Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 4 | 2 | 6 | 7.48 |
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. |
|---|---|---|---|---|---|---|---|---|
| LJGBGJFA_17 | 23134 | 24180 | clbA | ARO:3002814 | clbA | 92.77 | 99.71 | CP006845.1 |
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. |
|---|---|---|---|---|---|---|---|
| LJGBGJFA_17 | 23134 | 24177 | cfr(B) | Chloramphenicol, Florfenicol, Clindamycin, Lincomycin, Linezolid, Dalfopristin, Pristinamycin IIA, Virginiamycin M, Tiamulin | 88.90 | 99.33 | KR610408 |
| LJGBGJFA_6 | 137229 | 138605 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 87.15 | 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. |
|---|---|---|---|---|---|---|---|---|
| LJGBGJFA_17 | 23134 | 24177 | clbA | 23S rRNA (adenine(2503)-C(8))-methyltransferase ClbA | BLASTX | 92.24 | 99.71 | WP_012116915.1 |
| LJGBGJFA_6 | 137229 | 138599 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 86.43 | 99.78 | WP_003242953.1 |
| LJGBGJFA_17 | 20865 | 21383 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 82.66 | 100.00 | WP_003242546.1 |
| LJGBGJFA_1 | 5237 | 7834 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.06 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| LJGBGJFA_34 | 3492 | 4673 | capB | 0.0 | Capsule | Immune modulation | 81.87 | 99.66 | NP_391471 |
| LJGBGJFA_34 | 4688 | 5137 | capC | 1.16e-114 | Capsule | Immune modulation | 83.59 | 99.78 | NP_391470 |
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 |
|---|---|---|---|---|---|---|---|---|
| LJGBGJFA_20 | 27509 | 26373 | tufA | 0.0 | elongation factor Tu | 86.54 | 95.69 | AHM69299 |
| LJGBGJFA_40 | 4474 | 3605 | pdxS | 3.20e-153 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 84.83 | 98.31 | ACE61268 |
| LJGBGJFA_1 | 209039 | 208263 | CodY | 5.01e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| LJGBGJFA_56 | 41597 | 41205 | spxA1 | 3.93e-70 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| LJGBGJFA_17 | 6641 | 6838 | CspA | 1.07e-32 | cold shock protein | 92.42 | 100.00 | CAA62903 |
| LJGBGJFA_67 | 104840 | 105034 | CspD | 3.40e-28 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| LJGBGJFA_67 | 104840 | 105037 | CspB | 7.05e-28 | cold shock protein | 80.30 | 100.00 | CAD00094 |
| LJGBGJFA_17 | 6641 | 6835 | CspR | 5.29e-27 | cold shock protein | 80.00 | 98.48 | AAO82613 |
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 |
|---|---|---|---|
| LJGBGJFA_1 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_2 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_3 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_4 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_5 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_6 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_7 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_8 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_9 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_10 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_11 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_12 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_13 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_14 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_15 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_16 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_17 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_18 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_20 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_21 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_23 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_25 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_26 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_27 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_28 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_30 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_31 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_32 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_33 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_34 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_35 | 1.0 | 0.0 | 1.0 |
| LJGBGJFA_36 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_37 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_38 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_39 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_40 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_41 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_42 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_43 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_44 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_45 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_46 | 1.0 | 0.0 | 1.0 |
| LJGBGJFA_47 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_48 | 1.0 | 0.0 | 1.0 |
| LJGBGJFA_49 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_51 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_52 | 1.0 | 0.0 | 1.0 |
| LJGBGJFA_53 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_54 | 1.0 | 0.0 | 1.0 |
| LJGBGJFA_55 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_56 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_57 | 1.0 | 0.0 | 1.0 |
| LJGBGJFA_58 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_61 | 1.0 | 0.0 | 1.0 |
| LJGBGJFA_63 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_64 | 1.0 | 0.0 | 1.0 |
| LJGBGJFA_67 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_68 | 1.0 | 0.0 | 1.0 |
| LJGBGJFA_78 | 0.0 | 1.0 | 0.0 |
| LJGBGJFA_86 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LJGBGJFA_1 | 532727 | 561560 | False | Myoviridae | VOG0753, VOG4705, VOG3390, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG9667, VOG4602 |
| LJGBGJFA_3 | 148589 | 170611 | False | Siphoviridae | VOG4574, VOG0136, VOG0753, VOG5535, VOG3390, VOG1125, VOG4599, VOG4605, VOG4545, VOG0725, VOG0799, VOG0724, VOG5660, VOG0816, VOG4623, VOG5872, VOG2621, VOG1329, VOG4555, VOG6778, VOG4564, VOG0720, VOG10227 |
| LJGBGJFA_27 | 1199 | 22618 | False | Myoviridae | VOG4865, VOG6163, VOG3892, VOG6154, VOG0979, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG6480, VOG4688, VOG4773, VOG4773, VOG10227, VOG0796 |
| LJGBGJFA_33 | 732 | 23564 | False | Myoviridae | VOG10227, VOG0720, VOG4555, VOG4572, VOG1643, VOG4564, VOG4623, VOG1353, VOG1881, VOG1883, VOG1352, VOG4699, VOG6163, VOG1956, VOG1433, VOG1348, VOG0573, VOG4550, VOG4691, VOG4845, VOG7718, VOG3390, VOG4705, VOG0753, VOG0136, VOG10230 |
| LJGBGJFA_78 | 83050 | 109329 | False | Siphoviridae | VOG5534, VOG7718, VOG3390, VOG4705, VOG5008, VOG8610, VOG7930, VOG0275, VOG1637, VOG2091, VOG2090, VOG9312, VOG4910, VOG3389, VOG5042, VOG9712, VOG4660, VOG10230 |
Phigaro v2.4.0 (Database: Jan. 2024 release)