Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1354
  Reference Plasmid   NZ_LR883001.1
  Reference Plasmid Size   109853
  Reference Plasmid GC Content   0.51
  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
M0207083 KDEACCDJ_00033 29090 3 Gut 0.38 protein_coding synonymous_variant LOW 534C>T Gly178Gly
M0207084 KDEACCDJ_00033 29489 3 Gut 0.38 protein_coding synonymous_variant LOW 135G>A Val45Val
M0207085 KDEACCDJ_00033 29595 3 Gut 0.38 protein_coding missense_variant MODERATE 29T>C Ile10Thr
M0207086 KDEACCDJ_00035 30035 3 Gut 0.38 protein_coding synonymous_variant LOW 210C>T Ser70Ser
M0207087 KDEACCDJ_00035 30212 3 Gut 0.38 protein_coding synonymous_variant LOW 33T>G Val11Val
M0207088 KDEACCDJ_00032 30265 3 Gut 0.38 protein_coding upstream_gene_variant MODIFIER -1563G>A None
M0207089 KDEACCDJ_00036 30679 3 Gut 0.38 protein_coding synonymous_variant LOW 69A>G Glu23Glu
M0207090 KDEACCDJ_00037 30774 3 Gut 0.38 protein_coding synonymous_variant LOW 216C>G Gly72Gly






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
KDEACCDJ_00007 VFG042382 EtpA 99.3 0 1 603 1.0 1 Adherence two-partner secretion transporter EtpB experiment
KDEACCDJ_00007 VFG042382 EtpA 99.3 0 1 603 1.0 1 Adherence two-partner secretion transporter EtpB prediction
KDEACCDJ_00027 VFG033834 Pic 99.4 0 1 1364 1.0 0.9985 Effector delivery system Pic serine protease precursor, autotransporter prediction
KDEACCDJ_00030 VFG041000 AAI/SCI-II T6SS 92 4.8e-99 1 188 1.0 1 Effector delivery system hypothetical protein prediction
KDEACCDJ_00040 VFG017870 Icm/dot type IVB locus 77.9 1e-89 1 208 0.9905 0.9952 Effector delivery system ParA family 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






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
KDEACCDJ_00016 CBJ04457.1|GT41 99.1 0 1 636 1 0.9984
KDEACCDJ_00111 AHF22950.1|GH23 97.3 4.47e-133 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
KDEACCDJ_00007 1.B.20.3.3 99.3 0 1 603 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.20 The Two-Partner Secretion (TPS) Family
KDEACCDJ_00017 9.B.127.1.3 98.8 1.2e-93 1 164 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.127 The DUF2919 (PF11143) Family
KDEACCDJ_00075 3.A.7.10.1 99.1 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
KDEACCDJ_00076 3.A.7.10.1 96.9 1.2e-202 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
KDEACCDJ_00077 3.A.7.10.1 98 9.6e-241 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
KDEACCDJ_00085 9.B.40.1.2 86.3 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
KDEACCDJ_00096 3.A.7.10.1 99.1 9.7e-183 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
KDEACCDJ_00097 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
KDEACCDJ_00098 3.A.7.10.1 100 1.3e-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
KDEACCDJ_00101 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
KDEACCDJ_00102 3.A.7.10.1 99.5 2.8e-221 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
KDEACCDJ_00103 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
KDEACCDJ_00104 3.A.7.10.1 98.7 2.3e-86 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