae | VOG9667, VOG1563 |
| CLFMJCJL_27 | 38768 | 46969 | False | Unknown | VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773 |
Phigaro v2.4.0 (Database: Jan. 2024 release)