Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C901
  Reference Plasmid   NZ_CP075634.1
  Reference Plasmid Size   119130
  Reference Plasmid GC Content   0.50
  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
M0188227 JHCOCHDO_00096 77680 3 Gut 0.27 protein_coding missense_variant MODERATE 556A>G Ser186Gly
M0188228 JHCOCHDO_00121 100946 3 Gut 0.27 protein_coding missense_variant MODERATE 367C>A Leu123Ile






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
JHCOCHDO_00064 VFG012633 Iron-regulated element 98.7 0 1 682 1.0 1 Nutritional/Metabolic factor TonB-dependent siderophore receptor IreA 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
JHCOCHDO_00011 PHI:123867 NAL (LC602499) 78.1 2.5e-129 9 296 0.9697 0.9931 bony fishes gastroenteritis N-acetylneuraminate lyase increased virulence (hypervirulence)
JHCOCHDO_00012 PHI:124245 nanT 88.6 1.6e-250 1 481 0.9717 0.9698 rodents None sialic acid transporter reduced virulence
JHCOCHDO_00064 PHI:6654 ireA 98.5 0 1 682 1.0000 1.0000 birds avian colibacillosis iron-regulated outer membrane virulence protein unaffected pathogenicity
JHCOCHDO_00065 PHI:6654 ireA 73.5 1.2e-24 5 72 0.8947 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
JHCOCHDO_00125 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
JHCOCHDO_00012 2.A.1.12.1 88 8.1e-250 1 487 0.9838 0.9879 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
JHCOCHDO_00015 1.B.35.2.1 84.9 3.3e-124 1 237 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.35 The Oligogalacturonate-specific Porin (KdgM) Family
JHCOCHDO_00025 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
JHCOCHDO_00073 3.A.7.10.1 79.6 0 1 724 0.9439 7.5417 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
JHCOCHDO_00075 3.A.7.10.1 76.2 7e-189 1 399 0.9301 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
JHCOCHDO_00088 1.E.53.1.10 95.2 3.7e-17 9 50 0.8400 0.9767 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family
JHCOCHDO_00090 1.E.53.1.10 95.2 3.7e-17 9 50 0.8400 0.9767 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family
JHCOCHDO_00107 3.A.7.10.1 76.8 5.9e-140 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
JHCOCHDO_00108 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
JHCOCHDO_00109 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
JHCOCHDO_00111 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
JHCOCHDO_00112 3.A.7.10.1 78.5 4.2e-177 4 379 0.9843 3.9167 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
JHCOCHDO_00113 3.A.7.10.1 79 1.3e-124 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