Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1390
  Reference Plasmid   NZ_MW077915.1
  Reference Plasmid Size   91584
  Reference Plasmid GC Content   0.50
  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
M0208851 DBPHEMEG_00004 2877 3 Gut 0.60 protein_coding synonymous_variant LOW 228G>A Glu76Glu
M0208852 DBPHEMEG_00004 2926 3 Gut 0.60 protein_coding stop_lost&splice_region_variant HIGH 277T>G Ter93Gluext*?
M0208853 DBPHEMEG_00009 2992 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -1903C>T None
M0208854 DBPHEMEG_00009 3016 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -1879C>T None
M0208855 DBPHEMEG_00005 3079 3 Gut 0.60 protein_coding synonymous_variant LOW 93A>G Gln31Gln
M0208856 DBPHEMEG_00005 3144 3 Gut 0.60 protein_coding missense_variant MODERATE 28T>G Trp10Gly
M0208857 DBPHEMEG_00005 3150 3 Gut 0.60 protein_coding missense_variant MODERATE 22T>A Tyr8Asn
M0208858 DBPHEMEG_00005 3170 3 Gut 0.60 protein_coding start_lost HIGH 2T>C Met1?
M0208859 DBPHEMEG_00007 3513 3 Gut 0.60 protein_coding missense_variant MODERATE 371A>G His124Arg
M0208860 DBPHEMEG_00007 3585 3 Gut 0.60 protein_coding missense_variant MODERATE 299C>T Ala100Val
M0208861 DBPHEMEG_00007 3751 3 Gut 0.60 protein_coding synonymous_variant LOW 133T>C Leu45Leu
M0208862 DBPHEMEG_00007 3780 3 Gut 0.60 protein_coding stop_gained HIGH 104G>A Trp35*
M0208863 DBPHEMEG_00005 3911 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -740G>A None
M0208864 DBPHEMEG_00008 4485 3 Gut 0.60 protein_coding synonymous_variant LOW 57A>T Arg19Arg
M0208865 DBPHEMEG_00005 4547 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -1376G>A None
M0208866 DBPHEMEG_00005 4661 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -1490C>A None
M0208867 DBPHEMEG_00005 4666 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -1495A>T None
M0208868 DBPHEMEG_00005 4706 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -1535G>T 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
DBPHEMEG_00010 VFG044067 Colicin Ia 98.9 0 1 626 1.0 1 Exotoxin colicin-like pore-forming protein 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
DBPHEMEG_00055 Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)], Cetylpyridinium Chloride (CPC) [class: Quaternary Ammonium Compounds (QACs)], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Ethidium Bromide [class: Phenanthridine], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate] 82.9 9.9e-45 1 105 1.0000 1.0000 experiment
DBPHEMEG_00055 Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)], Cetylpyridinium Chloride (CPC) [class: Quaternary Ammonium Compounds (QACs)], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Ethidium Bromide [class: Phenanthridine], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate] 90.5 1.3e-45 1 105 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
DBPHEMEG_00057 ARO:3002013 100 2.33e-286 1 381 1.0000 1.0000 carbapenem CMY 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
DBPHEMEG_00057 PHI:6133 blaCMY-2 100 4.4e-227 1 381 1.0000 1.0000 rodents salmonellosis beta-lactamase 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
DBPHEMEG_00090 AHF22950.1|GH23 100 5.89e-138 1 186 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
DBPHEMEG_00010 1.C.1.1.1 100 0 1 626 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.1 The Channel-forming Colicin (Colicin) Family
DBPHEMEG_00051 3.A.7.10.1 100 0 1 763 1.0000 7.9479 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
DBPHEMEG_00052 3.A.7.10.1 96.9 2.3e-201 1 356 1.0000 3.7083 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
DBPHEMEG_00053 3.A.7.10.1 99.3 7.8e-243 1 402 1.0000 4.1875 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
DBPHEMEG_00055 2.A.7.1.10 86.7 9.7e-44 1 105 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.7 The Drug/Metabolite Transporter (DMT) Superfamily
DBPHEMEG_00057 8.A.212.1.4 76.1 5.1e-175 1 380 0.9974 1.0000 8 Accessory Factors Involved in Transport 8.A Auxiliary transport proteins 8.A.212 The d-Amino Acid Peptidase (dAAP) Family
DBPHEMEG_00063 9.B.40.1.2 85.5 0 1 722 1.0000 0.9691 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.40 The DotA/TraY (DotA/TraY) Family
DBPHEMEG_00074 3.A.7.10.1 99.7 1.4e-184 1 327 1.0000 3.4063 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
DBPHEMEG_00075 3.A.7.10.1 99.1 7.4e-129 1 230 1.0000 2.3958 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
DBPHEMEG_00076 3.A.7.10.1 99.1 2.9e-57 1 115 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
DBPHEMEG_00079 3.A.7.10.1 99 4.6e-56 1 96 1.0000 1.0000 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
DBPHEMEG_00080 3.A.7.10.1 100 3.3e-222 1 382 1.0000 3.9792 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
DBPHEMEG_00081 3.A.7.10.1 99.6 7.3e-160 1 272 1.0000 2.8333 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
DBPHEMEG_00082 3.A.7.10.1 100 6e-87 1 152 1.0000 1.5833 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