Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C866
  Reference Plasmid   NZ_CP072215.1
  Reference Plasmid Size   98239
  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
M0185319 HAPEGKJK_00024 27705 5 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4261G>T None
M0185320 HAPEGKJK_00024 27721 5 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4277G>T None
M0185321 HAPEGKJK_00024 27748 6 Gut 0.04 protein_coding upstream_gene_variant MODIFIER -4304A>G None
M0185322 HAPEGKJK_00024 27803 8 Gut 0.05 protein_coding upstream_gene_variant MODIFIER -4359A>G None
M0185323 HAPEGKJK_00092 74839 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -1888C>A None
M0185324 HAPEGKJK_00092 74842 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -1891C>T None
M0185325 HAPEGKJK_00098 77657 4 Gut 0.03 protein_coding missense_variant MODERATE 707A>G Asn236Ser
M0185326 HAPEGKJK_00098 77659 3 Gut 0.02 protein_coding synonymous_variant LOW 705A>G Gly235Gly
M0185327 HAPEGKJK_00034 36274 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -4302A>G None
M0185328 HAPEGKJK_00039 36334 4 Gut 0.03 protein_coding missense_variant MODERATE 1044G>C Glu348Asp
M0185329 HAPEGKJK_00039 36337 5 Gut 0.03 protein_coding synonymous_variant LOW 1041A>G Glu347Glu
M0185330 HAPEGKJK_00039 36650 4 Gut 0.03 protein_coding missense_variant MODERATE 728A>G Asn243Ser
M0185331 HAPEGKJK_00039 37066 3 Gut 0.02 protein_coding synonymous_variant LOW 312A>G Glu104Glu
M0185332 HAPEGKJK_00083 70108 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -1832G>T None
M0185333 HAPEGKJK_00083 70116 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -1840C>T None
M0185334 HAPEGKJK_00083 70137 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -1861T>C None
M0185335 HAPEGKJK_00083 70361 4 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -2085G>A None
M0185336 HAPEGKJK_00083 70363 4 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -2087A>G None
M0185337 HAPEGKJK_00091 71636 3 Gut 0.02 protein_coding synonymous_variant LOW 282T>C Asn94Asn
M0185338 HAPEGKJK_00091 71747 3 Gut 0.02 protein_coding synonymous_variant LOW 393G>A Glu131Glu
M0185339 HAPEGKJK_00091 71756 3 Gut 0.02 protein_coding synonymous_variant LOW 402T>C Asn134Asn
M0185340 HAPEGKJK_00024 27640 5 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4196T>G None
M0185341 HAPEGKJK_00039 37353 3 Gut 0.02 protein_coding missense_variant MODERATE 25T>A Ser9Thr
M0185342 HAPEGKJK_00039 37354 3 Gut 0.02 protein_coding synonymous_variant LOW 24C>T Ala8Ala
M0185343 HAPEGKJK_00041 38028 4 Gut 0.03 protein_coding missense_variant MODERATE 305A>G Lys102Arg
M0185344 HAPEGKJK_00042 39619 4 Gut 0.03 protein_coding synonymous_variant LOW 709T>C Leu237Leu
M0185345 HAPEGKJK_00042 39674 3 Gut 0.02 protein_coding missense_variant MODERATE 764G>A Gly255Asp
M0185346 HAPEGKJK_00042 39698 3 Gut 0.02 protein_coding missense_variant MODERATE 788T>C Val263Ala
M0185347 HAPEGKJK_00065 62264 6 Gut 0.04 protein_coding upstream_gene_variant MODIFIER -4827C>A None
M0185348 HAPEGKJK_00073 65497 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -4268T>G None
M0185349 HAPEGKJK_00073 65582 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -4353T>A None
M0185350 HAPEGKJK_00073 65585 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -4356G>A None
M0185351 HAPEGKJK_00087 69392 3 Gut 0.02 protein_coding synonymous_variant LOW 234A>G Ala78Ala
M0185352 HAPEGKJK_00024 22807 8 Gut 0.05 protein_coding missense_variant MODERATE 638C>T Ala213Val
M0185353 HAPEGKJK_00039 37276 3 Gut 0.02 protein_coding synonymous_variant LOW 102A>T Arg34Arg
M0185354 HAPEGKJK_00073 65103 4 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -3874G>A None
M0185355 HAPEGKJK_00073 65118 4 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -3889T>C None
M0185356 HAPEGKJK_00065 62174 4 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4737G>A None
M0185357 HAPEGKJK_00065 62178 4 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4741C>A None
M0185358 HAPEGKJK_00065 62228 5 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4791G>A None
M0185359 HAPEGKJK_00065 62279 4 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4842G>A None
M0185360 HAPEGKJK_00065 62310 5 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4873T>A None
M0185361 HAPEGKJK_00065 62325 5 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4888A>G None
M0185362 HAPEGKJK_00065 62334 4 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4897C>A None
M0185363 HAPEGKJK_00065 62346 4 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4909G>A None
M0185364 HAPEGKJK_00065 62357 4 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4920G>A None
M0185365 HAPEGKJK_00083 70334 4 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -2058G>A None
M0185366 HAPEGKJK_00092 73518 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -567A>G None
M0185367 HAPEGKJK_00092 73547 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -596G>A None
M0185368 HAPEGKJK_00039 37373 3 Gut 0.02 protein_coding missense_variant MODERATE 5A>G Lys2Arg
M0185369 HAPEGKJK_00043 40082 3 Gut 0.02 protein_coding missense_variant MODERATE 188A>G Asp63Gly
M0185370 HAPEGKJK_00043 40570 3 Gut 0.02 protein_coding missense_variant MODERATE 676G>A Gly226Ser
M0185371 HAPEGKJK_00097 76999 3 Gut 0.02 protein_coding missense_variant MODERATE 286G>A Glu96Lys
M0185372 HAPEGKJK_00098 78234 3 Gut 0.02 protein_coding missense_variant MODERATE 130G>A Val44Ile
M0185373 HAPEGKJK_00042 39323 3 Gut 0.02 protein_coding missense_variant MODERATE 413A>G Glu138Gly






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
HAPEGKJK_00021 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
HAPEGKJK_00009 QUT64421.1|GT4 100 1.11e-279 1 378 1 1
HAPEGKJK_00011 QUT55894.1|GT2 100 1.57e-228 1 304 1 1
HAPEGKJK_00013 QRP91616.1|GT4 100 5.41e-274 1 366 1 1
HAPEGKJK_00014 BBK89584.1|GT2 100 6.37e-226 1 300 1 1
HAPEGKJK_00015 QRP91614.1|GT4 100 4.79e-292 1 391 1 1
HAPEGKJK_00016 QUT83193.1|GT4 100 0 1 444 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