Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C868
  Reference Plasmid   NZ_CP072219.1
  Reference Plasmid Size   98230
  Reference Plasmid GC Content   0.43
  Reference Plasmid Mobility Type   non-mobilizable





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
M0185410 LCGMMOKH_00042 39674 3 Gut 0.05 protein_coding missense_variant MODERATE 764G>A Gly255Asp
M0185411 LCGMMOKH_00039 37247 3 Gut 0.05 protein_coding missense_variant MODERATE 131T>C Val44Ala
M0185412 LCGMMOKH_00039 37276 3 Gut 0.05 protein_coding synonymous_variant LOW 102A>T Arg34Arg
M0185413 LCGMMOKH_00039 37353 3 Gut 0.05 protein_coding missense_variant MODERATE 25T>A Ser9Thr
M0185414 LCGMMOKH_00039 37354 3 Gut 0.05 protein_coding synonymous_variant LOW 24C>T Ala8Ala






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






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
LCGMMOKH_00021 PHI:3281 AS87_04050 71.4 3e-136 1 325 1.0000 1.0000 birds fibrinous serositis; caseous salpingitis; vegetative disorder lipopolysaccharide biosynthesis and pathogenicity reduced virulence






        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
LCGMMOKH_00009 QUT64421.1|GT4 100 1.11e-279 1 378 1 1
LCGMMOKH_00011 QUT55894.1|GT2 100 1.57e-228 1 304 1 1
LCGMMOKH_00013 QRP91616.1|GT4 100 5.41e-274 1 366 1 1
LCGMMOKH_00014 BBK89584.1|GT2 100 6.37e-226 1 300 1 1
LCGMMOKH_00015 QRP91614.1|GT4 100 4.79e-292 1 391 1 1
LCGMMOKH_00016 QUT83193.1|GT4 100 0 1 444 1 1





        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