Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C729
  Reference Plasmid   NZ_CP053235.1
  Reference Plasmid Size   159399
  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
M0173692 COPBMBFO_00074 65224 3 Gut 0.43 protein_coding upstream_gene_variant MODIFIER -323T>C None
M0173693 COPBMBFO_00074 65241 3 Gut 0.43 protein_coding upstream_gene_variant MODIFIER -306C>T None
M0173694 COPBMBFO_00074 65355 3 Gut 0.43 protein_coding upstream_gene_variant MODIFIER -192T>A None
M0173695 COPBMBFO_00074 65386 3 Gut 0.43 protein_coding upstream_gene_variant MODIFIER -161T>C None
M0173696 COPBMBFO_00079 69870 4 Gut 0.57 protein_coding missense_variant MODERATE 287A>G Lys96Arg
M0173697 COPBMBFO_00079 69967 4 Gut 0.57 protein_coding synonymous_variant LOW 384T>C Ala128Ala






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
COPBMBFO_00113 VFG000844 EspP 90.9 0 1 1301 1.0 1.0008 Effector delivery system autotransporter, serine protease experiment
COPBMBFO_00010 VFG020186 VirK 98.7 2.7e-187 1 316 1.0 1 Others virulence factor VirK prediction
COPBMBFO_00011 VFG013087 MsbB2 96.4 2.5e-160 1 279 1.0 0.8885 Others lauroyl-Kdo(2)-lipid IV(A) myristoyltransferase prediction
COPBMBFO_00103 VFG012633 Iron-regulated element 98.7 0 1 682 1.0 1 Nutritional/Metabolic factor TonB-dependent siderophore receptor IreA prediction
COPBMBFO_00113 VFG000844 EspP 90.9 0 1 1301 1.0 1.0008 Effector delivery system autotransporter, serine protease 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
COPBMBFO_00009 PHI:10400 Sfgtr4 (ORF186) 95.3 8.1e-207 1 362 1.0000 1.0000 primates shigellosis putative lipopolysaccharides (LPS) glycosyltransferase (Gtr) reduced virulence
COPBMBFO_00092 PHI:6654 ireA 72.1 3.6e-24 9 76 0.8947 1.0000 birds avian colibacillosis iron-regulated outer membrane virulence protein unaffected pathogenicity
COPBMBFO_00103 PHI:6654 ireA 98.5 0 1 682 1.0000 1.0000 birds avian colibacillosis iron-regulated outer membrane virulence protein unaffected pathogenicity






        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
COPBMBFO_00009 QJS71303.1|GT4 100 2.67e-272 1 362 1 1
COPBMBFO_00160 AKF16924.1|GH23 100 9.46e-114 1 157 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
COPBMBFO_00034 2.A.123.2.16 100 1.7e-41 1 89 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.123 The Sweet; PQ-loop; Saliva; MtN3 (Sweet) Family
COPBMBFO_00094 3.A.7.10.1 79.3 0 1 723 0.9426 7.5313 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
COPBMBFO_00096 3.A.7.10.1 76.2 2.1e-190 1 399 0.9433 4.1563 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
COPBMBFO_00113 1.B.12.4.3 90.9 0 1 1301 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.12 The Autotransporter-1 (AT-1) Family
COPBMBFO_00141 3.A.7.10.1 76.1 6.5e-139 1 324 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
COPBMBFO_00142 3.A.7.10.1 70.7 2.3e-90 6 227 0.9610 2.2917 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
COPBMBFO_00143 3.A.7.10.1 73.3 1.2e-39 1 116 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
COPBMBFO_00145 3.A.7.10.1 71.3 1.3e-39 1 94 0.9792 0.9792 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
COPBMBFO_00146 3.A.7.10.1 78.1 5.4e-177 1 379 0.9921 3.9479 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
COPBMBFO_00147 3.A.7.10.1 78.2 1.1e-123 1 271 0.9748 2.8021 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