Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C896
  Reference Plasmid   NZ_CP074369.1
  Reference Plasmid Size   93492
  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
M0188187 CLNLNEAD_00039 40319 3 Gut 1.00 protein_coding missense_variant MODERATE 367A>G Ile123Val
M0188188 CLNLNEAD_00040 46560 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4276G>A None
M0188189 CLNLNEAD_00047 49658 3 Gut 1.00 protein_coding synonymous_variant LOW 225C>A Val75Val
M0188190 CLNLNEAD_00047 49659 3 Gut 1.00 protein_coding missense_variant MODERATE 224T>G Val75Gly
M0188191 CLNLNEAD_00047 49676 3 Gut 1.00 protein_coding synonymous_variant LOW 207A>C Thr69Thr
M0188192 CLNLNEAD_00047 49706 3 Gut 1.00 protein_coding synonymous_variant LOW 177T>C Ser59Ser
M0188193 CLNLNEAD_00047 49741 3 Gut 1.00 protein_coding synonymous_variant LOW 142T>C Leu48Leu
M0188194 CLNLNEAD_00047 49752 3 Gut 1.00 protein_coding missense_variant MODERATE 131T>C Ile44Thr
M0188195 CLNLNEAD_00047 49770 3 Gut 1.00 protein_coding missense_variant MODERATE 113A>T Gln38Leu
M0188196 CLNLNEAD_00047 49778 3 Gut 1.00 protein_coding synonymous_variant LOW 105G>A Thr35Thr
M0188197 CLNLNEAD_00047 49835 3 Gut 1.00 protein_coding synonymous_variant LOW 48A>C Ala16Ala
M0188198 CLNLNEAD_00043 50284 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -3801T>C None
M0188199 CLNLNEAD_00048 50371 3 Gut 1.00 protein_coding synonymous_variant LOW 27G>A Lys9Lys
M0188200 CLNLNEAD_00048 50567 3 Gut 1.00 protein_coding synonymous_variant LOW 223T>C Leu75Leu
M0188201 CLNLNEAD_00048 50581 3 Gut 1.00 protein_coding synonymous_variant LOW 237T>C Tyr79Tyr






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
CLNLNEAD_00007 VFG043568 OmpD 77.8 4.2e-163 8 370 0.9811 1.0028 Adherence phosphoporin PhoE 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
CLNLNEAD_00007 Methyl Viologen [class: Paraquat] 77.8 8.8e-165 8 370 1.0000 1.0221 experiment
CLNLNEAD_00007 Methyl Viologen [class: Paraquat] 98.6 2e-210 1 370 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






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
CLNLNEAD_00007 PHI:123435 ompD 77.8 1.5e-163 8 370 0.9811 0.9890 rodents salmonellosis porin OmpD unaffected pathogenicity






        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
CLNLNEAD_00005 AJS09995.1|GH24 100 4.67e-139 1 185 1 1
CLNLNEAD_00024 QMJ72311.1|GH23 98 0 1 1124 1 1
CLNLNEAD_00103 AYL89119.1|GH24 97.2 0 946 1448 0.3474 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
CLNLNEAD_00007 1.B.1.1.4 80.9 2.7e-173 1 370 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.1 The General Bacterial Porin (GBP) Family
CLNLNEAD_00014 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