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. |
|---|---|---|---|---|---|---|---|---|
| CJPGDABB_1 | 502836 | 503174 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| CJPGDABB_1 | 502519 | 502836 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| CJPGDABB_5 | 271322 | 273892 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| CJPGDABB_6 | 263998 | 264852 | aadK | ARO:3002627 | aadK | 98.94 | 100.00 | AL009126.1 |
| CJPGDABB_6 | 245372 | 246574 | blt | ARO:3003006 | blt | 100.00 | 100.00 | L32599.1 |
| CJPGDABB_4 | 153146 | 153739 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| CJPGDABB_4 | 102590 | 104029 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.42 | JYFL01000006.1 |
| CJPGDABB_4 | 89773 | 90693 | mphK | ARO:3004541 | mphK | 99.35 | 100.00 | CP010314.1 |
| CJPGDABB_8 | 29189 | 30835 | vmlR | ARO:3004476 | vmlR | 97.99 | 100.18 | NC_000964.3 |
| CJPGDABB_6 | 20386 | 21555 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
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. |
|---|---|---|---|---|---|---|---|
| CJPGDABB_4 | 89773 | 90693 | mph(K) | Spiramycin, Telithromycin | 99.24 | 100.00 | NC_000964 |
| CJPGDABB_2 | 36908 | 38284 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 99.06 | 100.00 | D12567 |
| CJPGDABB_6 | 264000 | 264852 | aadK | Streptomycin | 98.83 | 99.77 | 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. |
|---|---|---|---|---|---|---|---|---|
| CJPGDABB_4 | 89773 | 90690 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 99.35 | 100.00 | WP_003246254.1 |
| CJPGDABB_6 | 264001 | 264852 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.94 | 100.00 | WP_003229862.1 |
| CJPGDABB_2 | 36908 | 38281 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.69 | 100.00 | WP_063856081.1 |
| CJPGDABB_8 | 29189 | 30832 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 97.99 | 100.00 | WP_003234144.1 |
| CJPGDABB_2 | 40252 | 40770 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| CJPGDABB_3 | 154080 | 156677 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.83 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| CJPGDABB_2 | 985295 | 986233 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391077 |
| CJPGDABB_2 | 983648 | 985267 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391078 |
| CJPGDABB_3 | 263929 | 264570 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 100.00 | 100.00 | NP_390062 |
| CJPGDABB_2 | 982423 | 983619 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.67 | 100.00 | NP_391079 |
| CJPGDABB_2 | 534210 | 535391 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| CJPGDABB_2 | 535874 | 537016 | capA | 0.0 | Capsule | Immune modulation | 99.65 | 100.00 | NP_391469 |
| CJPGDABB_2 | 981612 | 982397 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| CJPGDABB_2 | 535406 | 535855 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| CJPGDABB_3 | 103990 | 105753 | dep/capD | 0.0 | Capsule | Immune modulation | 99.26 | 100.00 | NP_389723 |
| CJPGDABB_2 | 986253 | 993389 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.92 | 100.00 | NP_391076 |
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 |
|---|---|---|---|---|---|---|---|---|
| CJPGDABB_12 | 31854 | 32990 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| CJPGDABB_15 | 11387 | 10518 | pdxS | 1.13e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| CJPGDABB_1 | 193052 | 192276 | CodY | 7.61e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| CJPGDABB_2 | 689860 | 689291 | ClpP | 6.49e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| CJPGDABB_1 | 662253 | 661861 | spxA1 | 5.98e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| CJPGDABB_1 | 662253 | 661861 | spx | 3.57e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| CJPGDABB_13 | 34790 | 34548 | SpoVG | 7.53e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| CJPGDABB_8 | 78879 | 78682 | CspA | 9.36e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| CJPGDABB_3 | 276532 | 276726 | CspD | 2.80e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
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 |
|---|---|---|---|
| CJPGDABB_1 | 0.0 | 1.0 | 0.0 |
| CJPGDABB_2 | 0.0 | 1.0 | 0.0 |
| CJPGDABB_3 | 0.0 | 1.0 | 0.0 |
| CJPGDABB_4 | 0.0 | 1.0 | 0.0 |
| CJPGDABB_5 | 0.0 | 1.0 | 0.0 |
| CJPGDABB_6 | 0.0 | 1.0 | 0.0 |
| CJPGDABB_7 | 0.0 | 1.0 | 0.0 |
| CJPGDABB_8 | 0.0 | 1.0 | 0.0 |
| CJPGDABB_9 | 0.0 | 1.0 | 0.0 |
| CJPGDABB_10 | 1.0 | 0.0 | 1.0 |
| CJPGDABB_11 | 1.0 | 0.0 | 1.0 |
| CJPGDABB_12 | 0.0 | 1.0 | 0.0 |
| CJPGDABB_13 | 0.0 | 1.0 | 0.0 |
| CJPGDABB_15 | 0.0 | 1.0 | 0.0 |
| CJPGDABB_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 |
|---|---|---|---|---|---|
| CJPGDABB_1 | 532665 | 559149 | False | Myoviridae | VOG0753, VOG4705, VOG4612, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
| CJPGDABB_2 | 878379 | 910353 | False | Siphoviridae | VOG4602, VOG9667, VOG5353, VOG0181, VOG0549, VOG0550, VOG5651, VOG1638, VOG4552, VOG11060, VOG9600, VOG0025, VOG1884, VOG0198, VOG4841, VOG4581, VOG1886, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG4705, VOG5221 |
| CJPGDABB_6 | 198563 | 228412 | False | Myoviridae | VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG9315, VOG0796, VOG4673, VOG4693, VOG0189, VOG11060, VOG1309 |
| CJPGDABB_7 | 3975 | 10068 | False | Siphoviridae | VOG8241, VOG4552, VOG4603, VOG4600, VOG1309, VOG4566 |
| CJPGDABB_7 | 19844 | 40897 | False | Siphoviridae | VOG0796, VOG0720, VOG4564, VOG1183, VOG4555, VOG1329, VOG3480, VOG4623, VOG0816, VOG5660, VOG0724, VOG0799, VOG0725, VOG1323, VOG4545, VOG4605, VOG4599, VOG5535, VOG0753 |
Phigaro v2.4.0 (Database: Jan. 2024 release)