Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 8 | 18.25 |
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. |
|---|---|---|---|---|---|---|---|---|
| DNFCPGEP_1 | 288969 | 289823 | aadK | ARO:3002627 | aadK | 88.38 | 100.00 | AL009126.1 |
| DNFCPGEP_11 | 113810 | 114127 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| DNFCPGEP_11 | 113472 | 113810 | ykkC | ARO:3003063 | ykkC | 97.32 | 100.00 | AL009126.1 |
| DNFCPGEP_1 | 80764 | 81933 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| DNFCPGEP_7 | 48044 | 49483 | lmrB | ARO:3002813 | lmrB | 98.74 | 100.42 | JYFL01000006.1 |
| DNFCPGEP_13 | 29431 | 31077 | vmlR | ARO:3004476 | vmlR | 98.54 | 100.18 | NC_000964.3 |
| DNFCPGEP_43 | 12447 | 13649 | blt | ARO:3003006 | blt | 99.50 | 100.00 | L32599.1 |
| DNFCPGEP_35 | 7859 | 8713 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| DNFCPGEP_7 | 1048 | 1641 | tmrB | ARO:3003059 | tmrB | 96.95 | 100.00 | AL009126.3 |
| DNFCPGEP_47 | 128 | 2698 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.65 | 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. |
|---|---|---|---|---|---|---|---|
| DNFCPGEP_10 | 79942 | 81318 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 99.35 | 100.00 | X08034 |
| DNFCPGEP_35 | 7859 | 8713 | aadK | Streptomycin | 98.83 | 100.00 | M26879 |
| DNFCPGEP_7 | 74837 | 75756 | mph(K) | Spiramycin, Telithromycin | 97.83 | 99.89 | 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. |
|---|---|---|---|---|---|---|---|---|
| DNFCPGEP_10 | 79945 | 81318 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 99.13 | 100.00 | WP_003242953.1 |
| DNFCPGEP_35 | 7862 | 8713 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| DNFCPGEP_13 | 29431 | 31074 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.54 | 100.00 | WP_003234144.1 |
| DNFCPGEP_10 | 77443 | 77961 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| DNFCPGEP_1 | 288972 | 289823 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 88.38 | 100.00 | WP_003229862.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| DNFCPGEP_12 | 99770 | 100708 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.68 | 100.00 | NP_391077 |
| DNFCPGEP_12 | 103595 | 104380 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.62 | 100.00 | NP_391080 |
| DNFCPGEP_38 | 2871 | 3320 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| DNFCPGEP_24 | 33652 | 34293 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| DNFCPGEP_38 | 3335 | 4516 | capB | 0.0 | Capsule | Immune modulation | 99.41 | 100.00 | NP_391471 |
| DNFCPGEP_38 | 1710 | 2852 | capA | 0.0 | Capsule | Immune modulation | 99.30 | 100.00 | NP_391469 |
| DNFCPGEP_5 | 59134 | 60897 | dep/capD | 0.0 | Capsule | Immune modulation | 99.15 | 100.00 | NP_389723 |
| DNFCPGEP_12 | 92614 | 99750 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.95 | 100.00 | NP_391076 |
| DNFCPGEP_12 | 102373 | 103569 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.58 | 100.00 | NP_391079 |
| DNFCPGEP_12 | 100736 | 102355 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.84 | 100.00 | 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 |
|---|---|---|---|---|---|---|---|---|
| DNFCPGEP_26 | 31767 | 32903 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| DNFCPGEP_48 | 4418 | 5287 | pdxS | 1.13e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| DNFCPGEP_3 | 196813 | 196037 | CodY | 1.75e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| DNFCPGEP_4 | 153612 | 153043 | ClpP | 1.24e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| DNFCPGEP_20 | 52973 | 53365 | spxA1 | 5.22e-71 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| DNFCPGEP_20 | 52973 | 53365 | spx | 3.11e-69 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| DNFCPGEP_29 | 20633 | 20875 | SpoVG | 7.52e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| DNFCPGEP_13 | 83352 | 83155 | CspA | 4.53e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| DNFCPGEP_24 | 22419 | 22225 | CspD | 1.72e-28 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| DNFCPGEP_24 | 22419 | 22222 | CspB | 3.56e-28 | cold shock protein | 80.30 | 100.00 | CAD00094 |
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 |
|---|---|---|---|
| DNFCPGEP_1 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_2 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_3 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_4 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_5 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_6 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_7 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_8 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_9 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_10 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_11 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_12 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_13 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_14 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_15 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_16 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_17 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_18 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_19 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_20 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_21 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_22 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_23 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_24 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_25 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_26 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_27 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_28 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_29 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_30 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_31 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_32 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_33 | 1.0 | 0.0 | 1.0 |
| DNFCPGEP_34 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_35 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_36 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_37 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_38 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_39 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_40 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_41 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_42 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_43 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_44 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_45 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_46 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_47 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_48 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_49 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_50 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_51 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_52 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_53 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_54 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_56 | 1.0 | 0.0 | 1.0 |
| DNFCPGEP_57 | 0.0 | 1.0 | 0.0 |
| DNFCPGEP_58 | 1.0 | 0.0 | 1.0 |
| DNFCPGEP_60 | 1.0 | 0.0 | 1.0 |
| DNFCPGEP_61 | 1.0 | 0.0 | 1.0 |
| DNFCPGEP_62 | 1.0 | 0.0 | 1.0 |
| DNFCPGEP_63 | 1.0 | 0.0 | 1.0 |
| DNFCPGEP_64 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| DNFCPGEP_1 | 252665 | 277964 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG10227, VOG0796, VOG7060 |
| DNFCPGEP_3 | 56652 | 77406 | False | Siphoviridae | VOG8610, VOG7930, VOG0275, VOG4662, VOG9312, VOG4910, VOG3389, VOG5042, VOG9712, VOG7900, VOG10230 |
| DNFCPGEP_5 | 119600 | 141270 | False | Siphoviridae | VOG0136, VOG5221, VOG4705, VOG3390, VOG4612, VOG4626, VOG4619, VOG0801, VOG6163, VOG0541, VOG4586, VOG0704, VOG5660, VOG4589, VOG0204, VOG4553, VOG4568, VOG4556, VOG4544, VOG0519, VOG6154 |
| DNFCPGEP_11 | 56199 | 83608 | 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 |
Phigaro v2.4.0 (Database: Jan. 2024 release)