Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C256
  Reference Plasmid   LR962324.1
  Reference Plasmid Size   65146
  Reference Plasmid GC Content   0.33
  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
M0149931 DAPHLMFK_00055 45229 6 Gut 0.67 protein_coding synonymous_variant LOW 582C>A Gly194Gly
M0149932 DAPHLMFK_00055 45649 7 Gut 0.78 protein_coding synonymous_variant LOW 162T>C Tyr54Tyr
M0149933 DAPHLMFK_00055 45739 7 Gut 0.78 protein_coding synonymous_variant LOW 72T>C Tyr24Tyr
M0149934 DAPHLMFK_00058 46830 7 Gut 0.78 protein_coding missense_variant MODERATE 172C>T Pro58Ser
M0149935 DAPHLMFK_00060 49015 8 Gut 0.89 protein_coding missense_variant MODERATE 433G>A Glu145Lys
M0149936 DAPHLMFK_00060 49337 8 Gut 0.89 protein_coding synonymous_variant LOW 111A>C Ile37Ile
M0149937 DAPHLMFK_00060 49383 7 Gut 0.78 protein_coding missense_variant MODERATE 65C>A Ser22Tyr
M0149938 DAPHLMFK_00060 49388 8 Gut 0.89 protein_coding synonymous_variant LOW 60T>C His20His
M0149939 DAPHLMFK_00049 44688 5 Gut 0.56 protein_coding upstream_gene_variant MODIFIER -2971G>A None
M0149940 DAPHLMFK_00049 44816 5 Gut 0.56 protein_coding upstream_gene_variant MODIFIER -3099C>T None
M0149941 DAPHLMFK_00049 44839 5 Gut 0.56 protein_coding upstream_gene_variant MODIFIER -3122C>T 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
DAPHLMFK_00053 VFG002162 BSH 73.8 1.9e-147 1 324 1.0 0.9969 Stress survival bile salt hydrolase experiment
DAPHLMFK_00053 VFG019385 BSH 74.4 3.3e-148 1 324 1.0 0.9969 Stress survival bile salt hydrolase 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
DAPHLMFK_00003 PHI:5205 HMPREF0351_10118 (WxL locusC) 93.1 1.2e-123 1 231 1.0000 0.7704 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
DAPHLMFK_00035 PHI:5205 HMPREF0351_10118 (WxL locusC) 83.1 2.8e-30 1 71 0.8765 0.7704 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
DAPHLMFK_00060 PHI:5205 HMPREF0351_10118 (WxL locusC) 91.9 1.9e-83 1 160 1.0000 0.7704 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis 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
DAPHLMFK_00042 QTQ90882.1|GT4 99.2 4.15e-297 1 399 1 1
DAPHLMFK_00043 QMX55304.1|GT4 100 6.85e-273 1 376 1 1
DAPHLMFK_00044 QMX55303.1|GT2 100 2.02e-211 1 287 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
DAPHLMFK_00015 3.A.7.19.1 92.8 2.3e-243 3 447 0.9955 0.7932 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
DAPHLMFK_00018 3.A.7.19.1 86.8 2.3e-285 1 561 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
DAPHLMFK_00025 1.C.24.1.12 98.6 2.4e-38 1 71 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.24 The Pediocin (Pediocin) Family