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. |
|---|---|---|---|---|---|---|---|---|
| LABNAPHH_15 | 611197 | 612366 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| LABNAPHH_9 | 506360 | 506698 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| LABNAPHH_9 | 506043 | 506360 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| LABNAPHH_15 | 388852 | 390054 | blt | ARO:3003006 | blt | 100.00 | 100.00 | L32599.1 |
| LABNAPHH_15 | 370495 | 371349 | aadK | ARO:3002627 | aadK | 100.00 | 100.00 | AL009126.1 |
| LABNAPHH_2 | 108611 | 109531 | mphK | ARO:3004541 | mphK | 97.71 | 100.00 | CP010314.1 |
| LABNAPHH_2 | 95278 | 96717 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| LABNAPHH_2 | 45643 | 46236 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| LABNAPHH_6 | 29219 | 30862 | vmlR | ARO:3004476 | vmlR | 100.00 | 100.00 | NC_000964.3 |
| LABNAPHH_8 | 27286 | 29856 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 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. |
|---|---|---|---|---|---|---|---|
| LABNAPHH_15 | 370495 | 371349 | aadK | Streptomycin | 100.00 | 100.00 | M26879 |
| LABNAPHH_17 | 116731 | 118107 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 99.85 | 100.00 | X08034 |
| LABNAPHH_2 | 108611 | 109531 | mph(K) | Spiramycin, Telithromycin | 97.72 | 100.00 | 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. |
|---|---|---|---|---|---|---|---|---|
| LABNAPHH_15 | 370495 | 371346 | aadK | aminoglycoside 6-adenylyltransferase AadK | EXACTX | 100.00 | 100.00 | WP_003229862.1 |
| LABNAPHH_17 | 116731 | 118104 | tet(L) | tetracycline efflux MFS transporter Tet(L) | EXACTX | 100.00 | 100.00 | WP_003242953.1 |
| LABNAPHH_6 | 29219 | 30859 | vmlR | ABC-F type ribosomal protection protein VmlR | EXACTX | 100.00 | 100.00 | WP_003234144.1 |
| LABNAPHH_2 | 108614 | 109531 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.71 | 100.00 | WP_003246254.1 |
| LABNAPHH_17 | 120060 | 120578 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| LABNAPHH_13 | 18987 | 21581 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.15 | 99.88 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| LABNAPHH_13 | 66475 | 68238 | dep/capD | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_389723 |
| LABNAPHH_15 | 811102 | 811743 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 100.00 | 100.00 | NP_390062 |
| LABNAPHH_17 | 1006343 | 1007128 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.75 | 100.00 | NP_391080 |
| LABNAPHH_17 | 1010026 | 1010964 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.68 | 100.00 | NP_391077 |
| LABNAPHH_17 | 597146 | 598327 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| LABNAPHH_17 | 1008379 | 1009998 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.26 | 100.00 | NP_391078 |
| LABNAPHH_17 | 598810 | 599952 | capA | 0.0 | Capsule | Immune modulation | 98.95 | 100.00 | NP_391469 |
| LABNAPHH_17 | 1010984 | 1018120 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.95 | 100.00 | NP_391076 |
| LABNAPHH_17 | 1007154 | 1008350 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.91 | 100.00 | NP_391079 |
| LABNAPHH_17 | 598342 | 598791 | 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 |
|---|---|---|---|---|---|---|---|---|
| LABNAPHH_1 | 31674 | 32810 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| LABNAPHH_17 | 71307 | 70438 | pdxS | 1.93e-149 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.45 | 98.31 | ACE61268 |
| LABNAPHH_9 | 193029 | 192253 | CodY | 7.56e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| LABNAPHH_17 | 751416 | 750847 | ClpP | 6.73e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| LABNAPHH_9 | 657463 | 657071 | spxA1 | 5.95e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| LABNAPHH_9 | 657463 | 657071 | spx | 3.55e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| LABNAPHH_17 | 34691 | 34449 | SpoVG | 1.52e-37 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| LABNAPHH_6 | 76740 | 76543 | CspA | 3.75e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| LABNAPHH_15 | 799140 | 798946 | CspD | 5.15e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
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 |
|---|---|---|---|
| LABNAPHH_1 | 0.0 | 1.0 | 0.0 |
| LABNAPHH_2 | 0.0 | 1.0 | 0.0 |
| LABNAPHH_3 | 0.0 | 1.0 | 0.0 |
| LABNAPHH_4 | 0.0 | 1.0 | 0.0 |
| LABNAPHH_5 | 0.0 | 1.0 | 0.0 |
| LABNAPHH_6 | 0.0 | 1.0 | 0.0 |
| LABNAPHH_7 | 0.0 | 1.0 | 0.0 |
| LABNAPHH_8 | 0.0 | 1.0 | 0.0 |
| LABNAPHH_9 | 0.0 | 1.0 | 0.0 |
| LABNAPHH_10 | 0.0 | 1.0 | 0.0 |
| LABNAPHH_11 | 0.0 | 1.0 | 0.0 |
| LABNAPHH_12 | 0.0 | 1.0 | 0.0 |
| LABNAPHH_13 | 0.0 | 1.0 | 0.0 |
| LABNAPHH_14 | 0.0 | 1.0 | 0.0 |
| LABNAPHH_15 | 0.0 | 1.0 | 0.0 |
| LABNAPHH_16 | 0.0 | 1.0 | 0.0 |
| LABNAPHH_17 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LABNAPHH_9 | 536499 | 561827 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490 |
| LABNAPHH_14 | 36235 | 51469 | False | Myoviridae / Siphoviridae | VOG5534, VOG6940, VOG9713, VOG9219, VOG5495, VOG6036, VOG9867, VOG7134, VOG10940, VOG5721, VOG5779, VOG5722, VOG4570, VOG7567 |
| LABNAPHH_14 | 91133 | 95865 | False | Unknown | VOG6464, VOG0322, VOG7627 |
| LABNAPHH_15 | 409606 | 439983 | False | Myoviridae | VOG4600, VOG1309, VOG11060, VOG0189, VOG4693, VOG9587, VOG4673, VOG0796, VOG10227, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718 |
Phigaro v2.4.0 (Database: Jan. 2024 release)