Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C135
  Reference Plasmid   CP088415.1
  Reference Plasmid Size   95144
  Reference Plasmid GC Content   0.48
  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
M0145033 JCKICLOO_00044 41545 4 Gut 0.80 protein_coding synonymous_variant LOW 495C>T Arg165Arg
M0145034 JCKICLOO_00044 41581 4 Gut 0.80 protein_coding synonymous_variant LOW 531T>C Leu177Leu
M0145035 JCKICLOO_00044 41648 3 Gut 0.60 protein_coding synonymous_variant LOW 598C>T Leu200Leu
M0145036 JCKICLOO_00044 41656 4 Gut 0.80 protein_coding synonymous_variant LOW 606T>C Asn202Asn
M0145037 JCKICLOO_00044 41668 3 Gut 0.60 protein_coding synonymous_variant LOW 618C>T Ser206Ser
M0145038 JCKICLOO_00044 41713 3 Gut 0.60 protein_coding synonymous_variant LOW 663C>T Phe221Phe
M0145039 JCKICLOO_00044 42190 4 Gut 0.80 protein_coding synonymous_variant LOW 1140G>A Lys380Lys
M0145040 JCKICLOO_00044 42259 4 Gut 0.80 protein_coding synonymous_variant LOW 1209C>T Gly403Gly
M0145041 JCKICLOO_00044 42262 4 Gut 0.80 protein_coding synonymous_variant LOW 1212C>T Gly404Gly
M0145042 JCKICLOO_00044 42385 4 Gut 0.80 protein_coding synonymous_variant LOW 1335G>A Pro445Pro
M0145043 JCKICLOO_00044 42394 4 Gut 0.80 protein_coding synonymous_variant LOW 1344T>C Ser448Ser
M0145044 JCKICLOO_00044 42457 4 Gut 0.80 protein_coding synonymous_variant LOW 1407C>T Arg469Arg
M0145045 JCKICLOO_00044 42529 4 Gut 0.80 protein_coding missense_variant MODERATE 1479A>T Lys493Asn
M0145046 JCKICLOO_00044 42574 4 Gut 0.80 protein_coding synonymous_variant LOW 1524C>A Gly508Gly
M0145047 JCKICLOO_00044 42607 4 Gut 0.80 protein_coding synonymous_variant LOW 1557T>C Asp519Asp
M0145048 JCKICLOO_00044 42616 4 Gut 0.80 protein_coding synonymous_variant LOW 1566C>T Asp522Asp
M0145049 JCKICLOO_00044 42740 4 Gut 0.80 protein_coding missense_variant MODERATE 1690G>A Val564Ile
M0145050 JCKICLOO_00044 42940 4 Gut 0.80 protein_coding synonymous_variant LOW 1890T>G Arg630Arg
M0145051 JCKICLOO_00044 42986 4 Gut 0.80 protein_coding synonymous_variant LOW 1936C>A Arg646Arg
M0145052 JCKICLOO_00044 42994 4 Gut 0.80 protein_coding synonymous_variant LOW 1944T>C Ile648Ile
M0145053 JCKICLOO_00044 43042 4 Gut 0.80 protein_coding synonymous_variant LOW 1992T>G Thr664Thr
M0145054 JCKICLOO_00044 43186 4 Gut 0.80 protein_coding synonymous_variant LOW 2136G>T Leu712Leu
M0145055 JCKICLOO_00046 45023 3 Gut 0.60 protein_coding missense_variant MODERATE 105T>A Asp35Glu
M0145056 JCKICLOO_00046 45105 4 Gut 0.80 protein_coding missense_variant MODERATE 23T>A Leu8Gln
M0145057 JCKICLOO_00046 45124 3 Gut 0.60 protein_coding missense_variant MODERATE 4G>A Glu2Lys
M0145058 JCKICLOO_00047 45135 3 Gut 0.60 protein_coding splice_region_variant&stop_retained_variant LOW 677G>A Ter226Ter






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
JCKICLOO_00028 QMJ72311.1|GH23 98.2 0 1 1124 1 1
JCKICLOO_00049 AJS09995.1|GH24 100 4.67e-139 1 185 1 1
JCKICLOO_00052 AYL89119.1|GH24 97.2 0 1753 2255 0.2231 0.9031





        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
JCKICLOO_00038 1.E.4.1.1 100 1.3e-54 1 109 1.0000 1.0000 1 Channels/Pores 1.E Holins 1.E.4 The LydA Holin (LydA Holin) Family