Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 9 | 18.71 |
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. |
|---|---|---|---|---|---|---|---|---|
| GKAFKPJL_5 | 282743 | 283912 | bmr | ARO:3003007 | bmr | 99.23 | 100.00 | M33768.1 |
| GKAFKPJL_21 | 231650 | 232504 | aadK | ARO:3002627 | aadK | 97.54 | 100.00 | AL009126.1 |
| GKAFKPJL_4 | 195022 | 196665 | vmlR | ARO:3004476 | vmlR | 98.35 | 100.00 | NC_000964.3 |
| GKAFKPJL_20 | 124037 | 124630 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| GKAFKPJL_20 | 73515 | 74948 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.00 | JYFL01000006.1 |
| GKAFKPJL_20 | 60699 | 61619 | mphK | ARO:3004541 | mphK | 97.71 | 100.00 | CP010314.1 |
| GKAFKPJL_25 | 35952 | 36290 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| GKAFKPJL_25 | 35635 | 35952 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| GKAFKPJL_8 | 27208 | 29778 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 100.00 | AL009126.3 |
| GKAFKPJL_40 | 6529 | 7731 | blt | ARO:3003006 | blt | 99.75 | 100.00 | L32599.1 |
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. |
|---|---|---|---|---|---|---|---|
| GKAFKPJL_26 | 34419 | 35795 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 100.00 | 100.00 | X08034 |
| GKAFKPJL_21 | 231650 | 232502 | aadK | Streptomycin | 98.48 | 99.77 | M26879 |
| GKAFKPJL_20 | 60699 | 61619 | mph(K) | Spiramycin, Telithromycin | 97.50 | 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. |
|---|---|---|---|---|---|---|---|---|
| GKAFKPJL_26 | 34419 | 35792 | tet(L) | tetracycline efflux MFS transporter Tet(L) | EXACTX | 100.00 | 100.00 | WP_003242953.1 |
| GKAFKPJL_4 | 195025 | 196665 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.35 | 100.00 | WP_003234144.1 |
| GKAFKPJL_20 | 60699 | 61616 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.71 | 100.00 | WP_003246254.1 |
| GKAFKPJL_21 | 231650 | 232501 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.54 | 100.00 | WP_003229862.1 |
| GKAFKPJL_26 | 37736 | 38254 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| GKAFKPJL_29 | 14034 | 16631 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.40 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| GKAFKPJL_24 | 157749 | 158930 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| GKAFKPJL_12 | 8306 | 10069 | dep/capD | 0.0 | Capsule | Immune modulation | 99.49 | 100.00 | NP_389723 |
| GKAFKPJL_5 | 83335 | 83976 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.38 | 100.00 | NP_390062 |
| GKAFKPJL_23 | 349173 | 349958 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| GKAFKPJL_23 | 352856 | 353794 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391077 |
| GKAFKPJL_23 | 349984 | 351180 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.17 | 100.00 | NP_391079 |
| GKAFKPJL_23 | 353814 | 360948 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.06 | 99.97 | NP_391076 |
| GKAFKPJL_24 | 159413 | 160555 | capA | 0.0 | Capsule | Immune modulation | 98.95 | 100.00 | NP_391469 |
| GKAFKPJL_23 | 351209 | 352828 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.52 | 100.00 | NP_391078 |
| GKAFKPJL_24 | 158945 | 159394 | capC | 0.0 | Capsule | Immune modulation | 98.44 | 100.00 | NP_391470 |
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 |
|---|---|---|---|---|---|---|---|---|
| GKAFKPJL_28 | 31690 | 32826 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| GKAFKPJL_50 | 4505 | 5374 | pdxS | 2.61e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.45 | 98.31 | ACE61268 |
| GKAFKPJL_31 | 2942 | 3718 | CodY | 7.50e-126 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| GKAFKPJL_23 | 96809 | 96240 | ClpP | 2.78e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| GKAFKPJL_2 | 240478 | 240870 | spxA1 | 1.74e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| GKAFKPJL_2 | 240478 | 240870 | spx | 1.04e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| GKAFKPJL_37 | 34594 | 34352 | SpoVG | 7.48e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| GKAFKPJL_4 | 144332 | 144529 | CspA | 9.74e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| GKAFKPJL_5 | 95940 | 96134 | CspD | 2.72e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| GKAFKPJL_3 | 2772 | 2966 | CspB | 3.21e-28 | cold shock protein | 83.08 | 98.48 | 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 |
|---|---|---|---|
| GKAFKPJL_1 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_2 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_3 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_4 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_5 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_6 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_7 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_8 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_9 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_10 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_11 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_12 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_13 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_14 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_15 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_16 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_17 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_19 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_20 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_21 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_22 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_23 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_24 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_25 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_26 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_27 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_28 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_29 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_31 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_32 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_33 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_35 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_36 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_37 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_38 | 1.0 | 0.0 | 1.0 |
| GKAFKPJL_39 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_40 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_41 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_42 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_43 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_44 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_45 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_46 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_47 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_49 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_50 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_51 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_58 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_59 | 1.0 | 0.0 | 1.0 |
| GKAFKPJL_62 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_63 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_64 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_65 | 1.0 | 0.0 | 1.0 |
| GKAFKPJL_67 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_69 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_71 | 0.0 | 1.0 | 0.0 |
| GKAFKPJL_75 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| GKAFKPJL_9 | 13131 | 19760 | False | Siphoviridae | VOG4602, VOG4662, VOG9667, VOG9667, VOG0650, VOG4552, VOG4600 |
| GKAFKPJL_15 | 3360 | 25918 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773 |
| GKAFKPJL_16 | 6841 | 24505 | False | Siphoviridae | VOG0136, VOG0753, VOG10940, VOG5535, VOG4599, VOG4605, VOG9745, VOG0701, VOG10044, VOG6548, VOG0697, VOG0696, VOG0695, VOG2621, VOG4572, VOG9317, VOG0692, VOG0691 |
| GKAFKPJL_22 | 5619 | 15946 | False | Siphoviridae | VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
| GKAFKPJL_25 | 66100 | 73529 | False | Myoviridae | VOG4705, VOG4612, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894 |
Phigaro v2.4.0 (Database: Jan. 2024 release)