Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1217
  Reference Plasmid   NZ_CP135674.1
  Reference Plasmid Size   61392
  Reference Plasmid GC Content   0.48
  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
M0199676 MKODAMJP_00002 1007 3 Gut 0.75 protein_coding synonymous_variant LOW 255A>G Val85Val
M0199677 MKODAMJP_00002 1040 3 Gut 0.75 protein_coding synonymous_variant LOW 288C>T Asn96Asn
M0199678 MKODAMJP_00002 1100 3 Gut 0.75 protein_coding synonymous_variant LOW 348T>C Val116Val
M0199679 MKODAMJP_00002 1106 3 Gut 0.75 protein_coding synonymous_variant LOW 354G>A Arg118Arg
M0199680 MKODAMJP_00002 1139 3 Gut 0.75 protein_coding synonymous_variant LOW 387A>G Glu129Glu
M0199681 MKODAMJP_00002 1154 3 Gut 0.75 protein_coding synonymous_variant LOW 402T>G Ala134Ala
M0199682 MKODAMJP_00002 1157 3 Gut 0.75 protein_coding synonymous_variant LOW 405A>G Leu135Leu
M0199683 MKODAMJP_00002 1265 3 Gut 0.75 protein_coding synonymous_variant LOW 513A>G Leu171Leu
M0199684 MKODAMJP_00002 1284 3 Gut 0.75 protein_coding missense_variant MODERATE 532G>T Ala178Ser
M0199685 MKODAMJP_00002 1286 3 Gut 0.75 protein_coding synonymous_variant LOW 534C>T Ala178Ala
M0199686 MKODAMJP_00002 1295 3 Gut 0.75 protein_coding synonymous_variant LOW 543G>A Arg181Arg
M0199687 MKODAMJP_00002 1373 3 Gut 0.75 protein_coding synonymous_variant LOW 621A>T Ala207Ala
M0199688 MKODAMJP_00002 1394 3 Gut 0.75 protein_coding synonymous_variant LOW 642C>T Ser214Ser
M0199689 MKODAMJP_00002 1415 3 Gut 0.75 protein_coding synonymous_variant LOW 663C>T Val221Val
M0199690 MKODAMJP_00002 1559 3 Gut 0.75 protein_coding synonymous_variant LOW 807T>C His269His
M0199691 MKODAMJP_00002 1574 3 Gut 0.75 protein_coding synonymous_variant LOW 822C>G Gly274Gly
M0199692 MKODAMJP_00002 1592 3 Gut 0.75 protein_coding synonymous_variant LOW 840T>C Gly280Gly
M0199693 MKODAMJP_00002 1598 3 Gut 0.75 protein_coding synonymous_variant LOW 846A>G Arg282Arg
M0199694 MKODAMJP_00002 1655 3 Gut 0.75 protein_coding synonymous_variant LOW 903C>T Arg301Arg
M0199695 MKODAMJP_00002 1748 3 Gut 0.75 protein_coding synonymous_variant LOW 996G>A Thr332Thr
M0199696 MKODAMJP_00034 42366 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -1915G>T None
M0199697 MKODAMJP_00039 43907 3 Gut 0.75 protein_coding missense_variant MODERATE 1258T>C Cys420Arg
M0199698 MKODAMJP_00034 44497 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -4046T>G None
M0199699 MKODAMJP_00054 52678 3 Gut 0.75 protein_coding missense_variant MODERATE 497A>G Glu166Gly
M0199700 MKODAMJP_00054 52781 3 Gut 0.75 protein_coding synonymous_variant LOW 600C>T Ser200Ser
M0199701 MKODAMJP_00048 55386 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -4831A>G None






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
MKODAMJP_00032 PHI:10179 tnpA 74.3 8.2e-58 56 195 0.6604 0.9211 rodents salmonellosis regulatory RNA/ transposase for IS200 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
MKODAMJP_00011 AYL89119.1|GH24 96.6 0 903 1405 0.358 0.9031
MKODAMJP_00029 QIN74719.1|GT2 100 0 1 701 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
MKODAMJP_00033 1.B.55.3.1 99.2 0 1 1156 0.9991 0.9991 1 Channels/Pores 1.B β-Barrel Porins 1.B.55 The Poly Acetyl Glucosamine Porin (PgaA) Family