Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1016
  Reference Plasmid   NZ_CP095250.1
  Reference Plasmid Size   30116
  Reference Plasmid GC Content   0.58
  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
M0106676 CPGGDBME_00002 2481 4 Skin 0.50 protein_coding synonymous_variant LOW 1554T>C Thr518Thr
M0106677 CPGGDBME_00002 2514 4 Skin 0.50 protein_coding synonymous_variant LOW 1587T>G Thr529Thr
M0106678 CPGGDBME_00002 2592 4 Skin 0.50 protein_coding synonymous_variant LOW 1665A>T Gly555Gly
M0106679 CPGGDBME_00003 3323 3 Skin 0.38 protein_coding synonymous_variant LOW 78T>C His26His
M0106680 CPGGDBME_00003 3386 3 Skin 0.38 protein_coding synonymous_variant LOW 141G>T Ala47Ala
M0106681 CPGGDBME_00003 3389 3 Skin 0.38 protein_coding synonymous_variant LOW 144T>C Ile48Ile
M0106682 CPGGDBME_00003 3392 3 Skin 0.38 protein_coding synonymous_variant LOW 147A>G Gln49Gln
M0106683 CPGGDBME_00003 3401 3 Skin 0.38 protein_coding synonymous_variant LOW 156C>T Gly52Gly
M0106684 CPGGDBME_00003 3419 3 Skin 0.38 protein_coding synonymous_variant LOW 174T>C Gly58Gly
M0106685 CPGGDBME_00006 7818 3 Skin 0.38 protein_coding missense_variant MODERATE 763G>A Val255Met
M0106686 CPGGDBME_00006 8000 3 Skin 0.38 protein_coding synonymous_variant LOW 945T>C Ala315Ala
M0106687 CPGGDBME_00007 8509 3 Skin 0.38 protein_coding synonymous_variant LOW 135T>C Asn45Asn
M0106688 CPGGDBME_00009 10224 3 Skin 0.38 protein_coding synonymous_variant LOW 897A>G Glu299Glu
M0106689 CPGGDBME_00009 10666 3 Skin 0.38 protein_coding missense_variant MODERATE 455C>G Ala152Gly
M0106690 CPGGDBME_00010 11525 3 Skin 0.38 protein_coding missense_variant MODERATE 1094G>C Ser365Thr
M0106691 CPGGDBME_00010 11812 3 Skin 0.38 protein_coding synonymous_variant LOW 807A>G Leu269Leu
M0106692 CPGGDBME_00010 11904 3 Skin 0.38 protein_coding missense_variant MODERATE 715A>G Ile239Val
M0106693 CPGGDBME_00011 12734 3 Skin 0.38 protein_coding missense_variant MODERATE 8A>C Lys3Thr
M0106694 CPGGDBME_00001 208 3 Skin 0.38 protein_coding upstream_gene_variant MODIFIER -49T>C None
M0106695 CPGGDBME_00001 364 3 Skin 0.38 protein_coding synonymous_variant LOW 108G>A Lys36Lys
M0106696 CPGGDBME_00001 397 3 Skin 0.38 protein_coding synonymous_variant LOW 141T>C Thr47Thr
M0106697 CPGGDBME_00002 890 3 Skin 0.38 protein_coding upstream_gene_variant MODIFIER -38C>G None
M0106698 CPGGDBME_00002 1593 3 Skin 0.38 protein_coding synonymous_variant LOW 666T>C Arg222Arg
M0106699 CPGGDBME_00002 1980 3 Skin 0.38 protein_coding synonymous_variant LOW 1053A>G Lys351Lys
M0106700 CPGGDBME_00002 2189 3 Skin 0.38 protein_coding missense_variant MODERATE 1262G>A Ser421Asn
M0106701 CPGGDBME_00002 2193 3 Skin 0.38 protein_coding synonymous_variant LOW 1266C>T His422His






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
CPGGDBME_00020 Acriflavine [class: Acridine], Ethidium Bromide [class: Phenanthridine], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate] 99.8 3.3e-229 1 410 1.0000 1.0000 experiment
AGMEJPIN_00020 Acriflavine [class: Acridine], Ethidium Bromide [class: Phenanthridine], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate] 99.8 3.3e-229 1 410 1.0000 1.0000 experiment
CPGGDBME_00020 Acriflavine [class: Acridine], Ethidium Bromide [class: Phenanthridine], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate] 100 5.8e-227 1 410 1.0000 1.0000 prediction
AGMEJPIN_00020 Acriflavine [class: Acridine], Ethidium Bromide [class: Phenanthridine], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate] 100 5.8e-227 1 410 1.0000 1.0000 prediction






        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
CPGGDBME_00020 ARO:3001328 85.6 1.05e-251 1 410 1.0000 1.0000 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
AGMEJPIN_00020 ARO:3001328 85.6 1.05e-251 1 410 1.0000 1.0000 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux






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
CPGGDBME_00003 2.A.3.1.1 87.5 1.4e-224 1 456 0.9956 0.9978 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.3 The Amino Acid-Polyamine-Organocation (APC) Family
CPGGDBME_00009 1.A.23.4.5 81.9 1.8e-189 1 414 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.23 The Small Conductance Mechanosensitive Ion Channel (MscS) Family
CPGGDBME_00020 2.A.1.2.19 87.8 4.7e-203 1 410 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
CPGGDBME_00022 2.A.1.60.2 81.4 2.3e-178 1 400 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
AGMEJPIN_00003 2.A.3.1.1 87.5 1.4e-224 1 456 0.9956 0.9978 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.3 The Amino Acid-Polyamine-Organocation (APC) Family
AGMEJPIN_00009 1.A.23.4.5 81.9 1.8e-189 1 414 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.23 The Small Conductance Mechanosensitive Ion Channel (MscS) Family
AGMEJPIN_00020 2.A.1.2.19 87.8 4.7e-203 1 410 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
AGMEJPIN_00022 2.A.1.60.2 81.4 2.3e-178 1 400 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)