Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1164
  Reference Plasmid   NZ_CP124820.1
  Reference Plasmid Size   87527
  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
M0198627 MFKEMEIC_00018 12359 6 Gut 0.32 protein_coding synonymous_variant LOW 111C>T His37His
M0198628 MFKEMEIC_00021 14017 6 Gut 0.32 protein_coding upstream_gene_variant MODIFIER -117C>T None
M0198629 MFKEMEIC_00022 14371 6 Gut 0.32 protein_coding upstream_gene_variant MODIFIER -901T>G None
M0198630 MFKEMEIC_00022 14438 7 Gut 0.37 protein_coding upstream_gene_variant MODIFIER -834T>C None
M0198631 MFKEMEIC_00013 9048 3 Gut 0.16 protein_coding missense_variant MODERATE 106T>C Phe36Leu
M0198632 MFKEMEIC_00013 9056 3 Gut 0.16 protein_coding synonymous_variant LOW 114G>A Glu38Glu
M0198633 MFKEMEIC_00013 9059 3 Gut 0.16 protein_coding synonymous_variant LOW 117C>T Asp39Asp
M0198634 MFKEMEIC_00013 9093 3 Gut 0.16 protein_coding missense_variant MODERATE 151C>G Leu51Val
M0198635 MFKEMEIC_00013 9104 3 Gut 0.16 protein_coding synonymous_variant LOW 162C>A Gly54Gly
M0198636 MFKEMEIC_00013 9119 3 Gut 0.16 protein_coding synonymous_variant LOW 177G>A Ala59Ala
M0198637 MFKEMEIC_00013 9131 3 Gut 0.16 protein_coding synonymous_variant LOW 189T>C Tyr63Tyr
M0198638 MFKEMEIC_00013 9140 3 Gut 0.16 protein_coding synonymous_variant LOW 198C>T Ser66Ser
M0198639 MFKEMEIC_00013 9143 3 Gut 0.16 protein_coding missense_variant MODERATE 201T>G Asp67Glu
M0198640 MFKEMEIC_00013 9147 3 Gut 0.16 protein_coding missense_variant MODERATE 205C>G Leu69Val
M0198641 MFKEMEIC_00013 9149 3 Gut 0.16 protein_coding synonymous_variant LOW 207T>G Leu69Leu
M0198642 MFKEMEIC_00013 9152 3 Gut 0.16 protein_coding synonymous_variant LOW 210A>G Glu70Glu
M0198643 MFKEMEIC_00013 9214 3 Gut 0.16 protein_coding missense_variant MODERATE 272A>G Gln91Arg
M0198644 MFKEMEIC_00013 9215 3 Gut 0.16 protein_coding missense_variant MODERATE 273G>C Gln91His
M0198645 MFKEMEIC_00013 9229 3 Gut 0.16 protein_coding missense_variant MODERATE 287G>A Gly96Asp
M0198646 MFKEMEIC_00013 9242 3 Gut 0.16 protein_coding synonymous_variant LOW 300A>G Glu100Glu
M0198647 MFKEMEIC_00013 9245 3 Gut 0.16 protein_coding synonymous_variant LOW 303T>G Val101Val
M0198648 MFKEMEIC_00013 9254 3 Gut 0.16 protein_coding synonymous_variant LOW 312A>G Glu104Glu
M0198649 MFKEMEIC_00013 9290 3 Gut 0.16 protein_coding synonymous_variant LOW 348G>C Leu116Leu
M0198650 MFKEMEIC_00013 9303 3 Gut 0.16 protein_coding missense_variant MODERATE 361A>G Lys121Glu
M0198651 MFKEMEIC_00013 9304 3 Gut 0.16 protein_coding missense_variant MODERATE 362A>G Lys121Arg
M0198652 MFKEMEIC_00013 9305 3 Gut 0.16 protein_coding missense_variant MODERATE 363A>C Lys121Asn
M0198653 MFKEMEIC_00006 9323 3 Gut 0.16 protein_coding upstream_gene_variant MODIFIER -4963A>T None
M0198654 MFKEMEIC_00008 9362 3 Gut 0.16 protein_coding upstream_gene_variant MODIFIER -2379A>T None
M0198655 MFKEMEIC_00008 9377 3 Gut 0.16 protein_coding upstream_gene_variant MODIFIER -2394T>C None
M0198656 MFKEMEIC_00008 9412 3 Gut 0.16 protein_coding upstream_gene_variant MODIFIER -2429G>T None
M0198657 MFKEMEIC_00008 9445 3 Gut 0.16 protein_coding upstream_gene_variant MODIFIER -2462A>G None






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
MFKEMEIC_00040 VFG034721 Ibes 81.8 9e-286 1 572 0.9983 0.9913 Invasion phosphoethanolamine transferase CptA experiment
