Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C3227
  Reference Plasmid   MET0490_bin.4__k81_21430
  Reference Plasmid Size   84627
  Reference Plasmid GC Content   0.41
  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
M0080430 HDLNOAKB_00001 1316 3 Skin 0.38 protein_coding missense_variant MODERATE 148G>A Asp50Asn
M0080431 HDLNOAKB_00001 2270 3 Skin 0.38 protein_coding upstream_gene_variant MODIFIER -807T>G None
M0080432 HDLNOAKB_00004 2812 3 Skin 0.38 protein_coding missense_variant MODERATE 325G>A Val109Ile
M0080433 HDLNOAKB_00001 3187 4 Skin 0.50 protein_coding upstream_gene_variant MODIFIER -1724A>G None
M0080434 HDLNOAKB_00001 3210 3 Skin 0.38 protein_coding upstream_gene_variant MODIFIER -1747T>G None
M0080435 HDLNOAKB_00005 3437 3 Skin 0.38 protein_coding missense_variant MODERATE 79G>A Gly27Ser
M0080436 HDLNOAKB_00001 3636 4 Skin 0.50 protein_coding upstream_gene_variant MODIFIER -2173T>C None
M0080437 HDLNOAKB_00006 4037 3 Skin 0.38 protein_coding missense_variant MODERATE 554G>A Arg185His
M0080438 HDLNOAKB_00006 4435 3 Skin 0.38 protein_coding synonymous_variant LOW 156A>G Gly52Gly
M0080439 HDLNOAKB_00007 5055 3 Skin 0.38 protein_coding missense_variant MODERATE 190G>A Glu64Lys
M0080440 HDLNOAKB_00015 17345 4 Skin 0.50 protein_coding upstream_gene_variant MODIFIER -1985A>G None
M0080441 HDLNOAKB_00010 9200 3 Skin 0.38 protein_coding missense_variant MODERATE 539T>C Ile180Thr
M0080442 HDLNOAKB_00011 10260 3 Skin 0.38 protein_coding missense_variant MODERATE 531T>G Ser177Arg
M0080443 HDLNOAKB_00009 10919 3 Skin 0.38 protein_coding upstream_gene_variant MODIFIER -2363C>T None
M0080444 HDLNOAKB_00012 12219 3 Skin 0.38 protein_coding missense_variant MODERATE 85A>G Thr29Ala
M0080445 HDLNOAKB_00009 12366 3 Skin 0.38 protein_coding upstream_gene_variant MODIFIER -3810G>A None
M0080446 HDLNOAKB_00009 12590 3 Skin 0.38 protein_coding upstream_gene_variant MODIFIER -4034A>G None
M0080447 HDLNOAKB_00013 13201 3 Skin 0.38 protein_coding missense_variant MODERATE 542T>G Val181Gly
M0080448 HDLNOAKB_00013 13244 3 Skin 0.38 protein_coding synonymous_variant LOW 585T>C Ile195Ile
M0080449 HDLNOAKB_00013 14159 3 Skin 0.38 protein_coding synonymous_variant LOW 1500T>G Thr500Thr
M0080450 HDLNOAKB_00017 16173 3 Skin 0.38 protein_coding missense_variant MODERATE 46A>G Thr16Ala
M0080451 HDLNOAKB_00018 16929 3 Skin 0.38 protein_coding missense_variant MODERATE 398T>G Ile133Ser
M0080452 HDLNOAKB_00019 17926 3 Skin 0.38 protein_coding missense_variant MODERATE 491A>C Glu164Ala
M0080453 HDLNOAKB_00021 19113 3 Skin 0.38 protein_coding synonymous_variant LOW 642A>C Leu214Leu
M0080454 HDLNOAKB_00022 19678 3 Skin 0.38 protein_coding missense_variant MODERATE 367A>G Ile123Val
M0080455 HDLNOAKB_00023 20328 3 Skin 0.38 protein_coding missense_variant MODERATE 206T>G Val69Gly
M0080456 HDLNOAKB_00016 20508 3 Skin 0.38 protein_coding upstream_gene_variant MODIFIER -4748G>T None
M0080457 HDLNOAKB_00025 22941 3 Skin 0.38 protein_coding synonymous_variant LOW 264T>C Leu88Leu






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
HDLNOAKB_00008 Copper (Cu) 100 1.8e-32 1 69 1.0000 1.0000 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






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
HDLNOAKB_00030 PHI:6628 bcaP 73.2 2e-94 1 235 0.7886 0.8734 rodents skin infection; food poisoning; respiratory disease BCAA transporter unaffected pathogenicity
HDLNOAKB_00031 PHI:6628 bcaP 70.4 1e-72 1 186 0.9841 0.8734 rodents skin infection; food poisoning; respiratory disease BCAA transporter unaffected pathogenicity






        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
HDLNOAKB_00011 QQC38207.1|GH23 95.2 1.15e-123 1 250 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