Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 4 | 10 | 6 | 12.33 |
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. |
|---|---|---|---|---|---|---|---|---|
| NEJECHEI_2 | 702093 | 703718 | vmlR | ARO:3004476 | vmlR | 94.82 | 98.90 | NC_000964.3 |
| NEJECHEI_1 | 111638 | 111976 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
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. |
|---|---|---|---|---|---|---|---|
| NEJECHEI_2 | 971690 | 972612 | mph(K) | Spiramycin, Telithromycin | 97.72 | 100.00 | NC_000964 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| NEJECHEI_2 | 702093 | 703715 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 94.82 | 98.90 | WP_003234144.1 |
| NEJECHEI_2 | 1272985 | 1273356 | satA | streptothricin N-acetyltransferase SatA | PARTIALX | 91.13 | 71.68 | WP_003242546.1 |
| NEJECHEI_2 | 971904 | 972455 | mphK | macrolide 2'-phosphotransferase MphK | PARTIALX | 96.74 | 60.13 | WP_003246254.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| NEJECHEI_7 | 300516 | 301699 | capB | 0.0 | Capsule | Immune modulation | 99.49 | 100.00 | NP_391471 |
| NEJECHEI_3 | 660741 | 661383 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.07 | 100.00 | NP_390062 |
| NEJECHEI_7 | 748144 | 749083 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.94 | 100.00 | NP_391077 |
| NEJECHEI_5 | 280935 | 282700 | dep/capD | 0.0 | Capsule | Immune modulation | 98.92 | 100.00 | NP_389723 |
| NEJECHEI_7 | 302183 | 303325 | capA | 0.0 | Capsule | Immune modulation | 98.78 | 100.00 | NP_391469 |
| NEJECHEI_7 | 301714 | 302164 | capC | 0.0 | Capsule | Immune modulation | 98.67 | 100.00 | NP_391470 |
| NEJECHEI_7 | 744461 | 745249 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.61 | 99.87 | NP_391080 |
| NEJECHEI_7 | 745275 | 746471 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.25 | 100.00 | NP_391079 |
| NEJECHEI_7 | 749103 | 756244 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.93 | 99.96 | NP_391076 |
| NEJECHEI_7 | 746489 | 748116 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.67 | 100.19 | NP_391078 |
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 |
|---|---|---|---|---|---|---|---|---|
| NEJECHEI_2 | 1221342 | 1220692 | pdxS | 5.46e-128 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 86.64 | 73.56 | ACE61268 |
| NEJECHEI_5 | 35815 | 36591 | CodY | 2.38e-124 | nutrient-responsive regulator | 80.69 | 100.00 | ACJ80679 |
| NEJECHEI_2 | 107397 | 107005 | spxA1 | 6.57e-69 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| NEJECHEI_2 | 1184448 | 1184206 | SpoVG | 1.96e-37 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| NEJECHEI_2 | 726411 | 726214 | CspA | 6.23e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| NEJECHEI_3 | 649500 | 649306 | CspD | 4.82e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| NEJECHEI_2 | 1112821 | 1112012 | tufA | 2.78e-164 | elongation factor Tu | 86.30 | 68.27 | AHM69299 |
BLASTX v2.16.0 (Database: PHI base v4.16, May. 2024 release)
Plasmid
PlasmidFinder
| Query ID | Begin | End | Plasmid | Query / Template | Identity | Accession no. |
|---|---|---|---|---|---|---|
| NEJECHEI_4 | 2997 | 3164 | Col(SD853) | 168 / 194 | 86.90 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| NEJECHEI_1 | 0.0 | 1.0 | 0.0 |
| NEJECHEI_2 | 0.0 | 1.0 | 0.0 |
| NEJECHEI_3 | 0.0 | 1.0 | 0.0 |
| NEJECHEI_4 | 1.0 | 0.0 | 1.0 |
| NEJECHEI_5 | 0.0 | 1.0 | 0.0 |
| NEJECHEI_6 | 1.0 | 0.0 | 1.0 |
| NEJECHEI_7 | 0.0 | 1.0 | 0.0 |
| NEJECHEI_8 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| NEJECHEI_1 | 58006 | 78132 | False | Myoviridae | VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG0796, VOG9315, VOG10227, VOG4773, VOG4685, VOG4685, VOG0749, VOG0749, VOG10055, VOG3890, VOG3890, VOG3890, VOG3890, VOG3890, VOG3891, VOG3891, VOG3892, VOG9745, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4691 |
| NEJECHEI_2 | 2156 | 28887 | False | Siphoviridae | VOG7531, VOG0705, VOG0705, VOG6116, VOG6116, VOG8440, VOG0602, VOG4574, VOG0753, VOG4705, VOG4612, VOG4660, VOG4660, VOG4619, VOG4619, VOG0801, VOG0801, VOG6163, VOG6163, VOG4545, VOG6957, VOG4545, VOG0541, VOG4586, VOG0539, VOG4589, VOG0204, VOG5601, VOG4553, VOG4741, VOG4573, VOG4556, VOG4556, VOG1886, VOG4581, VOG4841, VOG0531, VOG2788 |
| NEJECHEI_5 | 241390 | 260279 | False | Siphoviridae | VOG0641, VOG0641, VOG3390, VOG4612, VOG4612, VOG4660, VOG4660, VOG4660, VOG4660, VOG4660, VOG4660, VOG4619, VOG4772, VOG0801, VOG5793, VOG5910, VOG0541, VOG4586, VOG0704, VOG1266, VOG0204, VOG4599, VOG4553, VOG4568, VOG4556, VOG4556, VOG1886 |
| NEJECHEI_5 | 272796 | 278017 | False | Siphoviridae | VOG6587, VOG6931, VOG0189, VOG0189, VOG4566, VOG0181, VOG9667, VOG9667, VOG1563 |
| NEJECHEI_7 | 643989 | 674310 | False | Siphoviridae | VOG0181, VOG4556, VOG0787, VOG1638, VOG4552, VOG4566, VOG9600, VOG0025, VOG0025, VOG0198, VOG4841, VOG4581, VOG4544, VOG3644, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0704, VOG4586, VOG0541, VOG5910, VOG4545, VOG6163, VOG0801, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG4705 |
Phigaro v2.4.0 (Database: Jan. 2024 release)