Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1376
  Reference Plasmid   NZ_MH287044.1
  Reference Plasmid Size   98766
  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
M0208552 EDMFNNPP_00040 34072 3 Gut 0.33 protein_coding upstream_gene_variant MODIFIER -4418C>G None
M0208553 EDMFNNPP_00040 34082 4 Gut 0.44 protein_coding upstream_gene_variant MODIFIER -4428A>G None
M0208554 EDMFNNPP_00048 34321 4 Gut 0.44 protein_coding synonymous_variant LOW 144C>T Ser48Ser
M0208555 EDMFNNPP_00049 34740 3 Gut 0.33 protein_coding synonymous_variant LOW 219A>G Lys73Lys
M0208556 EDMFNNPP_00049 35596 3 Gut 0.33 protein_coding missense_variant MODERATE 1075T>C Tyr359His
M0208557 EDMFNNPP_00049 35919 3 Gut 0.33 protein_coding missense_variant MODERATE 1398G>T Met466Ile
M0208558 EDMFNNPP_00049 35967 3 Gut 0.33 protein_coding synonymous_variant LOW 1446T>C Ser482Ser
M0208559 EDMFNNPP_00049 36200 3 Gut 0.33 protein_coding missense_variant MODERATE 1679T>C Leu560Pro
M0208560 EDMFNNPP_00049 36300 3 Gut 0.33 protein_coding synonymous_variant LOW 1779A>G Glu593Glu
M0208561 EDMFNNPP_00049 36302 3 Gut 0.33 protein_coding missense_variant MODERATE 1781C>T Pro594Leu
M0208562 EDMFNNPP_00049 36531 3 Gut 0.33 protein_coding synonymous_variant LOW 2010G>A Ala670Ala
M0208563 EDMFNNPP_00049 37067 3 Gut 0.33 protein_coding missense_variant MODERATE 2546A>G Asn849Ser
M0208564 EDMFNNPP_00050 37486 3 Gut 0.33 protein_coding synonymous_variant LOW 150G>A Gln50Gln
M0208565 EDMFNNPP_00047 37868 3 Gut 0.33 protein_coding upstream_gene_variant MODIFIER -3923A>G 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
EDMFNNPP_00011 VFG044067 Colicin Ia 98.7 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






        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
EDMFNNPP_00052 ARO:3002660 99.6 5.98e-177 15 257 0.9455 0.8741 aminoglycoside antibiotic APH(6) antibiotic inactivation
EDMFNNPP_00055 ARO:3000873 100 5.12e-208 1 286 1.0000 1.0000 monobactam TEM beta-lactamase antibiotic inactivation
EDMFNNPP_00056 ARO:3002639 99.6 5.98e-202 1 267 1.0000 1.0000 aminoglycoside antibiotic APH(3'') antibiotic inactivation
EDMFNNPP_00057 ARO:3000412 100 4.11e-186 1 271 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement






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
EDMFNNPP_00097 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
EDMFNNPP_00011 1.C.1.1.1 99.8 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
EDMFNNPP_00059 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
EDMFNNPP_00061 3.A.7.10.1 76.1 1.1e-189 1 401 0.9218 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
EDMFNNPP_00070 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
EDMFNNPP_00074 9.B.40.1.2 70.1 3.4e-289 1 720 0.9986 0.9678 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.40 The DotA/TraY (DotA/TraY) Family
EDMFNNPP_00085 3.A.7.10.1 74.6 4.2e-138 1 324 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
EDMFNNPP_00087 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
EDMFNNPP_00090 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
EDMFNNPP_00091 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