Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C486
  Reference Plasmid   NZ_CP022913.1
  Reference Plasmid Size   63392
  Reference Plasmid GC Content   0.48
  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
M0167245 NIEDAMDD_00042 41872 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4194T>A None
M0167246 NIEDAMDD_00042 41873 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4195G>A None
M0167247 NIEDAMDD_00042 41875 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4197C>G None
M0167248 NIEDAMDD_00042 41877 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4199C>T None
M0167249 NIEDAMDD_00042 41878 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4200C>A None
M0167250 NIEDAMDD_00042 41893 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4215A>C None
M0167251 NIEDAMDD_00042 41897 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4219C>T None
M0167252 NIEDAMDD_00042 41908 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4230A>G None
M0167253 NIEDAMDD_00042 41912 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4234C>A None
M0167254 NIEDAMDD_00042 41913 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4235A>C None
M0167255 NIEDAMDD_00042 41957 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4279A>C None
M0167256 NIEDAMDD_00042 41958 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4280A>T None
M0167257 NIEDAMDD_00042 41959 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4281A>T None
M0167258 NIEDAMDD_00042 42010 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4332G>A None
M0167259 NIEDAMDD_00042 42020 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4342G>A None
M0167260 NIEDAMDD_00042 42047 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4369C>G None
M0167261 NIEDAMDD_00042 42049 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4371G>A None
M0167262 NIEDAMDD_00042 42052 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4374T>A None
M0167263 NIEDAMDD_00042 42185 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4507A>G None
M0167264 NIEDAMDD_00042 42221 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4543C>G None
M0167265 NIEDAMDD_00042 42222 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4544T>C None
M0167266 NIEDAMDD_00042 42285 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4607T>A None
M0167267 NIEDAMDD_00042 42305 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4627G>A None
M0167268 NIEDAMDD_00042 42311 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4633A>C None
M0167269 NIEDAMDD_00042 42312 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4634C>G None
M0167270 NIEDAMDD_00042 42321 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4643C>T None
M0167271 NIEDAMDD_00042 42356 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4678T>A None
M0167272 NIEDAMDD_00042 42411 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4733T>A None
M0167273 NIEDAMDD_00047 42483 3 Gut 0.30 protein_coding synonymous_variant LOW 846A>C Thr282Thr
M0167274 NIEDAMDD_00047 42495 3 Gut 0.30 protein_coding synonymous_variant LOW 834T>C Ser278Ser
M0167275 NIEDAMDD_00047 42585 3 Gut 0.30 protein_coding synonymous_variant LOW 744G>A Gly248Gly
M0167276 NIEDAMDD_00047 42593 3 Gut 0.30 protein_coding missense_variant MODERATE 736T>G Ser246Ala
M0167277 NIEDAMDD_00047 42603 3 Gut 0.30 protein_coding synonymous_variant LOW 726T>G Thr242Thr
M0167278 NIEDAMDD_00047 42612 3 Gut 0.30 protein_coding synonymous_variant LOW 717G>A Arg239Arg
M0167279 NIEDAMDD_00047 42649 3 Gut 0.30 protein_coding missense_variant MODERATE 680A>G Asn227Ser
M0167280 NIEDAMDD_00047 42650 3 Gut 0.30 protein_coding missense_variant MODERATE 679A>G Asn227Asp
M0167281 NIEDAMDD_00047 42675 3 Gut 0.30 protein_coding synonymous_variant LOW 654A>G Lys218Lys
M0167282 NIEDAMDD_00047 42684 3 Gut 0.30 protein_coding synonymous_variant LOW 645T>G Arg215Arg
M0167283 NIEDAMDD_00006 10266 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4428G>A None
M0167284 NIEDAMDD_00006 10328 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4490A>C None






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
NIEDAMDD_00020 VFG042754 Adhesive fimbriae 100 9.8e-63 1 113 1.0 0.8968 Adherence LngX1 prediction
NIEDAMDD_00021 VFG042755 Adhesive fimbriae 100 1.5e-54 1 101 1.0 1 Adherence LngR prediction
NIEDAMDD_00022 VFG042756 Adhesive fimbriae 99.7 9.2e-169 1 298 1.0 1 Adherence LngS prediction
NIEDAMDD_00023 VFG042757 Adhesive fimbriae 100 5.5e-82 1 147 1.0 1 Adherence LngT prediction
NIEDAMDD_00024 VFG042758 Adhesive fimbriae 100 5.6e-35 1 73 1.0 1 Adherence LngX2 prediction
NIEDAMDD_00025 VFG042759 Adhesive fimbriae 87.3 1.4e-108 1 236 1.0 1 Adherence LngA prediction
NIEDAMDD_00026 VFG042760 Adhesive fimbriae 99.6 3e-300 1 523 1.0 1 Adherence LngB prediction
NIEDAMDD_00027 VFG042761 Adhesive fimbriae 100 2.4e-71 1 137 1.0 1 Adherence LngC prediction
NIEDAMDD_00028 VFG042762 Adhesive fimbriae 99.8 5.2e-270 1 485 1.0 0.9858 Adherence LngD prediction
NIEDAMDD_00029 VFG042763 Adhesive fimbriae 100 2.5e-103 1 186 1.0 1 Adherence LngE prediction
NIEDAMDD_00030 VFG042764 Adhesive fimbriae 99.6 1e-142 1 256 0.9309 0.9961 Adherence LngF prediction
NIEDAMDD_00031 VFG042765 Adhesive fimbriae 100 3e-81 1 161 1.0 1 Adherence LngG prediction
NIEDAMDD_00032 VFG042766 Adhesive fimbriae 100 1.1e-262 67 510 0.8706 1 Adherence LngH prediction
NIEDAMDD_00033 VFG042781 Adhesive fimbriae 95 1.1e-165 1 320 0.9467 0.9384 Adherence CofI prediction
NIEDAMDD_00034 VFG042768 Adhesive fimbriae 99.5 2.2e-220 1 373 1.0 1 Adherence LngJ prediction
NIEDAMDD_00035 VFG042769 Adhesive fimbriae 100 5.7e-160 1 284 1.0 1 Adherence LngP prediction







        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
NIEDAMDD_00023 AOT35488.1|GH23 100 7.36e-104 1 147 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
NIEDAMDD_00049 1.E.53.1.11 98 3.2e-21 1 49 1.0000 0.7206 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family