Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C288
  Reference Plasmid   NC_008790.1
  Reference Plasmid Size   45025
  Reference Plasmid GC Content   0.29
  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
M0151312 HMHIFHDA_00050 43605 14 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -18T>C None
M0151313 HMHIFHDA_00050 43658 3 Gut 0.11 protein_coding synonymous_variant LOW 36C>A Val12Val
M0151314 HMHIFHDA_00050 43796 3 Gut 0.11 protein_coding synonymous_variant LOW 174C>A Thr58Thr
M0151315 HMHIFHDA_00050 43829 9 Gut 0.32 protein_coding synonymous_variant LOW 207G>A Gly69Gly
M0151316 HMHIFHDA_00050 43850 7 Gut 0.25 protein_coding synonymous_variant LOW 228C>T His76His
M0151317 HMHIFHDA_00050 43949 6 Gut 0.21 protein_coding synonymous_variant LOW 327T>C Phe109Phe
M0151318 HMHIFHDA_00050 43961 8 Gut 0.29 protein_coding synonymous_variant LOW 339T>C Ser113Ser
M0151319 HMHIFHDA_00050 44142 13 Gut 0.46 protein_coding missense_variant MODERATE 520G>A Glu174Lys
M0151320 HMHIFHDA_00050 44261 3 Gut 0.11 protein_coding synonymous_variant LOW 639G>A Gly213Gly
M0151321 HMHIFHDA_00050 44266 3 Gut 0.11 protein_coding missense_variant MODERATE 644A>G Asp215Gly
M0151322 HMHIFHDA_00050 44275 4 Gut 0.14 protein_coding missense_variant MODERATE 653C>T Pro218Leu
M0151323 HMHIFHDA_00051 44421 7 Gut 0.25 protein_coding upstream_gene_variant MODIFIER -159T>G None
M0151324 HMHIFHDA_00051 44439 7 Gut 0.25 protein_coding upstream_gene_variant MODIFIER -141T>C None
M0151325 HMHIFHDA_00051 44445 7 Gut 0.25 protein_coding upstream_gene_variant MODIFIER -135T>C None
M0151326 HMHIFHDA_00050 43589 5 Gut 0.18 protein_coding upstream_gene_variant MODIFIER -34G>A None
M0151327 HMHIFHDA_00050 43592 5 Gut 0.18 protein_coding upstream_gene_variant MODIFIER -31C>T None
M0151328 HMHIFHDA_00050 43598 8 Gut 0.29 protein_coding upstream_gene_variant MODIFIER -25G>A None
M0151329 HMHIFHDA_00050 43730 6 Gut 0.21 protein_coding synonymous_variant LOW 108A>G Lys36Lys
M0151330 HMHIFHDA_00051 44391 4 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -189G>A None
M0151331 HMHIFHDA_00051 44430 4 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -150T>C None
M0151332 HMHIFHDA_00051 44460 5 Gut 0.18 protein_coding upstream_gene_variant MODIFIER -120G>A None
M0151333 HMHIFHDA_00051 44464 5 Gut 0.18 protein_coding upstream_gene_variant MODIFIER -116T>C None
M0151334 HMHIFHDA_00051 44493 5 Gut 0.18 protein_coding upstream_gene_variant MODIFIER -87C>T None
M0151335 HMHIFHDA_00050 43766 5 Gut 0.18 protein_coding synonymous_variant LOW 144T>C Asp48Asp
M0151336 HMHIFHDA_00050 43657 3 Gut 0.11 protein_coding missense_variant MODERATE 35T>C Val12Ala
M0151337 HMHIFHDA_00050 43682 3 Gut 0.11 protein_coding synonymous_variant LOW 60C>T Ser20Ser
M0151338 HMHIFHDA_00050 43709 3 Gut 0.11 protein_coding synonymous_variant LOW 87G>A Gln29Gln
M0151339 HMHIFHDA_00050 43733 3 Gut 0.11 protein_coding synonymous_variant LOW 111C>T Ser37Ser
M0151340 HMHIFHDA_00050 43754 3 Gut 0.11 protein_coding synonymous_variant LOW 132T>G Leu44Leu
M0151341 HMHIFHDA_00050 43760 4 Gut 0.14 protein_coding synonymous_variant LOW 138G>A Val46Val
M0151342 HMHIFHDA_00050 43783 3 Gut 0.11 protein_coding missense_variant MODERATE 161C>T Thr54Ile
M0151343 HMHIFHDA_00050 43791 3 Gut 0.11 protein_coding missense_variant MODERATE 169G>C Glu57Gln
M0151344 HMHIFHDA_00050 44068 5 Gut 0.18 protein_coding missense_variant MODERATE 446C>T Ser149Phe
M0151345 HMHIFHDA_00050 43578 3 Gut 0.11 protein_coding upstream_gene_variant MODIFIER -45T>C None
M0151346 HMHIFHDA_00001 536 3 Gut 0.11 protein_coding synonymous_variant LOW 471T>C Ile157Ile
M0151347 HMHIFHDA_00001 640 3 Gut 0.11 protein_coding missense_variant MODERATE 575T>C Val192Ala






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
HMHIFHDA_00049 ARO:3000190 99.8 0 1 639 1.0000 1.0000 tetracycline antibiotic tetracycline-resistant ribosomal protection protein antibiotic target protection






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