Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2988
  Reference Plasmid   DSKIN0031-1_bin.8__k141_19928
  Reference Plasmid Size   20122
  Reference Plasmid GC Content   0.67
  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
M0069072 COFOKFAB_00008 6620 3 Skin 0.33 protein_coding synonymous_variant LOW 219A>T Gly73Gly
M0069073 COFOKFAB_00008 6746 3 Skin 0.33 protein_coding synonymous_variant LOW 345G>C Arg115Arg
M0069074 COFOKFAB_00008 6776 3 Skin 0.33 protein_coding synonymous_variant LOW 375G>A Ala125Ala
M0069075 COFOKFAB_00008 6779 3 Skin 0.33 protein_coding synonymous_variant LOW 378G>A Ala126Ala
M0069076 COFOKFAB_00008 6833 3 Skin 0.33 protein_coding synonymous_variant LOW 432T>C Asn144Asn
M0069077 COFOKFAB_00007 7998 5 Skin 0.56 protein_coding upstream_gene_variant MODIFIER -1908C>G None
M0069078 COFOKFAB_00007 8022 5 Skin 0.56 protein_coding upstream_gene_variant MODIFIER -1932T>G None
M0069079 COFOKFAB_00009 8036 5 Skin 0.56 protein_coding stop_lost&splice_region_variant HIGH 736T>C Ter246Glnext*?
M0069080 COFOKFAB_00009 8277 4 Skin 0.44 protein_coding synonymous_variant LOW 495A>G Ser165Ser
M0069081 COFOKFAB_00009 8305 3 Skin 0.33 protein_coding missense_variant MODERATE 467A>G Asp156Gly
M0069082 COFOKFAB_00009 8337 3 Skin 0.33 protein_coding synonymous_variant LOW 435C>A Ala145Ala
M0069083 COFOKFAB_00009 8343 3 Skin 0.33 protein_coding synonymous_variant LOW 429C>A Ala143Ala
M0069084 COFOKFAB_00009 8346 3 Skin 0.33 protein_coding synonymous_variant LOW 426T>C Asp142Asp
M0069085 COFOKFAB_00009 8509 5 Skin 0.56 protein_coding missense_variant MODERATE 263T>C Val88Ala
M0069086 COFOKFAB_00010 9022 5 Skin 0.56 protein_coding synonymous_variant LOW 102A>G Glu34Glu
M0069087 COFOKFAB_00010 9052 5 Skin 0.56 protein_coding synonymous_variant LOW 132C>T Arg44Arg
M0069088 COFOKFAB_00010 9101 3 Skin 0.33 protein_coding synonymous_variant LOW 181C>T Leu61Leu
M0069089 COFOKFAB_00010 9396 5 Skin 0.56 protein_coding missense_variant MODERATE 476A>T Gln159Leu
M0069090 COFOKFAB_00010 9608 5 Skin 0.56 protein_coding missense_variant MODERATE 688A>G Asn230Asp
M0069091 COFOKFAB_00011 10296 4 Skin 0.44 protein_coding synonymous_variant LOW 381C>T Tyr127Tyr
M0069092 COFOKFAB_00011 10302 4 Skin 0.44 protein_coding synonymous_variant LOW 387T>C Asp129Asp
M0069093 COFOKFAB_00011 10326 3 Skin 0.33 protein_coding synonymous_variant LOW 411G>A Gly137Gly
M0069094 COFOKFAB_00011 10437 4 Skin 0.44 protein_coding synonymous_variant LOW 522T>C Asp174Asp
M0069095 COFOKFAB_00011 10467 3 Skin 0.33 protein_coding synonymous_variant LOW 552T>G Thr184Thr
M0069096 COFOKFAB_00011 10942 3 Skin 0.33 protein_coding missense_variant MODERATE 1027G>A Val343Ile
M0069097 COFOKFAB_00011 10959 3 Skin 0.33 protein_coding synonymous_variant LOW 1044G>A Val348Val
M0069098 COFOKFAB_00011 11007 3 Skin 0.33 protein_coding synonymous_variant LOW 1092C>T Arg364Arg
M0069099 COFOKFAB_00012 12364 3 Skin 0.33 protein_coding synonymous_variant LOW 306A>G Leu102Leu
M0069100 COFOKFAB_00012 12406 3 Skin 0.33 protein_coding synonymous_variant LOW 264T>C Gly88Gly
M0069101 COFOKFAB_00014 14743 3 Skin 0.33 protein_coding synonymous_variant LOW 633C>T Ala211Ala
M0069102 COFOKFAB_00012 15008 3 Skin 0.33 protein_coding upstream_gene_variant MODIFIER -2339A>G None
M0069103 COFOKFAB_00015 15790 4 Skin 0.44 protein_coding synonymous_variant LOW 699C>T Ser233Ser
M0069104 COFOKFAB_00007 4709 3 Skin 0.33 protein_coding missense_variant MODERATE 1382A>C Asp461Ala
M0069105 COFOKFAB_00010 9499 3 Skin 0.33 protein_coding synonymous_variant LOW 579T>C Thr193Thr
M0069106 COFOKFAB_00010 9509 3 Skin 0.33 protein_coding synonymous_variant LOW 589A>C Arg197Arg
M0069107 COFOKFAB_00010 9511 3 Skin 0.33 protein_coding missense_variant MODERATE 591G>C Arg197Ser
M0069108 COFOKFAB_00010 9535 3 Skin 0.33 protein_coding synonymous_variant LOW 615C>T Arg205Arg
M0069109 COFOKFAB_00011 10574 3 Skin 0.33 protein_coding missense_variant MODERATE 659G>A Arg220Lys
M0069110 COFOKFAB_00011 10593 3 Skin 0.33 protein_coding synonymous_variant LOW 678T>C Tyr226Tyr
M0069111 COFOKFAB_00011 10675 3 Skin 0.33 protein_coding missense_variant MODERATE 760C>A Gln254Lys
M0069112 COFOKFAB_00009 8136 3 Skin 0.33 protein_coding synonymous_variant LOW 636G>C Thr212Thr
M0069113 COFOKFAB_00014 14536 3 Skin 0.33 protein_coding synonymous_variant LOW 426C>G Arg142Arg
M0069114 COFOKFAB_00016 17085 3 Skin 0.33 protein_coding synonymous_variant LOW 624T>C Ala208Ala
M0069115 COFOKFAB_00016 17094 3 Skin 0.33 protein_coding synonymous_variant LOW 633C>T Arg211Arg
M0069116 COFOKFAB_00016 17133 3 Skin 0.33 protein_coding synonymous_variant LOW 672C>A Ala224Ala
M0069117 COFOKFAB_00016 18906 3 Skin 0.33 protein_coding synonymous_variant LOW 2445T>C Asp815Asp
M0069118 COFOKFAB_00016 19008 3 Skin 0.33 protein_coding synonymous_variant LOW 2547T>C Asp849Asp
M0069119 COFOKFAB_00016 19164 3 Skin 0.33 protein_coding synonymous_variant LOW 2703G>A Glu901Glu
M0069120 COFOKFAB_00016 19200 3 Skin 0.33 protein_coding synonymous_variant LOW 2739T>G Val913Val
M0069121 COFOKFAB_00015 19995 3 Skin 0.33 protein_coding downstream_gene_variant MODIFIER *3620G>A None
M0069122 COFOKFAB_00015 20003 3 Skin 0.33 protein_coding downstream_gene_variant MODIFIER *3628G>A None
M0069123 COFOKFAB_00015 20041 3 Skin 0.33 protein_coding downstream_gene_variant MODIFIER *3666T>C None
M0069124 COFOKFAB_00015 20072 3 Skin 0.33 protein_coding downstream_gene_variant MODIFIER *3697C>A None
M0069125 COFOKFAB_00015 20077 3 Skin 0.33 protein_coding downstream_gene_variant MODIFIER *3702C>G 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
COFOKFAB_00016 VFG037720 AdeFGH efflux pump 70.7 0 1 1065 0.9834 1.0057 Biofilm cation/multidrug efflux pump experiment
COFOKFAB_00016 VFG037718 AdeFGH efflux pump 70.7 0 1 1065 0.9834 1.0057 Biofilm cation/multidrug efflux pump 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
COFOKFAB_00016 Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Ethidium Bromide [class: Phenanthridine], Safranin O [class: Azin], Acridine Orange [class: Acridine] 70.7 0 1 1065 0.9834 1.0057 experiment
COFOKFAB_00016 Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Ethidium Bromide [class: Phenanthridine], Safranin O [class: Azin], Acridine Orange [class: Acridine] 70.5 0 1 1063 0.9815 1.0038 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
COFOKFAB_00016 ARO:3003010 71.6 0 1 1026 0.9474 0.9990 fluoroquinolone antibiotic resistance-nodulation-cell division (RND) 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
COFOKFAB_00016 2.A.6.2.44 70.7 0 1 1065 0.9834 2.6084 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily