Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C856
  Reference Plasmid   NZ_CP070295.1
  Reference Plasmid Size   98546
  Reference Plasmid GC Content   0.48
  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
M0185138 IIBDNADL_00016 15650 3 Gut 0.50 protein_coding synonymous_variant LOW 390T>C Ile130Ile
M0185139 IIBDNADL_00016 15779 3 Gut 0.50 protein_coding synonymous_variant LOW 519G>A Lys173Lys
M0185140 IIBDNADL_00016 15782 3 Gut 0.50 protein_coding synonymous_variant LOW 522T>A Pro174Pro
M0185141 IIBDNADL_00016 15785 3 Gut 0.50 protein_coding synonymous_variant LOW 525A>G Glu175Glu
M0185142 IIBDNADL_00020 15802 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -2807C>A None
M0185143 IIBDNADL_00020 15805 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -2804T>G None
M0185144 IIBDNADL_00020 15814 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -2795G>C None
M0185145 IIBDNADL_00017 15823 3 Gut 0.50 protein_coding synonymous_variant LOW 528T>A Pro176Pro
M0185146 IIBDNADL_00017 15838 3 Gut 0.50 protein_coding synonymous_variant LOW 513A>G Thr171Thr
M0185147 IIBDNADL_00017 15852 3 Gut 0.50 protein_coding missense_variant MODERATE 499A>G Ser167Gly
M0185148 IIBDNADL_00017 15856 3 Gut 0.50 protein_coding synonymous_variant LOW 495C>T Thr165Thr
M0185149 IIBDNADL_00018 16896 3 Gut 0.50 protein_coding synonymous_variant LOW 978T>C Tyr326Tyr
M0185150 IIBDNADL_00018 16951 3 Gut 0.50 protein_coding missense_variant MODERATE 923T>G Ile308Ser
M0185151 IIBDNADL_00018 17142 3 Gut 0.50 protein_coding synonymous_variant LOW 732C>T Phe244Phe
M0185152 IIBDNADL_00018 17148 3 Gut 0.50 protein_coding synonymous_variant LOW 726A>G Ala242Ala
M0185153 IIBDNADL_00018 17161 3 Gut 0.50 protein_coding missense_variant MODERATE 713C>T Thr238Ile
M0185154 IIBDNADL_00018 17162 3 Gut 0.50 protein_coding missense_variant MODERATE 712A>G Thr238Ala
M0185155 IIBDNADL_00018 17167 3 Gut 0.50 protein_coding missense_variant MODERATE 707A>G Asn236Ser
M0185156 IIBDNADL_00018 17223 3 Gut 0.50 protein_coding synonymous_variant LOW 651T>C Thr217Thr
M0185157 IIBDNADL_00018 17241 3 Gut 0.50 protein_coding synonymous_variant LOW 633T>A Pro211Pro
M0185158 IIBDNADL_00018 17250 3 Gut 0.50 protein_coding synonymous_variant LOW 624G>A Ala208Ala






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






        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
IIBDNADL_00009 QST66789.1|GH23 100 0 1 1110 1 1
IIBDNADL_00032 AJS09995.1|GH24 100 4.67e-139 1 185 1 1
IIBDNADL_00036 AYL89119.1|GH24 95.6 0 1753 2255 0.2231 0.9031





        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
IIBDNADL_00020 1.E.4.1.2 98.9 1.7e-47 1 93 1.0000 1.0000 1 Channels/Pores 1.E Holins 1.E.4 The LydA Holin (LydA Holin) Family
IIBDNADL_00021 1.E.4.1.1 100 1.3e-54 1 109 1.0000 1.0000 1 Channels/Pores 1.E Holins 1.E.4 The LydA Holin (LydA Holin) Family
IIBDNADL_00033 1.E.64.1.1 100 3.4e-39 1 84 1.0000 1.0000 1 Channels/Pores 1.E Holins 1.E.64 The P7 Phage Holin LydD (LydD) Family