Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C36
  Reference Plasmid   AP024695.1
  Reference Plasmid Size   147070
  Reference Plasmid GC Content   0.49
  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
M0142952 DMCBPIBN_00143 124957 3 Gut 0.33 protein_coding missense_variant MODERATE 323C>T Thr108Met
M0142953 DMCBPIBN_00143 124959 3 Gut 0.33 protein_coding synonymous_variant LOW 321C>T Asn107Asn
M0142954 DMCBPIBN_00143 124980 3 Gut 0.33 protein_coding synonymous_variant LOW 300T>C Ala100Ala
M0142955 DMCBPIBN_00143 124998 3 Gut 0.33 protein_coding synonymous_variant LOW 282A>C Thr94Thr
M0142956 DMCBPIBN_00143 125009 3 Gut 0.33 protein_coding missense_variant MODERATE 271G>A Val91Ile
M0142957 DMCBPIBN_00143 125016 3 Gut 0.33 protein_coding synonymous_variant LOW 264C>G Ser88Ser
M0142958 DMCBPIBN_00143 125069 3 Gut 0.33 protein_coding synonymous_variant LOW 211C>T Leu71Leu
M0142959 DMCBPIBN_00144 125366 3 Gut 0.33 protein_coding synonymous_variant LOW 267T>C Gly89Gly
M0142960 DMCBPIBN_00144 125498 3 Gut 0.33 protein_coding synonymous_variant LOW 135G>A Gly45Gly
M0142961 DMCBPIBN_00144 125603 3 Gut 0.33 protein_coding synonymous_variant LOW 30A>G Leu10Leu
M0142962 DMCBPIBN_00144 125618 3 Gut 0.33 protein_coding synonymous_variant LOW 15T>C Asn5Asn
M0142963 DMCBPIBN_00145 126973 3 Gut 0.33 protein_coding missense_variant MODERATE 2034T>G Asn678Lys
M0142964 DMCBPIBN_00145 126988 3 Gut 0.33 protein_coding synonymous_variant LOW 2019T>C Ala673Ala
M0142965 DMCBPIBN_00145 128198 3 Gut 0.33 protein_coding missense_variant MODERATE 809A>G Asn270Ser
M0142966 DMCBPIBN_00145 128269 3 Gut 0.33 protein_coding synonymous_variant LOW 738T>A Ser246Ser
M0142967 DMCBPIBN_00145 128293 3 Gut 0.33 protein_coding synonymous_variant LOW 714A>T Gly238Gly
M0142968 DMCBPIBN_00145 128296 3 Gut 0.33 protein_coding synonymous_variant LOW 711T>C Gly237Gly
M0142969 DMCBPIBN_00145 128314 3 Gut 0.33 protein_coding synonymous_variant LOW 693G>A Gly231Gly
M0142970 DMCBPIBN_00145 128329 3 Gut 0.33 protein_coding synonymous_variant LOW 678G>A Gly226Gly
M0142971 DMCBPIBN_00145 128335 3 Gut 0.33 protein_coding synonymous_variant LOW 672C>A Ala224Ala
M0142972 DMCBPIBN_00145 128368 3 Gut 0.33 protein_coding synonymous_variant LOW 639G>T Ala213Ala
M0142973 DMCBPIBN_00145 128380 3 Gut 0.33 protein_coding synonymous_variant LOW 627C>T Arg209Arg
M0142974 DMCBPIBN_00145 128440 3 Gut 0.33 protein_coding synonymous_variant LOW 567A>G Ser189Ser
M0142975 DMCBPIBN_00145 128532 3 Gut 0.33 protein_coding missense_variant MODERATE 475C>T Pro159Ser
M0142976 DMCBPIBN_00145 128666 3 Gut 0.33 protein_coding missense_variant MODERATE 341A>G Lys114Arg
M0142977 DMCBPIBN_00145 128673 3 Gut 0.33 protein_coding synonymous_variant LOW 334C>A Arg112Arg
M0142978 DMCBPIBN_00145 128687 3 Gut 0.33 protein_coding missense_variant MODERATE 320G>C Arg107Pro
M0142979 DMCBPIBN_00145 128689 3 Gut 0.33 protein_coding synonymous_variant LOW 318G>A Thr106Thr
M0142980 DMCBPIBN_00145 128708 3 Gut 0.33 protein_coding missense_variant MODERATE 299C>A Pro100Gln
M0142981 DMCBPIBN_00145 128717 3 Gut 0.33 protein_coding missense_variant MODERATE 290T>A Leu97Gln
