Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 7 | 17.83 |
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. |
|---|---|---|---|---|---|---|---|---|
| CMJKNIPP_2 | 567958 | 568812 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| CMJKNIPP_2 | 538741 | 539943 | blt | ARO:3003006 | blt | 99.50 | 100.00 | L32599.1 |
| CMJKNIPP_3 | 425485 | 425802 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| CMJKNIPP_3 | 425147 | 425485 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| CMJKNIPP_2 | 365493 | 366662 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| CMJKNIPP_4 | 359333 | 360253 | mphK | ARO:3004541 | mphK | 100.00 | 100.00 | CP010314.1 |
| CMJKNIPP_4 | 346061 | 347500 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.42 | JYFL01000006.1 |
| CMJKNIPP_4 | 296388 | 296981 | tmrB | ARO:3003059 | tmrB | 97.97 | 100.00 | AL009126.3 |
| CMJKNIPP_6 | 27416 | 29986 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 100.00 | AL009126.3 |
| CMJKNIPP_4 | 19096 | 20739 | vmlR | ARO:3004476 | vmlR | 99.45 | 100.00 | NC_000964.3 |
| CMJKNIPP_16 | 259 | 1011 | TEM-116 | ARO:3000979 | TEM-116 | 100.00 | 87.41 | U36911.1 |
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. |
|---|---|---|---|---|---|---|---|
| CMJKNIPP_16 | 259 | 1011 | blaTEM-116 | Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin | 100.00 | 87.46 | AY425988 |
| CMJKNIPP_4 | 359333 | 360253 | mph(K) | Spiramycin, Telithromycin | 99.67 | 100.00 | NC_000964 |
| CMJKNIPP_2 | 567958 | 568812 | aadK | Streptomycin | 98.83 | 100.00 | M26879 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| CMJKNIPP_4 | 359336 | 360253 | mphK | macrolide 2'-phosphotransferase MphK | EXACTX | 100.00 | 100.00 | WP_003246254.1 |
| CMJKNIPP_16 | 262 | 1011 | blaTEM | TEM family class A beta-lactamase | PARTIAL_CONTIG_ENDX | 100.00 | 87.41 | WP_000027050.1 |
| CMJKNIPP_4 | 19096 | 20736 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 99.45 | 100.00 | WP_003234144.1 |
| CMJKNIPP_2 | 567961 | 568812 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| CMJKNIPP_1 | 41549 | 42010 | satA | streptothricin N-acetyltransferase SatA | PARTIALX | 93.51 | 89.02 | WP_003242546.1 |
| CMJKNIPP_2 | 56187 | 58781 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.26 | 99.88 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| CMJKNIPP_2 | 9631 | 11394 | dep/capD | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_389723 |
| CMJKNIPP_1 | 529083 | 530264 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| CMJKNIPP_1 | 937923 | 938861 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.47 | 100.00 | NP_391077 |
| CMJKNIPP_2 | 165922 | 166563 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.38 | 100.00 | NP_390062 |
| CMJKNIPP_1 | 934241 | 935026 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| CMJKNIPP_1 | 530279 | 530728 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| CMJKNIPP_1 | 935052 | 936248 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.25 | 100.00 | NP_391079 |
| CMJKNIPP_1 | 530747 | 531889 | capA | 0.0 | Capsule | Immune modulation | 99.21 | 100.00 | NP_391469 |
| CMJKNIPP_1 | 938881 | 946017 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.99 | 100.00 | NP_391076 |
| CMJKNIPP_1 | 936277 | 937895 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.84 | 99.94 | 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 |
|---|---|---|---|---|---|---|---|---|
| CMJKNIPP_8 | 31748 | 32884 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| CMJKNIPP_12 | 11191 | 10322 | pdxS | 1.11e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| CMJKNIPP_3 | 735505 | 736281 | CodY | 7.54e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| CMJKNIPP_1 | 680665 | 680096 | ClpP | 6.30e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| CMJKNIPP_3 | 276409 | 276801 | spxA1 | 5.92e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| CMJKNIPP_3 | 276409 | 276801 | spx | 3.53e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| CMJKNIPP_9 | 20578 | 20820 | SpoVG | 7.50e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| CMJKNIPP_4 | 68729 | 68532 | CspA | 1.94e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
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 |
|---|---|---|---|
| CMJKNIPP_1 | 0.0 | 1.0 | 0.0 |
| CMJKNIPP_2 | 0.0 | 1.0 | 0.0 |
| CMJKNIPP_3 | 0.0 | 1.0 | 0.0 |
| CMJKNIPP_4 | 0.0 | 1.0 | 0.0 |
| CMJKNIPP_5 | 0.0 | 1.0 | 0.0 |
| CMJKNIPP_6 | 0.0 | 1.0 | 0.0 |
| CMJKNIPP_7 | 0.0 | 1.0 | 0.0 |
| CMJKNIPP_8 | 0.0 | 1.0 | 0.0 |
| CMJKNIPP_9 | 0.0 | 1.0 | 0.0 |
| CMJKNIPP_10 | 0.0 | 1.0 | 0.0 |
| CMJKNIPP_11 | 0.0 | 1.0 | 0.0 |
| CMJKNIPP_12 | 0.0 | 1.0 | 0.0 |
| CMJKNIPP_13 | 0.0 | 1.0 | 0.0 |
| CMJKNIPP_16 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| CMJKNIPP_3 | 369265 | 394928 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG4612, VOG4705 |
Phigaro v2.4.0 (Database: Jan. 2024 release)