Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 11 | 10 | 7 | 16.43 |
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. |
|---|---|---|---|---|---|---|---|---|
| GCCNJMJA_1 | 1634383 | 1634721 | ykkC | ARO:3003063 | ykkC | 99.11 | 100.00 | AL009126.1 |
| GCCNJMJA_1 | 1634066 | 1634383 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| GCCNJMJA_1 | 642623 | 643792 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| GCCNJMJA_1 | 444200 | 445402 | blt | ARO:3003006 | blt | 99.50 | 100.00 | L32599.1 |
| GCCNJMJA_1 | 427450 | 428304 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| GCCNJMJA_3 | 399156 | 400802 | vmlR | ARO:3004476 | vmlR | 98.54 | 100.18 | NC_000964.3 |
| GCCNJMJA_3 | 153866 | 154459 | tmrB | ARO:3003059 | tmrB | 97.97 | 100.00 | AL009126.3 |
| GCCNJMJA_3 | 103311 | 104750 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| GCCNJMJA_3 | 90490 | 91410 | mphK | ARO:3004541 | mphK | 99.02 | 100.00 | CP010314.1 |
| GCCNJMJA_4 | 27451 | 30021 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.53 | 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. |
|---|---|---|---|---|---|---|---|
| GCCNJMJA_3 | 90490 | 91410 | mph(K) | Spiramycin, Telithromycin | 99.35 | 100.00 | NC_000964 |
| GCCNJMJA_1 | 427450 | 428304 | aadK | Streptomycin | 98.71 | 100.00 | 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. |
|---|---|---|---|---|---|---|---|---|
| GCCNJMJA_3 | 90490 | 91407 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 99.02 | 100.00 | WP_003246254.1 |
| GCCNJMJA_1 | 427450 | 428301 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| GCCNJMJA_3 | 399159 | 400802 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.54 | 100.00 | WP_003234144.1 |
| GCCNJMJA_1 | 951717 | 954314 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| GCCNJMJA_1 | 844077 | 844718 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.84 | 100.00 | NP_390062 |
| GCCNJMJA_2 | 551477 | 552658 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| GCCNJMJA_2 | 1000914 | 1001699 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| GCCNJMJA_1 | 998323 | 1000086 | dep/capD | 0.0 | Capsule | Immune modulation | 99.32 | 100.00 | NP_389723 |
| GCCNJMJA_2 | 1001725 | 1002921 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.08 | 100.00 | NP_391079 |
| GCCNJMJA_2 | 553141 | 554283 | capA | 0.0 | Capsule | Immune modulation | 99.04 | 100.00 | NP_391469 |
| GCCNJMJA_2 | 1004597 | 1005535 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.04 | 100.00 | NP_391077 |
| GCCNJMJA_2 | 552673 | 553122 | capC | 0.0 | Capsule | Immune modulation | 98.44 | 100.00 | NP_391470 |
| GCCNJMJA_2 | 1005555 | 1012691 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.33 | 100.00 | NP_391076 |
| GCCNJMJA_2 | 1002950 | 1004569 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 96.61 | 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 |
|---|---|---|---|---|---|---|---|---|
| GCCNJMJA_5 | 31787 | 32923 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| GCCNJMJA_7 | 11248 | 10379 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| GCCNJMJA_1 | 1322776 | 1322000 | CodY | 1.68e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| GCCNJMJA_2 | 698391 | 697822 | ClpP | 6.70e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| GCCNJMJA_1 | 1793092 | 1792700 | spxA1 | 1.32e-69 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| GCCNJMJA_1 | 1793092 | 1792700 | spx | 7.88e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| GCCNJMJA_6 | 34705 | 34463 | SpoVG | 1.11e-38 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| GCCNJMJA_3 | 358368 | 358565 | CspA | 1.86e-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 |
|---|---|---|---|
| GCCNJMJA_1 | 0.0 | 1.0 | 0.0 |
| GCCNJMJA_2 | 0.0 | 1.0 | 0.0 |
| GCCNJMJA_3 | 0.0 | 1.0 | 0.0 |
| GCCNJMJA_4 | 0.0 | 1.0 | 0.0 |
| GCCNJMJA_5 | 0.0 | 1.0 | 0.0 |
| GCCNJMJA_6 | 0.0 | 1.0 | 0.0 |
| GCCNJMJA_7 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| GCCNJMJA_1 | 1664239 | 1690606 | 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 |
| GCCNJMJA_2 | 800680 | 805022 | False | Siphoviridae | VOG0275, VOG1563 |
| GCCNJMJA_2 | 812847 | 836092 | False | Siphoviridae | VOG8507, VOG4841, VOG0713, VOG4581, VOG1886, VOG3607, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG1266, VOG9583, VOG0704, VOG4586, VOG0541, VOG5910, VOG0801, VOG4772, VOG4660, VOG4612, VOG3390, VOG4705 |
Phigaro v2.4.0 (Database: Jan. 2024 release)