Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C823
  Reference Plasmid   NZ_CP068129.1
  Reference Plasmid Size   76161
  Reference Plasmid GC Content   0.36
  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
M0184018 CIFDNFPB_00086 66360 4 Gut 0.31 protein_coding upstream_gene_variant MODIFIER -460C>T None
M0184019 CIFDNFPB_00086 66496 3 Gut 0.23 protein_coding upstream_gene_variant MODIFIER -324C>T None
M0184020 CIFDNFPB_00086 66699 3 Gut 0.23 protein_coding upstream_gene_variant MODIFIER -121C>A None
M0184021 CIFDNFPB_00086 66720 3 Gut 0.23 protein_coding upstream_gene_variant MODIFIER -100T>C None
M0184022 CIFDNFPB_00087 67924 3 Gut 0.23 protein_coding missense_variant MODERATE 388G>A Ala130Thr
M0184023 CIFDNFPB_00087 67999 4 Gut 0.31 protein_coding missense_variant MODERATE 463T>G Leu155Val
M0184024 CIFDNFPB_00087 68090 3 Gut 0.23 protein_coding missense_variant MODERATE 554A>C Glu185Ala
M0184025 CIFDNFPB_00088 68359 3 Gut 0.23 protein_coding upstream_gene_variant MODIFIER -111T>C None
M0184026 CIFDNFPB_00088 68381 4 Gut 0.31 protein_coding upstream_gene_variant MODIFIER -89T>C None
M0184027 CIFDNFPB_00088 68395 4 Gut 0.31 protein_coding upstream_gene_variant MODIFIER -75T>C None
M0184028 CIFDNFPB_00088 68406 4 Gut 0.31 protein_coding upstream_gene_variant MODIFIER -64C>T None
M0184029 CIFDNFPB_00088 68437 4 Gut 0.31 protein_coding upstream_gene_variant MODIFIER -33C>T None
M0184030 CIFDNFPB_00088 68477 4 Gut 0.31 protein_coding missense_variant MODERATE 8A>G Tyr3Cys
M0184031 CIFDNFPB_00088 68700 4 Gut 0.31 protein_coding synonymous_variant LOW 231T>C Phe77Phe
M0184032 CIFDNFPB_00089 68796 4 Gut 0.31 protein_coding missense_variant MODERATE 5A>G Glu2Gly
M0184033 CIFDNFPB_00089 68811 4 Gut 0.31 protein_coding missense_variant MODERATE 20A>T Asp7Val
M0184034 CIFDNFPB_00089 68826 4 Gut 0.31 protein_coding missense_variant MODERATE 35C>T Ala12Val
M0184035 CIFDNFPB_00089 68856 3 Gut 0.23 protein_coding stop_gained HIGH 65G>A Trp22*
M0184036 CIFDNFPB_00089 68899 3 Gut 0.23 protein_coding synonymous_variant LOW 108G>A Gln36Gln
M0184037 CIFDNFPB_00089 69038 3 Gut 0.23 protein_coding missense_variant MODERATE 247C>T Pro83Ser
M0184038 CIFDNFPB_00089 69163 4 Gut 0.31 protein_coding synonymous_variant LOW 372C>T Ile124Ile
M0184039 CIFDNFPB_00089 69275 4 Gut 0.31 protein_coding missense_variant MODERATE 484T>C Tyr162His
M0184040 CIFDNFPB_00089 69276 4 Gut 0.31 protein_coding missense_variant MODERATE 485A>C Tyr162Ser
M0184041 CIFDNFPB_00089 69384 4 Gut 0.31 protein_coding missense_variant MODERATE 593A>G Gln198Arg
M0184042 CIFDNFPB_00090 69682 3 Gut 0.23 protein_coding upstream_gene_variant MODIFIER -111C>T None
M0184043 CIFDNFPB_00090 69727 3 Gut 0.23 protein_coding upstream_gene_variant MODIFIER -66G>A None
M0184044 CIFDNFPB_00091 70514 4 Gut 0.31 protein_coding synonymous_variant LOW 291T>C His97His
M0184045 CIFDNFPB_00091 70638 3 Gut 0.23 protein_coding missense_variant MODERATE 415A>G Ile139Val
M0184046 CIFDNFPB_00091 70694 3 Gut 0.23 protein_coding synonymous_variant LOW 471C>T Gly157Gly
M0184047 CIFDNFPB_00091 70696 3 Gut 0.23 protein_coding missense_variant MODERATE 473T>C Ile158Thr
M0184048 CIFDNFPB_00091 70754 4 Gut 0.31 protein_coding synonymous_variant LOW 531A>G Pro177Pro
M0184049 CIFDNFPB_00091 71009 3 Gut 0.23 protein_coding synonymous_variant LOW 786C>T Ile262Ile
M0184050 CIFDNFPB_00091 71072 4 Gut 0.31 protein_coding synonymous_variant LOW 849C>T Ile283Ile
M0184051 CIFDNFPB_00092 72239 4 Gut 0.31 protein_coding upstream_gene_variant MODIFIER -160G>T None
M0184052 CIFDNFPB_00092 72317 3 Gut 0.23 protein_coding upstream_gene_variant MODIFIER -82T>C None
M0184053 CIFDNFPB_00092 72526 4 Gut 0.31 protein_coding missense_variant MODERATE 128T>C Phe43Ser
M0184054 CIFDNFPB_00092 72620 5 Gut 0.38 protein_coding synonymous_variant LOW 222T>C Asp74Asp
M0184055 CIFDNFPB_00075 57258 3 Gut 0.23 protein_coding synonymous_variant LOW 225T>C Val75Val
M0184056 CIFDNFPB_00077 59109 3 Gut 0.23 protein_coding synonymous_variant LOW 615G>A Lys205Lys






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
CIFDNFPB_00021 Arsenic (As), Antimony (Sb) 79.2 1.7e-153 1 355 0.9889 0.9944 prediction






        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
CIFDNFPB_00030 PHI:7637 CspA 80.3 1.2e-26 1 66 1.0000 1.0000 bony fishes listeriosis cold shock protein reduced virulence
CIFDNFPB_00041 PHI:8586 mntH1 77.1 1.3e-221 1 514 0.9735 0.9699 moths nosocomial infection divalent metal cation transporter unaffected pathogenicity






        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
CIFDNFPB_00080 QZK92746.1|GH1 100 0 1 468 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
CIFDNFPB_00021 2.A.59.1.5 72.5 5.5e-139 6 347 0.9526 1.1554 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.59 The Arsenical Resistance-3 (ACR3) Family
CIFDNFPB_00079 4.A.3.1.1 71.7 2.6e-239 1 568 1.0000 0.9965 4 Group Translocators 4.A Phosphotransfer-driven Group Translocators (PTS) 4.A.3 The PTS Lactose-N,N'-Diacetylchitobiose-β-glucoside (Lac) Family