Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2283
  Reference Plasmid   1111525849758951_bin.8__k141_541259
  Reference Plasmid Size   17132
  Reference Plasmid GC Content   0.55
  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
M0033224 DNCGDJNA_00008 8069 3 Skin 0.16 protein_coding synonymous_variant LOW 708C>T Phe236Phe
M0033225 DNCGDJNA_00008 8078 3 Skin 0.16 protein_coding synonymous_variant LOW 717T>C Ser239Ser
M0033226 DNCGDJNA_00008 8081 3 Skin 0.16 protein_coding synonymous_variant LOW 720T>C Asp240Asp
M0033227 DNCGDJNA_00008 8090 3 Skin 0.16 protein_coding synonymous_variant LOW 729T>C Ser243Ser
M0033228 DNCGDJNA_00008 8102 3 Skin 0.16 protein_coding synonymous_variant LOW 741C>T Gly247Gly
M0033229 DNCGDJNA_00008 8105 3 Skin 0.16 protein_coding synonymous_variant LOW 744A>G Gln248Gln
M0033230 DNCGDJNA_00009 8223 12 Skin 0.63 protein_coding synonymous_variant LOW 30A>G Val10Val
M0033231 DNCGDJNA_00015 13815 6 Skin 0.32 protein_coding missense_variant MODERATE 142G>A Ala48Thr
M0033232 DNCGDJNA_00017 14727 5 Skin 0.26 protein_coding synonymous_variant LOW 1182T>C Arg394Arg
M0033233 DNCGDJNA_00017 14850 3 Skin 0.16 protein_coding synonymous_variant LOW 1059A>G Ser353Ser
M0033234 DNCGDJNA_00017 14871 3 Skin 0.16 protein_coding synonymous_variant LOW 1038G>A Glu346Glu
M0033235 DNCGDJNA_00017 15045 5 Skin 0.26 protein_coding synonymous_variant LOW 864C>A Arg288Arg
M0033236 DNCGDJNA_00017 15285 4 Skin 0.21 protein_coding synonymous_variant LOW 624T>C Ile208Ile
M0033237 DNCGDJNA_00017 15370 7 Skin 0.37 protein_coding missense_variant MODERATE 539C>A Thr180Lys
M0033238 DNCGDJNA_00017 15375 7 Skin 0.37 protein_coding synonymous_variant LOW 534G>A Glu178Glu
M0033239 DNCGDJNA_00017 15762 4 Skin 0.21 protein_coding synonymous_variant LOW 147A>G Pro49Pro
M0033240 DNCGDJNA_00017 15798 4 Skin 0.21 protein_coding synonymous_variant LOW 111A>C Val37Val
M0033241 DNCGDJNA_00012 15920 6 Skin 0.32 protein_coding upstream_gene_variant MODIFIER -4461A>G None
M0033242 DNCGDJNA_00018 16347 4 Skin 0.21 protein_coding missense_variant MODERATE 643G>T Gly215Cys
M0033243 DNCGDJNA_00018 16363 3 Skin 0.16 protein_coding missense_variant MODERATE 627C>A His209Gln
M0033244 DNCGDJNA_00018 16392 3 Skin 0.16 protein_coding synonymous_variant LOW 598T>C Leu200Leu
M0033245 DNCGDJNA_00018 16453 3 Skin 0.16 protein_coding synonymous_variant LOW 537A>G Leu179Leu
M0033246 DNCGDJNA_00003 3532 3 Skin 0.16 protein_coding missense_variant MODERATE 320T>C Leu107Pro
M0033247 DNCGDJNA_00014 13142 4 Skin 0.21 protein_coding synonymous_variant LOW 24C>T Thr8Thr
M0033248 DNCGDJNA_00015 13180 4 Skin 0.21 protein_coding synonymous_variant LOW 777G>T Arg259Arg
M0033249 DNCGDJNA_00015 13210 3 Skin 0.16 protein_coding synonymous_variant LOW 747T>G Pro249Pro
M0033250 DNCGDJNA_00015 13233 4 Skin 0.21 protein_coding missense_variant MODERATE 724A>G Thr242Ala
M0033251 DNCGDJNA_00016 14175 5 Skin 0.26 protein_coding missense_variant MODERATE 22G>A Glu8Lys
M0033252 DNCGDJNA_00016 14246 5 Skin 0.26 protein_coding synonymous_variant LOW 93C>T Thr31Thr
M0033253 DNCGDJNA_00016 14273 5 Skin 0.26 protein_coding synonymous_variant LOW 120T>C Asp40Asp
M0033254 DNCGDJNA_00016 14276 5 Skin 0.26 protein_coding synonymous_variant LOW 123T>C Arg41Arg
M0033255 DNCGDJNA_00016 14288 4 Skin 0.21 protein_coding synonymous_variant LOW 135T>G Gly45Gly
M0033256 DNCGDJNA_00016 14312 4 Skin 0.21 protein_coding synonymous_variant LOW 159T>C Asp53Asp
M0033257 DNCGDJNA_00016 14465 3 Skin 0.16 protein_coding synonymous_variant LOW 312C>T Cys104Cys
M0033258 DNCGDJNA_00017 15195 3 Skin 0.16 protein_coding synonymous_variant LOW 714A>G Gly238Gly






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
DNCGDJNA_00005 PHI:10052 STM14_RS15195 (srlA) 89 8.8e-93 1 182 1.0000 0.9733 eudicots infection PTS sorbitol transporter subunit IIC unaffected pathogenicity
DNCGDJNA_00006 PHI:10053 STM14_RS15200 (srlE) 82.3 1.3e-150 5 326 0.9877 0.9907 eudicots infection PTS sorbitol transporter subunit IIB unaffected pathogenicity
DNCGDJNA_00008 PHI:10055 STM14_RS15210 (srlD) 83.4 1.7e-118 1 259 1.0000 1.0000 eudicots infection sorbitol-6-phosphate dehydrogenase unaffected pathogenicity
DNCGDJNA_00010 PHI:10058 STM14_RS15225 70.8 8.6e-102 1 257 1.0000 1.0000 eudicots infection arabinose 5-phosphate isomerase unaffected pathogenicity
DNCGDJNA_00017 PHI:2472 lsc 77.1 6.7e-205 1 415 0.9976 1.0000 eudicots fire blight exopolysaccharides amylovoran 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
DNCGDJNA_00017 AHY08732.1|GH68 97.4 5.64000000171326e-315 1 416 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
DNCGDJNA_00006 4.A.4.1.1 81.1 1.3e-147 4 326 0.9908 0.9937 4 Group Translocators 4.A Phosphotransfer-driven Group Translocators (PTS) 4.A.4 The PTS Glucitol (Gut) Family