Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C125
  Reference Plasmid   CP077245.1
  Reference Plasmid Size   91885
  Reference Plasmid GC Content   0.53
  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
M0144781 ANDJCPDL_00014 14693 20 Gut 0.61 protein_coding missense_variant MODERATE 1445G>A Arg482Gln
M0144782 ANDJCPDL_00016 14879 19 Gut 0.58 protein_coding upstream_gene_variant MODIFIER -576T>A None
M0144783 ANDJCPDL_00015 15128 19 Gut 0.58 protein_coding upstream_gene_variant MODIFIER -3G>A None
M0144784 ANDJCPDL_00015 15441 19 Gut 0.58 protein_coding upstream_gene_variant MODIFIER -316T>C None
M0144785 ANDJCPDL_00017 16021 19 Gut 0.58 protein_coding missense_variant MODERATE 34A>G Thr12Ala
M0144786 ANDJCPDL_00020 17032 19 Gut 0.58 protein_coding missense_variant MODERATE 422C>T Ala141Val
M0144787 ANDJCPDL_00020 17136 19 Gut 0.58 protein_coding synonymous_variant LOW 318T>C Val106Val
M0144788 ANDJCPDL_00021 17570 20 Gut 0.61 protein_coding synonymous_variant LOW 15A>C Ile5Ile
M0144789 ANDJCPDL_00021 17597 20 Gut 0.61 protein_coding synonymous_variant LOW 42C>T Ala14Ala
M0144790 ANDJCPDL_00015 18444 19 Gut 0.58 protein_coding upstream_gene_variant MODIFIER -3319A>C None
M0144791 ANDJCPDL_00015 18445 19 Gut 0.58 protein_coding upstream_gene_variant MODIFIER -3320A>T None
M0144792 ANDJCPDL_00015 18923 20 Gut 0.61 protein_coding upstream_gene_variant MODIFIER -3798T>A None
M0144793 ANDJCPDL_00032 31208 12 Gut 0.36 protein_coding missense_variant MODERATE 2215G>A Asp739Asn
M0144794 ANDJCPDL_00021 17614 4 Gut 0.12 protein_coding missense_variant MODERATE 59A>T Gln20Leu
M0144795 ANDJCPDL_00031 28459 5 Gut 0.15 protein_coding synonymous_variant LOW 372G>A Glu124Glu
M0144796 ANDJCPDL_00030 27695 4 Gut 0.12 protein_coding synonymous_variant LOW 396G>T Ala132Ala






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
ANDJCPDL_00028 ARO:3000412 100 4.11e-186 1 271 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
ANDJCPDL_00029 ARO:3002639 99.6 5.98e-202 1 267 1.0000 1.0000 aminoglycoside antibiotic APH(3'') antibiotic inactivation
ANDJCPDL_00030 ARO:3000873 100 5.12e-208 1 286 1.0000 1.0000 monobactam TEM beta-lactamase antibiotic inactivation
ANDJCPDL_00033 ARO:3002660 99.6 5.98e-177 15 257 0.9455 0.8741 aminoglycoside antibiotic APH(6) 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






        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
ANDJCPDL_00087 SPE00673.1|GH23 100 1.33e-115 1 161 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
ANDJCPDL_00001 3.A.7.10.1 88.5 7.7e-38 1 78 1.0000 0.8125 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
ANDJCPDL_00015 1.E.53.1.10 100 2e-18 8 50 0.8600 1.0000 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family
ANDJCPDL_00024 3.A.7.10.1 76.1 1.1e-189 1 401 0.9282 4.1771 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
ANDJCPDL_00026 3.A.7.10.1 79.6 0 1 724 0.9439 7.5417 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
ANDJCPDL_00093 3.A.7.10.1 77.9 6.6e-124 1 271 0.9748 2.8021 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
ANDJCPDL_00094 3.A.7.10.1 77.8 1.7e-175 1 379 0.9921 3.9479 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
ANDJCPDL_00097 3.A.7.10.1 73.3 1.9e-40 1 116 1.0000 1.1979 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family