Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C840
  Reference Plasmid   NZ_CP069564.1
  Reference Plasmid Size   98235
  Reference Plasmid GC Content   0.43
  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
M0184539 HEJEOKCK_00026 23814 7 Gut 0.18 protein_coding upstream_gene_variant MODIFIER -1718T>C None
M0184540 HEJEOKCK_00026 23869 5 Gut 0.13 protein_coding upstream_gene_variant MODIFIER -1773T>C None
M0184541 HEJEOKCK_00026 23896 4 Gut 0.11 protein_coding upstream_gene_variant MODIFIER -1800C>A None
M0184542 HEJEOKCK_00026 23912 4 Gut 0.11 protein_coding upstream_gene_variant MODIFIER -1816C>T None
M0184543 HEJEOKCK_00026 23977 6 Gut 0.16 protein_coding upstream_gene_variant MODIFIER -1881A>C None
M0184544 HEJEOKCK_00039 33539 8 Gut 0.21 protein_coding missense_variant MODERATE 126A>G Ile42Met
M0184545 HEJEOKCK_00061 54535 6 Gut 0.16 protein_coding missense_variant MODERATE 686T>A Val229Glu
M0184546 HEJEOKCK_00019 13454 6 Gut 0.16 protein_coding missense_variant MODERATE 473T>G Leu158Trp
M0184547 HEJEOKCK_00019 13465 3 Gut 0.08 protein_coding synonymous_variant LOW 462C>T Asp154Asp
M0184548 HEJEOKCK_00019 13483 6 Gut 0.16 protein_coding synonymous_variant LOW 444C>A Val148Val
M0184549 HEJEOKCK_00019 13592 5 Gut 0.13 protein_coding missense_variant MODERATE 335A>G Lys112Arg
M0184550 HEJEOKCK_00014 14013 3 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -4902A>G None
M0184551 HEJEOKCK_00020 14246 3 Gut 0.08 protein_coding missense_variant MODERATE 7A>T Ile3Phe
M0184552 HEJEOKCK_00020 14263 4 Gut 0.11 protein_coding synonymous_variant LOW 24C>T Ala8Ala
M0184553 HEJEOKCK_00020 14264 4 Gut 0.11 protein_coding missense_variant MODERATE 25T>A Ser9Thr
M0184554 HEJEOKCK_00020 14341 4 Gut 0.11 protein_coding synonymous_variant LOW 102A>T Arg34Arg
M0184555 HEJEOKCK_00020 14370 5 Gut 0.13 protein_coding missense_variant MODERATE 131T>C Val44Ala
M0184556 HEJEOKCK_00018 11873 3 Gut 0.08 protein_coding synonymous_variant LOW 837T>A Val279Val
M0184557 HEJEOKCK_00018 11922 3 Gut 0.08 protein_coding missense_variant MODERATE 788T>C Val263Ala
M0184558 HEJEOKCK_00018 11946 3 Gut 0.08 protein_coding missense_variant MODERATE 764G>A Gly255Asp
M0184559 HEJEOKCK_00018 12001 3 Gut 0.08 protein_coding synonymous_variant LOW 709T>C Leu237Leu
M0184560 HEJEOKCK_00018 12129 3 Gut 0.08 protein_coding missense_variant MODERATE 581C>G Ala194Gly
M0184561 HEJEOKCK_00018 12248 3 Gut 0.08 protein_coding synonymous_variant LOW 462G>A Leu154Leu
M0184562 HEJEOKCK_00018 12297 3 Gut 0.08 protein_coding missense_variant MODERATE 413A>G Glu138Gly
M0184563 HEJEOKCK_00018 12323 3 Gut 0.08 protein_coding synonymous_variant LOW 387T>C Pro129Pro
M0184564 HEJEOKCK_00018 12360 3 Gut 0.08 protein_coding missense_variant MODERATE 350A>G Gln117Arg
M0184565 HEJEOKCK_00018 12362 3 Gut 0.08 protein_coding synonymous_variant LOW 348G>T Val116Val
M0184566 HEJEOKCK_00018 12467 3 Gut 0.08 protein_coding synonymous_variant LOW 243T>C Leu81Leu
M0184567 HEJEOKCK_00018 12527 3 Gut 0.08 protein_coding synonymous_variant LOW 183C>T Asp61Asp
M0184568 HEJEOKCK_00020 15280 5 Gut 0.13 protein_coding synonymous_variant LOW 1041A>G Glu347Glu
M0184569 HEJEOKCK_00020 15266 4 Gut 0.11 protein_coding missense_variant MODERATE 1027G>C Glu343Gln
M0184570 HEJEOKCK_00020 15268 4 Gut 0.11 protein_coding missense_variant MODERATE 1029A>C Glu343Asp
M0184571 HEJEOKCK_00018 12598 3 Gut 0.08 protein_coding missense_variant MODERATE 112A>G Ile38Val






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
HEJEOKCK_00038 PHI:3281 AS87_04050 71.4 3e-136 1 325 1.0000 1.0000 birds fibrinous serositis; caseous salpingitis; vegetative disorder lipopolysaccharide biosynthesis and pathogenicity 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
HEJEOKCK_00043 QUT83193.1|GT4 100 0 1 444 1 1
HEJEOKCK_00044 QRP91614.1|GT4 100 4.79e-292 1 391 1 1
HEJEOKCK_00045 BBK89584.1|GT2 100 6.37e-226 1 300 1 1
HEJEOKCK_00046 QRP91616.1|GT4 100 5.41e-274 1 366 1 1
HEJEOKCK_00048 QUT55894.1|GT2 100 1.57e-228 1 304 1 1
HEJEOKCK_00050 QUT64421.1|GT4 100 1.11e-279 1 378 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