Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 11 | 9 | 8 | 16.31 |
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. |
|---|---|---|---|---|---|---|---|---|
| NOCPLFFO_12 | 353141 | 354310 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| NOCPLFFO_21 | 109567 | 110487 | mphK | ARO:3004541 | mphK | 99.02 | 100.00 | CP010314.1 |
| NOCPLFFO_21 | 96235 | 97674 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| NOCPLFFO_21 | 46586 | 47179 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| NOCPLFFO_9 | 41571 | 41888 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| NOCPLFFO_9 | 41233 | 41571 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| NOCPLFFO_24 | 33343 | 34206 | aadK | ARO:3002627 | aadK | 97.89 | 101.06 | AL009126.1 |
| NOCPLFFO_19 | 28881 | 30527 | vmlR | ARO:3004476 | vmlR | 99.45 | 100.18 | NC_000964.3 |
| NOCPLFFO_17 | 27198 | 29768 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 100.00 | AL009126.3 |
| NOCPLFFO_24 | 14766 | 15968 | blt | ARO:3003006 | blt | 98.75 | 100.00 | L32599.1 |
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. |
|---|---|---|---|---|---|---|---|
| NOCPLFFO_21 | 109567 | 110487 | mph(K) | Spiramycin, Telithromycin | 99.35 | 100.00 | NC_000964 |
| NOCPLFFO_24 | 33354 | 34206 | aadK | Streptomycin | 98.12 | 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. |
|---|---|---|---|---|---|---|---|---|
| NOCPLFFO_19 | 28881 | 30524 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 99.45 | 100.00 | WP_003234144.1 |
| NOCPLFFO_21 | 109570 | 110487 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 99.02 | 100.00 | WP_003246254.1 |
| NOCPLFFO_24 | 33355 | 34206 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.89 | 100.00 | WP_003229862.1 |
| NOCPLFFO_12 | 62632 | 65229 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.06 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| NOCPLFFO_4 | 155024 | 156205 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| NOCPLFFO_12 | 155823 | 156464 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| NOCPLFFO_5 | 389577 | 390362 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| NOCPLFFO_5 | 390388 | 391584 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.25 | 100.00 | NP_391079 |
| NOCPLFFO_12 | 8257 | 10020 | dep/capD | 0.0 | Capsule | Immune modulation | 99.21 | 100.00 | NP_389723 |
| NOCPLFFO_4 | 156688 | 157830 | capA | 0.0 | Capsule | Immune modulation | 98.95 | 100.00 | NP_391469 |
| NOCPLFFO_5 | 393260 | 394198 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.72 | 100.00 | NP_391077 |
| NOCPLFFO_4 | 156220 | 156669 | capC | 0.0 | Capsule | Immune modulation | 98.00 | 100.00 | NP_391470 |
| NOCPLFFO_5 | 391613 | 393232 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.35 | 100.00 | NP_391078 |
| NOCPLFFO_6 | 1 | 4721 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.31 | 66.15 | NP_391076 |
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 |
|---|---|---|---|---|---|---|---|---|
| NOCPLFFO_23 | 31640 | 32776 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| NOCPLFFO_28 | 11122 | 10253 | pdxS | 1.10e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| NOCPLFFO_9 | 353112 | 353888 | CodY | 3.85e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| NOCPLFFO_5 | 126950 | 126381 | ClpP | 2.38e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| NOCPLFFO_8 | 275316 | 275708 | spxA1 | 2.44e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| NOCPLFFO_8 | 275316 | 275708 | spx | 1.46e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| NOCPLFFO_25 | 20477 | 20719 | SpoVG | 7.48e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| NOCPLFFO_19 | 77630 | 77433 | CspA | 4.61e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| NOCPLFFO_12 | 167695 | 167889 | CspD | 1.32e-27 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| NOCPLFFO_12 | 167695 | 167892 | CspB | 2.73e-27 | cold shock protein | 80.30 | 100.00 | 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 |
|---|---|---|---|
| NOCPLFFO_1 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_2 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_3 | 1.0 | 0.0 | 1.0 |
| NOCPLFFO_4 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_5 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_6 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_7 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_8 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_9 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_10 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_11 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_12 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_13 | 1.0 | 0.0 | 1.0 |
| NOCPLFFO_15 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_16 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_17 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_18 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_19 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_20 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_21 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_22 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_23 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_24 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_25 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_27 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_28 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_30 | 1.0 | 0.0 | 1.0 |
| NOCPLFFO_31 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_32 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_33 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_34 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_35 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_36 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_37 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_38 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_39 | 0.0 | 1.0 | 0.0 |
| NOCPLFFO_40 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| NOCPLFFO_8 | 367762 | 377685 | False | Siphoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685 |
| NOCPLFFO_9 | 4290 | 11360 | False | Myoviridae | VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG4705 |
| NOCPLFFO_27 | 5853 | 37725 | False | Myoviridae | VOG7718, VOG4862, VOG4691, VOG10120, VOG10989, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG10227, VOG0796, VOG9800, VOG9990, VOG0198, VOG4693, VOG0189, VOG11060, VOG1309 |
Phigaro v2.4.0 (Database: Jan. 2024 release)