Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C122
  Reference Plasmid   CP065520.1
  Reference Plasmid Size   266035
  Reference Plasmid GC Content   0.56
  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
M0059353 LCGBNJEE_00226 200559 3 Skin 0.03 protein_coding synonymous_variant LOW 183G>T Arg61Arg
M0059354 LCGBNJEE_00227 201240 3 Skin 0.03 protein_coding missense_variant MODERATE 506C>T Ala169Val
M0059355 LCGBNJEE_00227 201260 3 Skin 0.03 protein_coding missense_variant MODERATE 486T>G Asp162Glu
M0059356 LCGBNJEE_00227 201643 3 Skin 0.03 protein_coding missense_variant MODERATE 103C>A Pro35Thr
M0059357 LCGBNJEE_00229 202635 3 Skin 0.03 protein_coding synonymous_variant LOW 819C>T Ile273Ile
M0059358 LCGBNJEE_00229 202680 3 Skin 0.03 protein_coding synonymous_variant LOW 774G>A Lys258Lys
M0059359 LCGBNJEE_00229 202782 3 Skin 0.03 protein_coding synonymous_variant LOW 672G>A Gln224Gln
M0059360 LCGBNJEE_00229 202788 3 Skin 0.03 protein_coding synonymous_variant LOW 666C>T Tyr222Tyr
M0059361 LCGBNJEE_00229 202893 5 Skin 0.05 protein_coding synonymous_variant LOW 561C>A Gly187Gly
M0059362 LCGBNJEE_00229 202967 4 Skin 0.04 protein_coding synonymous_variant LOW 487T>C Leu163Leu
M0059363 LCGBNJEE_00229 202968 4 Skin 0.04 protein_coding synonymous_variant LOW 486T>G Gly162Gly
M0059364 LCGBNJEE_00229 202969 4 Skin 0.04 protein_coding missense_variant MODERATE 485G>A Gly162Asp
M0059365 LCGBNJEE_00229 202991 4 Skin 0.04 protein_coding missense_variant MODERATE 463G>A Ala155Thr
M0059366 LCGBNJEE_00229 203003 4 Skin 0.04 protein_coding synonymous_variant LOW 451T>C Leu151Leu
M0059367 LCGBNJEE_00229 203100 4 Skin 0.04 protein_coding synonymous_variant LOW 354G>A Ser118Ser
M0059368 LCGBNJEE_00229 203313 4 Skin 0.04 protein_coding synonymous_variant LOW 141T>A Arg47Arg
M0059369 LCGBNJEE_00229 203324 4 Skin 0.04 protein_coding synonymous_variant LOW 130C>T Leu44Leu
M0059370 LCGBNJEE_00229 203328 4 Skin 0.04 protein_coding synonymous_variant LOW 126C>G Ser42Ser
M0059371 LCGBNJEE_00229 203352 4 Skin 0.04 protein_coding synonymous_variant LOW 102C>G Ala34Ala
M0059372 LCGBNJEE_00229 203390 4 Skin 0.04 protein_coding missense_variant MODERATE 64C>G Leu22Val
M0059373 LCGBNJEE_00229 203399 4 Skin 0.04 protein_coding synonymous_variant LOW 55T>C Leu19Leu
M0059374 LCGBNJEE_00229 203421 4 Skin 0.04 protein_coding synonymous_variant LOW 33C>T Cys11Cys
M0059375 LCGBNJEE_00229 203424 4 Skin 0.04 protein_coding synonymous_variant LOW 30T>C Thr10Thr
M0059376 LCGBNJEE_00229 203436 4 Skin 0.04 protein_coding synonymous_variant LOW 18G>T Ala6Ala
M0059377 LCGBNJEE_00230 203475 3 Skin 0.03 protein_coding missense_variant MODERATE 803A>C Glu268Ala
M0059378 LCGBNJEE_00230 203489 3 Skin 0.03 protein_coding synonymous_variant LOW 789A>C Pro263Pro
M0059379 LCGBNJEE_00230 203491 3 Skin 0.03 protein_coding missense_variant MODERATE 787C>A Pro263Thr
M0059380 LCGBNJEE_00230 203505 3 Skin 0.03 protein_coding missense_variant MODERATE 773A>C Asn258Thr
M0059381 LCGBNJEE_00230 203507 3 Skin 0.03 protein_coding synonymous_variant LOW 771G>A Ala257Ala
M0059382 LCGBNJEE_00225 204358 5 Skin 0.05 protein_coding upstream_gene_variant MODIFIER -4594A>G None
M0059383 LCGBNJEE_00136 128941 6 Skin 0.06 protein_coding upstream_gene_variant MODIFIER -3849G>T None
M0059384 LCGBNJEE_00144 131475 10 Skin 0.11 protein_coding upstream_gene_variant MODIFIER -2880C>T None
M0059385 LCGBNJEE_00157 139459 8 Skin 0.08 protein_coding synonymous_variant LOW 249T>C Gly83Gly
M0059386 LCGBNJEE_00157 139555 6 Skin 0.06 protein_coding synonymous_variant LOW 153T>C Ser51Ser
M0059387 LCGBNJEE_00157 139600 8 Skin 0.08 protein_coding synonymous_variant LOW 108G>C Val36Val
M0059388 LCGBNJEE_00153 135218 3 Skin 0.03 protein_coding synonymous_variant LOW 153C>T Ser51Ser
M0059389 LCGBNJEE_00175 153233 3 Skin 0.03 protein_coding synonymous_variant LOW 205T>C Leu69Leu
M0059390 LCGBNJEE_00136 123284 6 Skin 0.06 protein_coding synonymous_variant LOW 1809T>C Gly603Gly
M0059391 LCGBNJEE_00136 123605 4 Skin 0.04 protein_coding synonymous_variant LOW 1488C>T Asp496Asp
M0059392 LCGBNJEE_00142 127501 3 Skin 0.03 protein_coding missense_variant MODERATE 242T>C Val81Ala
M0059393 LCGBNJEE_00228 202473 6 Skin 0.06 protein_coding missense_variant MODERATE 109T>C Phe37Leu
M0059394 LCGBNJEE_00228 202480 6 Skin 0.06 protein_coding synonymous_variant LOW 102G>A Ala34Ala
M0059395 LCGBNJEE_00225 204366 3 Skin 0.03 protein_coding upstream_gene_variant MODIFIER -4602C>A None
M0059396 LCGBNJEE_00225 204385 3 Skin 0.03 protein_coding upstream_gene_variant MODIFIER -4621T>C None
M0059397 LCGBNJEE_00136 123481 4 Skin 0.04 protein_coding missense_variant MODERATE 1612G>A Ala538Thr
M0059398 LCGBNJEE_00141 127032 3 Skin 0.03 protein_coding synonymous_variant LOW 96T>C Thr32Thr
M0059399 LCGBNJEE_00226 200437 4 Skin 0.04 protein_coding missense_variant MODERATE 305T>A Leu102Gln
M0059400 LCGBNJEE_00228 201970 3 Skin 0.03 protein_coding synonymous_variant LOW 612G>T Thr204Thr
M0059401 LCGBNJEE_00228 202300 8 Skin 0.08 protein_coding synonymous_variant LOW 282T>C Gly94Gly
M0059402 LCGBNJEE_00228 202320 8 Skin 0.08 protein_coding synonymous_variant LOW 262T>C Leu88Leu
M0059403 LCGBNJEE_00228 202321 8 Skin 0.08 protein_coding synonymous_variant LOW 261C>G Thr87Thr
M0059404 LCGBNJEE_00228 202333 8 Skin 0.08 protein_coding synonymous_variant LOW 249C>G Pro83Pro
M0059405 LCGBNJEE_00228 202432 4 Skin 0.04 protein_coding synonymous_variant LOW 150C>G Leu50Leu
M0059406 LCGBNJEE_00227 200758 4 Skin 0.04 protein_coding missense_variant MODERATE 988A>C Lys330Gln
M0059407 LCGBNJEE_00227 200801 3 Skin 0.03 protein_coding synonymous_variant LOW 945A>G Ala315Ala
M0059408 LCGBNJEE_00227 200814 3 Skin 0.03 protein_coding missense_variant MODERATE 932A>G Asn311Ser
M0059409 LCGBNJEE_00136 124984 3 Skin 0.03 protein_coding missense_variant MODERATE 109A>G Thr37Ala






