Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C609
  Reference Plasmid   NZ_CP035875.1
  Reference Plasmid Size   151583
  Reference Plasmid GC Content   0.48
  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
M0169481 GCJHBGDE_00150 119992 3 Gut 0.13 protein_coding missense_variant MODERATE 433A>G Thr145Ala






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
GCJHBGDE_00012 VFG042382 EtpA 98.8 0 1 603 1.0 1 Adherence two-partner secretion transporter EtpB experiment
GCJHBGDE_00058 VFG036066 Heat-labile toxin (LT) 99.5 5.3e-130 1 218 1.0 0.845 Exotoxin heat-labile enterotoxin A prepeptide (from human) experiment
GCJHBGDE_00059 VFG036068 Heat-labile toxin (LT) 98.4 2.6e-65 1 124 1.0 1 Exotoxin enterotoxin subunit B (from human) experiment
GCJHBGDE_00012 VFG042382 EtpA 98.8 0 1 603 1.0 1 Adherence two-partner secretion transporter EtpB prediction
GCJHBGDE_00019 VFG035930 Dispersin 100 8.1e-235 15 428 0.9673 1 Others AatD prediction
GCJHBGDE_00028 VFG035924 Dispersin 77.8 1.7e-89 1 207 0.9952 0.9952 Others ATP-binding protein AatC prediction
GCJHBGDE_00029 VFG035917 Dispersin 99.6 7.5e-143 3 257 0.9922 1 Others AatB prediction
GCJHBGDE_00030 VFG035910 Dispersin 100 2.4e-220 1 400 1.0 1 Others outer membrane protein AatA prediction
GCJHBGDE_00031 VFG035903 Dispersin 100 7.3e-195 4 379 0.9921 1 Others permease AatP prediction
GCJHBGDE_00042 VFG042470 Adhesive fimbriae 100 1.7e-82 1 168 1.0 1 Adherence CS3 pilin precursor polypeptide (AA -22 to 146) prediction
GCJHBGDE_00044 VFG042469 Adhesive fimbriae 100 0 260 810 0.6769 0.9616 Adherence unknown protein prediction
GCJHBGDE_00045 VFG042468 Adhesive fimbriae 99.2 1.4e-138 1 241 1.0 1 Adherence unknown protein prediction
GCJHBGDE_00058 VFG036065 Heat-labile toxin (LT) 100 1.1e-129 1 218 1.0 0.845 Exotoxin heat-labile enterotoxin A prepeptide (from human) prediction
GCJHBGDE_00059 VFG036068 Heat-labile toxin (LT) 98.4 2e-64 1 124 1.0 1 Exotoxin enterotoxin subunit B (from human) prediction
GCJHBGDE_00106 VFG013087 MsbB2 97.5 1.4e-183 1 314 1.0 1 Others lauroyl-Kdo(2)-lipid IV(A) myristoyltransferase prediction
GCJHBGDE_00107 VFG020186 VirK 98.7 4.2e-188 1 316 1.0 1 Others virulence factor VirK prediction
GCJHBGDE_00119 VFG033834 Pic 99.9 0 1 1364 1.0 0.9985 Effector delivery system Pic serine protease precursor, autotransporter prediction
GCJHBGDE_00122 VFG041000 AAI/SCI-II T6SS 90.3 1.7e-78 1 155 1.0 0.8245 Effector delivery system hypothetical protein prediction
GCJHBGDE_00173 VFG020186 VirK 98.4 2.1e-187 1 316 1.0 1 Others virulence factor VirK prediction
GCJHBGDE_00192 VFG043747 Heat-stable toxin (ST) 98.6 1.2e-34 1 72 1.0 1 Exotoxin unknown protein 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
GCJHBGDE_00058 PHI:698 CtxA 80.7 2.9e-106 1 218 1.0000 0.8450 primates cholera Cholera toxin (CT) reduced virulence
GCJHBGDE_00059 PHI:699 CtxB 79 7.9e-53 1 124 1.0000 1.0000 primates cholera Cholera toxin (CT) reduced virulence
GCJHBGDE_00108 PHI:10400 Sfgtr4 (ORF186) 95.6 7.3e-208 1 362 1.0000 1.0000 primates shigellosis putative lipopolysaccharides (LPS) glycosyltransferase (Gtr) reduced virulence
GCJHBGDE_00123 PHI:3113 stbA 97.9 2.8e-182 1 326 1.0000 1.0000 rodents neonatal meningitis stability protein for the plasmid reduced virulence
GCJHBGDE_00174 PHI:10400 Sfgtr4 (ORF186) 95.6 7.3e-208 1 362 1.0000 1.0000 primates shigellosis putative lipopolysaccharides (LPS) glycosyltransferase (Gtr) 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
GCJHBGDE_00007 APG37925.1|GT41 100 0 1 636 1 0.9984
GCJHBGDE_00072 APG37898.1|GH23 100 4.96e-124 1 169 1 1
GCJHBGDE_00108 AOT35667.1|GT4 100 7.65e-272 1 362 1 1
GCJHBGDE_00174 AOT35667.1|GT4 100 7.65e-272 1 362 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
GCJHBGDE_00006 9.B.127.1.3 100 1.4e-94 1 164 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.127 The DUF2919 (PF11143) Family
GCJHBGDE_00012 1.B.20.3.3 98.8 0 1 603 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.20 The Two-Partner Secretion (TPS) Family
GCJHBGDE_00058 1.C.72.4.1 99.5 3.1e-129 1 218 1.0000 0.8450 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.72 The Pertussis Toxin (PTX) Family