Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1128
  Reference Plasmid   NZ_CP118944.1
  Reference Plasmid Size   100830
  Reference Plasmid GC Content   0.53
  Reference Plasmid Mobility Type   conjugative





Mutation sites in the plasmid cluster


The table lists mutations identified in the plasmid cluster.
Note: Mutations identified in this plasmid cluster are listed below. Click on a mutation ID to view full details..

mutid gname pos count tissue frequnt biotype consequence impact nucchange aachange
M0109532 LNEGBHAO_00035 36042 3 Skin 0.23 protein_coding missense_variant MODERATE 2164C>G Pro722Ala
M0109533 LNEGBHAO_00035 36601 5 Skin 0.38 protein_coding synonymous_variant LOW 1605A>G Glu535Glu
M0109534 LNEGBHAO_00035 36741 7 Skin 0.54 protein_coding missense_variant MODERATE 1465T>G Ser489Ala
M0109535 LNEGBHAO_00035 36956 6 Skin 0.46 protein_coding missense_variant MODERATE 1250C>T Ala417Val
M0109536 LNEGBHAO_00035 37029 5 Skin 0.38 protein_coding missense_variant MODERATE 1177G>A Ala393Thr
M0109537 LNEGBHAO_00035 37031 5 Skin 0.38 protein_coding missense_variant MODERATE 1175A>T Tyr392Phe
M0109538 LNEGBHAO_00035 37103 5 Skin 0.38 protein_coding missense_variant MODERATE 1103C>T Thr368Ile
M0109539 LNEGBHAO_00035 37347 7 Skin 0.54 protein_coding missense_variant MODERATE 859A>G Thr287Ala
M0109540 LNEGBHAO_00035 37840 7 Skin 0.54 protein_coding missense_variant MODERATE 366C>G Ser122Arg
M0109541 LNEGBHAO_00031 38248 7 Skin 0.54 protein_coding upstream_gene_variant MODIFIER -3860C>T None
M0109542 LNEGBHAO_00036 38684 8 Skin 0.62 protein_coding synonymous_variant LOW 354G>A Leu118Leu
M0109543 LNEGBHAO_00037 39357 3 Skin 0.23 protein_coding missense_variant MODERATE 347C>T Ser116Leu
M0109544 LNEGBHAO_00038 40467 8 Skin 0.62 protein_coding synonymous_variant LOW 654T>C Pro218Pro
M0109545 LNEGBHAO_00035 40677 7 Skin 0.54 protein_coding upstream_gene_variant MODIFIER -2472C>G None
M0109546 LNEGBHAO_00035 37500 6 Skin 0.46 protein_coding missense_variant MODERATE 706A>G Ile236Val
M0109547 LNEGBHAO_00035 37644 3 Skin 0.23 protein_coding missense_variant MODERATE 562T>C Ser188Pro






Analysis of virulence factors contributing to bacterial pathogenicity


This table presents virulence factors identified within the plasmid cluster.
      Note: Virulence factor analysis was performed using VFDB. Genes in plasmid clusters showing strong homology (identity > 70%, coverage > 70%, E-value < 1e-5) to known virulence factors are listed.

Gene Name vf_gene_id vf_name identity evalue qstart qend query_coverage subject_coverage vf_category gene_description condition







        Analysis of biocide and heavy metal resistance genes to assess antimicrobial risk and environmental impact


This table presents biocides and heavy metals resistance genes identified within the plasmid cluster.
      Note: Analyzing biocide and heavy metal resistance genes based on BacMet to evaluate bacterial resistance risk and the potential impact of environmental heavy metal contamination. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, E-value < 1e-5) to known biocide and heavy metal resistance genes are listed.

Gene Name compound identity evalue qstart qend query_coverage subject_coverage group






        Analyzing antimicrobial resistance genes to assess bacterial resistance to antibiotics and other antimicrobial agents


This table presents antimicrobial resistance genes identified within the plasmid cluster.
      Note: Antimicrobial resistance was performed using CARD. Genes in plasmid clusters showing strong homology (identity > 70%, coverage > 70%, E-value < 1e-5) to known antimicrobial resistance genes are listed.

Gene Name aro_accession identity evalue qstart qend query_coverage subject_coverage drug_class amr_gene_family resistance_mechanism
LNEGBHAO_00037 ARO:3002639 99.6 5.98e-202 1 267 1.0000 1.0000 aminoglycoside antibiotic APH(3'') antibiotic inactivation
LNEGBHAO_00038 ARO:3002660 99.6 1.07e-205 1 278 1.0000 1.0000 aminoglycoside antibiotic APH(6) antibiotic inactivation






Analysis of pathogenicity genes to explore pathogen-host interactions


This table presents host pathogen-host interactions within the plasmid cluster.
      Note: Analyzing pathogenicity-related genes using PHI-base to understand pathogen virulence mechanisms and their impact on host interactions. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, and E-value < 1e-5) to known pathogenicity-related genes are listed.

Gene Name phi_molconn_id host gene_name identity evalue qstart qend query_coverage subject_coverage host_descripton disease_name function phenotype_of_mutant






        Analyzing carbohydrate-active enzyme genes to uncover mechanisms of nutrient degradation


This table presents carbohydrate-active enzyme genes identified within the plasmid cluster.
      Note: Annotation of carbohydrate-active enzyme genes was performed using CAZy to explore mechanisms of nutrient breakdown and utilization. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, and E-value < 1e−5) to known CAZyme genes are listed.

Gene Name cazy_id identity evalue qstart qend query_coverage subject_coverage
LNEGBHAO_00073 BBU06999.1|GH23 99.5 6.34e-131 85 267 0.6828 0.9946





        Analyzing transport proteins to understand bacterial strategies for substrate uptake and detoxification


This table presents transport proteins within the plasmid cluster.
      Note: Investigation of transport proteins based on TCDB to uncover bacterial mechanisms of substrate transport and environmental detoxification. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, and E-value < 1e−5) to known transport protein entries are listed.

Gene Name tcid identity evalue qstart qend query_coverage subject_coverage class_field class_term subclass subclass_term family family_term