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. |
|---|---|---|---|---|---|---|---|---|
| LOJCLDLB_2 | 495358 | 495696 | ykkC | ARO:3003063 | ykkC | 99.11 | 100.00 | AL009126.1 |
| LOJCLDLB_2 | 495041 | 495358 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| LOJCLDLB_1 | 481848 | 482702 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| LOJCLDLB_1 | 463160 | 464362 | blt | ARO:3003006 | blt | 99.50 | 100.00 | L32599.1 |
| LOJCLDLB_4 | 356791 | 358416 | vmlR | ARO:3004476 | vmlR | 98.52 | 98.90 | NC_000964.3 |
| LOJCLDLB_1 | 293045 | 294214 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| LOJCLDLB_4 | 98366 | 98959 | tmrB | ARO:3003059 | tmrB | 99.49 | 100.00 | AL009126.3 |
| LOJCLDLB_4 | 47831 | 49270 | lmrB | ARO:3002813 | lmrB | 99.79 | 100.42 | JYFL01000006.1 |
| LOJCLDLB_4 | 35019 | 35939 | mphK | ARO:3004541 | mphK | 97.06 | 100.00 | CP010314.1 |
| LOJCLDLB_6 | 27473 | 30043 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 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. |
|---|---|---|---|---|---|---|---|
| LOJCLDLB_3 | 655913 | 657289 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 99.42 | 100.00 | D12567 |
| LOJCLDLB_1 | 481848 | 482702 | aadK | Streptomycin | 98.83 | 100.00 | M26879 |
| LOJCLDLB_4 | 35019 | 35939 | mph(K) | Spiramycin, Telithromycin | 97.72 | 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. |
|---|---|---|---|---|---|---|---|---|
| LOJCLDLB_3 | 655916 | 657289 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 99.34 | 100.00 | WP_063856081.1 |
| LOJCLDLB_1 | 481851 | 482702 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| LOJCLDLB_4 | 356794 | 358416 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.52 | 98.90 | WP_003234144.1 |
| LOJCLDLB_4 | 35019 | 35936 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.06 | 100.00 | WP_003246254.1 |
| LOJCLDLB_3 | 653383 | 653901 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| LOJCLDLB_9 | 55012 | 57609 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.71 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| LOJCLDLB_5 | 265103 | 266722 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.81 | 100.00 | NP_391078 |
| LOJCLDLB_5 | 266750 | 267688 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.79 | 100.00 | NP_391077 |
| LOJCLDLB_3 | 142723 | 143904 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| LOJCLDLB_9 | 8316 | 10079 | dep/capD | 0.0 | Capsule | Immune modulation | 99.60 | 100.00 | NP_389723 |
| LOJCLDLB_5 | 263067 | 263852 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| LOJCLDLB_3 | 141098 | 142240 | capA | 0.0 | Capsule | Immune modulation | 99.47 | 100.00 | NP_391469 |
| LOJCLDLB_1 | 90013 | 90654 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.38 | 100.00 | NP_390062 |
| LOJCLDLB_3 | 142259 | 142708 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| LOJCLDLB_5 | 267708 | 274844 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.33 | 100.00 | NP_391076 |
| LOJCLDLB_5 | 263878 | 265074 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.00 | 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 |
|---|---|---|---|---|---|---|---|---|
| LOJCLDLB_12 | 31799 | 32935 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| LOJCLDLB_15 | 11334 | 10465 | pdxS | 1.14e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| LOJCLDLB_2 | 184734 | 183958 | CodY | 1.82e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| LOJCLDLB_5 | 8684 | 8115 | ClpP | 2.27e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| LOJCLDLB_2 | 646062 | 645670 | spxA1 | 2.22e-69 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| LOJCLDLB_14 | 20814 | 21056 | SpoVG | 7.55e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| LOJCLDLB_4 | 298140 | 298337 | CspA | 1.67e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| LOJCLDLB_1 | 102615 | 102809 | CspD | 6.09e-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 |
|---|---|---|---|
| LOJCLDLB_1 | 0.0 | 1.0 | 0.0 |
| LOJCLDLB_2 | 0.0 | 1.0 | 0.0 |
| LOJCLDLB_3 | 0.0 | 1.0 | 0.0 |
| LOJCLDLB_4 | 0.0 | 1.0 | 0.0 |
| LOJCLDLB_5 | 0.0 | 1.0 | 0.0 |
| LOJCLDLB_6 | 0.0 | 1.0 | 0.0 |
| LOJCLDLB_7 | 0.0 | 1.0 | 0.0 |
| LOJCLDLB_8 | 1.0 | 0.0 | 1.0 |
| LOJCLDLB_9 | 0.0 | 1.0 | 0.0 |
| LOJCLDLB_10 | 0.0 | 1.0 | 0.0 |
| LOJCLDLB_11 | 0.0 | 1.0 | 0.0 |
| LOJCLDLB_12 | 0.0 | 1.0 | 0.0 |
| LOJCLDLB_13 | 0.0 | 1.0 | 0.0 |
| LOJCLDLB_14 | 0.0 | 1.0 | 0.0 |
| LOJCLDLB_15 | 0.0 | 1.0 | 0.0 |
| LOJCLDLB_16 | 0.0 | 1.0 | 0.0 |
| LOJCLDLB_18 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LOJCLDLB_1 | 648183 | 675894 | False | Siphoviridae | VOG0705, VOG6116, VOG8440, VOG0602, VOG4574, VOG0753, VOG4705, VOG6243, VOG4612, VOG4626, VOG4619, VOG0801, VOG6163, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5601, VOG4553, VOG4573, VOG4556, VOG4544, VOG4581, VOG0531, VOG6430 |
| LOJCLDLB_1 | 695834 | 712802 | False | Myoviridae / Siphoviridae | VOG0371, VOG1093, VOG5543, VOG0026, VOG6497, VOG5385, VOG10937, VOG5753, VOG6546, VOG4134, VOG1563, VOG2215, VOG4551, VOG0025, VOG0943, VOG4907, VOG0189, VOG6168 |
| LOJCLDLB_2 | 525190 | 551511 | 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 |
| LOJCLDLB_8 | 29847 | 43964 | False | Siphoviridae | VOG1198, VOG0918, VOG4551, VOG0025, VOG7476, VOG0322, VOG6211, VOG4908, VOG0048 |
| LOJCLDLB_11 | 30774 | 47551 | False | Unknown | VOG7895, VOG8610, VOG0275, VOG9312, VOG4910, VOG3389, VOG5042, VOG9712 |
| LOJCLDLB_13 | 19307 | 38018 | False | Myoviridae | VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG10989, VOG4691, VOG4862 |
Phigaro v2.4.0 (Database: Jan. 2024 release)