Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C538
  Reference Plasmid   NZ_CP027545.1
  Reference Plasmid Size   101089
  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
M0168080 PCBKMEJD_00037 29449 9 Gut 0.26 protein_coding missense_variant MODERATE 426A>C Arg142Ser
M0168081 PCBKMEJD_00042 38537 8 Gut 0.23 protein_coding missense_variant MODERATE 304A>G Asn102Asp
M0168082 PCBKMEJD_00057 53074 4 Gut 0.11 protein_coding synonymous_variant LOW 279A>T Ala93Ala
M0168083 PCBKMEJD_00049 53306 4 Gut 0.11 protein_coding upstream_gene_variant MODIFIER -4485T>A None
M0168084 PCBKMEJD_00013 12906 7 Gut 0.20 protein_coding synonymous_variant LOW 1482C>T Thr494Thr
M0168085 PCBKMEJD_00014 14136 7 Gut 0.20 protein_coding missense_variant MODERATE 85A>G Met29Val
M0168086 PCBKMEJD_00016 15369 7 Gut 0.20 protein_coding missense_variant MODERATE 306G>A Met102Ile
M0168087 PCBKMEJD_00024 19406 5 Gut 0.14 protein_coding missense_variant MODERATE 760G>A Val254Met
M0168088 PCBKMEJD_00026 20533 6 Gut 0.17 protein_coding synonymous_variant LOW 207C>T Asp69Asp
M0168089 PCBKMEJD_00029 21727 6 Gut 0.17 protein_coding missense_variant MODERATE 16G>A Val6Met
M0168090 PCBKMEJD_00030 22140 6 Gut 0.17 protein_coding upstream_gene_variant MODIFIER -55G>T None
M0168091 PCBKMEJD_00034 27401 6 Gut 0.17 protein_coding missense_variant MODERATE 2732G>A Gly911Glu
M0168092 PCBKMEJD_00034 27423 6 Gut 0.17 protein_coding missense_variant MODERATE 2754T>G Ile918Met
M0168093 PCBKMEJD_00037 30745 6 Gut 0.17 protein_coding synonymous_variant LOW 1722G>T Pro574Pro
M0168094 PCBKMEJD_00037 30772 6 Gut 0.17 protein_coding synonymous_variant LOW 1749T>C Asn583Asn
M0168095 PCBKMEJD_00039 33048 6 Gut 0.17 protein_coding missense_variant MODERATE 103A>G Arg35Gly
M0168096 PCBKMEJD_00039 33196 5 Gut 0.14 protein_coding missense_variant MODERATE 251T>G Val84Gly
M0168097 PCBKMEJD_00039 33314 6 Gut 0.17 protein_coding synonymous_variant LOW 369C>A Ala123Ala
M0168098 PCBKMEJD_00039 33813 6 Gut 0.17 protein_coding synonymous_variant LOW 868T>C Leu290Leu
M0168099 PCBKMEJD_00039 34495 6 Gut 0.17 protein_coding missense_variant MODERATE 1550C>T Ala517Val
M0168100 PCBKMEJD_00039 35873 6 Gut 0.17 protein_coding synonymous_variant LOW 2928C>T Ser976Ser
M0168101 PCBKMEJD_00040 37075 6 Gut 0.17 protein_coding missense_variant MODERATE 610A>G Thr204Ala
M0168102 PCBKMEJD_00041 37612 6 Gut 0.17 protein_coding synonymous_variant LOW 342C>T Phe114Phe
M0168103 PCBKMEJD_00041 37682 6 Gut 0.17 protein_coding synonymous_variant LOW 412C>T Leu138Leu






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
PCBKMEJD_00047 VFG000843 Hemolysin 100 1.2e-267 1 479 1.0 1 Exotoxin Hemolysin D experiment
PCBKMEJD_00048 VFG000841 Hemolysin 99.6 0 1 706 1.0 1 Exotoxin Hemolysin B experiment
PCBKMEJD_00049 VFG000840 Hemolysin 99.5 0 7 1004 0.994 1 Exotoxin Hemolysin A experiment
PCBKMEJD_00050 VFG000842 Hemolysin 100 3.1e-101 1 171 1.0 1 Exotoxin Hemolysin C experiment
PCBKMEJD_00062 VFG034721 Ibes 81.8 9e-286 1 572 0.9983 0.9913 Invasion phosphoethanolamine transferase CptA experiment
PCBKMEJD_00080 VFG038285 Exe T2SS 80.6 2e-45 1 103 0.9537 0.7203 Effector delivery system general secretion pathway protein G experiment
PCBKMEJD_00047 VFG000843 Hemolysin 100 9e-267 1 479 1.0 1 Exotoxin Hemolysin D prediction
PCBKMEJD_00048 VFG033882 Hemolysin 100 0 1 706 1.0 1 Exotoxin Hemolysin B prediction
PCBKMEJD_00049 VFG033891 Hemolysin 100 0 7 1004 0.994 1 Exotoxin Hemolysin A prediction
PCBKMEJD_00050 VFG000842 Hemolysin 100 2.3e-100 1 171 1.0 1 Exotoxin Hemolysin C prediction
PCBKMEJD_00062 VFG034689 Ibes 100 0 1 573 1.0 1 Invasion phosphoethanolamine transferase CptA prediction
PCBKMEJD_00077 VFG040932 Etp 94.8 0 1 655 0.9985 1 Effector delivery system variant type II secretion system secretin EtpD prediction
PCBKMEJD_00078 VFG040933 Etp 96.1 2.6e-250 4 464 0.9872 0.9202 Effector delivery system type II secretion system ATPase GspE prediction
PCBKMEJD_00079 VFG040934 Etp 93.1 2.1e-203 1 407 1.0 1 Effector delivery system type II secretion system inner membrane protein GspF prediction
PCBKMEJD_00080 VFG040935 Etp 98.1 6.1e-54 1 104 0.963 0.7222 Effector delivery system type II secretion system major pseudopilin GspG prediction
PCBKMEJD_00082 VFG040937 Etp 85.2 1.1e-48 1 115 1.0 1 Effector delivery system type II secretion system minor pseudopilin GspI prediction
PCBKMEJD_00086 VFG040940 Etp 87.7 1.1e-202 36 425 0.9176 1 Effector delivery system type II secretion system protein GspL prediction
PCBKMEJD_00087 VFG040941 Etp 83.2 9.6e-78 1 167 0.9766 0.9824 Effector delivery system type II secretion system protein M prediction
PCBKMEJD_00090 VFG040943 Etp 80.6 2.3e-52 1 124 0.9688 0.9323 Effector delivery system GspS family T2SS pilot lipoprotein variant EptO 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
PCBKMEJD_00061 AHY68449.1|GT4 100 9.25e-267 1 368 1 1
PCBKMEJD_00112 QCH93330.1|GH24 100 3.49e-133 1 177 0.8634 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
PCBKMEJD_00048 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
PCBKMEJD_00049 1.C.11.1.6 97.9 0 7 1004 0.9940 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.11 The Pore-forming RTX Toxin (RTX-toxin) Family
PCBKMEJD_00077 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
PCBKMEJD_00078 3.A.15.1.1 74 9.6e-192 8 464 0.9786 2.0044 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
PCBKMEJD_00111 1.E.1.1.3 98.5 8.8e-32 1 67 0.3641 0.9853 1 Channels/Pores 1.E Holins 1.E.1 The P21 Holin S (P21 Holin) Family