Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 8 | 18.25 |
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. |
|---|---|---|---|---|---|---|---|---|
| MEGCPJPM_14 | 610553 | 611407 | aadK | ARO:3002627 | aadK | 98.24 | 100.00 | AL009126.1 |
| MEGCPJPM_14 | 581422 | 582624 | blt | ARO:3003006 | blt | 99.00 | 100.00 | L32599.1 |
| MEGCPJPM_14 | 379013 | 380182 | bmr | ARO:3003007 | bmr | 99.23 | 100.00 | M33768.1 |
| MEGCPJPM_17 | 224657 | 224995 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| MEGCPJPM_17 | 224340 | 224657 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| MEGCPJPM_12 | 195194 | 196837 | vmlR | ARO:3004476 | vmlR | 98.90 | 100.00 | NC_000964.3 |
| MEGCPJPM_10 | 109732 | 110652 | mphK | ARO:3004541 | mphK | 100.00 | 100.00 | CP010314.1 |
| MEGCPJPM_10 | 96399 | 97838 | lmrB | ARO:3002813 | lmrB | 99.79 | 100.42 | JYFL01000006.1 |
| MEGCPJPM_10 | 46692 | 47285 | tmrB | ARO:3003059 | tmrB | 96.95 | 100.00 | AL009126.3 |
| MEGCPJPM_6 | 27568 | 30138 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 100.00 | 100.00 | AL009126.3 |
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. |
|---|---|---|---|---|---|---|---|
| MEGCPJPM_10 | 109732 | 110652 | mph(K) | Spiramycin, Telithromycin | 99.78 | 100.00 | NC_000964 |
| MEGCPJPM_14 | 610555 | 611407 | aadK | Streptomycin | 98.59 | 99.77 | M26879 |
| MEGCPJPM_18 | 1022671 | 1024047 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 98.40 | 100.00 | D12567 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| MEGCPJPM_10 | 109735 | 110652 | mphK | macrolide 2'-phosphotransferase MphK | EXACTX | 100.00 | 100.00 | WP_003246254.1 |
| MEGCPJPM_12 | 195197 | 196837 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.90 | 100.00 | WP_003234144.1 |
| MEGCPJPM_18 | 1022674 | 1024047 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.25 | 100.00 | WP_063856081.1 |
| MEGCPJPM_14 | 610556 | 611407 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.24 | 100.00 | WP_003229862.1 |
| MEGCPJPM_18 | 1020148 | 1020666 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 91.91 | 100.00 | WP_003242546.1 |
| MEGCPJPM_14 | 75294 | 77891 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.94 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| MEGCPJPM_14 | 179828 | 180469 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.84 | 100.00 | NP_390062 |
| MEGCPJPM_18 | 527953 | 529134 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| MEGCPJPM_18 | 115223 | 116008 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.62 | 100.00 | NP_391080 |
| MEGCPJPM_18 | 526328 | 527470 | capA | 0.0 | Capsule | Immune modulation | 99.47 | 100.00 | NP_391469 |
| MEGCPJPM_18 | 527489 | 527938 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| MEGCPJPM_18 | 111387 | 112325 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.25 | 100.00 | NP_391077 |
| MEGCPJPM_18 | 114001 | 115197 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.25 | 100.00 | NP_391079 |
| MEGCPJPM_14 | 25154 | 26917 | dep/capD | 0.0 | Capsule | Immune modulation | 99.15 | 100.00 | NP_389723 |
| MEGCPJPM_18 | 104231 | 111367 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.77 | 100.00 | NP_391076 |
| MEGCPJPM_18 | 112353 | 113972 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.03 | 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 |
|---|---|---|---|---|---|---|---|---|
| MEGCPJPM_4 | 28013 | 26877 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| MEGCPJPM_9 | 11515 | 10646 | pdxS | 1.33e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| MEGCPJPM_20 | 310416 | 309640 | CodY | 3.28e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| MEGCPJPM_18 | 366604 | 367173 | ClpP | 6.40e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| MEGCPJPM_17 | 376543 | 376151 | spxA1 | 4.18e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| MEGCPJPM_17 | 376543 | 376151 | spx | 2.49e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| MEGCPJPM_7 | 34938 | 34696 | SpoVG | 7.90e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| MEGCPJPM_12 | 142299 | 142496 | CspA | 9.77e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| MEGCPJPM_17 | 619706 | 619900 | CspB | 6.02e-27 | 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 |
|---|---|---|---|
| MEGCPJPM_1 | 1.0 | 0.0 | 1.0 |
| MEGCPJPM_3 | 1.0 | 0.0 | 1.0 |
| MEGCPJPM_4 | 0.0 | 1.0 | 0.0 |
| MEGCPJPM_6 | 0.0 | 1.0 | 0.0 |
| MEGCPJPM_7 | 0.0 | 1.0 | 0.0 |
| MEGCPJPM_8 | 1.0 | 0.0 | 1.0 |
| MEGCPJPM_9 | 0.0 | 1.0 | 0.0 |
| MEGCPJPM_10 | 0.0 | 1.0 | 0.0 |
| MEGCPJPM_11 | 0.0 | 1.0 | 0.0 |
| MEGCPJPM_12 | 0.0 | 1.0 | 0.0 |
| MEGCPJPM_13 | 1.0 | 0.0 | 1.0 |
| MEGCPJPM_14 | 0.0 | 1.0 | 0.0 |
| MEGCPJPM_15 | 1.0 | 0.0 | 1.0 |
| MEGCPJPM_17 | 0.0 | 1.0 | 0.0 |
| MEGCPJPM_18 | 0.0 | 1.0 | 0.0 |
| MEGCPJPM_19 | 1.0 | 0.0 | 1.0 |
| MEGCPJPM_20 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| MEGCPJPM_17 | 254795 | 282209 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
Phigaro v2.4.0 (Database: Jan. 2024 release)