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
LCGBNJEE_00050 Cobalt (Co), Nickel (Ni) 71 9.1e-161 1 433 1.0000 1.0046 experiment
LCGBNJEE_00055 Nickel (Ni), Zinc (Zn) 73.9 4.3e-37 10 101 0.9109 0.9684 experiment
LCGBNJEE_00048 Chromium (Cr) 100 2.8e-262 1 455 1.0000 1.0000 prediction
LCGBNJEE_00049 Chromium (Cr), Methyl Viologen [class: Paraquat], Menadione [class: Naphthoquinone] 100 7.9e-168 20 313 0.9393 1.0000 prediction
LCGBNJEE_00050 Nickel (Ni), Cobalt (Co) 100 3.8e-229 1 434 1.0000 1.0000 prediction
LCGBNJEE_00055 Nickel (Ni), Zinc (Zn) 100 4.7e-53 1 101 1.0000 1.0000 prediction
LCGBNJEE_00063 Mercury (Hg) 96.7 9.7e-42 1 91 1.0000 1.0000 prediction
LCGBNJEE_00167 Mercury (Hg) 96.7 9.7e-42 1 91 1.0000 1.0000 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






        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





        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
LCGBNJEE_00048 2.A.51.1.4 73.9 3.4e-194 1 452 0.9934 0.9912 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.51 The Chromate Ion Transporter (CHR) Family