Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C110
  Reference Plasmid   CP057591.1
  Reference Plasmid Size   100275
  Reference Plasmid GC Content   0.49
  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
M0144450 LODLFBPM_00045 42370 4 Gut 0.67 protein_coding synonymous_variant LOW 441G>A Ala147Ala
M0144451 LODLFBPM_00056 51282 4 Gut 0.67 protein_coding missense_variant MODERATE 1396A>G Thr466Ala
M0144452 LODLFBPM_00056 52339 4 Gut 0.67 protein_coding synonymous_variant LOW 339C>A Ile113Ile
M0144453 LODLFBPM_00056 52504 4 Gut 0.67 protein_coding synonymous_variant LOW 174A>G Thr58Thr
M0144454 LODLFBPM_00057 52789 4 Gut 0.67 protein_coding missense_variant MODERATE 952A>G Thr318Ala
M0144455 LODLFBPM_00057 53027 4 Gut 0.67 protein_coding synonymous_variant LOW 714T>C Phe238Phe
M0144456 LODLFBPM_00058 54083 4 Gut 0.67 protein_coding synonymous_variant LOW 885A>G Thr295Thr
M0144457 LODLFBPM_00058 54230 3 Gut 0.50 protein_coding synonymous_variant LOW 738C>T Ser246Ser
M0144458 LODLFBPM_00058 54369 4 Gut 0.67 protein_coding missense_variant MODERATE 599T>C Phe200Ser
M0144459 LODLFBPM_00058 54620 4 Gut 0.67 protein_coding synonymous_variant LOW 348C>T Ser116Ser
M0144460 LODLFBPM_00058 54644 4 Gut 0.67 protein_coding synonymous_variant LOW 324A>G Glu108Glu
M0144461 LODLFBPM_00058 54857 4 Gut 0.67 protein_coding synonymous_variant LOW 111A>G Val37Val
M0144462 LODLFBPM_00057 52820 3 Gut 0.50 protein_coding synonymous_variant LOW 921A>T Val307Val
M0144463 LODLFBPM_00057 52829 3 Gut 0.50 protein_coding synonymous_variant LOW 912A>G Ala304Ala






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
LODLFBPM_00007 VFG043980 Colicin Ib 98.9 0 13 635 0.9811 0.9952 Exotoxin colicin-like pore-forming protein prediction
LODLFBPM_00016 VFG043979 Colicin B 99.6 1.8e-289 1 511 1.0 1 Exotoxin colicin B 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
LODLFBPM_00090 QDX42089.1|GH23 100 2.05e-138 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
LODLFBPM_00007 1.C.1.1.2 99.2 0 13 635 0.9811 0.9952 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.1 The Channel-forming Colicin (Colicin) Family
LODLFBPM_00008 8.B.24.2.1 97.3 4.6e-55 1 110 0.9565 0.8661 8 Accessory Factors Involved in Transport 8.B Ribosomally synthesized protein/peptide toxins/agonists that target channels and carriers 8.B.24 The Colicin Immunity Protein (ColIP) Functional Family
LODLFBPM_00013 8.B.24.3.1 99.1 3.2e-64 1 117 1.0000 0.8298 8 Accessory Factors Involved in Transport 8.B Ribosomally synthesized protein/peptide toxins/agonists that target channels and carriers 8.B.24 The Colicin Immunity Protein (ColIP) Functional Family
LODLFBPM_00016 1.C.1.3.2 99.6 1.4e-289 1 511 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.1 The Channel-forming Colicin (Colicin) Family
LODLFBPM_00056 3.A.7.10.1 99.6 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
LODLFBPM_00057 3.A.7.10.1 99.2 8e-207 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
LODLFBPM_00058 3.A.7.10.1 99.8 1.6e-243 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
LODLFBPM_00065 9.B.40.1.2 97.2 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
LODLFBPM_00076 3.A.7.10.1 100 6.1e-185 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
LODLFBPM_00077 3.A.7.10.1 99.6 3.3e-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
LODLFBPM_00078 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
LODLFBPM_00081 3.A.7.10.1 96.9 2.3e-55 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
LODLFBPM_00082 3.A.7.10.1 99.7 4.2e-222 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
LODLFBPM_00083 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
LODLFBPM_00084 3.A.7.10.1 100 6e-87 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