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. |
|---|---|---|---|---|---|---|---|---|
| PNLIMCFI_1 | 779400 | 779738 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| PNLIMCFI_1 | 779083 | 779400 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| PNLIMCFI_22 | 615707 | 616561 | aadK | ARO:3002627 | aadK | 97.89 | 100.00 | AL009126.1 |
| PNLIMCFI_22 | 586124 | 587326 | blt | ARO:3003006 | blt | 99.75 | 100.00 | L32599.1 |
| PNLIMCFI_22 | 356654 | 357823 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| PNLIMCFI_23 | 297009 | 299579 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 100.00 | AL009126.3 |
| PNLIMCFI_24 | 191509 | 193137 | vmlR | ARO:3004476 | vmlR | 98.52 | 99.09 | NC_000964.3 |
| PNLIMCFI_25 | 109988 | 110908 | mphK | ARO:3004541 | mphK | 98.68 | 100.00 | CP010314.1 |
| PNLIMCFI_25 | 96652 | 98091 | lmrB | ARO:3002813 | lmrB | 99.79 | 100.42 | JYFL01000006.1 |
| PNLIMCFI_25 | 46949 | 47542 | tmrB | ARO:3003059 | tmrB | 97.46 | 100.00 | AL009126.3 |
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. |
|---|---|---|---|---|---|---|---|
| PNLIMCFI_25 | 109988 | 110908 | mph(K) | Spiramycin, Telithromycin | 99.02 | 100.00 | NC_000964 |
| PNLIMCFI_22 | 615707 | 616561 | aadK | Streptomycin | 98.60 | 100.00 | M26879 |
| PNLIMCFI_12 | 1022760 | 1024136 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 98.47 | 100.00 | D12567 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| PNLIMCFI_12 | 1022763 | 1024136 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.69 | 100.00 | WP_063856081.1 |
| PNLIMCFI_25 | 110000 | 110908 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.68 | 99.02 | WP_003246254.1 |
| PNLIMCFI_24 | 191512 | 193137 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.52 | 98.90 | WP_003234144.1 |
| PNLIMCFI_22 | 615710 | 616561 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.89 | 100.00 | WP_003229862.1 |
| PNLIMCFI_12 | 1020210 | 1020728 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.75 | 100.00 | WP_003242546.1 |
| PNLIMCFI_22 | 57718 | 60315 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| PNLIMCFI_12 | 109350 | 110288 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.89 | 100.00 | NP_391077 |
| PNLIMCFI_12 | 525044 | 526225 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| PNLIMCFI_12 | 110316 | 111935 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.69 | 100.00 | NP_391078 |
| PNLIMCFI_22 | 156466 | 157107 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| PNLIMCFI_12 | 102194 | 109330 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.41 | 100.00 | NP_391076 |
| PNLIMCFI_12 | 111964 | 113160 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.33 | 100.00 | NP_391079 |
| PNLIMCFI_12 | 523419 | 524561 | capA | 0.0 | Capsule | Immune modulation | 99.30 | 100.00 | NP_391469 |
| PNLIMCFI_12 | 524580 | 525029 | capC | 0.0 | Capsule | Immune modulation | 99.11 | 100.00 | NP_391470 |
| PNLIMCFI_12 | 113186 | 113971 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.86 | 100.00 | NP_391080 |
| PNLIMCFI_22 | 8419 | 10182 | dep/capD | 0.0 | Capsule | Immune modulation | 98.75 | 100.00 | NP_389723 |
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 |
|---|---|---|---|---|---|---|---|---|
| PNLIMCFI_26 | 31635 | 32771 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| PNLIMCFI_28 | 4231 | 5100 | pdxS | 1.10e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| PNLIMCFI_1 | 466015 | 465239 | CodY | 9.80e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PNLIMCFI_12 | 368257 | 368826 | ClpP | 6.38e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| PNLIMCFI_1 | 934279 | 933887 | spxA1 | 7.70e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| PNLIMCFI_1 | 934279 | 933887 | spx | 4.60e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| PNLIMCFI_27 | 20482 | 20724 | SpoVG | 7.48e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| PNLIMCFI_24 | 138425 | 138622 | CspA | 9.59e-32 | 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 |
|---|---|---|---|
| PNLIMCFI_1 | 0.0 | 1.0 | 0.0 |
| PNLIMCFI_2 | 0.0 | 1.0 | 0.0 |
| PNLIMCFI_3 | 0.0 | 1.0 | 0.0 |
| PNLIMCFI_4 | 0.0 | 1.0 | 0.0 |
| PNLIMCFI_12 | 0.0 | 1.0 | 0.0 |
| PNLIMCFI_22 | 0.0 | 1.0 | 0.0 |
| PNLIMCFI_23 | 0.0 | 1.0 | 0.0 |
| PNLIMCFI_24 | 0.0 | 1.0 | 0.0 |
| PNLIMCFI_25 | 0.0 | 1.0 | 0.0 |
| PNLIMCFI_26 | 0.0 | 1.0 | 0.0 |
| PNLIMCFI_27 | 0.0 | 1.0 | 0.0 |
| PNLIMCFI_28 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PNLIMCFI_1 | 104017 | 127137 | False | Siphoviridae | VOG1659, VOG4574, VOG0136, VOG5221, VOG4705, VOG3390, VOG4612, VOG4705, VOG3390, VOG4626, VOG4619, VOG0801, VOG6163, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5361, VOG4553, VOG4568, VOG4556, VOG1886, VOG4581, VOG4841 |
| PNLIMCFI_1 | 178646 | 184201 | False | Unknown | VOG4551, VOG0025, VOG7476, VOG0322, VOG6211 |
| PNLIMCFI_1 | 245630 | 260989 | False | Unknown | VOG9312, VOG4910, VOG3389, VOG5042, VOG9712 |
| PNLIMCFI_1 | 809671 | 837166 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
| PNLIMCFI_22 | 534226 | 557075 | False | Myoviridae | VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG2381, VOG4688, VOG4773 |
| PNLIMCFI_23 | 13172 | 22093 | False | Myoviridae / Siphoviridae | VOG4602, VOG8483, VOG9667, VOG9667, VOG0650, VOG4552, VOG4600, VOG1309, VOG5263, VOG0189 |
| PNLIMCFI_23 | 28586 | 57993 | False | Siphoviridae | VOG4681, VOG0796, VOG10227, VOG0720, VOG4564, VOG4555, VOG4553, VOG1125, VOG0815, VOG4623, VOG0816, VOG5660, VOG0724, VOG0799, VOG2621, VOG0725, VOG4545, VOG4605, VOG4599, VOG5535, VOG4728, VOG0753, VOG0136, VOG4574, VOG1993, VOG2703, VOG9953, VOG3477 |
Phigaro v2.4.0 (Database: Jan. 2024 release)