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. |
|---|---|---|---|---|---|---|---|---|
| DNIIGGLF_12 | 531205 | 531543 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| DNIIGGLF_12 | 530888 | 531205 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| DNIIGGLF_23 | 446262 | 447116 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| DNIIGGLF_23 | 427508 | 428710 | blt | ARO:3003006 | blt | 99.00 | 100.00 | L32599.1 |
| DNIIGGLF_34 | 345022 | 345942 | mphK | ARO:3004541 | mphK | 99.02 | 100.00 | CP010314.1 |
| DNIIGGLF_34 | 331690 | 333129 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| DNIIGGLF_34 | 282015 | 282608 | tmrB | ARO:3003059 | tmrB | 97.46 | 100.00 | AL009126.3 |
| DNIIGGLF_45 | 255940 | 258510 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.53 | 100.00 | AL009126.3 |
| DNIIGGLF_23 | 206222 | 207391 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| DNIIGGLF_34 | 29066 | 30709 | 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. |
|---|---|---|---|---|---|---|---|
| DNIIGGLF_34 | 345022 | 345942 | mph(K) | Spiramycin, Telithromycin | 99.35 | 100.00 | NC_000964 |
| DNIIGGLF_23 | 446262 | 447116 | aadK | Streptomycin | 98.71 | 100.00 | 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. |
|---|---|---|---|---|---|---|---|---|
| DNIIGGLF_34 | 345025 | 345942 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 99.02 | 100.00 | WP_003246254.1 |
| DNIIGGLF_23 | 446265 | 447116 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| DNIIGGLF_34 | 29066 | 30706 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.17 | 100.00 | WP_003234144.1 |
| DNIIGGLF_1 | 1028682 | 1029200 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 93.64 | 100.00 | WP_003242546.1 |
| DNIIGGLF_77 | 4954 | 7551 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.65 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| DNIIGGLF_1 | 535617 | 536798 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| DNIIGGLF_1 | 112775 | 113560 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.75 | 100.00 | NP_391080 |
| DNIIGGLF_23 | 8913 | 9554 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.69 | 100.00 | NP_390062 |
| DNIIGGLF_1 | 111553 | 112749 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.33 | 100.00 | NP_391079 |
| DNIIGGLF_77 | 60032 | 61795 | dep/capD | 0.0 | Capsule | Immune modulation | 99.32 | 100.00 | NP_389723 |
| DNIIGGLF_1 | 535153 | 535602 | capC | 0.0 | Capsule | Immune modulation | 99.11 | 100.00 | NP_391470 |
| DNIIGGLF_1 | 533992 | 535134 | capA | 0.0 | Capsule | Immune modulation | 98.78 | 100.00 | NP_391469 |
| DNIIGGLF_1 | 101783 | 108919 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.74 | 100.00 | NP_391076 |
| DNIIGGLF_1 | 108939 | 109877 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.40 | 100.00 | NP_391077 |
| DNIIGGLF_1 | 109905 | 111524 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.41 | 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 |
|---|---|---|---|---|---|---|---|---|
| DNIIGGLF_2 | 27942 | 26806 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| DNIIGGLF_4 | 11224 | 10355 | pdxS | 1.11e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| DNIIGGLF_12 | 219788 | 219012 | CodY | 7.80e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| DNIIGGLF_1 | 376363 | 376932 | ClpP | 6.42e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| DNIIGGLF_12 | 684242 | 683850 | spxA1 | 6.13e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| DNIIGGLF_12 | 684242 | 683850 | spx | 3.66e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| DNIIGGLF_3 | 20553 | 20795 | SpoVG | 7.49e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| DNIIGGLF_34 | 79123 | 78926 | CspA | 1.89e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| DNIIGGLF_23 | 20786 | 20980 | CspD | 2.47e-27 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| DNIIGGLF_23 | 20786 | 20983 | CspB | 5.12e-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 |
|---|---|---|---|
| DNIIGGLF_1 | 0.0 | 1.0 | 0.0 |
| DNIIGGLF_2 | 0.0 | 1.0 | 0.0 |
| DNIIGGLF_3 | 0.0 | 1.0 | 0.0 |
| DNIIGGLF_4 | 0.0 | 1.0 | 0.0 |
| DNIIGGLF_5 | 0.0 | 1.0 | 0.0 |
| DNIIGGLF_12 | 0.0 | 1.0 | 0.0 |
| DNIIGGLF_23 | 0.0 | 1.0 | 0.0 |
| DNIIGGLF_34 | 0.0 | 1.0 | 0.0 |
| DNIIGGLF_45 | 0.0 | 1.0 | 0.0 |
| DNIIGGLF_56 | 0.0 | 1.0 | 0.0 |
| DNIIGGLF_66 | 0.0 | 1.0 | 0.0 |
| DNIIGGLF_76 | 0.0 | 1.0 | 0.0 |
| DNIIGGLF_77 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| DNIIGGLF_12 | 561087 | 587399 | False | Myoviridae | VOG0753, VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
| DNIIGGLF_23 | 379019 | 407946 | False | Myoviridae | VOG4862, VOG4691, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG10227, VOG0796, VOG4673, VOG9587, VOG4693, VOG0189, VOG11060, VOG1309, VOG4600 |
| DNIIGGLF_23 | 619434 | 645688 | False | Siphoviridae | VOG7531, VOG0705, VOG6116, VOG8440, VOG0602, VOG4666, VOG0753, VOG4705, VOG4626, VOG4619, VOG0801, VOG6163, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5601, VOG4553, VOG4573, VOG4556, VOG4544, VOG4581, VOG4841 |
| DNIIGGLF_23 | 655867 | 681253 | False | Siphoviridae | VOG9755, VOG0052, VOG4567, VOG0020, VOG1298, VOG4724, VOG4561, VOG1638, VOG0085, VOG4562, VOG2368, VOG4730, VOG1838, VOG3212, VOG0371, VOG1093, VOG5543, VOG0422, VOG0026, VOG6497, VOG10937, VOG5753, VOG7255, VOG0052, VOG1563, VOG11003, VOG2215, VOG4551, VOG0025 |
| DNIIGGLF_56 | 70913 | 96051 | False | Siphoviridae | VOG9219, VOG9713, VOG6940, VOG5534, VOG7718, VOG3390, VOG7895, VOG8610, VOG7930, VOG0275, VOG9312, VOG4910, VOG3389, VOG5042, VOG9712, VOG5070 |
Phigaro v2.4.0 (Database: Jan. 2024 release)