Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1170
  Reference Plasmid   NZ_CP127268.1
  Reference Plasmid Size   123716
  Reference Plasmid GC Content   0.49
  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
M0199150 ADJOALPO_00040 37588 3 Gut 0.15 protein_coding upstream_gene_variant MODIFIER -4759T>A None
M0199151 ADJOALPO_00040 37714 3 Gut 0.15 protein_coding upstream_gene_variant MODIFIER -4885T>C None
M0199152 ADJOALPO_00040 37796 3 Gut 0.15 protein_coding upstream_gene_variant MODIFIER -4967G>A None
M0199153 ADJOALPO_00040 37817 3 Gut 0.15 protein_coding upstream_gene_variant MODIFIER -4988A>G None
M0199154 ADJOALPO_00047 38525 3 Gut 0.15 protein_coding synonymous_variant LOW 417T>C Ile139Ile
M0199155 ADJOALPO_00047 38564 3 Gut 0.15 protein_coding synonymous_variant LOW 456T>C Tyr152Tyr
M0199156 ADJOALPO_00047 38615 3 Gut 0.15 protein_coding synonymous_variant LOW 507G>T Val169Val
M0199157 ADJOALPO_00047 38627 3 Gut 0.15 protein_coding synonymous_variant LOW 519C>T Ala173Ala
M0199158 ADJOALPO_00046 39111 3 Gut 0.15 protein_coding upstream_gene_variant MODIFIER -1789G>A None
M0199159 ADJOALPO_00046 39140 3 Gut 0.15 protein_coding upstream_gene_variant MODIFIER -1818T>A None
M0199160 ADJOALPO_00046 39142 3 Gut 0.15 protein_coding upstream_gene_variant MODIFIER -1820A>T None
M0199161 ADJOALPO_00046 39148 3 Gut 0.15 protein_coding upstream_gene_variant MODIFIER -1826C>T None
M0199162 ADJOALPO_00048 39180 3 Gut 0.15 protein_coding synonymous_variant LOW 102A>T Thr34Thr
M0199163 ADJOALPO_00048 39184 3 Gut 0.15 protein_coding missense_variant MODERATE 98G>A Gly33Glu
M0199164 ADJOALPO_00048 39197 3 Gut 0.15 protein_coding missense_variant MODERATE 85A>G Thr29Ala
M0199165 ADJOALPO_00048 39202 3 Gut 0.15 protein_coding missense_variant MODERATE 80T>C Leu27Pro
M0199166 ADJOALPO_00048 39233 3 Gut 0.15 protein_coding missense_variant MODERATE 49T>C Tyr17His
M0199167 ADJOALPO_00048 39237 3 Gut 0.15 protein_coding missense_variant MODERATE 45C>G Ile15Met
M0199168 ADJOALPO_00048 39239 3 Gut 0.15 protein_coding missense_variant MODERATE 43A>G Ile15Val
M0199169 ADJOALPO_00049 39416 3 Gut 0.15 protein_coding synonymous_variant LOW 696A>G Gly232Gly
M0199170 ADJOALPO_00024 19476 3 Gut 0.15 protein_coding missense_variant MODERATE 36C>A Asp12Glu
M0199171 ADJOALPO_00024 19485 3 Gut 0.15 protein_coding synonymous_variant LOW 27G>T Leu9Leu
M0199172 ADJOALPO_00024 19500 3 Gut 0.15 protein_coding synonymous_variant LOW 12A>C Ala4Ala
M0199173 ADJOALPO_00027 21100 3 Gut 0.15 protein_coding missense_variant MODERATE 406T>G Cys136Gly






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
ADJOALPO_00105 VFG035923 Dispersin 78.4 6.3e-88 1 208 0.9952 0.9952 Others ATP-binding protein AatC experiment
ADJOALPO_00126 VFG034541 EtpA 95 0 1 1513 1.0 0.9831 Adherence Two-partner secreted adhesin EtpA experiment
ADJOALPO_00127 VFG042382 EtpA 98.7 0 1 603 1.0 1 Adherence two-partner secretion transporter EtpB experiment
ADJOALPO_00001 VFG042503 Adhesive fimbriae 100 0 6 876 0.9943 1 Adherence outer membrane usher protein prediction
ADJOALPO_00002 VFG042504 Adhesive fimbriae 100 1e-209 1 361 1.0 1 Adherence CS14 minor fimbrial subunit prediction
ADJOALPO_00105 VFG035919 Dispersin 79.3 7.3e-88 1 208 0.9952 0.9952 Others ATP-binding protein AatC prediction
ADJOALPO_00126 VFG034541 EtpA 95 0 1 1513 1.0 0.9831 Adherence Two-partner secreted adhesin EtpA prediction
ADJOALPO_00127 VFG042382 EtpA 98.7 0 1 603 1.0 1 Adherence two-partner secretion transporter EtpB prediction
ADJOALPO_00158 VFG042500 Adhesive fimbriae 100 8.5e-133 1 238 1.0 1 Adherence CS14 periplasmic chaperone prediction
ADJOALPO_00159 VFG042501 Adhesive fimbriae 100 4.7e-85 1 169 1.0 1 Adherence CS14 major fimbrial subunit prediction
ADJOALPO_00160 VFG042502 Adhesive fimbriae 100 2.1e-88 1 175 1.0 1 Adherence CS14 major fimbrial subunit 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
ADJOALPO_00055 Arsenic (As), Antimony (Sb) 89.3 2.4e-70 1 140 0.9929 0.9929 experiment
ADJOALPO_00055 Arsenic (As) 97.9 3.9e-74 1 141 1.0000 1.0000 prediction






        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
ADJOALPO_00050 PHI:11470 STM14_3563 88 1.7e-33 5 87 0.9432 0.9121 rodents salmonellosis putative transcriptional regulator 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
ADJOALPO_00083 BAN82826.1|GH23 96.4 1.73e-114 1 168 1 0.7778
ADJOALPO_00124 CBJ04457.1|GT41 98.6 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
ADJOALPO_00001 1.B.11.4.1 93.9 0 9 876 0.9909 0.9988 1 Channels/Pores 1.B β-Barrel Porins 1.B.11 The Outer Membrane Fimbrial Usher Porin (FUP) Family
ADJOALPO_00057 2.A.53.3.1 98.4 2.1e-266 1 492 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.53 The Sulfate Permease (SulP) Family
ADJOALPO_00123 9.B.127.1.3 97.6 6.7e-92 1 164 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.127 The DUF2919 (PF11143) Family
ADJOALPO_00127 1.B.20.3.3 98.7 0 1 603 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.20 The Two-Partner Secretion (TPS) Family