Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 7 | 17.12 |
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. |
|---|---|---|---|---|---|---|---|---|
| MANCPEPA_2 | 1637398 | 1637736 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| MANCPEPA_2 | 1637081 | 1637398 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| MANCPEPA_2 | 684990 | 686159 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| MANCPEPA_2 | 464351 | 465553 | blt | ARO:3003006 | blt | 99.75 | 100.00 | L32599.1 |
| MANCPEPA_2 | 445962 | 446816 | aadK | ARO:3002627 | aadK | 97.89 | 100.00 | AL009126.1 |
| MANCPEPA_1 | 389426 | 391069 | vmlR | ARO:3004476 | vmlR | 98.54 | 100.00 | NC_000964.3 |
| MANCPEPA_4 | 304311 | 306881 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| MANCPEPA_1 | 147439 | 148032 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| MANCPEPA_1 | 96955 | 98388 | 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. |
|---|---|---|---|---|---|---|---|
| MANCPEPA_7 | 34586 | 35962 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 100.00 | 100.00 | D12567 |
| MANCPEPA_2 | 445962 | 446814 | aadK | Streptomycin | 98.59 | 99.77 | 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. |
|---|---|---|---|---|---|---|---|---|
| MANCPEPA_7 | 34586 | 35959 | tet(L) | tetracycline efflux MFS transporter Tet(L) | EXACTX | 100.00 | 100.00 | WP_063856081.1 |
| MANCPEPA_1 | 389429 | 391069 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.54 | 100.00 | WP_003234144.1 |
| MANCPEPA_2 | 445962 | 446813 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.89 | 100.00 | WP_003229862.1 |
| MANCPEPA_7 | 37942 | 38460 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| MANCPEPA_2 | 981144 | 983741 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.60 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| MANCPEPA_3 | 693938 | 694876 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.68 | 100.00 | NP_391077 |
| MANCPEPA_3 | 281535 | 282716 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| MANCPEPA_3 | 692291 | 693910 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.26 | 100.00 | NP_391078 |
| MANCPEPA_2 | 886954 | 887595 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.22 | 100.00 | NP_390062 |
| MANCPEPA_3 | 690255 | 691040 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.11 | 100.00 | NP_391080 |
| MANCPEPA_3 | 691066 | 692262 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.00 | 100.00 | NP_391079 |
| MANCPEPA_3 | 694896 | 702032 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.00 | 100.00 | NP_391076 |
| MANCPEPA_3 | 283199 | 284341 | capA | 0.0 | Capsule | Immune modulation | 98.95 | 100.00 | NP_391469 |
| MANCPEPA_2 | 1028919 | 1030682 | dep/capD | 0.0 | Capsule | Immune modulation | 98.87 | 100.00 | NP_389723 |
| MANCPEPA_3 | 282731 | 283180 | capC | 0.0 | Capsule | Immune modulation | 98.67 | 100.00 | NP_391470 |
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 |
|---|---|---|---|---|---|---|---|---|
| MANCPEPA_5 | 31692 | 32828 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| MANCPEPA_9 | 11330 | 10461 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| MANCPEPA_2 | 1327389 | 1326613 | CodY | 1.67e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| MANCPEPA_3 | 424135 | 423566 | ClpP | 4.83e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| MANCPEPA_2 | 1788210 | 1787818 | spxA1 | 1.32e-69 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| MANCPEPA_2 | 1788210 | 1787818 | spx | 7.85e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| MANCPEPA_8 | 34887 | 34645 | SpoVG | 7.52e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| MANCPEPA_1 | 342677 | 342874 | CspA | 1.81e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
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 |
|---|---|---|---|
| MANCPEPA_1 | 0.0 | 1.0 | 0.0 |
| MANCPEPA_2 | 0.0 | 1.0 | 0.0 |
| MANCPEPA_3 | 0.0 | 1.0 | 0.0 |
| MANCPEPA_4 | 0.0 | 1.0 | 0.0 |
| MANCPEPA_5 | 0.0 | 1.0 | 0.0 |
| MANCPEPA_7 | 0.0 | 1.0 | 0.0 |
| MANCPEPA_8 | 0.0 | 1.0 | 0.0 |
| MANCPEPA_9 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| MANCPEPA_2 | 490912 | 513470 | False | Myoviridae | VOG10227, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718 |
| MANCPEPA_2 | 1667217 | 1693700 | False | Myoviridae | VOG0753, VOG4705, VOG4612, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
| MANCPEPA_4 | 11916 | 18435 | False | Siphoviridae | VOG0275, VOG4602, VOG9667, VOG11075, VOG0650, VOG4552, VOG4603 |
| MANCPEPA_4 | 28884 | 56919 | False | Myoviridae | VOG0796, VOG0720, VOG4555, VOG4553, VOG0815, VOG4564, VOG4623, VOG1353, VOG1881, VOG1883, VOG1352, VOG4699, VOG1350, VOG6163, VOG1956, VOG1433, VOG1348, VOG0573, VOG4550, VOG4691, VOG4845, VOG7718, VOG3390, VOG4705, VOG5008, VOG0753, VOG0136, VOG4574, VOG1993, VOG2703, VOG6495, VOG9667, VOG3490 |
Phigaro v2.4.0 (Database: Jan. 2024 release)