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. |
|---|---|---|---|---|---|---|---|---|
| LHNGMDCD_37 | 84728 | 85066 | ykkC | ARO:3003063 | ykkC | 98.21 | 100.00 | AL009126.1 |
| LHNGMDCD_37 | 84411 | 84728 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| LHNGMDCD_1 | 46430 | 47023 | tmrB | ARO:3003059 | tmrB | 100.00 | 100.00 | AL009126.3 |
| LHNGMDCD_3 | 35016 | 35936 | mphK | ARO:3004541 | mphK | 98.68 | 100.00 | CP010314.1 |
| LHNGMDCD_30 | 28569 | 30212 | vmlR | ARO:3004476 | vmlR | 98.32 | 100.00 | NC_000964.3 |
| LHNGMDCD_39 | 27325 | 29895 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| LHNGMDCD_29 | 20862 | 22031 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| LHNGMDCD_2 | 7896 | 8747 | aadK | ARO:3002627 | aadK | 98.24 | 99.65 | AL009126.1 |
| LHNGMDCD_128 | 6846 | 8048 | blt | ARO:3003006 | blt | 99.25 | 100.00 | L32599.1 |
| LHNGMDCD_10 | 5816 | 7249 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.00 | JYFL01000006.1 |
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. |
|---|---|---|---|---|---|---|---|
| LHNGMDCD_2 | 7896 | 8747 | aadK | Streptomycin | 98.48 | 99.65 | M26879 |
| LHNGMDCD_3 | 35016 | 35936 | 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. |
|---|---|---|---|---|---|---|---|---|
| LHNGMDCD_3 | 35016 | 35924 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.68 | 99.02 | WP_003246254.1 |
| LHNGMDCD_2 | 7899 | 8747 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.24 | 100.00 | WP_003229862.1 |
| LHNGMDCD_30 | 28569 | 30209 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 96.71 | 99.82 | WP_003234144.1 |
| LHNGMDCD_4 | 22392 | 22784 | satA | streptothricin N-acetyltransferase SatA | PARTIALX | 91.60 | 75.72 | WP_003242546.1 |
| LHNGMDCD_80 | 3698 | 6295 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| LHNGMDCD_57 | 1941 | 3122 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| LHNGMDCD_75 | 6516 | 7301 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| LHNGMDCD_57 | 316 | 1458 | capA | 0.0 | Capsule | Immune modulation | 99.30 | 100.00 | NP_391469 |
| LHNGMDCD_80 | 57381 | 59144 | dep/capD | 0.0 | Capsule | Immune modulation | 98.98 | 100.00 | NP_389723 |
| LHNGMDCD_75 | 10188 | 11126 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.94 | 100.00 | NP_391077 |
| LHNGMDCD_38 | 74983 | 75624 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 98.91 | 100.00 | NP_390062 |
| LHNGMDCD_57 | 1477 | 1926 | capC | 0.0 | Capsule | Immune modulation | 98.89 | 100.00 | NP_391470 |
| LHNGMDCD_75 | 7327 | 8523 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.75 | 100.00 | NP_391079 |
| LHNGMDCD_75 | 11146 | 18282 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.57 | 100.00 | NP_391076 |
| LHNGMDCD_75 | 8541 | 10160 | 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 |
|---|---|---|---|---|---|---|---|---|
| LHNGMDCD_28 | 28040 | 26904 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| LHNGMDCD_74 | 4389 | 5258 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| LHNGMDCD_41 | 73981 | 74757 | CodY | 1.27e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| LHNGMDCD_32 | 45213 | 44644 | ClpP | 8.76e-100 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| LHNGMDCD_8 | 41570 | 41178 | spxA1 | 4.13e-71 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| LHNGMDCD_8 | 41570 | 41178 | spx | 2.47e-69 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| LHNGMDCD_7 | 20567 | 20809 | SpoVG | 6.47e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| LHNGMDCD_42 | 1924 | 1727 | CspA | 3.36e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| LHNGMDCD_38 | 86855 | 87049 | CspD | 1.01e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| LHNGMDCD_78 | 30233 | 30039 | CspB | 7.31e-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. |
|---|---|---|---|---|---|---|
| LHNGMDCD_105 | 934 | 1120 | Col(SD853) | 187 / 194 | 86.63 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| LHNGMDCD_1 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_2 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_3 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_4 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_5 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_7 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_8 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_9 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_10 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_11 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_12 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_13 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_14 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_15 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_16 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_17 | 1.0 | 0.0 | 1.0 |
| LHNGMDCD_18 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_19 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_20 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_21 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_22 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_23 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_24 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_25 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_26 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_27 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_28 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_29 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_30 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_31 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_32 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_33 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_34 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_35 | 1.0 | 0.0 | 1.0 |
| LHNGMDCD_36 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_37 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_38 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_39 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_40 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_41 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_42 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_43 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_44 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_45 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_46 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_47 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_48 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_49 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_50 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_51 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_52 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_53 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_54 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_55 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_56 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_57 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_58 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_59 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_60 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_61 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_62 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_64 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_65 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_66 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_67 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_68 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_69 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_70 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_71 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_72 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_73 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_74 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_75 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_76 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_77 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_78 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_79 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_80 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_81 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_82 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_83 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_84 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_86 | 1.0 | 0.0 | 1.0 |
| LHNGMDCD_87 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_88 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_89 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_90 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_91 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_92 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_93 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_94 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_95 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_97 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_99 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_100 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_101 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_102 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_103 | 1.0 | 0.0 | 1.0 |
| LHNGMDCD_104 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_105 | 1.0 | 0.0 | 1.0 |
| LHNGMDCD_106 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_107 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_108 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_109 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_110 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_112 | 1.0 | 0.0 | 1.0 |
| LHNGMDCD_114 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_115 | 1.0 | 0.0 | 1.0 |
| LHNGMDCD_117 | 1.0 | 0.0 | 1.0 |
| LHNGMDCD_118 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_119 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_120 | 1.0 | 0.0 | 1.0 |
| LHNGMDCD_121 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_122 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_123 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_124 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_125 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_126 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_127 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_128 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_129 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_130 | 1.0 | 0.0 | 1.0 |
| LHNGMDCD_131 | 0.0 | 1.0 | 0.0 |
| LHNGMDCD_132 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LHNGMDCD_32 | 131802 | 142084 | True | Siphoviridae | VOG3490, VOG0275, VOG0275, VOG1563, VOG9667, VOG9667, VOG7581, VOG4566, VOG0189 |
| LHNGMDCD_61 | 13450 | 40892 | False | Myoviridae | VOG0753, VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG6875, VOG0189, VOG3490, VOG9667 |
| LHNGMDCD_72 | 10178 | 20091 | False | Siphoviridae | VOG6513, VOG0275, VOG4602, VOG9667, VOG9667, VOG0650, VOG4552, VOG4603, VOG8233, VOG0186 |
| LHNGMDCD_72 | 22086 | 42621 | False | Siphoviridae | VOG1985, VOG0198, VOG0713, VOG4841, VOG4581, VOG1886, VOG0202, VOG4556, VOG4573, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801 |
Phigaro v2.4.0 (Database: Jan. 2024 release)