Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 3 | 2 | 8 | 8.77 |
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. |
|---|---|---|---|---|---|---|---|---|
| HBDLGIIM_42 | 145433 | 146482 | clbA | ARO:3002814 | clbA | 97.42 | 100.00 | 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. |
|---|---|---|---|---|---|---|---|
| HBDLGIIM_42 | 145433 | 146468 | cfr(B) | Chloramphenicol, Florfenicol, Clindamycin, Lincomycin, Linezolid, Dalfopristin, Pristinamycin IIA, Virginiamycin M, Tiamulin | 88.03 | 98.67 | KR610408 |
| HBDLGIIM_1 | 427163 | 428539 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 87.36 | 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. |
|---|---|---|---|---|---|---|---|---|
| HBDLGIIM_42 | 145433 | 146476 | clbA | 23S rRNA (adenine(2503)-C(8))-methyltransferase ClbA | BLASTX | 97.70 | 99.71 | WP_012116915.1 |
| HBDLGIIM_1 | 427169 | 428539 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 86.43 | 99.78 | WP_003242953.1 |
| HBDLGIIM_14 | 29834 | 32428 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.11 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| HBDLGIIM_13 | 24961 | 26142 | capB | 0.0 | Capsule | Immune modulation | 81.87 | 99.66 | NP_391471 |
| HBDLGIIM_13 | 26157 | 26606 | capC | 1.87e-115 | 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 |
|---|---|---|---|---|---|---|---|---|
| HBDLGIIM_6 | 27902 | 26766 | tufA | 0.0 | elongation factor Tu | 86.81 | 95.69 | AHM69299 |
| HBDLGIIM_19 | 4229 | 5098 | pdxS | 1.34e-152 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 84.83 | 98.31 | ACE61268 |
| HBDLGIIM_34 | 172123 | 171347 | CodY | 3.50e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| HBDLGIIM_40 | 257177 | 257569 | spxA1 | 6.23e-70 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| HBDLGIIM_42 | 114672 | 114869 | CspA | 1.05e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| HBDLGIIM_1 | 11254 | 11448 | CspD | 2.07e-27 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| HBDLGIIM_40 | 38478 | 38284 | CspB | 5.93e-27 | cold shock protein | 84.61 | 98.48 | CAD00094 |
| HBDLGIIM_42 | 114672 | 114866 | CspR | 1.37e-26 | cold shock protein | 80.00 | 98.48 | AAO82613 |
| HBDLGIIM_23 | 207401 | 208273 | lipA (SAUSA300_0829) | 1.11e-162 | lipoic acid synthetase | 80.82 | 95.41 | ABD22039 |
BLASTX v2.16.0 (Database: PHI base v4.16, May. 2024 release)
Plasmid
PlasmidFinder
| Query ID | Begin | End | Plasmid | Query / Template | Identity | Accession no. |
|---|---|---|---|---|---|---|
| HBDLGIIM_24 | 1 | 191 | Col(SD853) | 191 / 194 | 97.91 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| HBDLGIIM_1 | 0.0 | 1.0 | 0.0 |
| HBDLGIIM_2 | 0.0 | 1.0 | 0.0 |
| HBDLGIIM_3 | 0.0 | 1.0 | 0.0 |
| HBDLGIIM_4 | 0.0 | 1.0 | 0.0 |
| HBDLGIIM_5 | 0.0 | 1.0 | 0.0 |
| HBDLGIIM_6 | 0.0 | 1.0 | 0.0 |
| HBDLGIIM_7 | 0.0 | 1.0 | 0.0 |
| HBDLGIIM_8 | 0.0 | 1.0 | 0.0 |
| HBDLGIIM_9 | 0.0 | 1.0 | 0.0 |
| HBDLGIIM_10 | 0.0 | 1.0 | 0.0 |
| HBDLGIIM_11 | 0.0 | 1.0 | 0.0 |
| HBDLGIIM_12 | 0.0 | 1.0 | 0.0 |
| HBDLGIIM_13 | 0.0 | 1.0 | 0.0 |
| HBDLGIIM_14 | 0.0 | 1.0 | 0.0 |
| HBDLGIIM_15 | 0.0 | 1.0 | 0.0 |
| HBDLGIIM_16 | 0.0 | 1.0 | 0.0 |
| HBDLGIIM_17 | 0.0 | 1.0 | 0.0 |
| HBDLGIIM_18 | 0.0 | 1.0 | 0.0 |
| HBDLGIIM_19 | 0.0 | 1.0 | 0.0 |
| HBDLGIIM_20 | 0.0 | 1.0 | 0.0 |
| HBDLGIIM_21 | 0.0 | 1.0 | 0.0 |
| HBDLGIIM_22 | 0.0 | 1.0 | 0.0 |
| HBDLGIIM_23 | 0.0 | 1.0 | 0.0 |
| HBDLGIIM_24 | 1.0 | 0.0 | 1.0 |
| HBDLGIIM_25 | 0.0 | 1.0 | 0.0 |
| HBDLGIIM_27 | 0.0 | 1.0 | 0.0 |
| HBDLGIIM_30 | 1.0 | 0.0 | 1.0 |
| HBDLGIIM_31 | 1.0 | 0.0 | 1.0 |
| HBDLGIIM_34 | 0.0 | 1.0 | 0.0 |
| HBDLGIIM_40 | 0.0 | 1.0 | 0.0 |
| HBDLGIIM_41 | 0.0 | 1.0 | 0.0 |
| HBDLGIIM_42 | 0.0 | 1.0 | 0.0 |
| HBDLGIIM_43 | 0.0 | 1.0 | 0.0 |
| HBDLGIIM_44 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| HBDLGIIM_1 | 529887 | 558684 | False | Siphoviridae | VOG0641, VOG7896, VOG3390, VOG4612, VOG4660, VOG4772, VOG0801, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG1266, VOG0204, VOG5361, VOG4553, VOG4568, VOG4556, VOG3607, VOG1886, VOG4581, VOG4841, VOG2545, VOG0376, VOG0198, VOG7372, VOG2752, VOG4606 |
| HBDLGIIM_3 | 50707 | 75407 | False | Myoviridae | VOG0753, VOG4705, VOG3390, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861 |
Phigaro v2.4.0 (Database: Jan. 2024 release)