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. |
|---|---|---|---|---|---|---|---|---|
| LCANEFNB_2 | 36863 | 37909 | 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. |
|---|---|---|---|---|---|---|---|
| LCANEFNB_2 | 36863 | 37906 | cfr(B) | Chloramphenicol, Florfenicol, Clindamycin, Lincomycin, Linezolid, Dalfopristin, Pristinamycin IIA, Virginiamycin M, Tiamulin | 88.90 | 99.33 | KR610408 |
| LCANEFNB_29 | 362104 | 363480 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 87.07 | 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. |
|---|---|---|---|---|---|---|---|---|
| LCANEFNB_2 | 36863 | 37906 | clbA | 23S rRNA (adenine(2503)-C(8))-methyltransferase ClbA | BLASTX | 92.24 | 99.71 | WP_012116915.1 |
| LCANEFNB_29 | 362104 | 363474 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 86.43 | 99.78 | WP_003242953.1 |
| LCANEFNB_2 | 34594 | 35112 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 82.66 | 100.00 | WP_003242546.1 |
| LCANEFNB_11 | 5340 | 7937 | rphC | rifamycin-inactivating phosphotransferase RphC | INTERNAL_STOP | 80.94 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| LCANEFNB_22 | 377369 | 378550 | capB | 0.0 | Capsule | Immune modulation | 81.79 | 99.66 | NP_391471 |
| LCANEFNB_22 | 378565 | 379014 | capC | 3.53e-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 |
|---|---|---|---|---|---|---|---|---|
| LCANEFNB_3 | 31771 | 32907 | tufA | 0.0 | elongation factor Tu | 86.54 | 95.69 | AHM69299 |
| LCANEFNB_6 | 4401 | 5270 | pdxS | 6.45e-153 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 84.83 | 98.31 | ACE61268 |
| LCANEFNB_11 | 212052 | 211276 | CodY | 2.82e-124 | nutrient-responsive regulator | 80.69 | 100.00 | ACJ80679 |
| LCANEFNB_11 | 652327 | 651935 | spxA1 | 1.28e-69 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| LCANEFNB_2 | 20377 | 20574 | CspA | 1.31e-32 | cold shock protein | 92.42 | 100.00 | CAA62903 |
| LCANEFNB_28 | 104939 | 105133 | CspD | 1.13e-27 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| LCANEFNB_28 | 104939 | 105136 | CspB | 2.34e-27 | cold shock protein | 80.30 | 100.00 | CAD00094 |
| LCANEFNB_2 | 20377 | 20571 | CspR | 6.50e-27 | cold shock protein | 80.00 | 98.48 | AAO82613 |
| LCANEFNB_22 | 293298 | 294266 | atpA | 0.0 | ATP synthase subunit alpha | 81.11 | 64.34 | ABD31377 |
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 |
|---|---|---|---|
| LCANEFNB_1 | 0.0 | 1.0 | 0.0 |
| LCANEFNB_2 | 0.0 | 1.0 | 0.0 |
| LCANEFNB_3 | 0.0 | 1.0 | 0.0 |
| LCANEFNB_4 | 0.0 | 1.0 | 0.0 |
| LCANEFNB_5 | 0.0 | 1.0 | 0.0 |
| LCANEFNB_6 | 0.0 | 1.0 | 0.0 |
| LCANEFNB_7 | 0.0 | 1.0 | 0.0 |
| LCANEFNB_8 | 0.0 | 1.0 | 0.0 |
| LCANEFNB_11 | 0.0 | 1.0 | 0.0 |
| LCANEFNB_13 | 1.0 | 0.0 | 1.0 |
| LCANEFNB_22 | 0.0 | 1.0 | 0.0 |
| LCANEFNB_28 | 0.0 | 1.0 | 0.0 |
| LCANEFNB_29 | 0.0 | 1.0 | 0.0 |
| LCANEFNB_30 | 0.0 | 1.0 | 0.0 |
| LCANEFNB_31 | 0.0 | 1.0 | 0.0 |
| LCANEFNB_32 | 0.0 | 1.0 | 0.0 |
| LCANEFNB_33 | 0.0 | 1.0 | 0.0 |
| LCANEFNB_34 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LCANEFNB_11 | 535325 | 562258 | False | Myoviridae | VOG0753, VOG4705, VOG3390, VOG4612, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG0749, VOG4685, VOG4773, VOG10227, VOG4544, VOG0796, VOG5447, VOG4861, VOG0189, VOG9667 |
| LCANEFNB_11 | 912644 | 940695 | False | Siphoviridae | VOG0602, VOG4824, VOG5221, VOG4705, VOG3390, VOG4612, VOG4660, VOG4619, VOG0801, VOG0083, VOG11074, VOG2565, VOG0724, VOG5361, VOG3676, VOG4555, VOG0692, VOG2613, VOG3699, VOG5023, VOG0275, VOG1183, VOG5327, VOG6495, VOG7742, VOG7541 |
| LCANEFNB_11 | 960668 | 963926 | False | Unknown | VOG10564, VOG10937 |
| LCANEFNB_22 | 709116 | 742369 | False | Siphoviridae | VOG0181, VOG7438, VOG1047, VOG0021, VOG1565, VOG0026, VOG10500, VOG4609, VOG0327, VOG4548, VOG0198, VOG4581, VOG4544, VOG5051, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4772, VOG4619, VOG4660, VOG4612, VOG3390, VOG0641 |
| LCANEFNB_22 | 906716 | 929421 | False | Siphoviridae | VOG4841, VOG4556, VOG6052, VOG0531, VOG4581, VOG4544, VOG5051, VOG4556, VOG4568, VOG4553, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG4705, VOG0641 |
| LCANEFNB_30 | 130260 | 159327 | False | Siphoviridae | VOG4666, VOG4574, VOG0136, VOG0753, VOG5535, VOG3390, VOG4599, VOG4605, VOG4545, VOG0725, VOG0799, VOG0724, VOG5660, VOG0816, VOG4623, VOG5872, VOG2621, VOG1329, VOG4555, VOG6778, VOG4564, VOG0720, VOG10227, VOG0796, VOG4681, VOG4972, VOG5447 |
| LCANEFNB_30 | 161699 | 175645 | False | Siphoviridae | VOG0102, VOG6581, VOG0397, VOG8569, VOG4658, VOG1336, VOG0536, VOG0044, VOG0189, VOG9093, VOG1309, VOG4600, VOG4600, VOG4552, VOG0650, VOG11075, VOG9667, VOG8483 |
Phigaro v2.4.0 (Database: Jan. 2024 release)