Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1578
  Reference Plasmid   1111525849480358_bin.11__k141_274182
  Reference Plasmid Size   14189
  Reference Plasmid GC Content   0.70
  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
M0007806 GPNDGCNO_00001 1761 5 Skin 0.56 protein_coding synonymous_variant LOW 939A>G Ala313Ala
M0007807 GPNDGCNO_00001 2041 4 Skin 0.44 protein_coding missense_variant MODERATE 1219C>T Leu407Phe
M0007808 GPNDGCNO_00001 2100 4 Skin 0.44 protein_coding synonymous_variant LOW 1278A>G Gln426Gln
M0007809 GPNDGCNO_00001 2130 3 Skin 0.33 protein_coding synonymous_variant LOW 1308C>A Gly436Gly
M0007810 GPNDGCNO_00001 2141 3 Skin 0.33 protein_coding splice_region_variant&stop_retained_variant LOW 1319G>A Ter440Ter
M0007811 GPNDGCNO_00002 2146 4 Skin 0.44 protein_coding upstream_gene_variant MODIFIER -72C>G None
M0007812 GPNDGCNO_00002 2148 3 Skin 0.33 protein_coding upstream_gene_variant MODIFIER -70G>A None
M0007813 GPNDGCNO_00002 2183 4 Skin 0.44 protein_coding upstream_gene_variant MODIFIER -35G>A None
M0007814 GPNDGCNO_00002 2191 4 Skin 0.44 protein_coding upstream_gene_variant MODIFIER -27C>T None
M0007815 GPNDGCNO_00002 2260 4 Skin 0.44 protein_coding missense_variant MODERATE 43A>G Thr15Ala
M0007816 GPNDGCNO_00002 2447 4 Skin 0.44 protein_coding missense_variant MODERATE 230G>C Gly77Ala
M0007817 GPNDGCNO_00003 3140 5 Skin 0.56 protein_coding missense_variant MODERATE 43T>C Phe15Leu
M0007818 GPNDGCNO_00003 3418 4 Skin 0.44 protein_coding synonymous_variant LOW 321T>C Asp107Asp
M0007819 GPNDGCNO_00003 3445 4 Skin 0.44 protein_coding synonymous_variant LOW 348A>G Lys116Lys
M0007820 GPNDGCNO_00003 3757 3 Skin 0.33 protein_coding synonymous_variant LOW 660G>C Ala220Ala
M0007821 GPNDGCNO_00003 3796 3 Skin 0.33 protein_coding synonymous_variant LOW 699C>T Tyr233Tyr
M0007822 GPNDGCNO_00004 3977 4 Skin 0.44 protein_coding missense_variant MODERATE 37C>T Leu13Phe
M0007823 GPNDGCNO_00004 3992 4 Skin 0.44 protein_coding missense_variant MODERATE 52A>G Ile18Val
M0007824 GPNDGCNO_00004 4127 4 Skin 0.44 protein_coding missense_variant MODERATE 187A>G Asn63Asp
M0007825 GPNDGCNO_00004 4286 4 Skin 0.44 protein_coding missense_variant MODERATE 346A>C Lys116Gln
M0007826 GPNDGCNO_00004 4432 4 Skin 0.44 protein_coding synonymous_variant LOW 492T>C Leu164Leu
M0007827 GPNDGCNO_00004 4493 4 Skin 0.44 protein_coding missense_variant MODERATE 553G>A Ala185Thr
M0007828 GPNDGCNO_00004 4573 4 Skin 0.44 protein_coding synonymous_variant LOW 633G>T Arg211Arg
M0007829 GPNDGCNO_00004 4597 3 Skin 0.33 protein_coding synonymous_variant LOW 657T>C Leu219Leu
M0007830 GPNDGCNO_00004 4877 3 Skin 0.33 protein_coding missense_variant MODERATE 937G>A Val313Ile
M0007831 GPNDGCNO_00004 4899 3 Skin 0.33 protein_coding missense_variant MODERATE 959G>A Gly320Asp
M0007832 GPNDGCNO_00004 4903 3 Skin 0.33 protein_coding synonymous_variant LOW 963G>C Arg321Arg
M0007833 GPNDGCNO_00004 4904 3 Skin 0.33 protein_coding missense_variant MODERATE 964A>G Ile322Val
M0007834 GPNDGCNO_00004 4919 3 Skin 0.33 protein_coding missense_variant MODERATE 979A>C Lys327Gln
M0007835 GPNDGCNO_00005 5091 3 Skin 0.33 protein_coding synonymous_variant LOW 156T>G Arg52Arg
