Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 4 | 16.12 |
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. |
|---|---|---|---|---|---|---|---|---|
| PKPNCMNO_1 | 2524262 | 2525116 | aadK | ARO:3002627 | aadK | 98.94 | 100.00 | AL009126.1 |
| PKPNCMNO_1 | 2505518 | 2506720 | blt | ARO:3003006 | blt | 99.75 | 100.00 | L32599.1 |
| PKPNCMNO_1 | 2332281 | 2333450 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| PKPNCMNO_1 | 1289630 | 1289947 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| PKPNCMNO_1 | 1289292 | 1289630 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| PKPNCMNO_1 | 824144 | 826714 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.65 | 100.00 | AL009126.3 |
| PKPNCMNO_1 | 530447 | 532090 | vmlR | ARO:3004476 | vmlR | 98.90 | 100.00 | NC_000964.3 |
| PKPNCMNO_1 | 235881 | 237314 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.00 | JYFL01000006.1 |
| PKPNCMNO_1 | 223065 | 223985 | mphK | ARO:3004541 | mphK | 98.37 | 100.00 | CP010314.1 |
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. |
|---|---|---|---|---|---|---|---|
| PKPNCMNO_1 | 4020909 | 4022285 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 99.85 | 100.00 | X08034 |
| PKPNCMNO_1 | 2524264 | 2525116 | aadK | Streptomycin | 98.83 | 99.77 | M26879 |
| PKPNCMNO_1 | 223065 | 223985 | mph(K) | Spiramycin, Telithromycin | 98.05 | 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. |
|---|---|---|---|---|---|---|---|---|
| PKPNCMNO_1 | 4020912 | 4022285 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 99.56 | 100.00 | WP_003242953.1 |
| PKPNCMNO_1 | 2524265 | 2525116 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.94 | 100.00 | WP_003229862.1 |
| PKPNCMNO_1 | 530450 | 532090 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.90 | 100.00 | WP_003234144.1 |
| PKPNCMNO_1 | 223065 | 223982 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.37 | 100.00 | WP_003246254.1 |
| PKPNCMNO_1 | 4018403 | 4018921 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 91.33 | 100.00 | WP_003242546.1 |
| PKPNCMNO_1 | 2024961 | 2027558 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.94 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| PKPNCMNO_1 | 2132691 | 2133332 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 100.00 | 100.00 | NP_390062 |
| PKPNCMNO_1 | 3114029 | 3114967 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.89 | 100.00 | NP_391077 |
| PKPNCMNO_1 | 3114995 | 3116614 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.81 | 100.00 | NP_391078 |
| PKPNCMNO_1 | 3529227 | 3530408 | capB | 0.0 | Capsule | Immune modulation | 99.58 | 100.00 | NP_391471 |
| PKPNCMNO_1 | 3528763 | 3529212 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| PKPNCMNO_1 | 3527602 | 3528744 | capA | 0.0 | Capsule | Immune modulation | 99.39 | 100.00 | NP_391469 |
| PKPNCMNO_1 | 3117865 | 3118650 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| PKPNCMNO_1 | 1974428 | 1976191 | dep/capD | 0.0 | Capsule | Immune modulation | 99.26 | 100.00 | NP_389723 |
| PKPNCMNO_1 | 3106873 | 3114009 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.08 | 100.00 | NP_391076 |
| PKPNCMNO_1 | 3116643 | 3117839 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.00 | 100.00 | NP_391079 |
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 |
|---|---|---|---|---|---|---|---|---|
| PKPNCMNO_1 | 107599 | 108735 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| PKPNCMNO_1 | 8943 | 9812 | pdxS | 3.01e-149 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| PKPNCMNO_1 | 1631337 | 1632113 | CodY | 3.29e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PKPNCMNO_1 | 3373700 | 3374269 | ClpP | 2.44e-98 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
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 |
|---|---|---|---|
| PKPNCMNO_1 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PKPNCMNO_1 | 1233319 | 1259802 | 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 |
| PKPNCMNO_1 | 2981048 | 3004890 | False | Siphoviridae | VOG4574, VOG0136, VOG0753, VOG4728, VOG5535, VOG4599, VOG4605, VOG4545, VOG1323, VOG0725, VOG2621, VOG0799, VOG0724, VOG5660, VOG0816, VOG4623, VOG3480, VOG1329, VOG4555, VOG4564, VOG0720, VOG0796 |
Phigaro v2.4.0 (Database: Jan. 2024 release)