Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C106
  Reference Plasmid   CP056820.1
  Reference Plasmid Size   36067
  Reference Plasmid GC Content   0.41
  Reference Plasmid Mobility Type   conjugative





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
M0144150 NLPJCOIG_00015 10921 3 Gut 0.60 protein_coding synonymous_variant LOW 381A>G Gly127Gly
M0144151 NLPJCOIG_00015 10975 3 Gut 0.60 protein_coding synonymous_variant LOW 327G>A Arg109Arg
M0144152 NLPJCOIG_00015 11024 3 Gut 0.60 protein_coding missense_variant MODERATE 278C>A Ala93Asp
M0144153 NLPJCOIG_00016 11370 3 Gut 0.60 protein_coding synonymous_variant LOW 966T>G Arg322Arg
M0144154 NLPJCOIG_00016 11505 3 Gut 0.60 protein_coding synonymous_variant LOW 831T>C Ala277Ala
M0144155 NLPJCOIG_00016 11817 3 Gut 0.60 protein_coding synonymous_variant LOW 519T>G Gly173Gly
M0144156 NLPJCOIG_00016 11826 3 Gut 0.60 protein_coding synonymous_variant LOW 510T>A Gly170Gly
M0144157 NLPJCOIG_00016 11855 3 Gut 0.60 protein_coding missense_variant MODERATE 481C>A Arg161Ser
M0144158 NLPJCOIG_00016 11877 3 Gut 0.60 protein_coding missense_variant MODERATE 459T>A Asp153Glu
M0144159 NLPJCOIG_00016 11925 3 Gut 0.60 protein_coding synonymous_variant LOW 411G>C Ser137Ser
M0144160 NLPJCOIG_00016 11945 3 Gut 0.60 protein_coding missense_variant MODERATE 391A>G Ser131Gly
M0144161 NLPJCOIG_00016 12138 3 Gut 0.60 protein_coding synonymous_variant LOW 198C>T Ala66Ala
M0144162 NLPJCOIG_00016 12201 3 Gut 0.60 protein_coding synonymous_variant LOW 135A>G Lys45Lys
M0144163 NLPJCOIG_00016 12246 3 Gut 0.60 protein_coding synonymous_variant LOW 90T>C Ile30Ile
M0144164 NLPJCOIG_00016 12261 3 Gut 0.60 protein_coding missense_variant MODERATE 75G>T Glu25Asp
M0144165 NLPJCOIG_00017 12367 3 Gut 0.60 protein_coding synonymous_variant LOW 1176C>T Gly392Gly
M0144166 NLPJCOIG_00017 13063 3 Gut 0.60 protein_coding synonymous_variant LOW 480T>C Ser160Ser
M0144167 NLPJCOIG_00017 13117 3 Gut 0.60 protein_coding synonymous_variant LOW 426T>C Ser142Ser
M0144168 NLPJCOIG_00018 13752 3 Gut 0.60 protein_coding synonymous_variant LOW 717T>C Ser239Ser
M0144169 NLPJCOIG_00023 19802 3 Gut 0.60 protein_coding missense_variant MODERATE 580T>A Phe194Ile
M0144170 NLPJCOIG_00025 21016 3 Gut 0.60 protein_coding missense_variant MODERATE 309G>T Glu103Asp
M0144171 NLPJCOIG_00022 22205 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -4588A>G None
M0144172 NLPJCOIG_00027 22381 3 Gut 0.60 protein_coding missense_variant MODERATE 1156G>T Gly386Trp
M0144173 NLPJCOIG_00027 22519 3 Gut 0.60 protein_coding missense_variant MODERATE 1018G>A Ala340Thr






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
NLPJCOIG_00025 QJH52185.1|GH23 99.5 1.52e-152 1 215 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