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. |
|---|---|---|---|---|---|---|---|---|
| INLFLNLG_6 | 609962 | 610816 | aadK | ARO:3002627 | aadK | 97.54 | 100.00 | AL009126.1 |
| INLFLNLG_6 | 590793 | 591995 | blt | ARO:3003006 | blt | 99.75 | 100.00 | L32599.1 |
| INLFLNLG_6 | 363014 | 364183 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| INLFLNLG_5 | 323515 | 324435 | mphK | ARO:3004541 | mphK | 98.37 | 100.00 | CP010314.1 |
| INLFLNLG_5 | 310183 | 311622 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| INLFLNLG_5 | 260471 | 261064 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| INLFLNLG_8 | 255907 | 258477 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 100.00 | AL009126.3 |
| INLFLNLG_2 | 42057 | 42374 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| INLFLNLG_2 | 41719 | 42057 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| INLFLNLG_5 | 29142 | 30788 | vmlR | ARO:3004476 | vmlR | 98.54 | 100.18 | 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. |
|---|---|---|---|---|---|---|---|
| INLFLNLG_1 | 1023598 | 1024974 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 100.00 | 100.00 | X08034 |
| INLFLNLG_6 | 609964 | 610816 | aadK | Streptomycin | 98.12 | 99.77 | M26879 |
| INLFLNLG_5 | 323515 | 324435 | mph(K) | Spiramycin, Telithromycin | 97.94 | 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. |
|---|---|---|---|---|---|---|---|---|
| INLFLNLG_1 | 1023601 | 1024974 | tet(L) | tetracycline efflux MFS transporter Tet(L) | EXACTX | 100.00 | 100.00 | WP_003242953.1 |
| INLFLNLG_5 | 29142 | 30785 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.54 | 100.00 | WP_003234144.1 |
| INLFLNLG_5 | 323518 | 324435 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.37 | 100.00 | WP_003246254.1 |
| INLFLNLG_6 | 609965 | 610816 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.54 | 100.00 | WP_003229862.1 |
| INLFLNLG_1 | 1021126 | 1021644 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| INLFLNLG_6 | 59309 | 61906 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.40 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| INLFLNLG_6 | 163848 | 164489 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 100.00 | 100.00 | NP_390062 |
| INLFLNLG_1 | 527182 | 528363 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| INLFLNLG_1 | 525557 | 526699 | capA | 0.0 | Capsule | Immune modulation | 99.39 | 100.00 | NP_391469 |
| INLFLNLG_1 | 109093 | 110031 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391077 |
| INLFLNLG_1 | 526718 | 527167 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| INLFLNLG_1 | 112929 | 113714 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.24 | 100.00 | NP_391080 |
| INLFLNLG_1 | 111707 | 112903 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.17 | 100.00 | NP_391079 |
| INLFLNLG_6 | 9228 | 10991 | dep/capD | 0.0 | Capsule | Immune modulation | 99.15 | 100.00 | NP_389723 |
| INLFLNLG_1 | 101937 | 109073 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.06 | 100.00 | NP_391076 |
| INLFLNLG_1 | 110059 | 111678 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.52 | 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 |
|---|---|---|---|---|---|---|---|---|
| INLFLNLG_11 | 31842 | 32978 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| INLFLNLG_14 | 4350 | 5219 | pdxS | 1.11e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| INLFLNLG_2 | 352207 | 352983 | CodY | 5.79e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| INLFLNLG_1 | 365838 | 366407 | ClpP | 2.16e-98 | part of proteolytic complex | 80.53 | 97.44 | BAB94595 |
| INLFLNLG_4 | 110147 | 109755 | spxA1 | 9.29e-70 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| INLFLNLG_7 | 20518 | 20760 | SpoVG | 7.51e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| INLFLNLG_5 | 77543 | 77346 | CspA | 1.83e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| INLFLNLG_4 | 353346 | 353540 | CspB | 3.55e-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 |
|---|---|---|---|
| INLFLNLG_1 | 0.0 | 1.0 | 0.0 |
| INLFLNLG_2 | 0.0 | 1.0 | 0.0 |
| INLFLNLG_4 | 0.0 | 1.0 | 0.0 |
| INLFLNLG_5 | 0.0 | 1.0 | 0.0 |
| INLFLNLG_6 | 0.0 | 1.0 | 0.0 |
| INLFLNLG_7 | 0.0 | 1.0 | 0.0 |
| INLFLNLG_8 | 0.0 | 1.0 | 0.0 |
| INLFLNLG_10 | 0.0 | 1.0 | 0.0 |
| INLFLNLG_11 | 0.0 | 1.0 | 0.0 |
| INLFLNLG_13 | 0.0 | 1.0 | 0.0 |
| INLFLNLG_14 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| INLFLNLG_2 | 4482 | 12232 | False | Myoviridae | VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG3390, VOG4705 |
| INLFLNLG_2 | 627254 | 632816 | False | Unknown | VOG6211, VOG0322, VOG7476, VOG0025 |
| INLFLNLG_2 | 683206 | 706796 | False | Siphoviridae | VOG4841, VOG4581, VOG1886, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619, VOG4626, VOG3390, VOG4705, VOG4612, VOG3390, VOG7896 |
| INLFLNLG_4 | 5396 | 15316 | False | Siphoviridae | VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
| INLFLNLG_6 | 541521 | 563577 | False | Myoviridae | VOG7718, VOG4862, VOG4691, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773 |
Phigaro v2.4.0 (Database: Jan. 2024 release)