Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C646
  Reference Plasmid   NZ_CP040906.1
  Reference Plasmid Size   133232
  Reference Plasmid GC Content   0.35
  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
M0170271 KCHLDHLL_00061 55109 5 Gut 0.45 protein_coding synonymous_variant LOW 63C>T Ile21Ile
M0170272 KCHLDHLL_00061 55640 5 Gut 0.45 protein_coding synonymous_variant LOW 594C>T Ile198Ile
M0170273 KCHLDHLL_00064 57327 5 Gut 0.45 protein_coding synonymous_variant LOW 336C>T Arg112Arg
M0170274 KCHLDHLL_00064 57684 6 Gut 0.55 protein_coding synonymous_variant LOW 693A>G Leu231Leu
M0170275 KCHLDHLL_00065 57972 6 Gut 0.55 protein_coding missense_variant MODERATE 232T>C Ser78Pro
M0170276 KCHLDHLL_00065 58088 6 Gut 0.55 protein_coding synonymous_variant LOW 348A>T Ala116Ala
M0170277 KCHLDHLL_00067 59489 6 Gut 0.55 protein_coding missense_variant MODERATE 604A>G Arg202Gly
M0170278 KCHLDHLL_00067 59557 6 Gut 0.55 protein_coding missense_variant MODERATE 536T>G Ile179Ser
M0170279 KCHLDHLL_00067 59848 6 Gut 0.55 protein_coding missense_variant MODERATE 245A>C Asp82Ala
M0170280 KCHLDHLL_00067 60176 6 Gut 0.55 protein_coding upstream_gene_variant MODIFIER -84A>G None
M0170281 KCHLDHLL_00067 60299 5 Gut 0.45 protein_coding upstream_gene_variant MODIFIER -207A>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
KCHLDHLL_00047 VFG042984 PilA-type pili (PGS1, pilin gene clusters 1) 98 0 1 695 0.9986 0.9986 Adherence minor pilin subunit prediction
KCHLDHLL_00048 VFG042985 PilA-type pili (PGS1, pilin gene clusters 1) 98.8 4.9e-38 1 86 1.0 1 Adherence hypothetical hydrophobic peptide prediction
KCHLDHLL_00049 VFG042986 PilA-type pili (PGS1, pilin gene clusters 1) 98 1.2e-129 1 253 1.0 1.008 Adherence cell wall-associated LPXTG-like protein prediction
KCHLDHLL_00050 VFG042987 PilA-type pili (PGS1, pilin gene clusters 1) 99.2 1.2e-137 1 250 1.0 1 Adherence putative pilus-dedicated sortase prediction
KCHLDHLL_00051 VFG042988 PilA-type pili (PGS1, pilin gene clusters 1) 98.6 0 1 658 1.0 1 Adherence PilA prediction
KCHLDHLL_00052 VFG042989 PilA-type pili (PGS1, pilin gene clusters 1) 99.1 4.7e-125 1 223 1.0 1 Adherence putative housekeeping sortase 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
KCHLDHLL_00068 PHI:5205 HMPREF0351_10118 (WxL locusC) 90.3 2.1e-208 1 392 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
KCHLDHLL_00106 PHI:5205 HMPREF0351_10118 (WxL locusC) 90.3 2.1e-208 1 392 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis 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
KCHLDHLL_00033 QDA53360.1|GH73 100 5.02e-274 1 401 1 1
KCHLDHLL_00126 QZK92746.1|GH1 100 0 1 468 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
KCHLDHLL_00127 4.A.3.1.1 72.1 8.8e-240 1 568 1.0000 0.9965 4 Group Translocators 4.A Phosphotransfer-driven Group Translocators (PTS) 4.A.3 The PTS Lactose-N,N'-Diacetylchitobiose-β-glucoside (Lac) Family