Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1377
  Reference Plasmid   NZ_MH781719.1
  Reference Plasmid Size   93227
  Reference Plasmid GC Content   0.47
  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
M0208566 AMDDKCAG_00030 29621 3 Gut 0.75 protein_coding missense_variant MODERATE 1343T>C Val448Ala
M0208567 AMDDKCAG_00045 44771 3 Gut 0.75 protein_coding synonymous_variant LOW 366T>C Thr122Thr






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
AMDDKCAG_00040 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
AMDDKCAG_00040 Methyl Viologen [class: Paraquat] 77.8 8.8e-165 8 370 1.0000 1.0221 experiment
AMDDKCAG_00040 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
AMDDKCAG_00018 ARO:3007279 100 0 1 540 1.0000 1.0000 peptide antibiotic MCR phosphoethanolamine transferase antibiotic target alteration






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
AMDDKCAG_00018 PHI:11668 mcr-1 99.8 9.69999999999549e-313 1 540 1.0000 0.9982 moths infection probable phosphatidylethanolamine transferase increased virulence (hypervirulence)
AMDDKCAG_00040 PHI:123435 ompD 77.8 1.5e-163 8 370 0.9811 0.9890 rodents salmonellosis porin OmpD unaffected pathogenicity
AMDDKCAG_00068 PHI:3317 hsdR 73 0 1 1038 1.0000 1.0000 rodents Glasser's disease involved in pathogenicity 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
AMDDKCAG_00025 QHN43444.1|GH23 100 0 1 1130 1 1
AMDDKCAG_00042 AJS09995.1|GH24 100 4.67e-139 1 185 1 1
AMDDKCAG_00045 AYL89119.1|GH24 96.4 1.31999997843082e-316 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
AMDDKCAG_00033 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
AMDDKCAG_00040 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