Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C883
  Reference Plasmid   NZ_CP072245.1
  Reference Plasmid Size   102253
  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
M0187273 GOCEDPGL_00073 66167 9 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -4737G>A None
M0187274 GOCEDPGL_00073 66171 9 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -4741C>A None
M0187275 GOCEDPGL_00073 66221 6 Gut 0.06 protein_coding upstream_gene_variant MODIFIER -4791G>A None
M0187276 GOCEDPGL_00073 66257 7 Gut 0.07 protein_coding upstream_gene_variant MODIFIER -4827C>T None
M0187277 GOCEDPGL_00073 66026 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4596A>G None
M0187278 GOCEDPGL_00073 66168 4 Gut 0.04 protein_coding upstream_gene_variant MODIFIER -4738G>A None
M0187279 GOCEDPGL_00073 66244 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4814T>C None
M0187280 GOCEDPGL_00073 66247 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4817G>A None
M0187281 GOCEDPGL_00073 66256 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4826T>A None
M0187282 GOCEDPGL_00073 66303 5 Gut 0.05 protein_coding upstream_gene_variant MODIFIER -4873T>A None
M0187283 GOCEDPGL_00073 66318 5 Gut 0.05 protein_coding upstream_gene_variant MODIFIER -4888A>G None
M0187284 GOCEDPGL_00073 66327 5 Gut 0.05 protein_coding upstream_gene_variant MODIFIER -4897C>A None
M0187285 GOCEDPGL_00073 66339 5 Gut 0.05 protein_coding upstream_gene_variant MODIFIER -4909G>A None
M0187286 GOCEDPGL_00073 66350 5 Gut 0.05 protein_coding upstream_gene_variant MODIFIER -4920G>A None
M0187287 GOCEDPGL_00086 67756 4 Gut 0.04 protein_coding synonymous_variant LOW 270A>G Gly90Gly
M0187288 GOCEDPGL_00091 74327 4 Gut 0.04 protein_coding upstream_gene_variant MODIFIER -2058G>A None
M0187289 GOCEDPGL_00086 67606 4 Gut 0.04 protein_coding synonymous_variant LOW 120G>A Ala40Ala
M0187290 GOCEDPGL_00064 58568 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4019G>C None
M0187291 GOCEDPGL_00073 66272 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4842G>A None
M0187292 GOCEDPGL_00081 69314 4 Gut 0.04 protein_coding upstream_gene_variant MODIFIER -4092C>T None
M0187293 GOCEDPGL_00081 69317 4 Gut 0.04 protein_coding upstream_gene_variant MODIFIER -4095A>G None
M0187294 GOCEDPGL_00081 69326 4 Gut 0.04 protein_coding upstream_gene_variant MODIFIER -4104A>T None
M0187295 GOCEDPGL_00081 69327 4 Gut 0.04 protein_coding upstream_gene_variant MODIFIER -4105A>T None
M0187296 GOCEDPGL_00081 69342 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4120G>A None
M0187297 GOCEDPGL_00081 69575 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4353T>A None
M0187298 GOCEDPGL_00081 69578 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4356G>A None
M0187299 GOCEDPGL_00074 66656 4 Gut 0.04 protein_coding upstream_gene_variant MODIFIER -4855G>T None
M0187300 GOCEDPGL_00081 69096 4 Gut 0.04 protein_coding upstream_gene_variant MODIFIER -3874G>A None
M0187301 GOCEDPGL_00081 69111 4 Gut 0.04 protein_coding upstream_gene_variant MODIFIER -3889T>C None
M0187302 GOCEDPGL_00081 69138 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -3916A>G None
M0187303 GOCEDPGL_00081 69144 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -3922C>T None
M0187304 GOCEDPGL_00069 58354 3 Gut 0.03 protein_coding missense_variant MODERATE 58C>T Leu20Phe
M0187305 GOCEDPGL_00091 74165 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -1896T>C None
M0187306 GOCEDPGL_00099 77511 4 Gut 0.04 protein_coding upstream_gene_variant MODIFIER -181T>C None
M0187307 GOCEDPGL_00099 77538 4 Gut 0.04 protein_coding upstream_gene_variant MODIFIER -154T>C None
M0187308 GOCEDPGL_00099 77540 4 Gut 0.04 protein_coding upstream_gene_variant MODIFIER -152C>T None
M0187309 GOCEDPGL_00074 66667 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4866C>T None
M0187310 GOCEDPGL_00084 66747 3 Gut 0.03 protein_coding missense_variant MODERATE 76A>T Ser26Cys
M0187311 GOCEDPGL_00084 66777 3 Gut 0.03 protein_coding missense_variant MODERATE 106A>G Lys36Glu
M0187312 GOCEDPGL_00084 67029 3 Gut 0.03 protein_coding synonymous_variant LOW 358A>C Arg120Arg
M0187313 GOCEDPGL_00075 67187 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4517T>C None
M0187314 GOCEDPGL_00085 67269 3 Gut 0.03 protein_coding missense_variant MODERATE 62A>G His21Arg
M0187315 GOCEDPGL_00085 67410 3 Gut 0.03 protein_coding missense_variant MODERATE 203C>T Ser68Leu
M0187316 GOCEDPGL_00086 67785 3 Gut 0.03 protein_coding missense_variant MODERATE 299A>G Asp100Gly
M0187317 GOCEDPGL_00086 67804 3 Gut 0.03 protein_coding synonymous_variant LOW 318G>A Gly106Gly
M0187318 GOCEDPGL_00086 67813 3 Gut 0.03 protein_coding missense_variant MODERATE 327G>C Arg109Ser
M0187319 GOCEDPGL_00086 67830 3 Gut 0.03 protein_coding missense_variant MODERATE 344C>T Ser115Leu
M0187320 GOCEDPGL_00086 68107 3 Gut 0.03 protein_coding synonymous_variant LOW 621C>T Asp207Asp
M0187321 GOCEDPGL_00086 68109 3 Gut 0.03 protein_coding missense_variant MODERATE 623C>T Thr208Ile
M0187322 GOCEDPGL_00086 68116 3 Gut 0.03 protein_coding synonymous_variant LOW 630T>C Phe210Phe
M0187323 GOCEDPGL_00086 68190 3 Gut 0.03 protein_coding missense_variant MODERATE 704C>T Thr235Met
M0187324 GOCEDPGL_00087 68248 3 Gut 0.03 protein_coding missense_variant MODERATE 7G>A Ala3Thr
M0187325 GOCEDPGL_00087 68280 3 Gut 0.03 protein_coding synonymous_variant LOW 39C>T Val13Val
M0187326 GOCEDPGL_00087 68285 3 Gut 0.03 protein_coding missense_variant MODERATE 44C>T Ala15Val
M0187327 GOCEDPGL_00087 68294 3 Gut 0.03 protein_coding missense_variant MODERATE 53G>A Ser18Asn
M0187328 GOCEDPGL_00087 68314 3 Gut 0.03 protein_coding missense_variant MODERATE 73T>C Trp25Arg
M0187329 GOCEDPGL_00087 68341 3 Gut 0.03 protein_coding missense_variant MODERATE 100A>G Thr34Ala
M0187330 GOCEDPGL_00087 68391 3 Gut 0.03 protein_coding synonymous_variant LOW 150G>A Gly50Gly
M0187331 GOCEDPGL_00087 68415 3 Gut 0.03 protein_coding synonymous_variant LOW 174T>G Val58Val
M0187332 GOCEDPGL_00088 68634 3 Gut 0.03 protein_coding missense_variant MODERATE 70C>T Pro24Ser
M0187333 GOCEDPGL_00088 68687 3 Gut 0.03 protein_coding synonymous_variant LOW 123T>A Ile41Ile
M0187334 GOCEDPGL_00088 68816 3 Gut 0.03 protein_coding synonymous_variant LOW 252C>T Ala84Ala






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
GOCEDPGL_00023 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
GOCEDPGL_00010 QUT64421.1|GT4 100 1.11e-279 1 378 1 1
GOCEDPGL_00012 QUT55894.1|GT2 100 1.57e-228 1 304 1 1
GOCEDPGL_00015 QRP91616.1|GT4 100 5.41e-274 1 366 1 1
GOCEDPGL_00016 BBK89584.1|GT2 100 6.37e-226 1 300 1 1
GOCEDPGL_00017 QRP91614.1|GT4 100 4.79e-292 1 391 1 1
GOCEDPGL_00018 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