Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 9 | 18.03 |
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. |
|---|---|---|---|---|---|---|---|---|
| LHOCDELC_67 | 84623 | 84961 | ykkC | ARO:3003063 | ykkC | 98.21 | 100.00 | AL009126.1 |
| LHOCDELC_67 | 84306 | 84623 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| LHOCDELC_49 | 64888 | 65739 | aadK | ARO:3002627 | aadK | 98.24 | 99.65 | AL009126.1 |
| LHOCDELC_16 | 46431 | 47024 | tmrB | ARO:3003059 | tmrB | 100.00 | 100.00 | AL009126.3 |
| LHOCDELC_28 | 20862 | 22031 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| LHOCDELC_56 | 20734 | 22167 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.00 | JYFL01000006.1 |
| LHOCDELC_29 | 8893 | 11463 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| LHOCDELC_5 | 6372 | 7292 | mphK | ARO:3004541 | mphK | 98.68 | 100.00 | CP010314.1 |
| LHOCDELC_75 | 5902 | 7545 | vmlR | ARO:3004476 | vmlR | 98.32 | 100.00 | NC_000964.3 |
| LHOCDELC_108 | 793 | 1995 | 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. |
|---|---|---|---|---|---|---|---|
| LHOCDELC_49 | 64888 | 65739 | aadK | Streptomycin | 98.48 | 99.65 | M26879 |
| LHOCDELC_5 | 6372 | 7292 | mph(K) | Spiramycin, Telithromycin | 98.05 | 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. |
|---|---|---|---|---|---|---|---|---|
| LHOCDELC_5 | 6384 | 7292 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.68 | 99.02 | WP_003246254.1 |
| LHOCDELC_49 | 64888 | 65736 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.24 | 100.00 | WP_003229862.1 |
| LHOCDELC_75 | 5905 | 7545 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 96.71 | 99.82 | WP_003234144.1 |
| LHOCDELC_57 | 51220 | 51612 | satA | streptothricin N-acetyltransferase SatA | PARTIALX | 91.60 | 75.72 | WP_003242546.1 |
| LHOCDELC_63 | 1475 | 4072 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| LHOCDELC_135 | 1935 | 3116 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| LHOCDELC_53 | 107942 | 108727 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| LHOCDELC_135 | 310 | 1452 | capA | 0.0 | Capsule | Immune modulation | 99.30 | 100.00 | NP_391469 |
| LHOCDELC_73 | 49883 | 51646 | dep/capD | 0.0 | Capsule | Immune modulation | 98.98 | 100.00 | NP_389723 |
| LHOCDELC_53 | 104117 | 105055 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.94 | 100.00 | NP_391077 |
| LHOCDELC_33 | 88833 | 89474 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 98.91 | 100.00 | NP_390062 |
| LHOCDELC_135 | 1471 | 1920 | capC | 0.0 | Capsule | Immune modulation | 98.89 | 100.00 | NP_391470 |
| LHOCDELC_53 | 106720 | 107916 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.75 | 100.00 | NP_391079 |
| LHOCDELC_53 | 96961 | 104097 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.56 | 100.00 | NP_391076 |
| LHOCDELC_53 | 105083 | 106702 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.28 | 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 |
|---|---|---|---|---|---|---|---|---|
| LHOCDELC_45 | 28043 | 26907 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| LHOCDELC_69 | 4382 | 5251 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| LHOCDELC_41 | 82754 | 81978 | CodY | 1.27e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| LHOCDELC_54 | 45179 | 44610 | ClpP | 7.58e-100 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| LHOCDELC_4 | 23297 | 23689 | spxA1 | 4.11e-71 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| LHOCDELC_4 | 23297 | 23689 | spx | 2.45e-69 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| LHOCDELC_10 | 27046 | 26804 | SpoVG | 6.48e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| LHOCDELC_52 | 75818 | 76015 | CspA | 3.37e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| LHOCDELC_33 | 77602 | 77408 | CspD | 7.92e-29 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| LHOCDELC_12 | 49222 | 49416 | CspB | 7.27e-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. |
|---|---|---|---|---|---|---|
| LHOCDELC_43 | 1 | 484 | rep21 | 484 / 717 | 90.50 | FR821780 |
| LHOCDELC_43 | 2116 | 2280 | Col(SD853) | 165 / 194 | 86.06 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| LHOCDELC_1 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_2 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_3 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_4 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_5 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_6 | 1.0 | 0.0 | 1.0 |
| LHOCDELC_7 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_8 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_9 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_10 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_11 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_12 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_13 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_14 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_15 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_16 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_17 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_18 | 1.0 | 0.0 | 1.0 |
| LHOCDELC_19 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_20 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_21 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_22 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_23 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_24 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_25 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_26 | 1.0 | 0.0 | 1.0 |
| LHOCDELC_27 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_28 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_29 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_30 | 1.0 | 0.0 | 1.0 |
| LHOCDELC_31 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_32 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_33 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_34 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_35 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_36 | 1.0 | 0.0 | 1.0 |
| LHOCDELC_37 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_38 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_40 | 1.0 | 0.0 | 1.0 |
| LHOCDELC_41 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_42 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_43 | 1.0 | 0.0 | 1.0 |
| LHOCDELC_44 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_45 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_46 | 1.0 | 0.0 | 1.0 |
| LHOCDELC_47 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_48 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_49 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_50 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_51 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_52 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_53 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_54 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_55 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_56 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_57 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_58 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_59 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_60 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_61 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_62 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_63 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_64 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_65 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_66 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_67 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_68 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_69 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_70 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_71 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_72 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_73 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_74 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_75 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_76 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_77 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_78 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_79 | 1.0 | 0.0 | 1.0 |
| LHOCDELC_80 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_82 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_83 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_84 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_85 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_86 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_87 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_88 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_89 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_90 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_91 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_92 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_93 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_94 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_95 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_96 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_97 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_98 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_99 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_100 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_101 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_102 | 1.0 | 0.0 | 1.0 |
| LHOCDELC_103 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_104 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_105 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_106 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_107 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_108 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_109 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_110 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_114 | 1.0 | 0.0 | 1.0 |
| LHOCDELC_115 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_116 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_117 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_118 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_119 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_120 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_123 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_124 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_125 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_126 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_127 | 1.0 | 0.0 | 1.0 |
| LHOCDELC_128 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_129 | 1.0 | 0.0 | 1.0 |
| LHOCDELC_132 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_134 | 1.0 | 0.0 | 1.0 |
| LHOCDELC_135 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_136 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_137 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_139 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_140 | 0.0 | 1.0 | 0.0 |
| LHOCDELC_142 | 1.0 | 0.0 | 1.0 |
| LHOCDELC_143 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LHOCDELC_64 | 10296 | 30831 | False | Siphoviridae | VOG1985, VOG0198, VOG0713, VOG4841, VOG4581, VOG1886, VOG0202, VOG4556, VOG4573, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801 |
| LHOCDELC_67 | 114425 | 140588 | False | Myoviridae | VOG0753, VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490 |
Phigaro v2.4.0 (Database: Jan. 2024 release)