Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 4 | 2 | 5 | 6.71 |
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. |
|---|---|---|---|---|---|---|---|---|
| NMDLDNHH_2 | 166304 | 167350 | 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. |
|---|---|---|---|---|---|---|---|
| NMDLDNHH_2 | 166304 | 167347 | cfr(B) | Chloramphenicol, Florfenicol, Clindamycin, Lincomycin, Linezolid, Dalfopristin, Pristinamycin IIA, Virginiamycin M, Tiamulin | 88.90 | 99.33 | KR610408 |
| NMDLDNHH_1 | 1691112 | 1692488 | 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. |
|---|---|---|---|---|---|---|---|---|
| NMDLDNHH_2 | 166304 | 167347 | clbA | 23S rRNA (adenine(2503)-C(8))-methyltransferase ClbA | BLASTX | 92.24 | 99.71 | WP_012116915.1 |
| NMDLDNHH_1 | 1691118 | 1692488 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 87.09 | 99.78 | WP_003242953.1 |
| NMDLDNHH_2 | 164035 | 164553 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 82.66 | 100.00 | WP_003242546.1 |
| NMDLDNHH_1 | 953613 | 956210 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| NMDLDNHH_3 | 573093 | 574274 | capB | 0.0 | Capsule | Immune modulation | 82.04 | 99.66 | NP_391471 |
| NMDLDNHH_3 | 572629 | 573078 | capC | 3.93e-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 |
|---|---|---|---|---|---|---|---|---|
| NMDLDNHH_11 | 31665 | 32801 | tufA | 0.0 | elongation factor Tu | 86.54 | 95.69 | AHM69299 |
| NMDLDNHH_13 | 12530 | 11661 | pdxS | 6.37e-153 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 84.83 | 98.31 | ACE61268 |
| NMDLDNHH_1 | 752501 | 753277 | CodY | 1.70e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| NMDLDNHH_1 | 260677 | 261069 | spxA1 | 2.68e-69 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| NMDLDNHH_2 | 149817 | 150014 | CspA | 3.29e-32 | cold shock protein | 92.42 | 100.00 | CAA62903 |
| NMDLDNHH_2 | 149817 | 150011 | CspR | 1.63e-26 | 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 |
|---|---|---|---|
| NMDLDNHH_1 | 0.0 | 1.0 | 0.0 |
| NMDLDNHH_2 | 0.0 | 1.0 | 0.0 |
| NMDLDNHH_3 | 0.0 | 1.0 | 0.0 |
| NMDLDNHH_5 | 0.0 | 1.0 | 0.0 |
| NMDLDNHH_6 | 0.0 | 1.0 | 0.0 |
| NMDLDNHH_7 | 0.0 | 1.0 | 0.0 |
| NMDLDNHH_8 | 0.0 | 1.0 | 0.0 |
| NMDLDNHH_10 | 1.0 | 0.0 | 1.0 |
| NMDLDNHH_11 | 0.0 | 1.0 | 0.0 |
| NMDLDNHH_13 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| NMDLDNHH_1 | 298405 | 302344 | False | Unknown | VOG3304, VOG9576, VOG9667, VOG9667, VOG8241 |
| NMDLDNHH_1 | 302632 | 305923 | False | Unknown | VOG8233, VOG0186, VOG4566 |
| NMDLDNHH_1 | 315036 | 338321 | False | Myoviridae | VOG0796, VOG0720, VOG4555, VOG4572, VOG1643, VOG4564, VOG4623, VOG1353, VOG1881, VOG1883, VOG1352, VOG4699, VOG6163, VOG1956, VOG1433, VOG1348, VOG0573, VOG4550, VOG4691, VOG4845, VOG7718, VOG3390, VOG4705, VOG0753, VOG0136 |
| NMDLDNHH_1 | 402283 | 427670 | False | Myoviridae | VOG9667, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718 |
| NMDLDNHH_1 | 1255398 | 1266335 | False | Siphoviridae | VOG0918, VOG4551, VOG0025, VOG7627, VOG0322, VOG6464, VOG0156 |
| NMDLDNHH_1 | 1329661 | 1346514 | False | Unknown | VOG5008, VOG8610, VOG7930, VOG0275, VOG2091, VOG2090, VOG9312, VOG4910, VOG3389 |
| NMDLDNHH_3 | 21968 | 44674 | False | Siphoviridae | VOG4972, VOG0641, VOG4705, VOG3390, VOG4612, VOG4660, VOG4619, VOG0801, VOG6163, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG4553, VOG4568, VOG4556, VOG5051, VOG4544, VOG4581, VOG0531, VOG6052, VOG4556 |
| NMDLDNHH_3 | 163448 | 184256 | False | Siphoviridae | VOG5221, VOG4705, VOG3390, VOG4612, VOG4660, VOG4619, VOG0801, VOG6163, VOG11074, VOG0724, VOG4319, VOG9317, VOG0692, VOG2613, VOG3699, VOG5023 |
Phigaro v2.4.0 (Database: Jan. 2024 release)