Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C206
  Reference Plasmid   CP113227.1
  Reference Plasmid Size   194547
  Reference Plasmid GC Content   0.56
  Reference Plasmid Mobility Type   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
M0059644 GAHJGFOD_00089 67589 8 Skin 0.73 protein_coding missense_variant MODERATE 352A>G Lys118Glu
M0059645 GAHJGFOD_00089 67593 8 Skin 0.73 protein_coding synonymous_variant LOW 348T>G Val116Val
M0059646 GAHJGFOD_00089 67621 8 Skin 0.73 protein_coding missense_variant MODERATE 320G>A Gly107Glu
M0059647 GAHJGFOD_00089 67630 8 Skin 0.73 protein_coding missense_variant MODERATE 311T>C Val104Ala
M0059648 GAHJGFOD_00089 67648 8 Skin 0.73 protein_coding missense_variant MODERATE 293G>T Arg98Leu
M0059649 GAHJGFOD_00089 67701 8 Skin 0.73 protein_coding synonymous_variant LOW 240G>A Thr80Thr
M0059650 GAHJGFOD_00089 67704 8 Skin 0.73 protein_coding synonymous_variant LOW 237G>A Lys79Lys
M0059651 GAHJGFOD_00089 67750 8 Skin 0.73 protein_coding missense_variant MODERATE 191C>T Ala64Val
M0059652 GAHJGFOD_00089 67785 8 Skin 0.73 protein_coding synonymous_variant LOW 156G>A Glu52Glu
M0059653 GAHJGFOD_00089 67826 8 Skin 0.73 protein_coding missense_variant MODERATE 115G>A Glu39Lys
M0059654 GAHJGFOD_00089 67830 8 Skin 0.73 protein_coding synonymous_variant LOW 111C>T Leu37Leu
M0059655 GAHJGFOD_00089 67839 8 Skin 0.73 protein_coding synonymous_variant LOW 102T>C Ala34Ala
M0059656 GAHJGFOD_00089 67850 8 Skin 0.73 protein_coding missense_variant MODERATE 91A>G Asn31Asp
M0059657 GAHJGFOD_00089 67851 8 Skin 0.73 protein_coding synonymous_variant LOW 90A>G Arg30Arg
M0059658 GAHJGFOD_00089 67887 8 Skin 0.73 protein_coding missense_variant MODERATE 54C>G Asp18Glu
M0059659 GAHJGFOD_00089 67961 8 Skin 0.73 protein_coding upstream_gene_variant MODIFIER -21A>T None
M0059660 GAHJGFOD_00089 67965 8 Skin 0.73 protein_coding upstream_gene_variant MODIFIER -25C>T None
M0059661 GAHJGFOD_00089 67989 8 Skin 0.73 protein_coding upstream_gene_variant MODIFIER -49C>T None
M0059662 GAHJGFOD_00089 67991 8 Skin 0.73 protein_coding upstream_gene_variant MODIFIER -51A>G None
M0059663 GAHJGFOD_00090 68053 8 Skin 0.73 protein_coding synonymous_variant LOW 9C>G Thr3Thr
M0059664 GAHJGFOD_00090 68170 8 Skin 0.73 protein_coding synonymous_variant LOW 126C>T Arg42Arg
M0059665 GAHJGFOD_00167 147514 8 Skin 0.73 protein_coding upstream_gene_variant MODIFIER -4151T>C None
M0059666 GAHJGFOD_00167 147530 8 Skin 0.73 protein_coding upstream_gene_variant MODIFIER -4167T>A None
M0059667 GAHJGFOD_00167 147612 8 Skin 0.73 protein_coding upstream_gene_variant MODIFIER -4249T>C None
M0059668 GAHJGFOD_00167 147688 8 Skin 0.73 protein_coding upstream_gene_variant MODIFIER -4325A>G None
M0059669 GAHJGFOD_00173 147718 8 Skin 0.73 protein_coding synonymous_variant LOW 27G>A Gln9Gln
M0059670 GAHJGFOD_00173 147820 8 Skin 0.73 protein_coding synonymous_variant LOW 129C>G Leu43Leu
M0059671 GAHJGFOD_00173 147850 8 Skin 0.73 protein_coding synonymous_variant LOW 159A>T Ile53Ile
M0059672 GAHJGFOD_00173 147937 8 Skin 0.73 protein_coding synonymous_variant LOW 246T>C Asp82Asp
M0059673 GAHJGFOD_00173 147949 8 Skin 0.73 protein_coding synonymous_variant LOW 258G>C Gly86Gly
M0059674 GAHJGFOD_00173 148034 8 Skin 0.73 protein_coding missense_variant MODERATE 343A>G Ile115Val
M0059675 GAHJGFOD_00173 148048 8 Skin 0.73 protein_coding synonymous_variant LOW 357G>A Glu119Glu
M0059676 GAHJGFOD_00173 148090 8 Skin 0.73 protein_coding synonymous_variant LOW 399T>C Ala133Ala
M0059677 GAHJGFOD_00173 148105 8 Skin 0.73 protein_coding synonymous_variant LOW 414C>A Ile138Ile
