Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1193
  Reference Plasmid   NZ_CP130568.1
  Reference Plasmid Size   33265
  Reference Plasmid GC Content   0.30
  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
M0112833 APAGFDOH_00020 23275 3 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -3893G>A None
M0112834 APAGFDOH_00020 23278 3 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -3896G>A None
M0112835 APAGFDOH_00021 24862 5 Skin 0.19 protein_coding upstream_gene_variant MODIFIER -4631T>G None
M0112836 APAGFDOH_00015 14397 4 Skin 0.15 protein_coding synonymous_variant LOW 141C>T Ile47Ile
M0112837 APAGFDOH_00007 13584 3 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -4733A>G None
M0112838 APAGFDOH_00007 13589 3 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -4738G>A None
M0112839 APAGFDOH_00014 13653 3 Skin 0.12 protein_coding synonymous_variant LOW 33T>G Leu11Leu
M0112840 APAGFDOH_00014 13683 5 Skin 0.19 protein_coding synonymous_variant LOW 63A>G Val21Val
M0112841 APAGFDOH_00014 13689 3 Skin 0.12 protein_coding synonymous_variant LOW 69A>G Leu23Leu
M0112842 APAGFDOH_00014 13706 3 Skin 0.12 protein_coding missense_variant MODERATE 86G>A Arg29Lys
M0112843 APAGFDOH_00014 13718 3 Skin 0.12 protein_coding missense_variant MODERATE 98G>A Arg33Lys
M0112844 APAGFDOH_00014 13719 3 Skin 0.12 protein_coding synonymous_variant LOW 99G>A Arg33Arg
M0112845 APAGFDOH_00014 13722 3 Skin 0.12 protein_coding synonymous_variant LOW 102A>G Lys34Lys
M0112846 APAGFDOH_00014 13758 4 Skin 0.15 protein_coding synonymous_variant LOW 138T>A Gly46Gly
M0112847 APAGFDOH_00014 13765 3 Skin 0.12 protein_coding missense_variant MODERATE 145G>A Ala49Thr
M0112848 APAGFDOH_00014 13872 4 Skin 0.15 protein_coding synonymous_variant LOW 252A>G Val84Val
M0112849 APAGFDOH_00014 13968 5 Skin 0.19 protein_coding synonymous_variant LOW 348A>G Thr116Thr
M0112850 APAGFDOH_00014 13995 5 Skin 0.19 protein_coding synonymous_variant LOW 375C>T Ile125Ile
M0112851 APAGFDOH_00014 14145 3 Skin 0.12 protein_coding synonymous_variant LOW 525T>C Ser175Ser
M0112852 APAGFDOH_00014 14196 4 Skin 0.15 protein_coding synonymous_variant LOW 576T>A Ile192Ile
M0112853 APAGFDOH_00009 14245 4 Skin 0.15 protein_coding upstream_gene_variant MODIFIER -3620A>C None
M0112854 APAGFDOH_00009 14254 4 Skin 0.15 protein_coding upstream_gene_variant MODIFIER -3629A>G None
M0112855 APAGFDOH_00015 14508 5 Skin 0.19 protein_coding missense_variant MODERATE 252T>G Asp84Glu
M0112856 APAGFDOH_00015 14574 5 Skin 0.19 protein_coding synonymous_variant LOW 318G>A Glu106Glu
M0112857 APAGFDOH_00020 19115 3 Skin 0.12 protein_coding missense_variant MODERATE 268G>A Gly90Ser
M0112858 APAGFDOH_00023 21741 3 Skin 0.12 protein_coding synonymous_variant LOW 666A>G Ala222Ala
M0112859 APAGFDOH_00029 25184 3 Skin 0.12 protein_coding synonymous_variant LOW 303T>C Asp101Asp
M0112860 APAGFDOH_00032 28712 3 Skin 0.12 protein_coding synonymous_variant LOW 1239A>G Gly413Gly






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
APAGFDOH_00014 Cadmium (Cd), Zinc (Zn) 94.1 1.7e-101 1 205 1.0000 1.0000 experiment
HGPJNGCC_00014 Cadmium (Cd), Zinc (Zn) 94.1 1.7e-101 1 205 1.0000 1.0000 experiment
APAGFDOH_00014 Cadmium (Cd), Zinc (Zn) 100 1.3e-102 1 205 1.0000 1.0000 prediction
APAGFDOH_00022 Copper (Cu) 100 1.6e-33 1 69 1.0000 1.0000 prediction
APAGFDOH_00023 Copper (Cu), Silver (Ag) 78.9 2.1e-276 1 622 1.0000 0.7834 prediction
HGPJNGCC_00014 Cadmium (Cd), Zinc (Zn) 100 1.3e-102 1 205 1.0000 1.0000 prediction
HGPJNGCC_00022 Copper (Cu) 100 1.6e-33 1 69 1.0000 1.0000 prediction
HGPJNGCC_00023 Copper (Cu), Silver (Ag) 78.9 2.1e-276 1 622 1.0000 0.7834 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
APAGFDOH_00032 ARO:3000251 95.7 2.0997789948253e-320 1 488 1.0000 1.0000 macrolide antibiotic msr-type ABC-F protein antibiotic target protection
APAGFDOH_00033 ARO:3000319 98.7 1.82e-228 1 299 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
HGPJNGCC_00032 ARO:3000251 95.7 2.0997789948253e-320 1 488 1.0000 1.0000 macrolide antibiotic msr-type ABC-F protein antibiotic target protection
HGPJNGCC_00033 ARO:3000319 98.7 1.82e-228 1 299 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation






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
APAGFDOH_00014 2.A.77.1.1 93.7 1.4e-99 1 205 1.0000 0.9809 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.77 The Cadmium Resistance (CadD) Family
APAGFDOH_00023 3.A.3.5.19 77.7 3.3e-272 1 622 1.0000 0.7768 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.3 The P-type ATPase (P-ATPase) Superfamily
APAGFDOH_00032 3.A.1.121.1 98.8 5.7e-272 1 488 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
HGPJNGCC_00014 2.A.77.1.1 93.7 1.4e-99 1 205 1.0000 0.9809 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.77 The Cadmium Resistance (CadD) Family
HGPJNGCC_00023 3.A.3.5.19 77.7 3.3e-272 1 622 1.0000 0.7768 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.3 The P-type ATPase (P-ATPase) Superfamily
HGPJNGCC_00032 3.A.1.121.1 98.8 5.7e-272 1 488 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily