Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C156
  Reference Plasmid   CP088811.1
  Reference Plasmid Size   94402
  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
M0145678 JFIPDJDE_00006 6225 3 Gut 0.75 protein_coding synonymous_variant LOW 889A>C Arg297Arg
M0145679 JFIPDJDE_00006 6233 3 Gut 0.75 protein_coding synonymous_variant LOW 897A>G Pro299Pro
M0145680 JFIPDJDE_00007 6423 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -145G>A None
M0145681 JFIPDJDE_00007 6435 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -133T>C None
M0145682 JFIPDJDE_00007 6436 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -132A>T None
M0145683 JFIPDJDE_00007 6459 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -109C>T None
M0145684 JFIPDJDE_00007 6466 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -102A>T None
M0145685 JFIPDJDE_00007 6485 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -83C>T None
M0145686 JFIPDJDE_00007 6693 3 Gut 0.75 protein_coding synonymous_variant LOW 126G>A Ala42Ala
M0145687 JFIPDJDE_00007 6843 3 Gut 0.75 protein_coding synonymous_variant LOW 276T>G Leu92Leu
M0145688 JFIPDJDE_00007 6846 3 Gut 0.75 protein_coding synonymous_variant LOW 279A>C Ala93Ala
M0145689 JFIPDJDE_00007 6861 3 Gut 0.75 protein_coding synonymous_variant LOW 294G>T Thr98Thr
M0145690 JFIPDJDE_00007 6909 3 Gut 0.75 protein_coding synonymous_variant LOW 342T>C Thr114Thr
M0145691 JFIPDJDE_00007 7434 3 Gut 0.75 protein_coding synonymous_variant LOW 867C>T Gly289Gly
M0145692 JFIPDJDE_00007 7437 3 Gut 0.75 protein_coding synonymous_variant LOW 870T>A Thr290Thr
M0145693 JFIPDJDE_00007 7446 3 Gut 0.75 protein_coding synonymous_variant LOW 879A>C Ala293Ala
M0145694 JFIPDJDE_00007 7453 3 Gut 0.75 protein_coding missense_variant MODERATE 886A>G Thr296Ala
M0145695 JFIPDJDE_00007 7458 3 Gut 0.75 protein_coding synonymous_variant LOW 891A>G Glu297Glu
M0145696 JFIPDJDE_00007 7473 3 Gut 0.75 protein_coding synonymous_variant LOW 906C>A Ala302Ala
M0145697 JFIPDJDE_00007 7491 3 Gut 0.75 protein_coding synonymous_variant LOW 924G>A Pro308Pro
M0145698 JFIPDJDE_00007 7494 3 Gut 0.75 protein_coding synonymous_variant LOW 927G>T Leu309Leu
M0145699 JFIPDJDE_00007 7514 3 Gut 0.75 protein_coding missense_variant MODERATE 947A>G Lys316Arg
M0145700 JFIPDJDE_00007 7515 3 Gut 0.75 protein_coding missense_variant MODERATE 948A>T Lys316Asn
M0145701 JFIPDJDE_00007 7542 3 Gut 0.75 protein_coding synonymous_variant LOW 975T>C Val325Val
M0145702 JFIPDJDE_00007 7590 3 Gut 0.75 protein_coding synonymous_variant LOW 1023A>G Glu341Glu
M0145703 JFIPDJDE_00007 7608 3 Gut 0.75 protein_coding synonymous_variant LOW 1041T>G Gly347Gly
M0145704 JFIPDJDE_00007 7702 3 Gut 0.75 protein_coding missense_variant MODERATE 1135A>T Thr379Ser
M0145705 JFIPDJDE_00007 7761 3 Gut 0.75 protein_coding synonymous_variant LOW 1194T>C Arg398Arg






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
JFIPDJDE_00024 AOM57988.1|GH23 98.9 0 1 1124 1 1
JFIPDJDE_00046 AJS09995.1|GH24 100 4.67e-139 1 185 1 1
JFIPDJDE_00049 AYL89119.1|GH24 97 1.19999998039166e-317 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
JFIPDJDE_00035 1.E.4.1.2 90.3 4.3e-43 1 93 1.0000 1.0000 1 Channels/Pores 1.E Holins 1.E.4 The LydA Holin (LydA Holin) Family
JFIPDJDE_00036 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