Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C585
  Reference Plasmid   NZ_CP034945.1
  Reference Plasmid Size   46584
  Reference Plasmid GC Content   0.38
  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
M0168905 EFCJOJCK_00006 5943 5 Gut 0.15 protein_coding missense_variant MODERATE 8G>A Gly3Glu
M0168906 EFCJOJCK_00009 8671 9 Gut 0.27 protein_coding missense_variant MODERATE 380G>A Ser127Asn
M0168907 EFCJOJCK_00024 19806 3 Gut 0.09 protein_coding missense_variant MODERATE 100T>G Ser34Ala
M0168908 EFCJOJCK_00007 6827 3 Gut 0.09 protein_coding synonymous_variant LOW 255T>C Thr85Thr
M0168909 EFCJOJCK_00007 6897 3 Gut 0.09 protein_coding missense_variant MODERATE 185C>T Thr62Ile
M0168910 EFCJOJCK_00008 7639 6 Gut 0.18 protein_coding missense_variant MODERATE 568T>G Ser190Ala
M0168911 EFCJOJCK_00009 8911 5 Gut 0.15 protein_coding missense_variant MODERATE 140C>A Thr47Lys
M0168912 EFCJOJCK_00009 8969 6 Gut 0.18 protein_coding synonymous_variant LOW 82C>T Leu28Leu
M0168913 EFCJOJCK_00006 9165 6 Gut 0.18 protein_coding upstream_gene_variant MODIFIER -3215T>C None
M0168914 EFCJOJCK_00011 10944 9 Gut 0.27 protein_coding missense_variant MODERATE 710T>G Leu237Arg
M0168915 EFCJOJCK_00012 11071 6 Gut 0.18 protein_coding missense_variant MODERATE 74A>T Tyr25Phe
M0168916 EFCJOJCK_00013 12093 5 Gut 0.15 protein_coding missense_variant MODERATE 320A>T Asn107Ile
M0168917 EFCJOJCK_00014 12662 6 Gut 0.18 protein_coding missense_variant MODERATE 104A>C His35Pro
M0168918 EFCJOJCK_00019 16003 3 Gut 0.09 protein_coding synonymous_variant LOW 627T>A Pro209Pro
M0168919 EFCJOJCK_00019 16009 3 Gut 0.09 protein_coding synonymous_variant LOW 621C>T Asn207Asn
M0168920 EFCJOJCK_00019 16039 3 Gut 0.09 protein_coding synonymous_variant LOW 591T>C Ile197Ile
M0168921 EFCJOJCK_00019 16106 4 Gut 0.12 protein_coding missense_variant MODERATE 524T>A Val175Glu
M0168922 EFCJOJCK_00019 16164 4 Gut 0.12 protein_coding missense_variant MODERATE 466G>A Val156Ile
M0168923 EFCJOJCK_00019 16269 3 Gut 0.09 protein_coding missense_variant MODERATE 361A>G Ile121Val
M0168924 EFCJOJCK_00019 16272 3 Gut 0.09 protein_coding synonymous_variant LOW 358C>A Arg120Arg
M0168925 EFCJOJCK_00019 16292 3 Gut 0.09 protein_coding missense_variant MODERATE 338T>C Val113Ala
M0168926 EFCJOJCK_00019 16341 3 Gut 0.09 protein_coding synonymous_variant LOW 289C>T Leu97Leu
M0168927 EFCJOJCK_00019 16342 3 Gut 0.09 protein_coding synonymous_variant LOW 288A>G Gly96Gly
M0168928 EFCJOJCK_00019 16372 3 Gut 0.09 protein_coding synonymous_variant LOW 258A>G Arg86Arg
M0168929 EFCJOJCK_00019 16378 3 Gut 0.09 protein_coding synonymous_variant LOW 252T>G Thr84Thr
M0168930 EFCJOJCK_00019 16381 3 Gut 0.09 protein_coding synonymous_variant LOW 249A>C Thr83Thr
M0168931 EFCJOJCK_00019 16408 3 Gut 0.09 protein_coding synonymous_variant LOW 222T>C Thr74Thr
M0168932 EFCJOJCK_00019 16441 3 Gut 0.09 protein_coding synonymous_variant LOW 189T>C Asp63Asp
M0168933 EFCJOJCK_00019 16449 3 Gut 0.09 protein_coding missense_variant MODERATE 181T>A Phe61Ile
M0168934 EFCJOJCK_00019 16483 3 Gut 0.09 protein_coding synonymous_variant LOW 147G>A Ser49Ser
M0168935 EFCJOJCK_00019 16517 3 Gut 0.09 protein_coding missense_variant MODERATE 113T>G Leu38Trp






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
EFCJOJCK_00005 PHI:5205 HMPREF0351_10118 (WxL locusC) 78.1 9.7e-44 1 105 1.0000 0.8571 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence






        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