Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C532
  Reference Plasmid   NZ_CP026416.1
  Reference Plasmid Size   127843
  Reference Plasmid GC Content   0.38
  Reference Plasmid Mobility Type   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
M0093266 PNDEIBGD_00102 98417 3 Skin 0.13 protein_coding missense_variant MODERATE 10T>C Tyr4His
M0093267 PNDEIBGD_00123 116766 3 Skin 0.13 protein_coding missense_variant MODERATE 9T>A Asn3Lys
M0093268 PNDEIBGD_00123 116779 3 Skin 0.13 protein_coding missense_variant MODERATE 22G>A Val8Ile
M0093269 PNDEIBGD_00123 117042 3 Skin 0.13 protein_coding synonymous_variant LOW 285G>A Val95Val
M0093270 PNDEIBGD_00066 67150 3 Skin 0.13 protein_coding missense_variant MODERATE 271T>G Ser91Ala
M0093271 PNDEIBGD_00063 67450 3 Skin 0.13 protein_coding upstream_gene_variant MODIFIER -3516C>A 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







        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
PNDEIBGD_00129 Arsenic (As) 71.3 2.8e-69 27 193 0.8653 0.7198 experiment
PNDEIBGD_00118 Copper (Cu) 99.6 0 1 791 1.0000 1.0000 prediction
PNDEIBGD_00121 Cadmium (Cd), Zinc (Zn) 82.7 4.6e-109 1 226 1.0000 0.9869 prediction
PNDEIBGD_00129 Arsenic (As) 77.9 2.2e-75 22 193 0.8912 0.7167 prediction
PNDEIBGD_00130 Arsenic (As) 91.2 2.2e-201 4 365 0.9918 0.9972 prediction






        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
PNDEIBGD_00014 PHI:7520 VK055_1952 74.3 8.4e-207 9 490 0.9837 0.9897 rodents pneumonia betaine aldehyde dehydrogenase unaffected pathogenicity
PNDEIBGD_00112 PHI:10395 copD (ABUW_3327) 73.7 1.6e-120 1 293 1.0000 1.0000 moths nosocomial infection copper resistance D reduced virulence
PNDEIBGD_00113 PHI:10398 copC (ABUW_3326) 78.6 2.3e-52 1 126 1.0000 1.0000 moths nosocomial infection copper resistance protein reduced virulence
PNDEIBGD_00120 PHI:10394 cusS (ABUW_3324) 75.1 5.5e-200 1 457 0.9807 0.9978 moths nosocomial infection sensor kinase reduced virulence
PNDEIBGD_00121 PHI:10397 cusR (ABUW_3323) 95.1 2.5e-121 1 226 1.0000 0.9956 moths nosocomial infection DNA-binding response regulator reduced virulence
PNDEIBGD_00123 PHI:10392 pcoA (ABUW_3228) 71.8 3.9e-265 1 627 1.0000 1.0000 moths nosocomial infection copper resistance protein A reduced virulence
PNDEIBGD_00124 PHI:10396 copB (ABUW_3320) 70.8 2.3e-122 1 306 1.0000 1.0000 moths nosocomial infection autotransporter domain-containing protein 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
PNDEIBGD_00058 QXX86794.1|CE4 100 3e-250 1 320 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
PNDEIBGD_00112 9.B.62.1.6 73.7 3.6e-120 1 293 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.62 The Copper Resistance (CopD) Family