Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2733
  Reference Plasmid   1111525849861727_bin.16__k141_87231
  Reference Plasmid Size   4266
  Reference Plasmid GC Content   0.42
  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
M0132459 JNLGINIM_00002 1810 3 Oral 0.60 protein_coding synonymous_variant LOW 591T>C Asn197Asn
M0132460 JNLGINIM_00002 1821 3 Oral 0.60 protein_coding missense_variant MODERATE 580G>A Ala194Thr
M0132461 JNLGINIM_00002 1825 3 Oral 0.60 protein_coding synonymous_variant LOW 576A>G Leu192Leu
M0132462 JNLGINIM_00002 1827 3 Oral 0.60 protein_coding synonymous_variant LOW 574C>T Leu192Leu
M0132463 JNLGINIM_00002 2014 4 Oral 0.80 protein_coding synonymous_variant LOW 387T>C Asn129Asn
M0132464 JNLGINIM_00002 2122 3 Oral 0.60 protein_coding synonymous_variant LOW 279C>G Leu93Leu
M0132465 JNLGINIM_00002 2233 4 Oral 0.80 protein_coding synonymous_variant LOW 168T>C His56His
M0132466 JNLGINIM_00003 2457 5 Oral 1.00 protein_coding missense_variant MODERATE 884C>T Thr295Ile
M0132467 JNLGINIM_00003 2540 3 Oral 0.60 protein_coding synonymous_variant LOW 801A>G Gln267Gln
M0132468 JNLGINIM_00003 2555 5 Oral 1.00 protein_coding synonymous_variant LOW 786C>T Phe262Phe
M0132469 JNLGINIM_00003 2564 4 Oral 0.80 protein_coding synonymous_variant LOW 777T>C Arg259Arg
M0132470 JNLGINIM_00003 2960 4 Oral 0.80 protein_coding synonymous_variant LOW 381T>C Ile127Ile
M0132471 JNLGINIM_00001 3396 5 Oral 1.00 protein_coding upstream_gene_variant MODIFIER -2197G>T None
M0132472 JNLGINIM_00004 3419 5 Oral 1.00 protein_coding synonymous_variant LOW 786T>C Asp262Asp
M0132473 JNLGINIM_00004 3572 5 Oral 1.00 protein_coding missense_variant MODERATE 633G>C Leu211Phe
M0132474 JNLGINIM_00004 3581 4 Oral 0.80 protein_coding synonymous_variant LOW 624A>G Leu208Leu
M0132475 JNLGINIM_00004 3674 3 Oral 0.60 protein_coding synonymous_variant LOW 531C>A Ala177Ala
M0132476 JNLGINIM_00004 4085 4 Oral 0.80 protein_coding synonymous_variant LOW 120T>C Asn40Asn
M0132477 JNLGINIM_00004 4109 5 Oral 1.00 protein_coding synonymous_variant LOW 96T>C Phe32Phe
M0132478 JNLGINIM_00002 1906 3 Oral 0.60 protein_coding synonymous_variant LOW 495T>G Gly165Gly
M0132479 JNLGINIM_00001 3401 3 Oral 0.60 protein_coding upstream_gene_variant MODIFIER -2202T>A None
M0132480 JNLGINIM_00004 4190 3 Oral 0.60 protein_coding synonymous_variant LOW 15C>T Asp5Asp
M0132481 JNLGINIM_00004 4193 3 Oral 0.60 protein_coding synonymous_variant LOW 12C>A Ile4Ile






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
JNLGINIM_00002 EFC71205.1|GT4 94 3.34e-264 1 385 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