Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1439
  Reference Plasmid   NZ_OY725967.1
  Reference Plasmid Size   5947
  Reference Plasmid GC Content   0.40
  Reference Plasmid Mobility Type   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
M0210946 JCHPHFCM_00001 403 44 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -60C>T None
M0210947 JCHPHFCM_00005 4411 10 Gut 0.17 protein_coding synonymous_variant LOW 126T>C Gly42Gly
M0210948 JCHPHFCM_00005 4417 10 Gut 0.17 protein_coding synonymous_variant LOW 120T>C Cys40Cys
M0210949 JCHPHFCM_00005 4483 12 Gut 0.20 protein_coding synonymous_variant LOW 54T>C Asp18Asp
M0210950 JCHPHFCM_00006 4581 10 Gut 0.17 protein_coding synonymous_variant LOW 252A>G Glu84Glu
M0210951 JCHPHFCM_00006 4614 11 Gut 0.19 protein_coding synonymous_variant LOW 219T>C Tyr73Tyr
M0210952 JCHPHFCM_00006 4638 7 Gut 0.12 protein_coding synonymous_variant LOW 195A>G Gly65Gly
M0210953 JCHPHFCM_00006 4701 9 Gut 0.15 protein_coding synonymous_variant LOW 132C>A Arg44Arg
M0210954 JCHPHFCM_00006 4719 6 Gut 0.10 protein_coding synonymous_variant LOW 114A>G Thr38Thr
M0210955 JCHPHFCM_00006 4731 6 Gut 0.10 protein_coding synonymous_variant LOW 102G>A Glu34Glu
M0210956 JCHPHFCM_00006 4740 9 Gut 0.15 protein_coding synonymous_variant LOW 93T>C Ser31Ser
M0210957 JCHPHFCM_00006 4746 7 Gut 0.12 protein_coding synonymous_variant LOW 87C>T Gly29Gly
M0210958 JCHPHFCM_00005 4084 7 Gut 0.12 protein_coding synonymous_variant LOW 453G>A Glu151Glu
M0210959 JCHPHFCM_00005 4098 6 Gut 0.10 protein_coding missense_variant MODERATE 439G>A Gly147Ser
M0210960 JCHPHFCM_00005 4105 4 Gut 0.07 protein_coding synonymous_variant LOW 432C>T Ala144Ala
M0210961 JCHPHFCM_00005 4114 8 Gut 0.14 protein_coding synonymous_variant LOW 423A>T Ala141Ala
M0210962 JCHPHFCM_00005 4270 8 Gut 0.14 protein_coding synonymous_variant LOW 267T>C Asp89Asp
M0210963 JCHPHFCM_00005 4276 3 Gut 0.05 protein_coding synonymous_variant LOW 261C>T Gly87Gly
M0210964 JCHPHFCM_00006 4791 4 Gut 0.07 protein_coding synonymous_variant LOW 42G>C Thr14Thr
M0210965 JCHPHFCM_00005 3811 3 Gut 0.05 protein_coding synonymous_variant LOW 726A>G Leu242Leu
M0210966 JCHPHFCM_00005 3814 3 Gut 0.05 protein_coding missense_variant MODERATE 723C>A Asn241Lys
M0210967 JCHPHFCM_00005 3829 4 Gut 0.07 protein_coding synonymous_variant LOW 708A>G Glu236Glu
M0210968 JCHPHFCM_00005 4014 3 Gut 0.05 protein_coding missense_variant MODERATE 523A>G Ile175Val
M0210969 JCHPHFCM_00005 4054 3 Gut 0.05 protein_coding synonymous_variant LOW 483C>T Gly161Gly
M0210970 JCHPHFCM_00005 4111 6 Gut 0.10 protein_coding synonymous_variant LOW 426G>A Thr142Thr
M0210971 JCHPHFCM_00005 4228 4 Gut 0.07 protein_coding synonymous_variant LOW 309T>C Ile103Ile
M0210972 JCHPHFCM_00005 4243 4 Gut 0.07 protein_coding synonymous_variant LOW 294C>T Asn98Asn
M0210973 JCHPHFCM_00005 4522 3 Gut 0.05 protein_coding synonymous_variant LOW 15A>G Gly5Gly
M0210974 JCHPHFCM_00004 4921 12 Gut 0.20 protein_coding upstream_gene_variant MODIFIER -1136G>A None
M0210975 JCHPHFCM_00005 4333 3 Gut 0.05 protein_coding synonymous_variant LOW 204C>T Val68Val
M0210976 JCHPHFCM_00005 4354 3 Gut 0.05 protein_coding synonymous_variant LOW 183C>T Asn61Asn






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






        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





        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