Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C842
  Reference Plasmid   NZ_CP069648.1
  Reference Plasmid Size   67974
  Reference Plasmid GC Content   0.51
  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
M0184573 JHADMINC_00027 22945 4 Gut 0.50 protein_coding synonymous_variant LOW 243A>G Glu81Glu
M0184574 JHADMINC_00027 22948 4 Gut 0.50 protein_coding synonymous_variant LOW 246T>G Gly82Gly
M0184575 JHADMINC_00027 22951 4 Gut 0.50 protein_coding synonymous_variant LOW 249G>A Gln83Gln
M0184576 JHADMINC_00027 22954 4 Gut 0.50 protein_coding synonymous_variant LOW 252T>C Leu84Leu
M0184577 JHADMINC_00027 22957 4 Gut 0.50 protein_coding synonymous_variant LOW 255C>T Arg85Arg
M0184578 JHADMINC_00027 22972 4 Gut 0.50 protein_coding synonymous_variant LOW 270G>A Glu90Glu
M0184579 JHADMINC_00027 22999 4 Gut 0.50 protein_coding synonymous_variant LOW 297C>T Thr99Thr
M0184580 JHADMINC_00028 23234 4 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -52C>A None
M0184581 JHADMINC_00028 23235 4 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -51T>A None
M0184582 JHADMINC_00028 23239 4 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -47T>A None
M0184583 JHADMINC_00028 23280 4 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -6C>A None






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
JHADMINC_00040 VFG001445 TraJ 98.5 1.2e-113 1 200 0.8772 0.995 Invasion unknown protein experiment
JHADMINC_00040 VFG001445 TraJ 98.5 9.3e-113 1 200 0.8772 0.995 Invasion unknown protein prediction







        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
JHADMINC_00006 ARO:3000873 100 5.12e-208 1 286 1.0000 1.0000 monobactam TEM beta-lactamase antibiotic inactivation
JHADMINC_00021 ARO:3000166 99.3 3.06e-283 1 401 1.0000 1.0000 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
JHADMINC_00022 ARO:3003479 99.5 8.47e-152 1 207 1.0000 0.9952 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic target alteration






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
JHADMINC_00038 AWM63927.1|GH23 99.1 7.84e-155 1 215 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
JHADMINC_00021 2.A.1.2.68 99.8 6.4e-221 1 401 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)