Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2098
  Reference Plasmid   1111525849742797_bin.26__k141_325281
  Reference Plasmid Size   28688
  Reference Plasmid GC Content   0.54
  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
M0024716 MIEBEGKC_00009 11573 5 Skin 0.16 protein_coding synonymous_variant LOW 1059T>C His353His
M0024717 MIEBEGKC_00001 174 9 Skin 0.29 protein_coding synonymous_variant LOW 129C>T Thr43Thr
M0024718 MIEBEGKC_00001 213 10 Skin 0.32 protein_coding synonymous_variant LOW 168G>A Gly56Gly
M0024719 MIEBEGKC_00001 216 10 Skin 0.32 protein_coding synonymous_variant LOW 171T>G Pro57Pro
M0024720 MIEBEGKC_00001 228 10 Skin 0.32 protein_coding synonymous_variant LOW 183A>G Gln61Gln
M0024721 MIEBEGKC_00001 276 13 Skin 0.42 protein_coding synonymous_variant LOW 231A>G Gly77Gly
M0024722 MIEBEGKC_00001 285 13 Skin 0.42 protein_coding synonymous_variant LOW 240C>T Ile80Ile
M0024723 MIEBEGKC_00001 315 13 Skin 0.42 protein_coding synonymous_variant LOW 270A>G Pro90Pro
M0024724 MIEBEGKC_00001 1395 3 Skin 0.10 protein_coding synonymous_variant LOW 1350C>G Thr450Thr
M0024725 MIEBEGKC_00005 4543 4 Skin 0.13 protein_coding synonymous_variant LOW 198C>T Ser66Ser






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
MIEBEGKC_00006 VFG048779 T6SS 81.4 9.3e-180 1 361 1.0 1 Effector delivery system type VI secretion system baseplate subunit TssG experiment
MIEBEGKC_00007 VFG048771 T6SS 87.3 1.09999999999999e-310 1 584 1.0 1 Effector delivery system type VI secretion system baseplate subunit TssF experiment
MIEBEGKC_00008 VFG048762 T6SS 77.9 1.4e-237 1 533 1.0 1.0019 Effector delivery system type VI secretion system protein TssA experiment
MIEBEGKC_00009 VFG048755 T6SS 78.3 0 108 1156 0.9074 0.9114 Effector delivery system type VI secretion protein TssM experiment
MIEBEGKC_00019 VFG048697 T6SS 81.6 0 1 877 0.9921 0.9921 Effector delivery system type VI secretion system ATPase TssH experiment
MIEBEGKC_00020 VFG048687 T6SS 95.7 6.9e-90 1 163 1.0 1 Effector delivery system type VI secretion system protein, Hcp family experiment
MIEBEGKC_00022 VFG048665 T6SS 78.6 3e-107 1 229 1.0 1 Effector delivery system type VI secretion system protein, DotU/TssL family experiment
MIEBEGKC_00004 VFG049292 T6SS-III 82.9 1.3e-67 1 146 0.9799 0.9669 Effector delivery system type VI secretion system baseplate subunit TssE prediction
MIEBEGKC_00005 VFG048782 T6SS 76.1 3.6e-75 1 180 0.9945 0.9945 Effector delivery system type VI secretion system lipoprotein TssJ prediction
MIEBEGKC_00006 VFG048773 T6SS 86.7 1.8e-190 1 361 1.0 1 Effector delivery system type VI secretion system baseplate subunit TssG prediction
MIEBEGKC_00007 VFG048765 T6SS 91.8 0 1 584 1.0 1 Effector delivery system type VI secretion system baseplate subunit TssF prediction
MIEBEGKC_00008 VFG048762 T6SS 77.9 1.1e-236 1 533 1.0 1.0019 Effector delivery system type VI secretion system protein TssA prediction
MIEBEGKC_00009 VFG048749 T6SS 82.4 0 87 1156 0.9256 0.9256 Effector delivery system type VI secretion protein TssM prediction
MIEBEGKC_00018 VFG048701 T6SS 88.1 3.7e-294 1 555 0.9391 0.7115 Effector delivery system type VI secretion system tip protein VgrG prediction
MIEBEGKC_00019 VFG048692 T6SS 81.8 0 1 877 0.9921 0.9921 Effector delivery system type VI secretion system ATPase TssH prediction
MIEBEGKC_00020 VFG048679 T6SS 98.2 2.9e-92 1 163 1.0 1 Effector delivery system type VI secretion system protein, Hcp family prediction
MIEBEGKC_00021 VFG048669 T6SS 83 2.4e-282 1 570 1.0 1 Effector delivery system OmpA family protein prediction
MIEBEGKC_00022 VFG048657 T6SS 88.6 3.9e-119 1 229 1.0 1 Effector delivery system type VI secretion system protein, DotU/TssL family 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
MIEBEGKC_00004 PHI:7082 tssE-2 76.4 1.7e-57 6 145 0.9396 0.9333 eudicots fire blight T6SS-3 component reduced virulence
MIEBEGKC_00019 PHI:7094 clpV-2 75.3 0 5 877 0.9876 0.9842 eudicots fire blight T6SS-3 component reduced virulence
MIEBEGKC_00020 PHI:7108 hcp-2 82.2 8.4e-79 1 163 1.0000 1.0000 eudicots fire blight T6SS effector protein effector (plant avirulence determinant)






        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





        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