Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 8 | 17.55 |
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. |
|---|---|---|---|---|---|---|---|---|
| GKMCNJLD_12 | 416716 | 417054 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| GKMCNJLD_12 | 416399 | 416716 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| GKMCNJLD_11 | 350337 | 351983 | vmlR | ARO:3004476 | vmlR | 98.91 | 100.18 | NC_000964.3 |
| GKMCNJLD_10 | 301892 | 304462 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.65 | 100.00 | AL009126.3 |
| GKMCNJLD_16 | 294231 | 295085 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| GKMCNJLD_16 | 277138 | 278340 | blt | ARO:3003006 | blt | 99.50 | 100.00 | L32599.1 |
| GKMCNJLD_11 | 97219 | 97812 | tmrB | ARO:3003059 | tmrB | 100.00 | 100.00 | AL009126.3 |
| GKMCNJLD_16 | 56367 | 57536 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| GKMCNJLD_11 | 46746 | 48179 | lmrB | ARO:3002813 | lmrB | 99.58 | 100.00 | JYFL01000006.1 |
| GKMCNJLD_11 | 33932 | 34852 | mphK | ARO:3004541 | mphK | 97.71 | 100.00 | CP010314.1 |
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. |
|---|---|---|---|---|---|---|---|
| GKMCNJLD_16 | 294231 | 295085 | aadK | Streptomycin | 98.83 | 100.00 | M26879 |
| GKMCNJLD_9 | 547261 | 548637 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 98.33 | 100.00 | D12567 |
| GKMCNJLD_11 | 33932 | 34852 | mph(K) | Spiramycin, Telithromycin | 97.72 | 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. |
|---|---|---|---|---|---|---|---|---|
| GKMCNJLD_11 | 350340 | 351983 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.91 | 100.00 | WP_003234144.1 |
| GKMCNJLD_16 | 294234 | 295085 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| GKMCNJLD_9 | 547264 | 548637 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.47 | 100.00 | WP_063856081.1 |
| GKMCNJLD_11 | 33932 | 34849 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.71 | 100.00 | WP_003246254.1 |
| GKMCNJLD_9 | 544772 | 545290 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 91.33 | 100.00 | WP_003242546.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| GKMCNJLD_22 | 61606 | 62247 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.69 | 100.00 | NP_390062 |
| GKMCNJLD_9 | 51037 | 52218 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| GKMCNJLD_14 | 423407 | 424192 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| GKMCNJLD_14 | 424218 | 425414 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.33 | 100.00 | NP_391079 |
| GKMCNJLD_22 | 220121 | 221884 | dep/capD | 0.0 | Capsule | Immune modulation | 98.98 | 100.00 | NP_389723 |
| GKMCNJLD_9 | 49412 | 50554 | capA | 0.0 | Capsule | Immune modulation | 98.69 | 100.00 | NP_391469 |
| GKMCNJLD_9 | 50573 | 51022 | capC | 0.0 | Capsule | Immune modulation | 98.67 | 100.00 | NP_391470 |
| GKMCNJLD_14 | 427090 | 428028 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.40 | 100.00 | NP_391077 |
| GKMCNJLD_14 | 428048 | 435184 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.38 | 100.00 | NP_391076 |
| GKMCNJLD_14 | 425443 | 427062 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.41 | 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 |
|---|---|---|---|---|---|---|---|---|
| GKMCNJLD_18 | 13628 | 12492 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| GKMCNJLD_21 | 4539 | 5408 | pdxS | 1.15e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| GKMCNJLD_12 | 107926 | 107150 | CodY | 4.33e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| GKMCNJLD_14 | 107366 | 106797 | ClpP | 3.23e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| GKMCNJLD_7 | 46351 | 45959 | spxA1 | 2.06e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| GKMCNJLD_7 | 46351 | 45959 | spx | 1.23e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| GKMCNJLD_20 | 19267 | 19509 | SpoVG | 7.20e-38 | RNA-binding protein | 80.25 | 79.41 | AAT02994 |
| GKMCNJLD_11 | 306564 | 306761 | CspA | 1.65e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| GKMCNJLD_22 | 50374 | 50180 | CspD | 5.93e-28 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| GKMCNJLD_22 | 50374 | 50177 | CspB | 1.23e-27 | 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 |
|---|---|---|---|
| GKMCNJLD_2 | 0.0 | 1.0 | 0.0 |
| GKMCNJLD_3 | 0.0 | 1.0 | 0.0 |
| GKMCNJLD_4 | 0.0 | 1.0 | 0.0 |
| GKMCNJLD_5 | 0.0 | 1.0 | 0.0 |
| GKMCNJLD_6 | 0.0 | 1.0 | 0.0 |
| GKMCNJLD_7 | 0.0 | 1.0 | 0.0 |
| GKMCNJLD_8 | 0.0 | 1.0 | 0.0 |
| GKMCNJLD_9 | 0.0 | 1.0 | 0.0 |
| GKMCNJLD_10 | 0.0 | 1.0 | 0.0 |
| GKMCNJLD_11 | 0.0 | 1.0 | 0.0 |
| GKMCNJLD_12 | 0.0 | 1.0 | 0.0 |
| GKMCNJLD_13 | 0.0 | 1.0 | 0.0 |
| GKMCNJLD_14 | 0.0 | 1.0 | 0.0 |
| GKMCNJLD_15 | 0.0 | 1.0 | 0.0 |
| GKMCNJLD_16 | 0.0 | 1.0 | 0.0 |
| GKMCNJLD_17 | 0.0 | 1.0 | 0.0 |
| GKMCNJLD_18 | 0.0 | 1.0 | 0.0 |
| GKMCNJLD_19 | 0.0 | 1.0 | 0.0 |
| GKMCNJLD_20 | 0.0 | 1.0 | 0.0 |
| GKMCNJLD_21 | 0.0 | 1.0 | 0.0 |
| GKMCNJLD_22 | 0.0 | 1.0 | 0.0 |
| GKMCNJLD_23 | 0.0 | 1.0 | 0.0 |
| GKMCNJLD_24 | 0.0 | 1.0 | 0.0 |
| GKMCNJLD_25 | 0.0 | 1.0 | 0.0 |
| GKMCNJLD_26 | 0.0 | 1.0 | 0.0 |
| GKMCNJLD_27 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| GKMCNJLD_10 | 24833 | 47417 | False | Myoviridae | VOG0720, VOG4555, VOG4553, VOG4564, VOG4623, VOG1353, VOG1881, VOG1883, VOG1352, VOG4699, VOG6163, VOG1956, VOG1433, VOG1348, VOG0573, VOG4550, VOG4691, VOG4845, VOG7718, VOG3390, VOG4705, VOG5008, VOG0753, VOG0136 |
| GKMCNJLD_12 | 446870 | 474151 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
| GKMCNJLD_14 | 330089 | 356176 | False | Siphoviridae | VOG4566, VOG9600, VOG0025, VOG1884, VOG0198, VOG4841, VOG4556, VOG4581, VOG1886, VOG3644, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619, VOG4626, VOG4612, VOG6243, VOG4705, VOG0641, VOG4574 |
| GKMCNJLD_16 | 227524 | 257143 | False | Myoviridae | VOG4705, VOG7718, VOG0906, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG10227, VOG0796, VOG4673, VOG4693, VOG0189, VOG11060, VOG1309 |
Phigaro v2.4.0 (Database: Jan. 2024 release)