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. |
|---|---|---|---|---|---|---|---|---|
| PKNAILHA_1 | 2632748 | 2633602 | aadK | ARO:3002627 | aadK | 97.89 | 100.00 | AL009126.1 |
| PKNAILHA_1 | 2614015 | 2615217 | blt | ARO:3003006 | blt | 99.75 | 100.00 | L32599.1 |
| PKNAILHA_1 | 2441353 | 2442522 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| PKNAILHA_1 | 1402436 | 1402753 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| PKNAILHA_1 | 1402098 | 1402436 | ykkC | ARO:3003063 | ykkC | 98.21 | 100.00 | AL009126.1 |
| PKNAILHA_1 | 904367 | 906937 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.65 | 100.00 | AL009126.3 |
| PKNAILHA_1 | 613951 | 615579 | vmlR | ARO:3004476 | vmlR | 98.52 | 99.09 | NC_000964.3 |
| PKNAILHA_1 | 292209 | 293642 | lmrB | ARO:3002813 | lmrB | 98.95 | 100.00 | JYFL01000006.1 |
| PKNAILHA_1 | 279396 | 280316 | 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. |
|---|---|---|---|---|---|---|---|
| PKNAILHA_1 | 4196797 | 4198173 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 99.35 | 100.00 | X08034 |
| PKNAILHA_1 | 2632750 | 2633602 | aadK | Streptomycin | 98.59 | 99.77 | M26879 |
| PKNAILHA_1 | 279396 | 280316 | 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. |
|---|---|---|---|---|---|---|---|---|
| PKNAILHA_1 | 4196800 | 4198173 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 99.13 | 100.00 | WP_003242953.1 |
| PKNAILHA_1 | 613954 | 615579 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.52 | 98.90 | WP_003234144.1 |
| PKNAILHA_1 | 279396 | 280313 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.37 | 100.00 | WP_003246254.1 |
| PKNAILHA_1 | 2632751 | 2633602 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.89 | 100.00 | WP_003229862.1 |
| PKNAILHA_1 | 4194298 | 4194816 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| PKNAILHA_1 | 1994413 | 1997010 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.71 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| PKNAILHA_1 | 3691681 | 3692862 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| PKNAILHA_1 | 3690056 | 3691198 | capA | 0.0 | Capsule | Immune modulation | 99.65 | 100.00 | NP_391469 |
| PKNAILHA_1 | 2242552 | 2243193 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| PKNAILHA_1 | 3233665 | 3234450 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| PKNAILHA_1 | 3691217 | 3691666 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| PKNAILHA_1 | 1945327 | 1947090 | dep/capD | 0.0 | Capsule | Immune modulation | 99.21 | 100.00 | NP_389723 |
| PKNAILHA_1 | 3230795 | 3232414 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.64 | 100.00 | NP_391078 |
| PKNAILHA_1 | 3222673 | 3229809 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.38 | 100.00 | NP_391076 |
| PKNAILHA_1 | 3229829 | 3230767 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.08 | 100.00 | NP_391077 |
| PKNAILHA_1 | 3232443 | 3233639 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.00 | 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 |
|---|---|---|---|---|---|---|---|---|
| PKNAILHA_1 | 132395 | 133531 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| PKNAILHA_1 | 18663 | 19532 | pdxS | 3.14e-149 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| PKNAILHA_1 | 1718183 | 1718959 | CodY | 3.43e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PKNAILHA_1 | 3533674 | 3534243 | ClpP | 2.54e-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 |
|---|---|---|---|
| PKNAILHA_1 | 0.0 | 1.0 | 0.0 |
| PKNAILHA_2 | 0.0 | 1.0 | 0.0 |
| PKNAILHA_3 | 0.0 | 1.0 | 0.0 |
| PKNAILHA_4 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PKNAILHA_1 | 1344844 | 1372615 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG4705 |
| PKNAILHA_1 | 2202380 | 2217183 | False | Unknown | VOG4705, VOG8610, VOG7930, VOG0275, VOG9312, VOG4910, VOG3389, VOG5042 |
| PKNAILHA_1 | 2801043 | 2826788 | False | Myoviridae | VOG0221, VOG6116, VOG6613, VOG4574, VOG0136, VOG0753, VOG4705, VOG3390, VOG7718, VOG4845, VOG4691, VOG4550, VOG0573, VOG1348, VOG1433, VOG1956, VOG6163, VOG4699, VOG1352, VOG1883, VOG1881, VOG1353, VOG4623, VOG4564, VOG4553, VOG4555, VOG0720 |
| PKNAILHA_1 | 3406509 | 3431536 | False | Siphoviridae | VOG4574, VOG0641, VOG4705, VOG3390, VOG4612, VOG4705, VOG3390, VOG4626, VOG4772, VOG0801, VOG5910, VOG0541, VOG4586, VOG0704, VOG9583, VOG4589, VOG5361, VOG8908, VOG4553, VOG4568, VOG4556, VOG3607, VOG1886, VOG4581, VOG0713, VOG4841, VOG0275 |
Phigaro v2.4.0 (Database: Jan. 2024 release)