Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C404
  Reference Plasmid   NZ_CP006263.1
  Reference Plasmid Size   98066
  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
M0163787 FHAIKJIH_00097 84394 5 Gut 0.23 protein_coding upstream_gene_variant MODIFIER -1042G>A None
M0163788 FHAIKJIH_00102 86388 5 Gut 0.23 protein_coding missense_variant MODERATE 1045G>T Ala349Ser
M0163789 FHAIKJIH_00102 87785 3 Gut 0.14 protein_coding synonymous_variant LOW 2442G>A Leu814Leu
M0163790 FHAIKJIH_00104 90648 5 Gut 0.23 protein_coding synonymous_variant LOW 135C>T His45His






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
FHAIKJIH_00001 VFG000846 StcE 86.8 0 1 886 1.0 0.9866 Exoenzyme metalloprotease experiment
FHAIKJIH_00006 VFG038285 Exe T2SS 75.9 1.6e-58 1 137 0.9514 0.958 Effector delivery system general secretion pathway protein G experiment
FHAIKJIH_00035 VFG034721 Ibes 81.8 9e-286 1 572 0.9983 0.9913 Invasion phosphoethanolamine transferase CptA experiment
FHAIKJIH_00065 VFG001445 TraJ 98 6.2e-113 1 200 0.8772 0.995 Invasion unknown protein experiment
FHAIKJIH_00101 VFG000842 Hemolysin 100 3.1e-101 1 171 1.0 1 Exotoxin Hemolysin C experiment
FHAIKJIH_00102 VFG000840 Hemolysin 99.5 0 1 998 1.0 1 Exotoxin Hemolysin A experiment
FHAIKJIH_00103 VFG000841 Hemolysin 99.6 0 1 706 1.0 1 Exotoxin Hemolysin B experiment
FHAIKJIH_00104 VFG000843 Hemolysin 100 1.2e-267 1 479 1.0 1 Exotoxin Hemolysin D experiment
FHAIKJIH_00001 VFG000846 StcE 86.8 0 1 886 1.0 0.9866 Exoenzyme metalloprotease prediction
FHAIKJIH_00002 VFG040931 Etp 81.5 6.7e-118 1 270 1.0 0.9278 Effector delivery system type II secretion system protein GspC prediction
FHAIKJIH_00003 VFG040932 Etp 94.8 0 1 655 0.9985 1 Effector delivery system variant type II secretion system secretin EtpD prediction
FHAIKJIH_00004 VFG040933 Etp 96.2 7e-270 4 500 0.994 0.992 Effector delivery system type II secretion system ATPase GspE prediction
FHAIKJIH_00005 VFG040934 Etp 93.1 2.1e-203 1 407 1.0 1 Effector delivery system type II secretion system inner membrane protein GspF prediction
FHAIKJIH_00006 VFG040935 Etp 95.1 6.8e-77 1 144 1.0 1 Effector delivery system type II secretion system major pseudopilin GspG prediction
FHAIKJIH_00007 VFG040936 Etp 88 1.1e-87 1 183 1.0 0.9946 Effector delivery system type II secretion system minor pseudopilin GspH prediction
FHAIKJIH_00008 VFG040937 Etp 85.2 1.1e-48 1 115 1.0 1 Effector delivery system type II secretion system minor pseudopilin GspI prediction
FHAIKJIH_00009 VFG040938 Etp 92 2.9e-102 1 199 1.0 1 Effector delivery system type II secretion system minor pseudopilin GspJ prediction
FHAIKJIH_00010 VFG040939 Etp 89.2 6.5e-160 1 325 1.0 1 Effector delivery system type II secretion system minor pseudopilin GspK prediction
FHAIKJIH_00011 VFG040940 Etp 87.9 5.7e-203 1 390 1.0 1 Effector delivery system type II secretion system protein GspL prediction
FHAIKJIH_00012 VFG040941 Etp 83.6 3.6e-77 1 165 0.9706 0.9706 Effector delivery system type II secretion system protein M prediction
FHAIKJIH_00015 VFG040942 Etp 87.7 1.4e-139 1 277 1.0 1 Effector delivery system A24 family peptidase prediction
FHAIKJIH_00016 VFG040943 Etp 80.6 2.3e-52 1 124 0.9688 0.9323 Effector delivery system GspS family T2SS pilot lipoprotein variant EptO prediction
FHAIKJIH_00035 VFG034689 Ibes 100 0 1 573 1.0 1 Invasion phosphoethanolamine transferase CptA prediction
FHAIKJIH_00065 VFG001445 TraJ 98 4.6e-112 1 200 0.8772 0.995 Invasion unknown protein prediction
FHAIKJIH_00101 VFG000842 Hemolysin 100 2.3e-100 1 171 1.0 1 Exotoxin Hemolysin C prediction
FHAIKJIH_00102 VFG033891 Hemolysin 100 0 1 998 1.0 1 Exotoxin Hemolysin A prediction
FHAIKJIH_00103 VFG033882 Hemolysin 100 0 1 706 1.0 1 Exotoxin Hemolysin B prediction
FHAIKJIH_00104 VFG000843 Hemolysin 100 9e-267 1 479 1.0 1 Exotoxin Hemolysin D 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
FHAIKJIH_00034 AHY68449.1|GT4 100 9.25e-267 1 368 1 1
FHAIKJIH_00067 AHG18083.1|GH23 100 8.17e-157 1 215 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
FHAIKJIH_00003 1.B.22.1.1 72.1 2.2e-255 10 654 0.9832 0.9803 1 Channels/Pores 1.B β-Barrel Porins 1.B.22 The Outer Bacterial Membrane Secretin (Secretin) Family
FHAIKJIH_00004 3.A.15.1.1 72.9 1.3e-202 8 498 0.9820 2.1535 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.15 The Outer Membrane Protein Secreting Main Terminal Branch (MTB) Family
FHAIKJIH_00102 1.C.11.1.6 97.9 0 1 998 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.11 The Pore-forming RTX Toxin (RTX-toxin) Family
FHAIKJIH_00103 3.A.1.109.1 73.3 2.9e-301 11 706 0.9858 0.9844 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily