Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C381
  Reference Plasmid   NZ_AP025236.1
  Reference Plasmid Size   7659
  Reference Plasmid GC Content   0.38
  Reference Plasmid Mobility Type   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
M0163615 LHAJEFPH_00003 791 3 Gut 1.00 protein_coding synonymous_variant LOW 444C>T Ile148Ile
M0163616 LHAJEFPH_00003 854 3 Gut 1.00 protein_coding synonymous_variant LOW 381A>G Ala127Ala
M0163617 LHAJEFPH_00003 881 3 Gut 1.00 protein_coding synonymous_variant LOW 354G>A Glu118Glu
M0163618 LHAJEFPH_00003 1178 3 Gut 1.00 protein_coding synonymous_variant LOW 57T>G Gly19Gly
M0163619 LHAJEFPH_00005 1734 3 Gut 1.00 protein_coding synonymous_variant LOW 243A>G Ala81Ala
M0163620 LHAJEFPH_00005 1736 3 Gut 1.00 protein_coding missense_variant MODERATE 241G>A Ala81Thr
M0163621 LHAJEFPH_00005 1749 3 Gut 1.00 protein_coding synonymous_variant LOW 228A>G Lys76Lys
M0163622 LHAJEFPH_00005 1752 3 Gut 1.00 protein_coding synonymous_variant LOW 225G>A Leu75Leu
M0163623 LHAJEFPH_00001 4311 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -3868A>G None
M0163624 LHAJEFPH_00001 4469 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4026T>C None
M0163625 LHAJEFPH_00010 5291 3 Gut 1.00 protein_coding synonymous_variant LOW 195C>A Gly65Gly
M0163626 LHAJEFPH_00010 5344 3 Gut 1.00 protein_coding missense_variant MODERATE 248C>A Ala83Glu
M0163627 LHAJEFPH_00010 5355 3 Gut 1.00 protein_coding missense_variant MODERATE 259G>A Glu87Lys
M0163628 LHAJEFPH_00010 5432 3 Gut 1.00 protein_coding synonymous_variant LOW 336G>A Ala112Ala
M0163629 LHAJEFPH_00010 5525 3 Gut 1.00 protein_coding synonymous_variant LOW 429T>C His143His
M0163630 LHAJEFPH_00010 5677 3 Gut 1.00 protein_coding missense_variant MODERATE 581A>G His194Arg
M0163631 LHAJEFPH_00010 5774 3 Gut 1.00 protein_coding synonymous_variant LOW 678T>C Ala226Ala
M0163632 LHAJEFPH_00010 5861 3 Gut 1.00 protein_coding missense_variant MODERATE 765A>T Glu255Asp
M0163633 LHAJEFPH_00011 6063 3 Gut 1.00 protein_coding synonymous_variant LOW 174T>C Ala58Ala
M0163634 LHAJEFPH_00011 6948 3 Gut 1.00 protein_coding synonymous_variant LOW 1059C>T Val353Val
M0163635 LHAJEFPH_00011 7209 3 Gut 1.00 protein_coding synonymous_variant LOW 1320G>A Gly440Gly
M0163636 LHAJEFPH_00011 7218 3 Gut 1.00 protein_coding synonymous_variant LOW 1329A>G Thr443Thr
M0163637 LHAJEFPH_00011 7239 3 Gut 1.00 protein_coding missense_variant MODERATE 1350G>T Leu450Phe
M0163638 LHAJEFPH_00011 7242 3 Gut 1.00 protein_coding synonymous_variant LOW 1353G>T Gly451Gly
M0163639 LHAJEFPH_00011 7500 3 Gut 1.00 protein_coding synonymous_variant LOW 1611G>A Arg537Arg
M0163640 LHAJEFPH_00007 7577 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4888G>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







        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





        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