Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1155
  Reference Plasmid   NZ_CP123608.1
  Reference Plasmid Size   218594
  Reference Plasmid GC Content   0.36
  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
M0198125 KAKGEAIE_00071 61029 4 Gut 0.22 protein_coding upstream_gene_variant MODIFIER -4868T>G None
M0198126 KAKGEAIE_00078 61278 3 Gut 0.17 protein_coding synonymous_variant LOW 165T>C Val55Val
M0198127 KAKGEAIE_00072 61684 3 Gut 0.17 protein_coding upstream_gene_variant MODIFIER -4630A>G None
M0198128 KAKGEAIE_00079 62035 3 Gut 0.17 protein_coding missense_variant MODERATE 2090A>C Asp697Ala
M0198129 KAKGEAIE_00079 62313 5 Gut 0.28 protein_coding synonymous_variant LOW 1812C>T Arg604Arg
M0198130 KAKGEAIE_00079 62378 4 Gut 0.22 protein_coding missense_variant MODERATE 1747G>A Glu583Lys
M0198131 KAKGEAIE_00079 62393 4 Gut 0.22 protein_coding missense_variant MODERATE 1732T>G Ser578Ala
M0198132 KAKGEAIE_00079 62522 3 Gut 0.17 protein_coding missense_variant MODERATE 1603C>G His535Asp
M0198133 KAKGEAIE_00079 62580 4 Gut 0.22 protein_coding synonymous_variant LOW 1545C>T Thr515Thr
M0198134 KAKGEAIE_00079 63639 4 Gut 0.22 protein_coding synonymous_variant LOW 486T>G Ser162Ser
M0198135 KAKGEAIE_00079 63891 3 Gut 0.17 protein_coding synonymous_variant LOW 234G>A Gly78Gly
M0198136 KAKGEAIE_00079 64030 4 Gut 0.22 protein_coding missense_variant MODERATE 95G>A Gly32Glu
M0198137 KAKGEAIE_00079 62091 3 Gut 0.17 protein_coding synonymous_variant LOW 2034A>G Thr678Thr
M0198138 KAKGEAIE_00079 62184 3 Gut 0.17 protein_coding synonymous_variant LOW 1941C>T Ala647Ala
M0198139 KAKGEAIE_00076 64189 3 Gut 0.17 protein_coding upstream_gene_variant MODIFIER -3911C>T 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
KAKGEAIE_00126 VFG042984 PilA-type pili (PGS1, pilin gene clusters 1) 81.1 1.2e-242 1 532 0.8567 0.7644 Adherence minor pilin subunit prediction
KAKGEAIE_00127 VFG042985 PilA-type pili (PGS1, pilin gene clusters 1) 97.7 1.4e-37 1 86 1.0 1 Adherence hypothetical hydrophobic peptide prediction
KAKGEAIE_00128 VFG042986 PilA-type pili (PGS1, pilin gene clusters 1) 99.6 2.4e-133 1 251 1.0 1 Adherence cell wall-associated LPXTG-like protein prediction
KAKGEAIE_00129 VFG042987 PilA-type pili (PGS1, pilin gene clusters 1) 98.4 1.6e-137 1 250 1.0 1 Adherence putative pilus-dedicated sortase prediction
KAKGEAIE_00130 VFG042988 PilA-type pili (PGS1, pilin gene clusters 1) 98.5 0 1 658 1.0 1 Adherence PilA prediction
KAKGEAIE_00131 VFG042989 PilA-type pili (PGS1, pilin gene clusters 1) 99.1 3.6e-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
KAKGEAIE_00212 Copper (Cu) 100 2.8e-85 1 151 1.0000 1.0000 experiment
KAKGEAIE_00213 Copper (Cu) 99.3 0 11 821 0.9878 1.0000 experiment
KAKGEAIE_00214 Copper (Cu) 98.5 5.2e-31 1 67 0.9853 0.9853 experiment
KAKGEAIE_00215 Copper (Cu) 94.6 0 1 740 1.0000 1.0423 experiment
KAKGEAIE_00196 Copper (Cu), Cobalt (Co) 100 1.39999999999998e-310 1 527 1.0000 1.0000 prediction
KAKGEAIE_00212 Copper (Cu) 100 6.5e-83 1 151 1.0000 1.0000 prediction
KAKGEAIE_00213 Copper (Cu) 100 0 1 821 1.0000 1.0000 prediction
KAKGEAIE_00214 Copper (Cu) 100 2.4e-29 1 68 1.0000 1.0000 prediction
KAKGEAIE_00215 Copper (Cu) 97.3 0 1 740 1.0000 1.0137 prediction






        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
KAKGEAIE_00011 PHI:5205 HMPREF0351_10118 (WxL locusC) 84.4 2.6e-75 1 160 0.9756 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
KAKGEAIE_00012 PHI:5205 HMPREF0351_10118 (WxL locusC) 88.6 5.6e-107 1 211 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
KAKGEAIE_00101 PHI:5205 HMPREF0351_10118 (WxL locusC) 89.3 1.7e-205 1 394 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
KAKGEAIE_00162 PHI:5205 HMPREF0351_10118 (WxL locusC) 91.7 4.3e-33 1 72 0.9474 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
KAKGEAIE_00163 PHI:5205 HMPREF0351_10118 (WxL locusC) 72.1 2.5e-115 4 272 0.9890 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
KAKGEAIE_00245 PHI:5205 HMPREF0351_10118 (WxL locusC) 94.6 6.1e-216 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
KAKGEAIE_00001 QXM04906.1|GT4 99.7 0 1 1183 1 1
KAKGEAIE_00019 AWV59846.1|GH4 100 0 1 436 1 1
KAKGEAIE_00024 QOG29405.1|GH36 100 0 1 727 1 1
KAKGEAIE_00026 QDA39721.1|GH13_31 99.7 2.74e-238 1 322 1 1
KAKGEAIE_00027 AOM14759.1|GH13_18 100 0 1 486 1 1
KAKGEAIE_00086 QZK92746.1|GH1 100 0 1 468 1 1
KAKGEAIE_00259 QXM04907.1|GT2 99.8 0 1 495 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
KAKGEAIE_00022 3.A.1.1.28 74.1 2.8e-125 1 290 1.0000 0.7692 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
KAKGEAIE_00023 3.A.1.1.28 75.3 5.4e-118 5 276 0.9855 0.7294 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
KAKGEAIE_00087 4.A.3.1.1 71.7 4.4e-239 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
KAKGEAIE_00213 3.A.3.5.15 99.3 0 11 821 0.9878 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.3 The P-type ATPase (P-ATPase) Superfamily
KAKGEAIE_00215 3.A.3.5.16 94.6 0 1 740 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.3 The P-type ATPase (P-ATPase) Superfamily