Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1348
  Reference Plasmid   NZ_LR135227.1
  Reference Plasmid Size   169998
  Reference Plasmid GC Content   0.35
  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
M0207019 LMCMPAOA_00081 76577 3 Gut 0.19 protein_coding synonymous_variant LOW 297T>C Asn99Asn
M0207020 LMCMPAOA_00065 65340 3 Gut 0.19 protein_coding upstream_gene_variant MODIFIER -3961G>A None
M0207021 LMCMPAOA_00065 65681 3 Gut 0.19 protein_coding upstream_gene_variant MODIFIER -4302G>A None
M0207022 LMCMPAOA_00070 66527 3 Gut 0.19 protein_coding synonymous_variant LOW 649T>C Leu217Leu
M0207023 LMCMPAOA_00073 69207 3 Gut 0.19 protein_coding missense_variant MODERATE 238G>A Gly80Ser
M0207024 LMCMPAOA_00070 69479 3 Gut 0.19 protein_coding upstream_gene_variant MODIFIER -2304A>T None
M0207025 LMCMPAOA_00070 69516 3 Gut 0.19 protein_coding upstream_gene_variant MODIFIER -2341T>C None
M0207026 LMCMPAOA_00075 70788 3 Gut 0.19 protein_coding missense_variant MODERATE 380T>C Val127Ala
M0207027 LMCMPAOA_00078 74946 3 Gut 0.19 protein_coding missense_variant MODERATE 591T>A Asp197Glu
M0207028 LMCMPAOA_00078 75102 3 Gut 0.19 protein_coding synonymous_variant LOW 747G>A Lys249Lys
M0207029 LMCMPAOA_00078 75274 3 Gut 0.19 protein_coding missense_variant MODERATE 919T>G Leu307Val
M0207030 LMCMPAOA_00078 75280 3 Gut 0.19 protein_coding missense_variant MODERATE 925G>C Gly309Arg
M0207031 LMCMPAOA_00078 75281 3 Gut 0.19 protein_coding missense_variant MODERATE 926G>A Gly309Glu
M0207032 LMCMPAOA_00078 75285 3 Gut 0.19 protein_coding synonymous_variant LOW 930C>G Arg310Arg
M0207033 LMCMPAOA_00078 75286 3 Gut 0.19 protein_coding missense_variant MODERATE 931C>T Pro311Ser
M0207034 LMCMPAOA_00078 75351 3 Gut 0.19 protein_coding synonymous_variant LOW 996G>A Arg332Arg
M0207035 LMCMPAOA_00078 75372 3 Gut 0.19 protein_coding synonymous_variant LOW 1017A>G Val339Val
M0207036 LMCMPAOA_00078 75390 3 Gut 0.19 protein_coding synonymous_variant LOW 1035T>C Cys345Cys
M0207037 LMCMPAOA_00078 75405 3 Gut 0.19 protein_coding synonymous_variant LOW 1050T>C Leu350Leu
M0207038 LMCMPAOA_00078 75420 3 Gut 0.19 protein_coding synonymous_variant LOW 1065A>G Val355Val
M0207039 LMCMPAOA_00078 75429 3 Gut 0.19 protein_coding synonymous_variant LOW 1074T>C Ile358Ile






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






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
LMCMPAOA_00025 PHI:5205 HMPREF0351_10118 (WxL locusC) 100 1e-226 1 392 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
LMCMPAOA_00036 PHI:5205 HMPREF0351_10118 (WxL locusC) 77.9 2e-23 13 80 0.8095 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
LMCMPAOA_00069 PHI:5205 HMPREF0351_10118 (WxL locusC) 99.7 5e-226 1 392 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
LMCMPAOA_00092 PHI:5205 HMPREF0351_10118 (WxL locusC) 71 7.7e-163 1 388 0.9974 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
LMCMPAOA_00042 QMV94891.1|GH32 100 0 1 479 1 1
LMCMPAOA_00077 ADX80433.1|GH35 100 0 1 592 1 1
LMCMPAOA_00102 AAN34803.1|GH84 100 0 1 553 1 1
LMCMPAOA_00103 QEW99892.1|GH2 100 0 1 993 1 1
LMCMPAOA_00104 QSQ01358.1|GH20 100 0 1 637 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
LMCMPAOA_00023 1.C.90.3.3 100 2.3e-38 1 87 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.90 The Carnocyclin A (Carnocyclin) Family