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. |
|---|---|---|---|---|---|---|---|---|
| GCJBNFKD_12 | 600385 | 601239 | aadK | ARO:3002627 | aadK | 98.24 | 100.00 | AL009126.1 |
| GCJBNFKD_12 | 574389 | 575591 | blt | ARO:3003006 | blt | 100.00 | 100.00 | L32599.1 |
| GCJBNFKD_16 | 502618 | 502956 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| GCJBNFKD_16 | 502301 | 502618 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| GCJBNFKD_17 | 435190 | 436833 | vmlR | ARO:3004476 | vmlR | 98.72 | 100.00 | NC_000964.3 |
| GCJBNFKD_12 | 377750 | 378919 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| GCJBNFKD_17 | 160114 | 160707 | tmrB | ARO:3003059 | tmrB | 97.46 | 100.00 | AL009126.3 |
| GCJBNFKD_17 | 109555 | 110988 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.00 | JYFL01000006.1 |
| GCJBNFKD_17 | 96740 | 97660 | mphK | ARO:3004541 | mphK | 98.37 | 100.00 | CP010314.1 |
| GCJBNFKD_18 | 27249 | 29819 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 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. |
|---|---|---|---|---|---|---|---|
| GCJBNFKD_1 | 1021547 | 1022923 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 99.42 | 100.00 | D12567 |
| GCJBNFKD_12 | 600387 | 601239 | aadK | Streptomycin | 98.71 | 99.77 | M26879 |
| GCJBNFKD_17 | 96740 | 97660 | mph(K) | Spiramycin, Telithromycin | 97.94 | 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. |
|---|---|---|---|---|---|---|---|---|
| GCJBNFKD_1 | 1021550 | 1022923 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 99.56 | 100.00 | WP_063856081.1 |
| GCJBNFKD_17 | 435193 | 436833 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.72 | 100.00 | WP_003234144.1 |
| GCJBNFKD_17 | 96740 | 97657 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.37 | 100.00 | WP_003246254.1 |
| GCJBNFKD_12 | 600388 | 601239 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.24 | 100.00 | WP_003229862.1 |
| GCJBNFKD_1 | 1019030 | 1019548 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 91.91 | 100.00 | WP_003242546.1 |
| GCJBNFKD_12 | 69911 | 72508 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.60 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| GCJBNFKD_1 | 529556 | 530698 | capA | 0.0 | Capsule | Immune modulation | 99.83 | 100.00 | NP_391469 |
| GCJBNFKD_12 | 171285 | 171926 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.69 | 100.00 | NP_390062 |
| GCJBNFKD_1 | 531181 | 532362 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| GCJBNFKD_1 | 109056 | 109994 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.57 | 100.00 | NP_391077 |
| GCJBNFKD_1 | 530717 | 531166 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| GCJBNFKD_1 | 111670 | 112866 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.33 | 100.00 | NP_391079 |
| GCJBNFKD_1 | 101906 | 109036 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.22 | 99.99 | NP_391076 |
| GCJBNFKD_12 | 24563 | 26326 | dep/capD | 0.0 | Capsule | Immune modulation | 99.21 | 100.00 | NP_389723 |
| GCJBNFKD_1 | 112892 | 113677 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.98 | 100.00 | NP_391080 |
| GCJBNFKD_1 | 110022 | 111641 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.33 | 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 |
|---|---|---|---|---|---|---|---|---|
| GCJBNFKD_20 | 27920 | 26784 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| GCJBNFKD_2 | 4229 | 5098 | pdxS | 1.10e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| GCJBNFKD_16 | 192433 | 191657 | CodY | 7.54e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| GCJBNFKD_1 | 374678 | 375247 | ClpP | 6.37e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| GCJBNFKD_16 | 653307 | 652915 | spxA1 | 5.93e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| GCJBNFKD_16 | 653307 | 652915 | spx | 3.53e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| GCJBNFKD_21 | 34636 | 34394 | SpoVG | 7.48e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| GCJBNFKD_17 | 379947 | 380144 | CspA | 2.01e-31 | 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 |
|---|---|---|---|
| GCJBNFKD_1 | 0.0 | 1.0 | 0.0 |
| GCJBNFKD_2 | 0.0 | 1.0 | 0.0 |
| GCJBNFKD_3 | 0.0 | 1.0 | 0.0 |
| GCJBNFKD_12 | 0.0 | 1.0 | 0.0 |
| GCJBNFKD_16 | 0.0 | 1.0 | 0.0 |
| GCJBNFKD_17 | 0.0 | 1.0 | 0.0 |
| GCJBNFKD_18 | 0.0 | 1.0 | 0.0 |
| GCJBNFKD_19 | 0.0 | 1.0 | 0.0 |
| GCJBNFKD_20 | 0.0 | 1.0 | 0.0 |
| GCJBNFKD_21 | 0.0 | 1.0 | 0.0 |
| GCJBNFKD_22 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| GCJBNFKD_16 | 532445 | 558776 | False | Myoviridae | VOG0753, VOG4705, VOG3390, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
| GCJBNFKD_18 | 280698 | 306776 | False | Siphoviridae | VOG5417, VOG3490, VOG9667, VOG6495, VOG2703, VOG4574, VOG0136, VOG0753, VOG4728, VOG5535, VOG4599, VOG4605, VOG9745, VOG0701, VOG10044, VOG0698, VOG0697, VOG0696, VOG0695, VOG2621, VOG4572, VOG9317, VOG0692, VOG0691, VOG10227, VOG0796, VOG7983, VOG0198 |
| GCJBNFKD_18 | 316314 | 319936 | False | Siphoviridae | VOG4552, VOG0650, VOG9667, VOG9667, VOG4662 |
Phigaro v2.4.0 (Database: Jan. 2024 release)