Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C3313
  Reference Plasmid   MGYG000298317__MGYG000298317_58
  Reference Plasmid Size   17085
  Reference Plasmid GC Content   0.39
  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
M0135149 NCOCNEKG_00001 216 3 Oral 0.75 protein_coding missense_variant MODERATE 245G>A Arg82Lys
M0135150 NCOCNEKG_00001 320 3 Oral 0.75 protein_coding synonymous_variant LOW 141T>A Gly47Gly
M0135151 NCOCNEKG_00001 326 3 Oral 0.75 protein_coding synonymous_variant LOW 135C>T Leu45Leu
M0135152 NCOCNEKG_00001 335 3 Oral 0.75 protein_coding synonymous_variant LOW 126A>G Glu42Glu
M0135153 NCOCNEKG_00001 338 3 Oral 0.75 protein_coding synonymous_variant LOW 123C>A Gly41Gly
M0135154 NCOCNEKG_00001 341 3 Oral 0.75 protein_coding synonymous_variant LOW 120A>C Ala40Ala
M0135155 NCOCNEKG_00001 1876 4 Oral 1.00 protein_coding upstream_gene_variant MODIFIER -1416T>C None
M0135156 NCOCNEKG_00003 2297 3 Oral 0.75 protein_coding synonymous_variant LOW 4167C>T Asn1389Asn
M0135157 NCOCNEKG_00003 2324 3 Oral 0.75 protein_coding synonymous_variant LOW 4140A>G Ser1380Ser
M0135158 NCOCNEKG_00003 2582 4 Oral 1.00 protein_coding synonymous_variant LOW 3882A>T Leu1294Leu
M0135159 NCOCNEKG_00003 2690 3 Oral 0.75 protein_coding synonymous_variant LOW 3774G>A Leu1258Leu
M0135160 NCOCNEKG_00003 3161 4 Oral 1.00 protein_coding synonymous_variant LOW 3303T>C Gly1101Gly
M0135161 NCOCNEKG_00003 4694 4 Oral 1.00 protein_coding synonymous_variant LOW 1770C>T Thr590Thr
M0135162 NCOCNEKG_00003 4739 3 Oral 0.75 protein_coding synonymous_variant LOW 1725A>C Val575Val
M0135163 NCOCNEKG_00003 5045 4 Oral 1.00 protein_coding synonymous_variant LOW 1419T>C His473His
M0135164 NCOCNEKG_00003 5246 4 Oral 1.00 protein_coding synonymous_variant LOW 1218A>C Arg406Arg
M0135165 NCOCNEKG_00003 5618 3 Oral 0.75 protein_coding synonymous_variant LOW 846T>C Arg282Arg
M0135166 NCOCNEKG_00003 5807 3 Oral 0.75 protein_coding synonymous_variant LOW 657A>G Ala219Ala
M0135167 NCOCNEKG_00004 7224 4 Oral 1.00 protein_coding synonymous_variant LOW 3075C>T Leu1025Leu
M0135168 NCOCNEKG_00004 7254 4 Oral 1.00 protein_coding missense_variant MODERATE 3045T>G Asn1015Lys
M0135169 NCOCNEKG_00004 9480 4 Oral 1.00 protein_coding synonymous_variant LOW 819A>G Glu273Glu
M0135170 NCOCNEKG_00003 10422 4 Oral 1.00 protein_coding upstream_gene_variant MODIFIER -3959G>A None
M0135171 NCOCNEKG_00003 10423 4 Oral 1.00 protein_coding upstream_gene_variant MODIFIER -3960C>T None
M0135172 NCOCNEKG_00003 10427 4 Oral 1.00 protein_coding upstream_gene_variant MODIFIER -3964A>C None
M0135173 NCOCNEKG_00006 10938 3 Oral 0.75 protein_coding missense_variant MODERATE 470G>C Gly157Ala
M0135174 NCOCNEKG_00006 11377 3 Oral 0.75 protein_coding missense_variant MODERATE 31A>G Thr11Ala
M0135175 NCOCNEKG_00007 11894 3 Oral 0.75 protein_coding synonymous_variant LOW 225A>G Val75Val
M0135176 NCOCNEKG_00001 1894 3 Oral 0.75 protein_coding upstream_gene_variant MODIFIER -1434A>G None
M0135177 NCOCNEKG_00003 5444 3 Oral 0.75 protein_coding synonymous_variant LOW 1020G>A Lys340Lys
M0135178 NCOCNEKG_00004 8187 3 Oral 0.75 protein_coding synonymous_variant LOW 2112A>G Glu704Glu
M0135179 NCOCNEKG_00004 9021 3 Oral 0.75 protein_coding synonymous_variant LOW 1278T>C Ile426Ile
M0135180 NCOCNEKG_00004 9036 3 Oral 0.75 protein_coding synonymous_variant LOW 1263T>C Ala421Ala
M0135181 NCOCNEKG_00004 9351 3 Oral 0.75 protein_coding synonymous_variant LOW 948C>T Ser316Ser
M0135182 NCOCNEKG_00004 9369 3 Oral 0.75 protein_coding synonymous_variant LOW 930G>A Thr310Thr






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
NCOCNEKG_00011 ARO:3003368 71.6 5.48e-207 1 393 0.9949 1.0000 elfamycin antibiotic elfamycin resistant EF-Tu antibiotic target alteration






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