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. |
|---|---|---|---|---|---|---|---|---|
| LDHOENAK_1 | 503015 | 503353 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| LDHOENAK_1 | 502698 | 503015 | ykkD | ARO:3003064 | ykkD | 100.00 | 100.00 | AL009126.1 |
| LDHOENAK_23 | 459253 | 460107 | aadK | ARO:3002627 | aadK | 100.00 | 100.00 | AL009126.1 |
| LDHOENAK_23 | 440544 | 441746 | blt | ARO:3003006 | blt | 100.00 | 100.00 | L32599.1 |
| LDHOENAK_23 | 218226 | 219395 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| LDHOENAK_45 | 162828 | 163421 | tmrB | ARO:3003059 | tmrB | 100.00 | 100.00 | AL009126.3 |
| LDHOENAK_45 | 112325 | 113764 | lmrB | ARO:3002813 | lmrB | 99.79 | 100.42 | JYFL01000006.1 |
| LDHOENAK_45 | 99510 | 100430 | mphK | ARO:3004541 | mphK | 100.00 | 100.00 | CP010314.1 |
| LDHOENAK_2 | 47355 | 48998 | vmlR | ARO:3004476 | vmlR | 100.00 | 100.00 | NC_000964.3 |
| LDHOENAK_34 | 27249 | 29819 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 100.00 | 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. |
|---|---|---|---|---|---|---|---|
| LDHOENAK_23 | 459253 | 460107 | aadK | Streptomycin | 100.00 | 100.00 | M26879 |
| LDHOENAK_45 | 99510 | 100430 | mph(K) | Spiramycin, Telithromycin | 100.00 | 100.00 | NC_000964 |
| LDHOENAK_67 | 90371 | 91747 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 100.00 | 100.00 | X08034 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| LDHOENAK_23 | 459256 | 460107 | aadK | aminoglycoside 6-adenylyltransferase AadK | EXACTX | 100.00 | 100.00 | WP_003229862.1 |
| LDHOENAK_45 | 99510 | 100427 | mphK | macrolide 2'-phosphotransferase MphK | EXACTX | 100.00 | 100.00 | WP_003246254.1 |
| LDHOENAK_67 | 87853 | 88371 | satA | streptothricin N-acetyltransferase SatA | EXACTX | 100.00 | 100.00 | WP_003242546.1 |
| LDHOENAK_67 | 90374 | 91747 | tet(L) | tetracycline efflux MFS transporter Tet(L) | EXACTX | 100.00 | 100.00 | WP_003242953.1 |
| LDHOENAK_2 | 47358 | 48998 | vmlR | ABC-F type ribosomal protection protein VmlR | EXACTX | 100.00 | 100.00 | WP_003234144.1 |
| LDHOENAK_3 | 54786 | 57380 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| LDHOENAK_12 | 398113 | 399255 | capA | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_391469 |
| LDHOENAK_12 | 396449 | 397630 | capB | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_391471 |
| LDHOENAK_12 | 397645 | 398094 | capC | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_391470 |
| LDHOENAK_3 | 8128 | 9891 | dep/capD | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_389723 |
| LDHOENAK_12 | 804780 | 805565 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391080 |
| LDHOENAK_12 | 808463 | 809401 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391077 |
| LDHOENAK_12 | 805591 | 806787 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391079 |
| LDHOENAK_12 | 806816 | 808435 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391078 |
| LDHOENAK_12 | 809421 | 816557 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391076 |
| LDHOENAK_23 | 18871 | 19512 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 100.00 | 100.00 | NP_390062 |
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 |
|---|---|---|---|---|---|---|---|---|
| LDHOENAK_4 | 31638 | 32774 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| LDHOENAK_8 | 11182 | 10313 | pdxS | 1.10e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| LDHOENAK_1 | 189751 | 188975 | CodY | 7.52e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| LDHOENAK_12 | 550842 | 550273 | ClpP | 5.52e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| LDHOENAK_1 | 652176 | 651784 | spxA1 | 2.23e-69 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| LDHOENAK_5 | 34575 | 34333 | SpoVG | 2.72e-38 | RNA-binding protein | 80.25 | 79.41 | AAT02994 |
| LDHOENAK_2 | 1883 | 2080 | CspA | 3.37e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| LDHOENAK_23 | 31474 | 31668 | CspD | 5.51e-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 |
|---|---|---|---|
| LDHOENAK_1 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_2 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_3 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_4 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_5 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_6 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_7 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_8 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_9 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_10 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_11 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_12 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_13 | 1.0 | 0.0 | 1.0 |
| LDHOENAK_14 | 1.0 | 0.0 | 1.0 |
| LDHOENAK_15 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_16 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_17 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_18 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_19 | 1.0 | 0.0 | 1.0 |
| LDHOENAK_20 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_21 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_22 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_23 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_24 | 1.0 | 0.0 | 1.0 |
| LDHOENAK_25 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_26 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_27 | 1.0 | 0.0 | 1.0 |
| LDHOENAK_28 | 1.0 | 0.0 | 1.0 |
| LDHOENAK_29 | 1.0 | 0.0 | 1.0 |
| LDHOENAK_30 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_31 | 1.0 | 0.0 | 1.0 |
| LDHOENAK_33 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_34 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_35 | 1.0 | 0.0 | 1.0 |
| LDHOENAK_36 | 1.0 | 0.0 | 1.0 |
| LDHOENAK_37 | 1.0 | 0.0 | 1.0 |
| LDHOENAK_39 | 1.0 | 0.0 | 1.0 |
| LDHOENAK_40 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_41 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_42 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_43 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_44 | 1.0 | 0.0 | 1.0 |
| LDHOENAK_45 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_46 | 1.0 | 0.0 | 1.0 |
| LDHOENAK_47 | 1.0 | 0.0 | 1.0 |
| LDHOENAK_48 | 1.0 | 0.0 | 1.0 |
| LDHOENAK_56 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_67 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_78 | 0.0 | 1.0 | 0.0 |
| LDHOENAK_89 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LDHOENAK_1 | 533192 | 559300 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
| LDHOENAK_23 | 390616 | 420860 | False | Myoviridae | VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG10227, VOG0796, VOG4673, VOG9587, VOG4693, VOG0189, VOG11060, VOG1309, VOG4600 |
Phigaro v2.4.0 (Database: Jan. 2024 release)