M0007836 GPNDGCNO_00005 5151 3 Skin 0.33 protein_coding synonymous_variant LOW 216G>C Val72Val
M0007837 GPNDGCNO_00005 5163 4 Skin 0.44 protein_coding synonymous_variant LOW 228C>T Gly76Gly
M0007838 GPNDGCNO_00005 5529 4 Skin 0.44 protein_coding synonymous_variant LOW 594C>T His198His
M0007839 GPNDGCNO_00005 5625 4 Skin 0.44 protein_coding synonymous_variant LOW 690A>C Val230Val
M0007840 GPNDGCNO_00006 5989 3 Skin 0.33 protein_coding synonymous_variant LOW 288C>A Ile96Ile
M0007841 GPNDGCNO_00006 5994 3 Skin 0.33 protein_coding missense_variant MODERATE 293T>C Val98Ala
M0007842 GPNDGCNO_00006 6003 3 Skin 0.33 protein_coding missense_variant MODERATE 302G>A Gly101Asp
M0007843 GPNDGCNO_00006 6008 3 Skin 0.33 protein_coding missense_variant MODERATE 307A>C Met103Leu
M0007844 GPNDGCNO_00006 6061 3 Skin 0.33 protein_coding synonymous_variant LOW 360C>G Thr120Thr
M0007845 GPNDGCNO_00006 6074 3 Skin 0.33 protein_coding missense_variant MODERATE 373A>C Met125Leu
M0007846 GPNDGCNO_00007 7546 3 Skin 0.33 protein_coding missense_variant MODERATE 391G>A Ala131Thr
M0007847 GPNDGCNO_00007 7597 3 Skin 0.33 protein_coding missense_variant MODERATE 442A>G Asn148Asp
M0007848 GPNDGCNO_00007 7731 3 Skin 0.33 protein_coding synonymous_variant LOW 576A>G Ala192Ala
M0007849 GPNDGCNO_00008 7989 3 Skin 0.33 protein_coding synonymous_variant LOW 741T>C Ile247Ile
M0007850 GPNDGCNO_00008 8225 3 Skin 0.33 protein_coding missense_variant MODERATE 505A>G Ile169Val
M0007851 GPNDGCNO_00008 8505 3 Skin 0.33 protein_coding synonymous_variant LOW 225T>C Ala75Ala
M0007852 GPNDGCNO_00008 8715 3 Skin 0.33 protein_coding synonymous_variant LOW 15A>C Leu5Leu
M0007853 GPNDGCNO_00008 8732 3 Skin 0.33 protein_coding upstream_gene_variant MODIFIER -3T>C None
M0007854 GPNDGCNO_00009 8861 3 Skin 0.33 protein_coding synonymous_variant LOW 15T>C Gly5Gly
M0007855 GPNDGCNO_00009 8873 3 Skin 0.33 protein_coding synonymous_variant LOW 27C>G Leu9Leu
M0007856 GPNDGCNO_00009 8897 3 Skin 0.33 protein_coding synonymous_variant LOW 51C>G Ala17Ala
M0007857 GPNDGCNO_00009 9209 4 Skin 0.44 protein_coding synonymous_variant LOW 363T>C Gly121Gly
M0007858 GPNDGCNO_00001 1338 4 Skin 0.44 protein_coding synonymous_variant LOW 516T>C Thr172Thr
M0007859 GPNDGCNO_00006 6643 3 Skin 0.33 protein_coding synonymous_variant LOW 942C>T His314His
M0007860 GPNDGCNO_00006 6739 3 Skin 0.33 protein_coding synonymous_variant LOW 1038C>G Leu346Leu
M0007861 GPNDGCNO_00007 7266 3 Skin 0.33 protein_coding synonymous_variant LOW 111T>C Ala37Ala






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






        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
GPNDGCNO_00013 QQO46424.1|GT51 78.9 1.57e-119 15 235 0.8911 0.9701





        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
GPNDGCNO_00002 3.A.1.1.5 74.7 4.3e-118 1 289 1.0000 0.8705 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
GPNDGCNO_00003 3.A.1.1.5 76.4 1.9e-118 1 276 1.0000 0.8313 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
GPNDGCNO_00004 3.A.1.1.5 72.5 8.2e-137 1 331 0.9970 0.9970 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily