Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1349
  Reference Plasmid   NZ_LR135334.1
  Reference Plasmid Size   72466
  Reference Plasmid GC Content   0.34
  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
M0207040 GMLELPKF_00005 3009 4 Gut 0.80 protein_coding synonymous_variant LOW 33G>T Val11Val
M0207041 GMLELPKF_00006 3152 4 Gut 0.80 protein_coding synonymous_variant LOW 462A>T Ile154Ile
M0207042 GMLELPKF_00006 3553 4 Gut 0.80 protein_coding synonymous_variant LOW 61T>C Leu21Leu
M0207043 GMLELPKF_00006 3559 3 Gut 0.60 protein_coding synonymous_variant LOW 55C>T Leu19Leu
M0207044 GMLELPKF_00007 3747 4 Gut 0.80 protein_coding synonymous_variant LOW 810C>T Ile270Ile
M0207045 GMLELPKF_00007 4027 4 Gut 0.80 protein_coding missense_variant MODERATE 530G>A Ser177Asn
M0207046 GMLELPKF_00004 4586 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -1779C>T None
M0207047 GMLELPKF_00004 4938 4 Gut 0.80 protein_coding upstream_gene_variant MODIFIER -2131C>T None
M0207048 GMLELPKF_00004 5123 4 Gut 0.80 protein_coding upstream_gene_variant MODIFIER -2316T>C None
M0207049 GMLELPKF_00004 5125 4 Gut 0.80 protein_coding upstream_gene_variant MODIFIER -2318T>C None
M0207050 GMLELPKF_00004 5147 4 Gut 0.80 protein_coding upstream_gene_variant MODIFIER -2340T>C None
M0207051 GMLELPKF_00004 5149 4 Gut 0.80 protein_coding upstream_gene_variant MODIFIER -2342A>T None
M0207052 GMLELPKF_00004 5158 4 Gut 0.80 protein_coding upstream_gene_variant MODIFIER -2351C>T None
M0207053 GMLELPKF_00004 5168 4 Gut 0.80 protein_coding upstream_gene_variant MODIFIER -2361A>G None
M0207054 GMLELPKF_00004 5252 4 Gut 0.80 protein_coding upstream_gene_variant MODIFIER -2445T>G None
M0207055 GMLELPKF_00009 5377 4 Gut 0.80 protein_coding synonymous_variant LOW 639T>C Ser213Ser
M0207056 GMLELPKF_00009 5413 4 Gut 0.80 protein_coding synonymous_variant LOW 603C>T Ala201Ala
M0207057 GMLELPKF_00009 5458 4 Gut 0.80 protein_coding synonymous_variant LOW 558T>C Pro186Pro
M0207058 GMLELPKF_00009 5473 4 Gut 0.80 protein_coding synonymous_variant LOW 543T>C Gly181Gly
M0207059 GMLELPKF_00009 5527 4 Gut 0.80 protein_coding synonymous_variant LOW 489C>T Val163Val
M0207060 GMLELPKF_00009 5530 4 Gut 0.80 protein_coding synonymous_variant LOW 486G>A Ala162Ala
M0207061 GMLELPKF_00009 5539 4 Gut 0.80 protein_coding synonymous_variant LOW 477A>T Val159Val
M0207062 GMLELPKF_00009 5545 4 Gut 0.80 protein_coding synonymous_variant LOW 471C>T Ile157Ile
M0207063 GMLELPKF_00009 5563 4 Gut 0.80 protein_coding synonymous_variant LOW 453T>C Asn151Asn
M0207064 GMLELPKF_00009 5568 4 Gut 0.80 protein_coding synonymous_variant LOW 448C>T Leu150Leu
M0207065 GMLELPKF_00009 5569 4 Gut 0.80 protein_coding missense_variant MODERATE 447G>A Met149Ile
M0207066 GMLELPKF_00009 5653 4 Gut 0.80 protein_coding synonymous_variant LOW 363T>C Gly121Gly
M0207067 GMLELPKF_00009 5697 3 Gut 0.60 protein_coding missense_variant MODERATE 319A>G Thr107Ala
M0207068 GMLELPKF_00009 5708 3 Gut 0.60 protein_coding missense_variant MODERATE 308C>T Ser103Leu
M0207069 GMLELPKF_00009 5710 3 Gut 0.60 protein_coding synonymous_variant LOW 306A>G Glu102Glu
M0207070 GMLELPKF_00009 5713 3 Gut 0.60 protein_coding synonymous_variant LOW 303T>C Tyr101Tyr
M0207071 GMLELPKF_00009 5728 3 Gut 0.60 protein_coding synonymous_variant LOW 288C>A Ala96Ala
M0207072 GMLELPKF_00009 5746 3 Gut 0.60 protein_coding synonymous_variant LOW 270T>C Asn90Asn
M0207073 GMLELPKF_00009 5778 3 Gut 0.60 protein_coding synonymous_variant LOW 238T>C Leu80Leu
M0207074 GMLELPKF_00009 5783 3 Gut 0.60 protein_coding missense_variant MODERATE 233A>G Lys78Arg
M0207075 GMLELPKF_00009 5785 3 Gut 0.60 protein_coding synonymous_variant LOW 231T>A Ile77Ile
M0207076 GMLELPKF_00009 5799 3 Gut 0.60 protein_coding missense_variant MODERATE 217G>A Val73Ile
M0207077 GMLELPKF_00009 5824 3 Gut 0.60 protein_coding synonymous_variant LOW 192T>C Ala64Ala






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
GMLELPKF_00006 ARO:3004629 100 5.08e-134 1 178 1.0000 1.0000 aminoglycoside antibiotic AAC(6') antibiotic inactivation
GMLELPKF_00007 ARO:3002635 99.7 7.34e-219 1 299 1.0000 1.0000 aminoglycoside antibiotic APH(2'') antibiotic inactivation






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
GMLELPKF_00078 PHI:5205 HMPREF0351_10118 (WxL locusC) 100 1e-226 1 392 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis 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
GMLELPKF_00045 BBI27878.1|GH32 100 0 1 475 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