Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 9 | 18.71 |
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. |
|---|---|---|---|---|---|---|---|---|
| DNMLIFGM_2 | 696450 | 697619 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| DNMLIFGM_2 | 497882 | 499084 | blt | ARO:3003006 | blt | 100.00 | 100.00 | L32599.1 |
| DNMLIFGM_2 | 479445 | 480299 | aadK | ARO:3002627 | aadK | 98.94 | 100.00 | AL009126.1 |
| DNMLIFGM_16 | 433635 | 433973 | ykkC | ARO:3003063 | ykkC | 98.21 | 100.00 | AL009126.1 |
| DNMLIFGM_16 | 433318 | 433635 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| DNMLIFGM_6 | 342321 | 343241 | mphK | ARO:3004541 | mphK | 98.69 | 100.00 | CP010314.1 |
| DNMLIFGM_6 | 330160 | 331599 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.42 | JYFL01000006.1 |
| DNMLIFGM_6 | 280484 | 281077 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| DNMLIFGM_3 | 247787 | 250357 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.65 | 100.00 | AL009126.3 |
| DNMLIFGM_6 | 29343 | 30986 | vmlR | ARO:3004476 | vmlR | 98.17 | 100.00 | NC_000964.3 |
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. |
|---|---|---|---|---|---|---|---|
| DNMLIFGM_2 | 479445 | 480299 | aadK | Streptomycin | 99.18 | 100.00 | M26879 |
| DNMLIFGM_1 | 42677 | 44053 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 98.98 | 100.00 | D12567 |
| DNMLIFGM_6 | 342321 | 343241 | mph(K) | Spiramycin, Telithromycin | 98.05 | 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. |
|---|---|---|---|---|---|---|---|---|
| DNMLIFGM_2 | 479445 | 480296 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.94 | 100.00 | WP_003229862.1 |
| DNMLIFGM_6 | 342324 | 343241 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.69 | 100.00 | WP_003246254.1 |
| DNMLIFGM_1 | 42677 | 44050 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.47 | 100.00 | WP_063856081.1 |
| DNMLIFGM_6 | 29343 | 30983 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.17 | 100.00 | WP_003234144.1 |
| DNMLIFGM_1 | 46020 | 46538 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.75 | 100.00 | WP_003242546.1 |
| DNMLIFGM_17 | 9215 | 11812 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| DNMLIFGM_2 | 899784 | 900425 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 100.00 | 100.00 | NP_390062 |
| DNMLIFGM_1 | 544387 | 545568 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| DNMLIFGM_7 | 113072 | 113857 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| DNMLIFGM_1 | 546051 | 547193 | capA | 0.0 | Capsule | Immune modulation | 99.39 | 100.00 | NP_391469 |
| DNMLIFGM_1 | 545583 | 546032 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| DNMLIFGM_17 | 59373 | 61136 | dep/capD | 0.0 | Capsule | Immune modulation | 99.15 | 100.00 | NP_389723 |
| DNMLIFGM_7 | 102080 | 109216 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.80 | 100.00 | NP_391076 |
| DNMLIFGM_7 | 110202 | 111821 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.39 | 100.00 | NP_391078 |
| DNMLIFGM_7 | 109236 | 110174 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.30 | 100.00 | NP_391077 |
| DNMLIFGM_7 | 111850 | 113046 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.08 | 100.00 | NP_391079 |
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 |
|---|---|---|---|---|---|---|---|---|
| DNMLIFGM_4 | 28155 | 27019 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| DNMLIFGM_14 | 4251 | 5120 | pdxS | 1.11e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| DNMLIFGM_16 | 123550 | 122774 | CodY | 4.81e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| DNMLIFGM_1 | 712040 | 711471 | ClpP | 4.83e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| DNMLIFGM_16 | 583815 | 583423 | spxA1 | 3.78e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| DNMLIFGM_16 | 583815 | 583423 | spx | 2.26e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| DNMLIFGM_15 | 34691 | 34449 | SpoVG | 7.49e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| DNMLIFGM_6 | 80985 | 80788 | CspA | 1.90e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| DNMLIFGM_2 | 887824 | 887630 | CspD | 6.14e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| DNMLIFGM_8 | 232785 | 232979 | CspB | 2.56e-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 |
|---|---|---|---|
| DNMLIFGM_1 | 0.0 | 1.0 | 0.0 |
| DNMLIFGM_2 | 0.0 | 1.0 | 0.0 |
| DNMLIFGM_3 | 0.0 | 1.0 | 0.0 |
| DNMLIFGM_4 | 0.0 | 1.0 | 0.0 |
| DNMLIFGM_5 | 0.0 | 1.0 | 0.0 |
| DNMLIFGM_6 | 0.0 | 1.0 | 0.0 |
| DNMLIFGM_7 | 0.0 | 1.0 | 0.0 |
| DNMLIFGM_8 | 0.0 | 1.0 | 0.0 |
| DNMLIFGM_9 | 0.0 | 1.0 | 0.0 |
| DNMLIFGM_12 | 0.0 | 1.0 | 0.0 |
| DNMLIFGM_13 | 0.0 | 1.0 | 0.0 |
| DNMLIFGM_14 | 0.0 | 1.0 | 0.0 |
| DNMLIFGM_15 | 0.0 | 1.0 | 0.0 |
| DNMLIFGM_16 | 0.0 | 1.0 | 0.0 |
| DNMLIFGM_17 | 0.0 | 1.0 | 0.0 |
| DNMLIFGM_19 | 1.0 | 0.0 | 1.0 |
| DNMLIFGM_20 | 0.0 | 1.0 | 0.0 |
| DNMLIFGM_22 | 1.0 | 0.0 | 1.0 |
| DNMLIFGM_23 | 1.0 | 0.0 | 1.0 |
| DNMLIFGM_24 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| DNMLIFGM_2 | 282909 | 309234 | False | Myoviridae | VOG6282, VOG0796, VOG10227, VOG0720, VOG4555, VOG4553, VOG0815, VOG4564, VOG4623, VOG1353, VOG1881, VOG1883, VOG1352, VOG4699, VOG6163, VOG1956, VOG1433, VOG1348, VOG0573, VOG4550, VOG4691, VOG4845, VOG7718, VOG3390, VOG4705, VOG0753, VOG0136, VOG4574, VOG5859 |
| DNMLIFGM_16 | 463842 | 489883 | 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)