Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C3410
  Reference Plasmid   SRR1950730_bin.2__k91_7742
  Reference Plasmid Size   12744
  Reference Plasmid GC Content   0.31
  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
M0116886 IIMONLLA_00012 7935 4 Skin 0.67 protein_coding synonymous_variant LOW 1278T>G Val426Val
M0116887 IIMONLLA_00012 8196 4 Skin 0.67 protein_coding missense_variant MODERATE 1017T>A Phe339Leu
M0116888 IIMONLLA_00012 8312 4 Skin 0.67 protein_coding missense_variant MODERATE 901A>G Ile301Val
M0116889 IIMONLLA_00012 8316 3 Skin 0.50 protein_coding synonymous_variant LOW 897G>T Ser299Ser
M0116890 IIMONLLA_00012 8394 4 Skin 0.67 protein_coding synonymous_variant LOW 819T>A Thr273Thr
M0116891 IIMONLLA_00012 8397 4 Skin 0.67 protein_coding synonymous_variant LOW 816C>T Ile272Ile
M0116892 IIMONLLA_00012 8402 4 Skin 0.67 protein_coding missense_variant MODERATE 811T>A Ser271Thr
M0116893 IIMONLLA_00012 8522 3 Skin 0.50 protein_coding synonymous_variant LOW 691T>C Leu231Leu
M0116894 IIMONLLA_00012 8774 3 Skin 0.50 protein_coding missense_variant MODERATE 439A>G Ser147Gly
M0116895 IIMONLLA_00012 9126 4 Skin 0.67 protein_coding synonymous_variant LOW 87T>C Ile29Ile
M0116896 IIMONLLA_00013 9329 4 Skin 0.67 protein_coding missense_variant MODERATE 632A>G His211Arg
M0116897 IIMONLLA_00013 9400 3 Skin 0.50 protein_coding missense_variant MODERATE 561A>C Glu187Asp
M0116898 IIMONLLA_00013 9442 4 Skin 0.67 protein_coding synonymous_variant LOW 519T>A Leu173Leu
M0116899 IIMONLLA_00013 9490 4 Skin 0.67 protein_coding synonymous_variant LOW 471T>C Phe157Phe
M0116900 IIMONLLA_00013 9574 3 Skin 0.50 protein_coding synonymous_variant LOW 387T>G Ala129Ala
M0116901 IIMONLLA_00013 9597 3 Skin 0.50 protein_coding missense_variant MODERATE 364T>C Tyr122His
M0116902 IIMONLLA_00013 9675 4 Skin 0.67 protein_coding synonymous_variant LOW 286T>C Leu96Leu
M0116903 IIMONLLA_00013 9679 4 Skin 0.67 protein_coding synonymous_variant LOW 282C>T Ser94Ser
M0116904 IIMONLLA_00013 9711 4 Skin 0.67 protein_coding missense_variant MODERATE 250G>A Ala84Thr
M0116905 IIMONLLA_00013 9715 4 Skin 0.67 protein_coding synonymous_variant LOW 246T>C Arg82Arg
M0116906 IIMONLLA_00013 9820 4 Skin 0.67 protein_coding synonymous_variant LOW 141T>C Thr47Thr
M0116907 IIMONLLA_00013 9832 4 Skin 0.67 protein_coding synonymous_variant LOW 129A>C Ser43Ser
M0116908 IIMONLLA_00013 9919 4 Skin 0.67 protein_coding synonymous_variant LOW 42T>C Gly14Gly
M0116909 IIMONLLA_00013 9931 4 Skin 0.67 protein_coding synonymous_variant LOW 30C>A Ser10Ser
M0116910 IIMONLLA_00011 10044 4 Skin 0.67 protein_coding upstream_gene_variant MODIFIER -2750A>G None
M0116911 IIMONLLA_00006 7104 3 Skin 0.50 protein_coding upstream_gene_variant MODIFIER -3323C>T None
M0116912 IIMONLLA_00011 7172 3 Skin 0.50 protein_coding synonymous_variant LOW 123T>A Ile41Ile
M0116913 IIMONLLA_00011 7181 3 Skin 0.50 protein_coding synonymous_variant LOW 114G>A Leu38Leu
M0116914 IIMONLLA_00011 7240 3 Skin 0.50 protein_coding missense_variant MODERATE 55A>G Ile19Val
M0116915 IIMONLLA_00012 8903 3 Skin 0.50 protein_coding synonymous_variant LOW 310T>C Leu104Leu
M0116916 IIMONLLA_00012 8913 3 Skin 0.50 protein_coding synonymous_variant LOW 300A>T Ile100Ile
M0116917 IIMONLLA_00012 8961 3 Skin 0.50 protein_coding synonymous_variant LOW 252G>A Thr84Thr






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
IIMONLLA_00011 PHI:6581 VraH 70.5 4.1e-18 1 61 0.9839 0.9683 moths skin infection; food poisoning; respiratory disease involved in gallidermin and daptomycin resistance reduced virulence
IIMONLLA_00013 PHI:6579 VraD 74.2 3.8e-102 1 252 1.0000 1.0000 moths skin infection; food poisoning; respiratory disease involved in gallidermin and daptomycin resistance 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





        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
IIMONLLA_00013 3.A.1.134.11 74.2 8.4e-102 1 252 1.0000 4.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily