Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C46
  Reference Plasmid   AP028537.1
  Reference Plasmid Size   120373
  Reference Plasmid GC Content   0.52
  Reference Plasmid Mobility Type   conjugative





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
M0143070 DDLIIDDG_00089 78499 5 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -3476T>G None
M0143071 DDLIIDDG_00096 79306 5 Gut 0.50 protein_coding synonymous_variant LOW 342T>C Val114Val
M0143072 DDLIIDDG_00097 79584 5 Gut 0.50 protein_coding synonymous_variant LOW 429G>C Leu143Leu
M0143073 DDLIIDDG_00097 79634 5 Gut 0.50 protein_coding missense_variant MODERATE 379C>A Gln127Lys
M0143074 DDLIIDDG_00097 80240 5 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -228C>A None
M0143075 DDLIIDDG_00098 80519 4 Gut 0.40 protein_coding missense_variant MODERATE 73A>G Thr25Ala
M0143076 DDLIIDDG_00098 80524 4 Gut 0.40 protein_coding missense_variant MODERATE 78G>T Glu26Asp
M0143077 DDLIIDDG_00098 80532 4 Gut 0.40 protein_coding missense_variant MODERATE 86G>A Arg29Lys
M0143078 DDLIIDDG_00098 80677 4 Gut 0.40 protein_coding synonymous_variant LOW 231G>A Thr77Thr
M0143079 DDLIIDDG_00098 80791 3 Gut 0.30 protein_coding synonymous_variant LOW 345A>G Glu115Glu
M0143080 DDLIIDDG_00090 75285 3 Gut 0.30 protein_coding missense_variant MODERATE 73A>G Ile25Val
M0143081 DDLIIDDG_00090 75477 3 Gut 0.30 protein_coding missense_variant MODERATE 265A>G Asn89Asp
M0143082 DDLIIDDG_00091 75538 3 Gut 0.30 protein_coding synonymous_variant LOW 57A>G Ala19Ala
M0143083 DDLIIDDG_00089 76029 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -1006C>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
DDLIIDDG_00008 VFG002901 O-antigen 71.5 2.8e-85 1 228 1.0 1 Immune modulation histidine ABC transporter permease HisQ 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
DDLIIDDG_00033 AUY68670.1|GH1 99.2 0 1 479 1 1
DDLIIDDG_00038 QAX13367.1|GH1 99.8 0 1 467 1 1
DDLIIDDG_00097 QJO48544.1|GH23 100 9.06e-113 1 159 1 1





        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
DDLIIDDG_00006 3.A.1.3.29 86 4.4e-122 1 257 1.0000 1.1272 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
DDLIIDDG_00007 3.A.1.3.29 82.6 2.8e-107 1 235 0.9874 1.0307 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
DDLIIDDG_00008 3.A.1.3.29 73.2 1.4e-87 1 228 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
DDLIIDDG_00088 1.E.53.1.7 72 9e-14 1 50 0.9434 0.7042 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family