Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 11 | 10 | 9 | 17.38 |
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. |
|---|---|---|---|---|---|---|---|---|
| APCKLLDC_46 | 84664 | 85002 | ykkC | ARO:3003063 | ykkC | 98.21 | 100.00 | AL009126.1 |
| APCKLLDC_46 | 84347 | 84664 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| APCKLLDC_62 | 41757 | 44327 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| APCKLLDC_88 | 41017 | 41781 | mphK | ARO:3004541 | mphK | 97.61 | 83.01 | CP010314.1 |
| APCKLLDC_88 | 27689 | 29122 | lmrB | ARO:3002813 | lmrB | 98.95 | 100.00 | JYFL01000006.1 |
| APCKLLDC_7 | 7178 | 7771 | tmrB | ARO:3003059 | tmrB | 99.49 | 100.00 | AL009126.3 |
| APCKLLDC_2 | 3653 | 4507 | aadK | ARO:3002627 | aadK | 98.94 | 100.00 | AL009126.1 |
| APCKLLDC_106 | 872 | 2074 | blt | ARO:3003006 | blt | 99.25 | 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. |
|---|---|---|---|---|---|---|---|
| APCKLLDC_2 | 3653 | 4507 | aadK | Streptomycin | 98.83 | 100.00 | M26879 |
| APCKLLDC_88 | 41017 | 41775 | mph(K) | Spiramycin, Telithromycin | 97.63 | 82.41 | 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. |
|---|---|---|---|---|---|---|---|---|
| APCKLLDC_2 | 3656 | 4507 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.94 | 100.00 | WP_003229862.1 |
| APCKLLDC_88 | 41029 | 41775 | mphK | macrolide 2'-phosphotransferase MphK | PARTIALX | 98.39 | 81.37 | WP_003246254.1 |
| APCKLLDC_9 | 8516 | 10123 | vmlR | ABC-F type ribosomal protection protein VmlR | INTERNAL_STOP | 95.61 | 100.00 | WP_003234144.1 |
| APCKLLDC_55 | 61892 | 62410 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 91.91 | 100.00 | WP_003242546.1 |
| APCKLLDC_58 | 54416 | 57013 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.48 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| APCKLLDC_60 | 21359 | 22540 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| APCKLLDC_16 | 112921 | 113706 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| APCKLLDC_60 | 23023 | 24165 | capA | 0.0 | Capsule | Immune modulation | 99.30 | 100.00 | NP_391469 |
| APCKLLDC_16 | 109085 | 110023 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.15 | 100.00 | NP_391077 |
| APCKLLDC_16 | 111699 | 112895 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.08 | 100.00 | NP_391079 |
| APCKLLDC_11 | 15146 | 15787 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 98.91 | 100.00 | NP_390062 |
| APCKLLDC_60 | 22555 | 23004 | capC | 0.0 | Capsule | Immune modulation | 98.89 | 100.00 | NP_391470 |
| APCKLLDC_16 | 101929 | 109065 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.66 | 100.00 | NP_391076 |
| APCKLLDC_58 | 1613 | 3365 | dep/capD | 0.0 | Capsule | Immune modulation | 98.36 | 99.94 | NP_389723 |
| APCKLLDC_16 | 110051 | 111670 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.04 | 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 |
|---|---|---|---|---|---|---|---|---|
| APCKLLDC_10 | 28056 | 26920 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| APCKLLDC_15 | 11360 | 10491 | pdxS | 1.99e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.45 | 98.31 | ACE61268 |
| APCKLLDC_1 | 156068 | 156844 | CodY | 2.05e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| APCKLLDC_47 | 73841 | 74410 | ClpP | 5.77e-100 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| APCKLLDC_35 | 23397 | 23789 | spxA1 | 4.48e-71 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| APCKLLDC_35 | 23397 | 23789 | spx | 2.67e-69 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| APCKLLDC_8 | 34686 | 34444 | SpoVG | 7.52e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| APCKLLDC_49 | 1926 | 1729 | CspA | 5.31e-33 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| APCKLLDC_11 | 27017 | 27211 | CspD | 6.95e-29 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| APCKLLDC_12 | 24910 | 25104 | CspB | 4.58e-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. |
|---|---|---|---|---|---|---|
| APCKLLDC_67 | 7723 | 7916 | Col(SD853) | 194 / 194 | 97.42 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| APCKLLDC_1 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_2 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_3 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_4 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_5 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_6 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_7 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_8 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_9 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_10 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_11 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_12 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_13 | 1.0 | 0.0 | 1.0 |
| APCKLLDC_14 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_15 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_16 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_17 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_19 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_21 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_22 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_23 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_24 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_25 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_26 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_27 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_28 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_29 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_30 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_31 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_32 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_33 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_34 | 1.0 | 0.0 | 1.0 |
| APCKLLDC_35 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_36 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_37 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_38 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_39 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_40 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_41 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_42 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_43 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_44 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_45 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_46 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_47 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_48 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_49 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_50 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_51 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_52 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_53 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_54 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_55 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_56 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_57 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_58 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_59 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_60 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_61 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_62 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_63 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_64 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_65 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_66 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_67 | 1.0 | 0.0 | 1.0 |
| APCKLLDC_68 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_69 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_70 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_71 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_72 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_73 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_74 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_75 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_76 | 1.0 | 0.0 | 1.0 |
| APCKLLDC_77 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_78 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_79 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_80 | 1.0 | 0.0 | 1.0 |
| APCKLLDC_81 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_82 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_83 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_84 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_85 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_86 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_87 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_88 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_89 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_92 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_93 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_94 | 1.0 | 0.0 | 1.0 |
| APCKLLDC_95 | 1.0 | 0.0 | 1.0 |
| APCKLLDC_96 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_97 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_98 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_99 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_100 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_101 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_102 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_104 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_105 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_106 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_108 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_109 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_110 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_111 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_112 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_113 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_114 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_115 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_117 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_120 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_122 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_123 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_124 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_126 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_127 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_132 | 0.0 | 1.0 | 0.0 |
| APCKLLDC_133 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| APCKLLDC_13 | 5637 | 19738 | False | Siphoviridae | VOG0189, VOG5446, VOG0025, VOG4813, VOG4551, VOG2215, VOG1563, VOG0052, VOG6546, VOG5753, VOG10937, VOG5324, VOG7980, VOG0026 |
| APCKLLDC_25 | 534 | 26614 | False | Siphoviridae | VOG4626, VOG4619, VOG0801, VOG6163, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5361, VOG4553, VOG4573, VOG4556, VOG0202, VOG1886, VOG4581, VOG4841, VOG0713, VOG7884, VOG0275, VOG0198, VOG0044, VOG0397, VOG3444, VOG4567, VOG5836, VOG1336, VOG0536 |
| APCKLLDC_46 | 114466 | 141142 | False | Myoviridae | VOG0753, VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490 |
| APCKLLDC_82 | 4941 | 15466 | True | Siphoviridae | VOG6587, VOG0189, VOG4566, VOG7581, VOG9667, VOG9667, VOG1563, VOG0275, VOG0275 |
Phigaro v2.4.0 (Database: Jan. 2024 release)