Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 4 | 16.88 |
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. |
|---|---|---|---|---|---|---|---|---|
| LHHNJJHM_1 | 2683581 | 2684435 | aadK | ARO:3002627 | aadK | 98.94 | 100.00 | AL009126.1 |
| LHHNJJHM_1 | 2666314 | 2667516 | blt | ARO:3003006 | blt | 99.25 | 100.00 | L32599.1 |
| LHHNJJHM_1 | 2381228 | 2382397 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| LHHNJJHM_1 | 1395182 | 1395499 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| LHHNJJHM_1 | 1394844 | 1395182 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| LHHNJJHM_1 | 933654 | 936224 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| LHHNJJHM_1 | 582495 | 584123 | vmlR | ARO:3004476 | vmlR | 99.08 | 99.09 | NC_000964.3 |
| LHHNJJHM_1 | 330098 | 330691 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| LHHNJJHM_1 | 279573 | 281006 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.00 | JYFL01000006.1 |
| LHHNJJHM_1 | 266758 | 267624 | mphK | ARO:3004541 | mphK | 98.61 | 94.12 | CP010314.1 |
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. |
|---|---|---|---|---|---|---|---|
| LHHNJJHM_1 | 4150761 | 4152137 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 99.06 | 100.00 | D12567 |
| LHHNJJHM_1 | 2683583 | 2684435 | aadK | Streptomycin | 98.94 | 99.77 | M26879 |
| LHHNJJHM_1 | 266758 | 267678 | 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. |
|---|---|---|---|---|---|---|---|---|
| LHHNJJHM_1 | 582498 | 584123 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 99.08 | 98.90 | WP_003234144.1 |
| LHHNJJHM_1 | 2683584 | 2684435 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.94 | 100.00 | WP_003229862.1 |
| LHHNJJHM_1 | 4150764 | 4152137 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.91 | 100.00 | WP_063856081.1 |
| LHHNJJHM_1 | 266758 | 267675 | mphK | macrolide 2'-phosphotransferase MphK | INTERNAL_STOP | 98.04 | 100.00 | WP_003246254.1 |
| LHHNJJHM_1 | 4148298 | 4148816 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.75 | 100.00 | WP_003242546.1 |
| LHHNJJHM_1 | 2075137 | 2077725 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.37 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| LHHNJJHM_1 | 3657370 | 3658512 | capA | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_391469 |
| LHHNJJHM_1 | 3658531 | 3658980 | capC | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_391470 |
| LHHNJJHM_1 | 3255580 | 3256365 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391080 |
| LHHNJJHM_1 | 3244588 | 3251724 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.99 | 100.00 | NP_391076 |
| LHHNJJHM_1 | 3658995 | 3660176 | capB | 0.0 | Capsule | Immune modulation | 99.92 | 100.00 | NP_391471 |
| LHHNJJHM_1 | 3251744 | 3252682 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.89 | 100.00 | NP_391077 |
| LHHNJJHM_1 | 3252710 | 3254329 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.57 | 100.00 | NP_391078 |
| LHHNJJHM_1 | 3254358 | 3255554 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.50 | 100.00 | NP_391079 |
| LHHNJJHM_1 | 2178433 | 2179074 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.38 | 100.00 | NP_390062 |
| LHHNJJHM_1 | 2020733 | 2022496 | dep/capD | 0.0 | Capsule | Immune modulation | 98.92 | 100.00 | NP_389723 |
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 |
|---|---|---|---|---|---|---|---|---|
| LHHNJJHM_1 | 132363 | 133499 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| LHHNJJHM_1 | 18660 | 19529 | pdxS | 3.10e-149 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| LHHNJJHM_1 | 1705184 | 1705960 | CodY | 3.39e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| LHHNJJHM_1 | 3504907 | 3505476 | ClpP | 2.51e-98 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
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 |
|---|---|---|---|
| LHHNJJHM_1 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LHHNJJHM_1 | 631698 | 640469 | False | Myoviridae | VOG8483, VOG9667, VOG9667, VOG0650, VOG4552, VOG4600, VOG1309, VOG5263, VOG0189 |
| LHHNJJHM_1 | 646336 | 668828 | False | Siphoviridae | VOG0796, VOG10227, VOG0720, VOG4564, VOG4555, VOG4553, VOG1125, VOG0815, VOG4623, VOG0816, VOG5660, VOG0724, VOG0799, VOG0725, VOG4545, VOG4605, VOG4599, VOG5535, VOG10940, VOG0753, VOG0136, VOG4707 |
| LHHNJJHM_1 | 1338875 | 1365357 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG4612, VOG4705 |
| LHHNJJHM_1 | 2405142 | 2430760 | False | Siphoviridae | VOG0275, VOG5216, VOG10051, VOG6116, VOG8440, VOG0602, VOG4574, VOG5221, VOG4705, VOG3390, VOG4612, VOG4660, VOG4619, VOG0801, VOG6163, VOG0725, VOG0799, VOG0704, VOG5589, VOG4564, VOG5504, VOG3676, VOG4555, VOG5012, VOG5023, VOG0275 |
| LHHNJJHM_1 | 2453882 | 2462591 | False | Myoviridae / Siphoviridae | VOG10937, VOG7255, VOG4134, VOG1563, VOG2215, VOG4551, VOG0025, VOG0943 |
| LHHNJJHM_1 | 2617147 | 2639762 | False | Myoviridae | VOG7718, VOG4862, VOG4691, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG10227 |
Phigaro v2.4.0 (Database: Jan. 2024 release)