MFKEMEIC_00056 VFG000842 Hemolysin 100 3.1e-101 1 171 1.0 1 Exotoxin Hemolysin C experiment
MFKEMEIC_00057 VFG000840 Hemolysin 99.5 0 1 998 1.0 1 Exotoxin Hemolysin A experiment
MFKEMEIC_00058 VFG000841 Hemolysin 99.6 0 1 706 1.0 1 Exotoxin Hemolysin B experiment
MFKEMEIC_00059 VFG000843 Hemolysin 100 1.2e-267 1 479 1.0 1 Exotoxin Hemolysin D experiment
MFKEMEIC_00068 VFG000846 StcE 86.9 0 1 886 1.0 0.9866 Exoenzyme metalloprotease experiment
MFKEMEIC_00073 VFG038285 Exe T2SS 75.9 1.6e-58 1 137 0.9514 0.958 Effector delivery system general secretion pathway protein G experiment
MFKEMEIC_00040 VFG034689 Ibes 100 0 1 573 1.0 1 Invasion phosphoethanolamine transferase CptA prediction
MFKEMEIC_00056 VFG000842 Hemolysin 100 2.3e-100 1 171 1.0 1 Exotoxin Hemolysin C prediction
MFKEMEIC_00057 VFG033891 Hemolysin 100 0 1 998 1.0 1 Exotoxin Hemolysin A prediction
MFKEMEIC_00058 VFG033882 Hemolysin 100 0 1 706 1.0 1 Exotoxin Hemolysin B prediction
MFKEMEIC_00059 VFG000843 Hemolysin 100 9e-267 1 479 1.0 1 Exotoxin Hemolysin D prediction
MFKEMEIC_00068 VFG000846 StcE 86.9 0 1 886 1.0 0.9866 Exoenzyme metalloprotease prediction
MFKEMEIC_00069 VFG040931 Etp 81.5 6.7e-118 1 270 1.0 0.9278 Effector delivery system type II secretion system protein GspC prediction
MFKEMEIC_00070 VFG040932 Etp 94.8 0 1 655 0.9985 1 Effector delivery system variant type II secretion system secretin EtpD prediction
MFKEMEIC_00071 VFG040933 Etp 96.2 7e-270 4 500 0.994 0.992 Effector delivery system type II secretion system ATPase GspE prediction
MFKEMEIC_00072 VFG040934 Etp 93.1 2.1e-203 1 407 1.0 1 Effector delivery system type II secretion system inner membrane protein GspF prediction
MFKEMEIC_00073 VFG040935 Etp 95.1 6.8e-77 1 144 1.0 1 Effector delivery system type II secretion system major pseudopilin GspG prediction
MFKEMEIC_00074 VFG040936 Etp 88 1.1e-87 1 183 1.0 0.9946 Effector delivery system type II secretion system minor pseudopilin GspH prediction
MFKEMEIC_00075 VFG040937 Etp 85.2 1.1e-48 1 115 1.0 1 Effector delivery system type II secretion system minor pseudopilin GspI prediction
MFKEMEIC_00076 VFG040938 Etp 92 2.9e-102 1 199 1.0 1 Effector delivery system type II secretion system minor pseudopilin GspJ prediction
MFKEMEIC_00077 VFG040939 Etp 89.2 6.5e-160 1 325 1.0 1 Effector delivery system type II secretion system minor pseudopilin GspK prediction
MFKEMEIC_00078 VFG040940 Etp 87.9 5.7e-203 1 390 1.0 1 Effector delivery system type II secretion system protein GspL prediction
MFKEMEIC_00079 VFG040941 Etp 83.6 3.6e-77 1 165 0.9706 0.9706 Effector delivery system type II secretion system protein M prediction
MFKEMEIC_00082 VFG040942 Etp 88.1 1.3e-140 1 277 1.0 1 Effector delivery system A24 family peptidase prediction
MFKEMEIC_00083 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
MFKEMEIC_00024 AHG18083.1|GH23 100 8.17e-157 1 215 1 1
MFKEMEIC_00041 AHY68449.1|GT4 100 9.25e-267 1 368 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
MFKEMEIC_00057 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
MFKEMEIC_00058 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
MFKEMEIC_00070 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
MFKEMEIC_00071 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