Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2620
  Reference Plasmid   1111525849858229_bin.11__k141_19080
  Reference Plasmid Size   4999
  Reference Plasmid GC Content   0.60
  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
M0049410 JCMFOCHF_00001 720 10 Skin 0.59 protein_coding synonymous_variant LOW 624A>G Val208Val
M0049411 JCMFOCHF_00001 1083 8 Skin 0.47 protein_coding synonymous_variant LOW 987C>G Gly329Gly
M0049412 JCMFOCHF_00002 1498 6 Skin 0.35 protein_coding synonymous_variant LOW 207G>C Pro69Pro
M0049413 JCMFOCHF_00003 2485 8 Skin 0.47 protein_coding synonymous_variant LOW 858T>C Asp286Asp
M0049414 JCMFOCHF_00003 2494 8 Skin 0.47 protein_coding synonymous_variant LOW 849C>T His283His
M0049415 JCMFOCHF_00003 3061 9 Skin 0.53 protein_coding synonymous_variant LOW 282A>G Ala94Ala
M0049416 JCMFOCHF_00003 3067 9 Skin 0.53 protein_coding synonymous_variant LOW 276T>C Ile92Ile
M0049417 JCMFOCHF_00002 3758 9 Skin 0.53 protein_coding upstream_gene_variant MODIFIER -2054C>T None
M0049418 JCMFOCHF_00004 4137 5 Skin 0.29 protein_coding synonymous_variant LOW 726A>G Ala242Ala
M0049419 JCMFOCHF_00001 339 8 Skin 0.47 protein_coding synonymous_variant LOW 243C>T Leu81Leu
M0049420 JCMFOCHF_00001 384 8 Skin 0.47 protein_coding synonymous_variant LOW 288T>G Ala96Ala
M0049421 JCMFOCHF_00001 916 4 Skin 0.24 protein_coding missense_variant MODERATE 820T>C Phe274Leu
M0049422 JCMFOCHF_00001 948 5 Skin 0.29 protein_coding missense_variant MODERATE 852T>G Asp284Glu
M0049423 JCMFOCHF_00002 1809 10 Skin 0.59 protein_coding upstream_gene_variant MODIFIER -105G>C None
M0049424 JCMFOCHF_00003 2392 5 Skin 0.29 protein_coding synonymous_variant LOW 951C>T Gly317Gly
M0049425 JCMFOCHF_00003 2815 7 Skin 0.41 protein_coding synonymous_variant LOW 528G>A Glu176Glu
M0049426 JCMFOCHF_00003 2914 6 Skin 0.35 protein_coding synonymous_variant LOW 429G>A Pro143Pro
M0049427 JCMFOCHF_00003 3202 6 Skin 0.35 protein_coding synonymous_variant LOW 141A>C Gly47Gly
M0049428 JCMFOCHF_00002 3999 5 Skin 0.29 protein_coding upstream_gene_variant MODIFIER -2295T>C None
M0049429 JCMFOCHF_00002 3969 3 Skin 0.18 protein_coding upstream_gene_variant MODIFIER -2265C>T None
M0049430 JCMFOCHF_00002 3974 3 Skin 0.18 protein_coding upstream_gene_variant MODIFIER -2270C>T None
M0049431 JCMFOCHF_00002 4039 4 Skin 0.24 protein_coding upstream_gene_variant MODIFIER -2335A>G None
M0049432 JCMFOCHF_00002 4073 3 Skin 0.18 protein_coding upstream_gene_variant MODIFIER -2369G>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
JCMFOCHF_00003 VFG000133 Alginate 80.5 3.4e-230 1 473 0.9834 0.9834 Biofilm phosphomannose isomerase / guanosine 5'-diphospho-D-mannose pyrophosphorylase experiment
JCMFOCHF_00003 VFG014892 Alginate 99.6 9.6e-285 1 481 1.0 1 Biofilm phosphomannose isomerase / guanosine 5'-diphospho-D-mannose pyrophosphorylase 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






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