Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2709
  Reference Plasmid   1111525849861219_bin.29__k141_296755
  Reference Plasmid Size   14927
  Reference Plasmid GC Content   0.38
  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
M0053231 IGGPBKBD_00006 6518 3 Skin 0.50 protein_coding synonymous_variant LOW 1413C>A Ser471Ser
M0053232 IGGPBKBD_00006 6584 3 Skin 0.50 protein_coding synonymous_variant LOW 1347T>G Ser449Ser
M0053233 IGGPBKBD_00006 6671 3 Skin 0.50 protein_coding synonymous_variant LOW 1260G>A Ala420Ala
M0053234 IGGPBKBD_00006 6674 3 Skin 0.50 protein_coding synonymous_variant LOW 1257A>T Val419Val
M0053235 IGGPBKBD_00006 6677 3 Skin 0.50 protein_coding synonymous_variant LOW 1254A>C Ser418Ser
M0053236 IGGPBKBD_00006 7155 3 Skin 0.50 protein_coding missense_variant MODERATE 776A>G Tyr259Cys
M0053237 IGGPBKBD_00006 7712 3 Skin 0.50 protein_coding synonymous_variant LOW 219C>T Ser73Ser
M0053238 IGGPBKBD_00006 7859 3 Skin 0.50 protein_coding synonymous_variant LOW 72T>A Arg24Arg
M0053239 IGGPBKBD_00007 8297 4 Skin 0.67 protein_coding missense_variant MODERATE 82A>G Ile28Val
M0053240 IGGPBKBD_00007 8306 4 Skin 0.67 protein_coding missense_variant MODERATE 91A>G Ile31Val
M0053241 IGGPBKBD_00007 8327 4 Skin 0.67 protein_coding missense_variant MODERATE 112G>T Ala38Ser
M0053242 IGGPBKBD_00007 8368 4 Skin 0.67 protein_coding synonymous_variant LOW 153A>C Ser51Ser
M0053243 IGGPBKBD_00006 8515 4 Skin 0.67 protein_coding upstream_gene_variant MODIFIER -585A>G None
M0053244 IGGPBKBD_00008 8688 4 Skin 0.67 protein_coding missense_variant MODERATE 160G>A Val54Ile
M0053245 IGGPBKBD_00008 8763 4 Skin 0.67 protein_coding missense_variant MODERATE 235C>T His79Tyr
M0053246 IGGPBKBD_00008 8792 4 Skin 0.67 protein_coding missense_variant MODERATE 264A>C Lys88Asn
M0053247 IGGPBKBD_00008 8801 3 Skin 0.50 protein_coding synonymous_variant LOW 273G>A Leu91Leu
M0053248 IGGPBKBD_00008 8816 3 Skin 0.50 protein_coding synonymous_variant LOW 288A>T Ser96Ser
M0053249 IGGPBKBD_00009 9185 3 Skin 0.50 protein_coding missense_variant MODERATE 73G>A Val25Ile
M0053250 IGGPBKBD_00006 9316 3 Skin 0.50 protein_coding upstream_gene_variant MODIFIER -1386G>A None
M0053251 IGGPBKBD_00010 9519 3 Skin 0.50 protein_coding missense_variant MODERATE 190A>G Ile64Val
M0053252 IGGPBKBD_00010 9764 3 Skin 0.50 protein_coding synonymous_variant LOW 435T>C Arg145Arg
M0053253 IGGPBKBD_00010 9923 3 Skin 0.50 protein_coding missense_variant MODERATE 594C>A Asn198Lys






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
IGGPBKBD_00006 PHI:11789 spd_1587 (MgaSpn) 97.8 3.3e-275 1 492 1.0000 0.9980 rodents pneumonia transcriptional activator, putative increased virulence (hypervirulence)






        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