M0142982 DMCBPIBN_00145 128724 3 Gut 0.33 protein_coding missense_variant MODERATE 283G>A Val95Ile
M0142983 DMCBPIBN_00145 128725 3 Gut 0.33 protein_coding synonymous_variant LOW 282T>C Asp94Asp
M0142984 DMCBPIBN_00145 128726 3 Gut 0.33 protein_coding missense_variant MODERATE 281A>G Asp94Gly






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
DMCBPIBN_00072 Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)] 93.6 4.2e-54 1 110 1.0000 1.0000 experiment
DMCBPIBN_00072 Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)] 100 1.7e-53 1 110 1.0000 1.0000 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
DMCBPIBN_00068 ARO:3002858 100 4.78e-119 1 165 1.0000 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
DMCBPIBN_00069 ARO:3002602 100 5.68e-187 1 259 1.0000 1.0000 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
DMCBPIBN_00070 ARO:3002693 99.8 7.16e-298 1 419 1.0000 1.0000 phenicol antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
DMCBPIBN_00071 ARO:3002601 99.6 1.33e-186 1 259 1.0000 0.9848 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
DMCBPIBN_00072 ARO:3005098 93.6 1.69e-70 1 110 1.0000 1.0000 disinfecting agents and antiseptics small multidrug resistance (SMR) antibiotic efflux pump antibiotic efflux
DMCBPIBN_00074 ARO:3000413 100 3.83e-187 1 263 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
DMCBPIBN_00079 ARO:3003107 100 9.23e-289 1 409 1.0000 1.0000 macrolide antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
DMCBPIBN_00098 ARO:3000186 96.1 0 1 639 1.0000 1.0000 tetracycline antibiotic tetracycline-resistant ribosomal protection protein antibiotic target protection
DMCBPIBN_00103 ARO:3000873 100 5.12e-208 1 286 1.0000 1.0000 monobactam TEM beta-lactamase 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
DMCBPIBN_00067 PHI:9804 int 97.3 1.2e-13 1 37 0.1098 1.0000 rodents gastroenteritis integrase 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
DMCBPIBN_00118 AYL89119.1|GH24 97.2 1.19999998039166e-317 1753 2255 0.2231 0.9031
DMCBPIBN_00122 ART19930.1|GH24 100 1.72e-162 1 214 1 1
DMCBPIBN_00145 QMJ72311.1|GH23 98.2 0 1 1124 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
DMCBPIBN_00070 2.A.1.2.3 100 1e-232 1 419 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
DMCBPIBN_00083 5.A.3.5.1 88.3 0 1 757 1.0000 2.9843 5 Transmembrane Electron Carriers 5.A Transmembrane 2-electron transfer carriers 5.A.3 The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family
DMCBPIBN_00084 5.A.3.5.1 85.8 2.1e-100 1 190 0.9896 0.7480 5 Transmembrane Electron Carriers 5.A Transmembrane 2-electron transfer carriers 5.A.3 The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family
DMCBPIBN_00085 5.A.3.5.1 85.4 9.1e-128 1 253 0.9922 0.9764 5 Transmembrane Electron Carriers 5.A Transmembrane 2-electron transfer carriers 5.A.3 The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family
DMCBPIBN_00121 1.E.64.1.1 100 3.4e-39 1 84 1.0000 1.0000 1 Channels/Pores 1.E Holins 1.E.64 The P7 Phage Holin LydD (LydD) Family
DMCBPIBN_00134 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