Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C113
  Reference Plasmid   CP057937.1
  Reference Plasmid Size   97047
  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
M0144483 DLOLGPCD_00004 4658 3 Gut 0.30 protein_coding synonymous_variant LOW 966T>C Ser322Ser
M0144484 DLOLGPCD_00004 4811 3 Gut 0.30 protein_coding synonymous_variant LOW 1119C>T Arg373Arg
M0144485 DLOLGPCD_00004 5213 3 Gut 0.30 protein_coding synonymous_variant LOW 1521C>T Ala507Ala
M0144486 DLOLGPCD_00004 5261 3 Gut 0.30 protein_coding synonymous_variant LOW 1569G>A Thr523Thr
M0144487 DLOLGPCD_00005 5534 3 Gut 0.30 protein_coding synonymous_variant LOW 75G>T Ala25Ala
M0144488 DLOLGPCD_00005 5705 3 Gut 0.30 protein_coding synonymous_variant LOW 246A>G Val82Val
M0144489 DLOLGPCD_00005 5729 3 Gut 0.30 protein_coding synonymous_variant LOW 270A>T Ser90Ser
M0144490 DLOLGPCD_00005 5741 3 Gut 0.30 protein_coding synonymous_variant LOW 282T>C Val94Val
M0144491 DLOLGPCD_00005 5822 3 Gut 0.30 protein_coding synonymous_variant LOW 363C>T Tyr121Tyr
M0144492 DLOLGPCD_00005 5846 3 Gut 0.30 protein_coding synonymous_variant LOW 387T>C Ser129Ser
M0144493 DLOLGPCD_00005 5987 3 Gut 0.30 protein_coding synonymous_variant LOW 528C>T Gly176Gly
M0144494 DLOLGPCD_00005 6119 3 Gut 0.30 protein_coding missense_variant MODERATE 660G>T Glu220Asp
M0144495 DLOLGPCD_00005 6128 3 Gut 0.30 protein_coding synonymous_variant LOW 669G>T Ser223Ser
M0144496 DLOLGPCD_00005 6131 3 Gut 0.30 protein_coding synonymous_variant LOW 672G>A Thr224Thr
M0144497 DLOLGPCD_00005 6146 3 Gut 0.30 protein_coding synonymous_variant LOW 687T>C Asn229Asn
M0144498 DLOLGPCD_00074 75255 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4755C>T None
M0144499 DLOLGPCD_00092 80168 4 Gut 0.40 protein_coding missense_variant MODERATE 554C>G Ala185Gly
M0144500 DLOLGPCD_00094 81403 3 Gut 0.30 protein_coding synonymous_variant LOW 171G>A Lys57Lys
M0144501 DLOLGPCD_00086 81501 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -4382T>C None
M0144502 DLOLGPCD_00095 81809 3 Gut 0.30 protein_coding synonymous_variant LOW 307T>C Leu103Leu
M0144503 DLOLGPCD_00108 93049 3 Gut 0.30 protein_coding synonymous_variant LOW 219T>C Val73Val
M0144504 DLOLGPCD_00108 93084 3 Gut 0.30 protein_coding synonymous_variant LOW 184T>C Leu62Leu
M0144505 DLOLGPCD_00108 96866 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -3599T>C 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






        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
DLOLGPCD_00023 AOM57988.1|GH23 100 0 1 1124 1 1
DLOLGPCD_00045 AJS09995.1|GH24 99.5 7.75e-138 1 185 1 1
DLOLGPCD_00049 AYL89119.1|GH24 96.2 1.19999998039166e-317 1753 2255 0.2231 0.9031





        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
DLOLGPCD_00033 1.E.4.1.2 100 8.9e-49 1 93 1.0000 1.0000 1 Channels/Pores 1.E Holins 1.E.4 The LydA Holin (LydA Holin) Family
DLOLGPCD_00034 1.E.4.1.1 100 1.3e-54 1 109 1.0000 1.0000 1 Channels/Pores 1.E Holins 1.E.4 The LydA Holin (LydA Holin) Family
DLOLGPCD_00046 1.E.64.1.1 100 5.7e-39 1 83 1.0000 0.9881 1 Channels/Pores 1.E Holins 1.E.64 The P7 Phage Holin LydD (LydD) Family