Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C965
  Reference Plasmid   NZ_CP085293.1
  Reference Plasmid Size   35757
  Reference Plasmid GC Content   0.34
  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
M0191123 PEFHHHMO_00010 13569 8 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4752T>G None
M0191124 PEFHHHMO_00010 13575 8 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4758T>A None
M0191125 PEFHHHMO_00010 13583 8 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4766A>C None
M0191126 PEFHHHMO_00019 13650 8 Gut 1.00 protein_coding missense_variant MODERATE 859A>C Ile287Leu
M0191127 PEFHHHMO_00019 13651 8 Gut 1.00 protein_coding synonymous_variant LOW 858T>A Gly286Gly
M0191128 PEFHHHMO_00019 13691 8 Gut 1.00 protein_coding missense_variant MODERATE 818C>T Pro273Leu
M0191129 PEFHHHMO_00019 13867 8 Gut 1.00 protein_coding synonymous_variant LOW 642C>T Ser214Ser






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
PEFHHHMO_00024 ARO:3000375 98 4.61e-173 1 245 1.0000 0.9879 macrolide antibiotic Erm 23S ribosomal RNA methyltransferase antibiotic target alteration
PEFHHHMO_00032 ARO:3005021 99.7 1.77e-260 37 393 0.9084 1.0000 lincosamide antibiotic Cfr 23S ribosomal RNA methyltransferase antibiotic target alteration
PEFHHHMO_00033 ARO:3004470 100 0 1 531 0.9852 0.9797 tetracycline antibiotic Miscellaneous ABC-F subfamily ATP-binding cassette ribosomal protection proteins antibiotic target protection
PEFHHHMO_00035 ARO:3002704 98.9 0 1 475 1.0000 1.0000 phenicol antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux






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
PEFHHHMO_00004 UDM45518.1|GH23 100 1.61e-272 1 369 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
PEFHHHMO_00001 3.A.7.14.1 98.9 1.90000000000005e-311 1 551 1.0000 3.0109 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
PEFHHHMO_00002 3.A.7.14.1 96.5 3.5e-68 1 143 1.0000 0.7814 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
PEFHHHMO_00003 3.A.7.14.1 96.7 8.3e-91 1 183 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
PEFHHHMO_00004 3.A.7.14.1 99.2 7e-214 1 369 1.0000 2.0164 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
PEFHHHMO_00005 3.A.7.14.1 98.9 7.9e-244 1 450 1.0000 2.4590 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
PEFHHHMO_00006 3.A.7.14.1 99.5 1.5e-100 1 182 1.0000 0.9945 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
PEFHHHMO_00007 3.A.7.14.1 98.5 5.6e-261 1 461 0.9978 2.5191 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
PEFHHHMO_00008 3.A.7.14.1 97.4 1.9e-102 23 212 0.8962 1.0383 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
PEFHHHMO_00012 3.A.7.14.1 96 0 1 649 1.0000 3.5738 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
PEFHHHMO_00038 3.A.7.14.1 83.4 2.8e-108 1 259 1.0000 1.5410 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
PEFHHHMO_00040 3.A.7.14.1 98.8 3.9e-168 1 323 1.0000 1.7596 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
PEFHHHMO_00041 3.A.7.14.1 92.3 2.2e-152 1 310 1.0000 1.6940 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
PEFHHHMO_00042 3.A.7.14.1 80.8 9.6e-81 1 172 0.9942 0.9399 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