Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 2 | 1 | 7 | 7.35 |
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. |
|---|---|---|---|---|---|---|---|---|
| JCCMGDGN_8 | 182255 | 183304 | clbA | ARO:3002814 | clbA | 97.13 | 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. |
|---|---|---|---|---|---|---|---|
| JCCMGDGN_8 | 182255 | 183290 | cfr(B) | Chloramphenicol, Florfenicol, Clindamycin, Lincomycin, Linezolid, Dalfopristin, Pristinamycin IIA, Virginiamycin M, Tiamulin | 87.64 | 98.67 | KR610408 |
| JCCMGDGN_7 | 194818 | 196194 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 86.86 | 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. |
|---|---|---|---|---|---|---|---|---|
| JCCMGDGN_8 | 182255 | 183298 | clbA | 23S rRNA (adenine(2503)-C(8))-methyltransferase ClbA | BLASTX | 97.41 | 99.71 | WP_012116915.1 |
| JCCMGDGN_7 | 194824 | 196194 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 86.43 | 99.78 | WP_003242953.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| JCCMGDGN_2 | 482265 | 483446 | capB | 0.0 | Capsule | Immune modulation | 82.46 | 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 |
|---|---|---|---|---|---|---|---|---|
| JCCMGDGN_12 | 34817 | 35953 | tufA | 0.0 | elongation factor Tu | 86.54 | 95.69 | AHM69299 |
| JCCMGDGN_15 | 14046 | 13177 | pdxS | 9.73e-153 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 84.83 | 98.31 | ACE61268 |
| JCCMGDGN_3 | 330996 | 330220 | CodY | 9.74e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| JCCMGDGN_6 | 48300 | 47908 | spxA1 | 6.55e-70 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| JCCMGDGN_8 | 152957 | 153154 | CspA | 1.36e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| JCCMGDGN_5 | 144709 | 144903 | CspD | 8.67e-28 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| JCCMGDGN_5 | 144709 | 144906 | CspB | 1.80e-27 | cold shock protein | 80.30 | 100.00 | CAD00094 |
| JCCMGDGN_8 | 152957 | 153151 | CspR | 1.78e-26 | cold shock protein | 80.00 | 98.48 | AAO82613 |
| JCCMGDGN_2 | 850007 | 850879 | lipA (SAUSA300_0829) | 3.19e-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 |
|---|---|---|---|
| JCCMGDGN_1 | 1.0 | 0.0 | 1.0 |
| JCCMGDGN_2 | 0.0 | 1.0 | 0.0 |
| JCCMGDGN_3 | 0.0 | 1.0 | 0.0 |
| JCCMGDGN_4 | 0.0 | 1.0 | 0.0 |
| JCCMGDGN_5 | 0.0 | 1.0 | 0.0 |
| JCCMGDGN_6 | 0.0 | 1.0 | 0.0 |
| JCCMGDGN_7 | 0.0 | 1.0 | 0.0 |
| JCCMGDGN_8 | 0.0 | 1.0 | 0.0 |
| JCCMGDGN_9 | 0.0 | 1.0 | 0.0 |
| JCCMGDGN_10 | 0.0 | 1.0 | 0.0 |
| JCCMGDGN_11 | 0.0 | 1.0 | 0.0 |
| JCCMGDGN_12 | 0.0 | 1.0 | 0.0 |
| JCCMGDGN_13 | 0.0 | 1.0 | 0.0 |
| JCCMGDGN_14 | 0.0 | 1.0 | 0.0 |
| JCCMGDGN_15 | 0.0 | 1.0 | 0.0 |
| JCCMGDGN_16 | 0.0 | 1.0 | 0.0 |
| JCCMGDGN_17 | 0.0 | 1.0 | 0.0 |
| JCCMGDGN_22 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| JCCMGDGN_3 | 704955 | 730613 | 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 |
| JCCMGDGN_3 | 798896 | 820107 | False | Siphoviridae | VOG5535, VOG4599, VOG4605, VOG4545, VOG1323, VOG0725, VOG0799, VOG0724, VOG5660, VOG0816, VOG4623, VOG0815, VOG1125, VOG4553, VOG4555, VOG4564, VOG0720, VOG0796 |
| JCCMGDGN_4 | 4131 | 8002 | False | Unknown | VOG6587, VOG6931, VOG0189, VOG4566, VOG0650, VOG9667 |
| JCCMGDGN_6 | 7675 | 10561 | False | Unknown | VOG4552, VOG8241, VOG9667, VOG9667 |
| JCCMGDGN_7 | 229689 | 258504 | False | Siphoviridae | VOG6048, VOG4707, VOG0641, VOG7896, VOG3390, VOG4612, VOG4660, VOG4619, VOG0801, VOG6163, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5361, VOG4553, VOG4568, VOG4556, VOG1886, VOG4581, VOG1796, VOG0713, VOG0531, VOG0275, VOG0198, VOG5447, VOG1137, VOG4376 |
Phigaro v2.4.0 (Database: Jan. 2024 release)