Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C133
  Reference Plasmid   CP088357.1
  Reference Plasmid Size   150952
  Reference Plasmid GC Content   0.52
  Reference Plasmid Mobility Type   conjugative





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
M0144882 GJDKCLLI_00031 28973 3 Gut 0.75 protein_coding synonymous_variant LOW 48T>C Ile16Ile
M0144883 GJDKCLLI_00031 28975 3 Gut 0.75 protein_coding missense_variant MODERATE 46A>G Ile16Val
M0144884 GJDKCLLI_00031 28976 3 Gut 0.75 protein_coding synonymous_variant LOW 45G>A Ala15Ala
M0144885 GJDKCLLI_00031 28981 3 Gut 0.75 protein_coding synonymous_variant LOW 40A>C Arg14Arg
M0144886 GJDKCLLI_00031 28982 3 Gut 0.75 protein_coding synonymous_variant LOW 39G>A Gln13Gln
M0144887 GJDKCLLI_00027 29042 4 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -2209C>T None
M0144888 GJDKCLLI_00027 29117 4 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -2284T>C None
M0144889 GJDKCLLI_00033 29667 4 Gut 1.00 protein_coding missense_variant MODERATE 289C>A Leu97Met
M0144890 GJDKCLLI_00033 29669 4 Gut 1.00 protein_coding synonymous_variant LOW 291G>C Leu97Leu
M0144891 GJDKCLLI_00033 29679 4 Gut 1.00 protein_coding missense_variant MODERATE 301C>G Leu101Val
M0144892 GJDKCLLI_00033 29681 4 Gut 1.00 protein_coding synonymous_variant LOW 303G>A Leu101Leu
M0144893 GJDKCLLI_00033 29838 4 Gut 1.00 protein_coding missense_variant MODERATE 460A>T Arg154Trp
M0144894 GJDKCLLI_00033 29887 4 Gut 1.00 protein_coding missense_variant MODERATE 509A>C Gln170Pro
M0144895 GJDKCLLI_00034 29992 4 Gut 1.00 protein_coding synonymous_variant LOW 324G>A Arg108Arg
M0144896 GJDKCLLI_00034 30049 4 Gut 1.00 protein_coding synonymous_variant LOW 267G>T Gly89Gly
M0144897 GJDKCLLI_00035 30494 4 Gut 1.00 protein_coding synonymous_variant LOW 51G>A Gly17Gly
M0144898 GJDKCLLI_00035 30649 4 Gut 1.00 protein_coding missense_variant MODERATE 206G>T Gly69Val
M0144899 GJDKCLLI_00035 30657 4 Gut 1.00 protein_coding missense_variant MODERATE 214A>G Thr72Ala
M0144900 GJDKCLLI_00036 31176 4 Gut 1.00 protein_coding missense_variant MODERATE 167T>C Met56Thr






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
GJDKCLLI_00042 VFG001827 ShET2 99.7 7.9e-225 1 391 1.0 1 Exotoxin enterotoxin experiment
GJDKCLLI_00161 VFG048621 Aerobactin 99.7 0 1 732 1.0 0.9986 Nutritional/Metabolic factor ferric aerobactin receptor IutA experiment
GJDKCLLI_00042 VFG036084 Enterotoxin SenB/TieB 100 1.2e-224 1 391 1.0 1 Exotoxin enterotoxin production-related protein TieB prediction
GJDKCLLI_00161 VFG033944 Aerobactin 100 0 1 732 1.0 0.9986 Nutritional/Metabolic factor ferric aerobactin receptor precusor IutA prediction







        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
GJDKCLLI_00061 ARO:3000165 99.7 7.17e-278 1 390 0.9774 0.9198 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux






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
GJDKCLLI_00039 PHI:10792 cjrA 100 5.6e-166 1 291 1.0000 1.0000 primates neonatal meningitis iron-regulated protein increased virulence (hypervirulence)
GJDKCLLI_00040 PHI:10793 cjrB 100 1.7e-137 1 258 1.0000 1.0000 primates neonatal meningitis colicin Js sensitivity protein increased virulence (hypervirulence)
GJDKCLLI_00041 PHI:10794 cjrC 100 0 1 753 1.0000 1.0000 primates neonatal meningitis TonB-dependent colicin J protein increased virulence (hypervirulence)
GJDKCLLI_00042 PHI:10795 senB 100 4.2e-225 1 391 1.0000 1.0000 primates neonatal meningitis enterotoxin increased virulence (hypervirulence)
GJDKCLLI_00161 PHI:6563 iucA 99.7 0 1 732 1.0000 0.9986 rodents pneumonia aerobactin 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
GJDKCLLI_00124 AKD26598.1|GH23 100 3.49e-124 1 169 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
GJDKCLLI_00018 2.A.108.2.10 99.7 0 1 646 1.0000 3.7341 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.108 The Iron/Lead Transporter (ILT) Family
GJDKCLLI_00019 2.A.108.2.10 100 5e-101 3 175 0.9886 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.108 The Iron/Lead Transporter (ILT) Family
GJDKCLLI_00040 2.C.1.1.3 100 3.7e-137 1 258 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.C Ion-gradient-driven energizers 2.C.1 The TonB-ExbB-ExbD/TolA-TolQ-TolR Outer Membrane Receptor Energizers and Stabilizers (TonB/TolA) Family
GJDKCLLI_00041 1.B.14.7.1 100 0 1 753 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.14 The Outer Membrane Receptor (OMR) Family
GJDKCLLI_00061 2.A.1.2.4 100 2.4e-223 1 399 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
GJDKCLLI_00062 2.A.7.3.67 100 1.8e-159 1 294 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.7 The Drug/Metabolite Transporter (DMT) Superfamily
GJDKCLLI_00083 1.E.53.1.11 98.5 2.5e-32 1 68 1.0000 1.0000 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family