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PlasmidVar Mutation Annotation Categories







Summary information of mutation

Basic Information about Mutation.

  Gene Information   Gene Name   ODBHLOBF_00029
  Gene Type   protein_coding
  Mutation type   synonymous_variant
  Genome position   23895
  Reference   genome   1111525849736575_bin.9__k141_15879
  DNA Level   DNA Mutation: 171A>G
  Ref Seq: T
  Mut Seq: C
  Protein Level   Protein 1-letter Mutation: K57K
  Protein 3-letter Mutation: Lys57Lys





Analyzing the distribution of mutation across skin, oral, gut, and vaginal tissues.


The table summarizes the frequency and tissue-specific distribution of plasmid mutations detected in human skin, oral, gut, and vaginal microbiomes.
      Note: The mutation frequency of each mutation was calculated separately for each plasmid cluster and tissue. The biological effects of the identified mutations were annotated using SnpEff.

Mutation ID Gene Name Position Mutation Count Mutation Frequency Tissue Distribution Biotype Consequence Mutation Impact
M0021847 ODBHLOBF_00029 23895 4 0.11 Skin protein_coding synonymous_variant LOW






Investigating natural selection at mutation site for genetic adaptation and diversity


The MEME method within the HyPhy software was employed to analyze positive selection. MEME: episodic selection.
      Note: List of sites found to be under episodic selection by MEME (p < 0.05). "Protein Start" corresponds to the protein's starting genomic position. "Protein End" corresponds to the protein's ending genomic position. The term 'site' represents a selection site within the protein.

Protein name Protein start Protein end Protein length Site P-value Plasmid cluster Method


The FEL method within the HyPhy software was employed to analyze both positive and negative selection. FEL: pervasive selection on samll datasets.
      Note: List of sites found to be under pervasive selection by FEL (p < 0.05). A beta value greater than alpha signifies positive selection, while a beta value smaller than alpha signifies negative selection. "Protein Start" corresponds to the protein's starting genomic position. "Protein End" corresponds to the protein's ending genomic position. The term 'site' represents a selection site within the protein.

Protein name Protein start Protein end Protein length Site Alpha Beta P-value Plasmid cluster Method






Alterations in protein physicochemical properties induced by mutation

Understanding the alterations in protein physicochemical properties can reveal the evolutionary processes and adaptive changes of viruses
      Note: ProtParam software was used for the analysis of physicochemical properties. Significant change threshold: A change exceeding 10% compared to the reference is considered a significant change. "GRAVY" is an abbreviation for "grand average of hydropathicity".

Group Protein name Molecular weight Theoretical PI Extinction coefficients Aliphatic index instability_index instability_classifies




Alterations in protein stability induced by mutation

The impact of mutations on protein stability directly or indirectly affects the biological characteristics, adaptability, and transmission capacity of the virus
      Note: iMutant 2.0 was utilized to analyze the effects of mutations on protein stability. pH 7 and a temperature of 25°C are employed to replicate the in vitro environment. pH 7.4 and a temperature of 37°C are utilized to simulate the in vivo environment.

Mutation Mutation type Position ΔDDG Stability pH Temperature Condition Tissue




Alterations in enzyme cleavage sites induced by mutation

Exploring the impact of mutations on the cleavage sites of 28 enzymes.
      Note: The PeptideCutter software was used for detecting enzymes cleavage sites. The increased enzymes cleavage sites refer to the cleavage sites in the mutated protein that are added compared to the reference protein. Conversely, the decreased enzymes cleavage sites indicate the cleavage sites in the mutated protein that are reduced compared to the reference protein.

Mutation Protein name Genome position Enzyme name Increased cleavage sites Decreased cleavage sites




Impact of mutation on antigenicity and immunogenicity

Investigating the impact of mutations on antigenicity and immunogenicity carries important implications for vaccine design and our understanding of immune responses.
      Note: An absolute change greater than 0.0102 (three times the median across sites) in antigenicity score is considered significant. An absolute changegreater than 0.2754 (three times the median across sites) in immunogenicity score is considered significant. The VaxiJen tool was utilized for antigenicity analysis. The IEDB tool was used for immunogenicity analysis. Antigens with a prediction score of more than 0.4 for this tool are considered candidate antigens. MHC I immunogenicity score >0, indicating a higher probability to stimulate an immune response.

Group Protein name Protein region Antigenicity score Immunogenicity score




Analysis of virulence factors contributing to bacterial pathogenicity

The table lists virulence factors linked to this mutation.
      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.

gname vf_name vf_gene_id vf_category q_start q_end query_coverage subject_coverage identity evalue gene_description group




        Analysis of biocide and heavy metal resistance genes to assess antimicrobial risk and environmental impact

The table lists biocide and heavy metal resistance genes linked to this mutation.
      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.

gname subject accession q_start q_end query_coverage subject_coverage identity evalue compound group
ODBHLOBF_00029 gi|544752042 WP_021178954.1 1 159 1.0252 1.0795 77.3 3.7e-36 Hydrochloric acid (HCl) [class: Acid] prediction




        Analyzing antimicrobial resistance genes to assess bacterial resistance to antibiotics and other antimicrobial agents

The table lists antimicrobial resistance genes linked to this mutation.
      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.

gname aro_name amr_gene_family aro_accession q_start q_end query_coverage subject_coverage identity evalue drug_class resistance_mechanism





Analysis of pathogenicity genes to explore pathogen-host interactions

The table lists pathogenicity genes linked to this mutation.
      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.

gname phi_molconn_id gene_name function phenotype_of_mutant q_start q_end query_coverage subject_coverage identity evalue source pathogen_species disease_name host_descripton





Analyzing carbohydrate-active enzyme genes to uncover mechanisms of nutrient degradation

The table lists carbohydrate-active enzyme genes linked to this mutation.
      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.

gname cazy_id q_start q_end query_coverage subject_coverage identity evalue




Analyzing transport proteins to understand bacterial strategies for substrate uptake and detoxification

The table lists transport proteins linked to this mutation.
      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.

class_field >
gname tcid q_start q_end query_coverage subject_coverage identity evalue class_term subclass subclass_term family family_term