Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 8 | 17.55 |
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. |
|---|---|---|---|---|---|---|---|---|
| GHMONIFL_19 | 198566 | 199735 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| GHMONIFL_15 | 94415 | 95008 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| GHMONIFL_11 | 86582 | 86920 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| GHMONIFL_11 | 86265 | 86582 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| GHMONIFL_15 | 43858 | 45291 | lmrB | ARO:3002813 | lmrB | 99.58 | 100.00 | JYFL01000006.1 |
| GHMONIFL_16 | 31436 | 33082 | vmlR | ARO:3004476 | vmlR | 98.91 | 100.18 | NC_000964.3 |
| GHMONIFL_15 | 31042 | 31962 | mphK | ARO:3004541 | mphK | 98.68 | 100.00 | CP010314.1 |
| GHMONIFL_7 | 27347 | 29917 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| GHMONIFL_53 | 17774 | 18976 | blt | ARO:3003006 | blt | 99.25 | 100.00 | L32599.1 |
| GHMONIFL_59 | 2613 | 3467 | aadK | ARO:3002627 | aadK | 97.54 | 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. |
|---|---|---|---|---|---|---|---|
| GHMONIFL_15 | 31042 | 31962 | mph(K) | Spiramycin, Telithromycin | 98.91 | 100.00 | NC_000964 |
| GHMONIFL_59 | 2615 | 3467 | aadK | Streptomycin | 98.71 | 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. |
|---|---|---|---|---|---|---|---|---|
| GHMONIFL_16 | 31436 | 33079 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.91 | 100.00 | WP_003234144.1 |
| GHMONIFL_15 | 31042 | 31950 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.68 | 99.02 | WP_003246254.1 |
| GHMONIFL_59 | 2616 | 3467 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.54 | 100.00 | WP_003229862.1 |
| GHMONIFL_45 | 42854 | 43372 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 93.06 | 100.00 | WP_003242546.1 |
| GHMONIFL_63 | 1473 | 4070 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.07 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| GHMONIFL_18 | 78418 | 79059 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.84 | 100.00 | NP_390062 |
| GHMONIFL_10 | 23307 | 24488 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| GHMONIFL_17 | 35389 | 36174 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| GHMONIFL_17 | 34167 | 35363 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.25 | 100.00 | NP_391079 |
| GHMONIFL_10 | 21682 | 22824 | capA | 0.0 | Capsule | Immune modulation | 99.21 | 100.00 | NP_391469 |
| GHMONIFL_10 | 22843 | 23292 | capC | 0.0 | Capsule | Immune modulation | 99.11 | 100.00 | NP_391470 |
| GHMONIFL_22 | 25459 | 27222 | dep/capD | 0.0 | Capsule | Immune modulation | 99.09 | 100.00 | NP_389723 |
| GHMONIFL_17 | 24397 | 31533 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.02 | 100.00 | NP_391076 |
| GHMONIFL_17 | 31553 | 32491 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.83 | 100.00 | NP_391077 |
| GHMONIFL_17 | 32519 | 34138 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.35 | 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 |
|---|---|---|---|---|---|---|---|---|
| GHMONIFL_21 | 27938 | 26802 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| GHMONIFL_40 | 4283 | 5152 | pdxS | 1.10e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| GHMONIFL_1 | 157487 | 158263 | CodY | 1.61e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| GHMONIFL_3 | 180101 | 180670 | ClpP | 1.30e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| GHMONIFL_55 | 8871 | 8479 | spxA1 | 1.09e-71 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| GHMONIFL_55 | 8871 | 8479 | spx | 6.48e-70 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| GHMONIFL_47 | 10528 | 10770 | SpoVG | 6.12e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| GHMONIFL_38 | 3353 | 3156 | CspA | 5.06e-33 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| GHMONIFL_32 | 107292 | 107098 | CspD | 2.89e-28 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| GHMONIFL_32 | 107292 | 107095 | CspB | 5.99e-28 | 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 |
|---|---|---|---|
| GHMONIFL_1 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_2 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_3 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_4 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_5 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_6 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_7 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_8 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_9 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_10 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_11 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_12 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_13 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_14 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_15 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_16 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_17 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_18 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_19 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_21 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_22 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_23 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_24 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_25 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_26 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_27 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_28 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_29 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_30 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_31 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_32 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_33 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_34 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_35 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_36 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_37 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_38 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_39 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_40 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_41 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_42 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_43 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_44 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_45 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_46 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_47 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_48 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_49 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_50 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_51 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_52 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_53 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_54 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_55 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_56 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_57 | 1.0 | 0.0 | 1.0 |
| GHMONIFL_58 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_59 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_61 | 1.0 | 0.0 | 1.0 |
| GHMONIFL_62 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_63 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_64 | 1.0 | 0.0 | 1.0 |
| GHMONIFL_65 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_66 | 1.0 | 0.0 | 1.0 |
| GHMONIFL_67 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_69 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_70 | 1.0 | 0.0 | 1.0 |
| GHMONIFL_72 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_73 | 1.0 | 0.0 | 1.0 |
| GHMONIFL_74 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_75 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_78 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_82 | 1.0 | 0.0 | 1.0 |
| GHMONIFL_89 | 0.0 | 1.0 | 0.0 |
| GHMONIFL_90 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| GHMONIFL_19 | 7967 | 24838 | False | Myoviridae | VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4691, VOG4862, VOG7718 |
| GHMONIFL_28 | 25560 | 53319 | False | Myoviridae | VOG0136, VOG0753, VOG4705, VOG3390, VOG4612, 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)