Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 3 | 1 | 7 | 7.68 |
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. |
|---|---|---|---|---|---|---|---|---|
| NCMCLLKC_31 | 50874 | 51923 | 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. |
|---|---|---|---|---|---|---|---|
| NCMCLLKC_31 | 50888 | 51923 | cfr(B) | Chloramphenicol, Florfenicol, Clindamycin, Lincomycin, Linezolid, Dalfopristin, Pristinamycin IIA, Virginiamycin M, Tiamulin | 87.64 | 98.67 | KR610408 |
| NCMCLLKC_23 | 193569 | 194945 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 86.64 | 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. |
|---|---|---|---|---|---|---|---|---|
| NCMCLLKC_31 | 50880 | 51923 | clbA | 23S rRNA (adenine(2503)-C(8))-methyltransferase ClbA | BLASTX | 97.70 | 99.71 | WP_012116915.1 |
| NCMCLLKC_23 | 193575 | 194945 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 86.43 | 99.78 | WP_003242953.1 |
| NCMCLLKC_23 | 195158 | 195676 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 80.35 | 100.00 | WP_003242546.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| NCMCLLKC_12 | 371956 | 373137 | capB | 0.0 | Capsule | Immune modulation | 82.29 | 99.66 | NP_391471 |
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 |
|---|---|---|---|---|---|---|---|---|
| NCMCLLKC_3 | 31685 | 32821 | tufA | 0.0 | elongation factor Tu | 86.54 | 95.69 | AHM69299 |
| NCMCLLKC_8 | 4275 | 5144 | pdxS | 8.92e-153 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 84.83 | 98.31 | ACE61268 |
| NCMCLLKC_1 | 328990 | 328214 | CodY | 1.28e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| NCMCLLKC_1 | 829023 | 828631 | spxA1 | 2.33e-69 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| NCMCLLKC_31 | 70469 | 70272 | CspA | 1.24e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| NCMCLLKC_32 | 186483 | 186677 | CspD | 5.17e-28 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| NCMCLLKC_32 | 186483 | 186680 | CspB | 1.07e-27 | cold shock protein | 80.30 | 100.00 | CAD00094 |
| NCMCLLKC_31 | 70469 | 70275 | CspR | 1.62e-26 | cold shock protein | 80.00 | 98.48 | AAO82613 |
| NCMCLLKC_12 | 15055 | 14183 | lipA (SAUSA300_0829) | 2.77e-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. |
|---|---|---|---|---|---|---|
| No hit found | ||||||
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| NCMCLLKC_1 | 0.0 | 1.0 | 0.0 |
| NCMCLLKC_2 | 0.0 | 1.0 | 0.0 |
| NCMCLLKC_3 | 0.0 | 1.0 | 0.0 |
| NCMCLLKC_4 | 0.0 | 1.0 | 0.0 |
| NCMCLLKC_5 | 0.0 | 1.0 | 0.0 |
| NCMCLLKC_6 | 0.0 | 1.0 | 0.0 |
| NCMCLLKC_7 | 0.0 | 1.0 | 0.0 |
| NCMCLLKC_8 | 0.0 | 1.0 | 0.0 |
| NCMCLLKC_9 | 0.0 | 1.0 | 0.0 |
| NCMCLLKC_10 | 0.0 | 1.0 | 0.0 |
| NCMCLLKC_11 | 1.0 | 0.0 | 1.0 |
| NCMCLLKC_12 | 0.0 | 1.0 | 0.0 |
| NCMCLLKC_13 | 0.0 | 1.0 | 0.0 |
| NCMCLLKC_14 | 1.0 | 0.0 | 1.0 |
| NCMCLLKC_15 | 0.0 | 1.0 | 0.0 |
| NCMCLLKC_16 | 0.0 | 1.0 | 0.0 |
| NCMCLLKC_18 | 1.0 | 0.0 | 1.0 |
| NCMCLLKC_19 | 1.0 | 0.0 | 1.0 |
| NCMCLLKC_23 | 0.0 | 1.0 | 0.0 |
| NCMCLLKC_31 | 0.0 | 1.0 | 0.0 |
| NCMCLLKC_32 | 0.0 | 1.0 | 0.0 |
| NCMCLLKC_33 | 0.0 | 1.0 | 0.0 |
| NCMCLLKC_34 | 0.0 | 1.0 | 0.0 |
| NCMCLLKC_35 | 0.0 | 1.0 | 0.0 |
| NCMCLLKC_36 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| NCMCLLKC_1 | 701590 | 727905 | 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 |
| NCMCLLKC_6 | 12339 | 36486 | False | Siphoviridae | VOG2703, VOG4581, VOG1886, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390 |
| NCMCLLKC_32 | 11850 | 37004 | False | Siphoviridae | VOG0641, VOG7896, VOG3390, VOG4612, VOG4660, VOG4772, VOG0801, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG1266, VOG0204, VOG5361, VOG4553, VOG4568, VOG4556, VOG3607, VOG1886, VOG4581, VOG0713, VOG4841, VOG0275, VOG0198 |
Phigaro v2.4.0 (Database: Jan. 2024 release)