Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C3089
  Reference Plasmid   MET0107_bin.1__k81_4629
  Reference Plasmid Size   61384
  Reference Plasmid GC Content   0.33
  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
M0074233 DMPHFPGH_00034 33867 3 Skin 0.30 protein_coding synonymous_variant LOW 66G>A Leu22Leu
M0074234 DMPHFPGH_00034 34033 3 Skin 0.30 protein_coding missense_variant MODERATE 232A>G Asn78Asp
M0074235 DMPHFPGH_00034 34048 3 Skin 0.30 protein_coding missense_variant MODERATE 247A>G Thr83Ala
M0074236 DMPHFPGH_00034 34054 3 Skin 0.30 protein_coding synonymous_variant LOW 253T>C Leu85Leu
M0074237 DMPHFPGH_00034 34191 3 Skin 0.30 protein_coding synonymous_variant LOW 390C>T Ile130Ile
M0074238 DMPHFPGH_00034 34254 3 Skin 0.30 protein_coding synonymous_variant LOW 453T>C Asp151Asp
M0074239 DMPHFPGH_00034 34513 3 Skin 0.30 protein_coding synonymous_variant LOW 712T>C Leu238Leu
M0074240 DMPHFPGH_00034 34521 3 Skin 0.30 protein_coding synonymous_variant LOW 720A>G Val240Val
M0074241 DMPHFPGH_00034 34575 3 Skin 0.30 protein_coding synonymous_variant LOW 774T>A Thr258Thr
M0074242 DMPHFPGH_00034 34684 3 Skin 0.30 protein_coding missense_variant MODERATE 883G>A Gly295Arg
M0074243 DMPHFPGH_00034 34685 3 Skin 0.30 protein_coding missense_variant MODERATE 884G>T Gly295Val
M0074244 DMPHFPGH_00034 34701 3 Skin 0.30 protein_coding synonymous_variant LOW 900G>A Thr300Thr
M0074245 DMPHFPGH_00035 34916 3 Skin 0.30 protein_coding synonymous_variant LOW 51C>G Thr17Thr
M0074246 DMPHFPGH_00035 35150 3 Skin 0.30 protein_coding synonymous_variant LOW 285G>A Val95Val
M0074247 DMPHFPGH_00035 35156 3 Skin 0.30 protein_coding synonymous_variant LOW 291T>C Phe97Phe






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
DMPHFPGH_00003 VFG001295 Staphopain 73.5 3.4e-167 1 396 1.0 1.0076 Exoenzyme staphopain cysteine proteinase SspB experiment
DMPHFPGH_00003 VFG001295 Staphopain 73.5 2.5e-166 1 396 1.0 1.0076 Exoenzyme staphopain cysteine proteinase SspB 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
DMPHFPGH_00003 PHI:11915 sspB 73 3.8e-165 1 396 1.0000 1.0000 primates abscess; sepsis staphopain B 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
DMPHFPGH_00062 UJC87785.1|GT4 99.9 0 1 1008 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
DMPHFPGH_00017 2.A.118.1.7 73.4 5.3e-215 7 521 0.9885 0.9981 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.118 The Basic Amino Acid Antiporter (ArcD) Family
DMPHFPGH_00031 2.A.52.1.5 83.5 3.7e-164 1 351 1.0000 0.9971 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.52 The Ni2+-Co2+ Transporter (NiCoT) Family