M0059678 GAHJGFOD_00173 148216 8 Skin 0.73 protein_coding missense_variant MODERATE 525T>G His175Gln
M0059679 GAHJGFOD_00173 148246 8 Skin 0.73 protein_coding synonymous_variant LOW 555A>G Lys185Lys
M0059680 GAHJGFOD_00173 148252 8 Skin 0.73 protein_coding synonymous_variant LOW 561C>T Ala187Ala
M0059681 GAHJGFOD_00173 148325 8 Skin 0.73 protein_coding synonymous_variant LOW 634C>T Leu212Leu
M0059682 GAHJGFOD_00173 148331 8 Skin 0.73 protein_coding missense_variant MODERATE 640A>G Thr214Ala
M0059683 GAHJGFOD_00173 148339 8 Skin 0.73 protein_coding synonymous_variant LOW 648C>T Ser216Ser
M0059684 GAHJGFOD_00173 148355 8 Skin 0.73 protein_coding missense_variant MODERATE 664T>C Ser222Pro
M0059685 GAHJGFOD_00173 148614 8 Skin 0.73 protein_coding missense_variant MODERATE 923C>G Thr308Arg
M0059686 GAHJGFOD_00173 148884 8 Skin 0.73 protein_coding missense_variant MODERATE 1193G>C Arg398Pro
M0059687 GAHJGFOD_00173 148940 8 Skin 0.73 protein_coding missense_variant MODERATE 1249T>G Trp417Gly
M0059688 GAHJGFOD_00173 148972 8 Skin 0.73 protein_coding missense_variant MODERATE 1281T>G His427Gln
M0059689 GAHJGFOD_00169 149117 7 Skin 0.64 protein_coding upstream_gene_variant MODIFIER -4744A>T None
M0059690 GAHJGFOD_00169 149164 7 Skin 0.64 protein_coding upstream_gene_variant MODIFIER -4791A>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







        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
GAHJGFOD_00182 Cobalt (Co), Nickel (Ni) 71.1 1.5e-169 14 467 0.9560 0.9520 experiment
GAHJGFOD_00182 Triclosan [class: Phenolic compounds], n-hexane [class: Alkane], p-xylene [class: Aromatic hydrocarbons] 71.1 1.5e-169 14 467 0.9560 0.9520 experiment
GAHJGFOD_00183 Triclosan [class: Phenolic compounds], n-hexane [class: Alkane], p-xylene [class: Aromatic hydrocarbons] 76.7 0 1 1032 0.9981 0.9990 experiment
GAHJGFOD_00074 Ethidium Bromide [class: Phenanthridine], Rhodamine 6G [class: Xanthene], 4,6-diamidino-2-phenylindole (DAPI) [class: Diamidine], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], Acridine Orange [class: Acridine] 70.3 4.7e-241 5 613 0.9935 0.9870 prediction
GAHJGFOD_00182 Triclosan [class: Phenolic compounds], n-hexane [class: Alkane], p-xylene [class: Aromatic hydrocarbons] 97.7 3.7e-249 1 477 1.0000 1.0000 prediction
GAHJGFOD_00183 Triclosan [class: Phenolic compounds], n-hexane [class: Alkane], p-xylene [class: Aromatic hydrocarbons] 100 0 1 1044 1.0000 1.0000 prediction
GAHJGFOD_00184 Triclosan [class: Phenolic compounds], n-hexane [class: Alkane], p-xylene [class: Aromatic hydrocarbons] 99.2 2.2e-207 1 387 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
GAHJGFOD_00069 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
GAHJGFOD_00076 ARO:3002363 100 7.02e-217 1 308 1.0000 1.0000 monobactam PER beta-lactamase antibiotic inactivation
GAHJGFOD_00080 ARO:3002803 100 9.75e-87 1 218 1.0000 1.0000 fluoroquinolone antibiotic quinolone resistance protein (qnr) antibiotic target protection
GAHJGFOD_00082 ARO:3000410 100 2e-198 6 283 0.9823 0.9964 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
GAHJGFOD_00083 ARO:3002601 98.8 1.09e-185 1 259 1.0000 0.9848 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
GAHJGFOD_00084 ARO:3002578 99 7.83e-152 1 210 1.0000 0.8046 aminoglycoside antibiotic AAC(6') antibiotic inactivation
GAHJGFOD_00167 ARO:3002272 100 1.91e-193 1 266 1.0000 1.0000 carbapenem VIM beta-lactamase antibiotic inactivation
GAHJGFOD_00168 ARO:3002577 99.5 2.91e-136 1 184 1.0000 1.0000 aminoglycoside antibiotic AAC(6') antibiotic inactivation
GAHJGFOD_00169 ARO:3002864 98.7 1.44e-54 1 78 1.0000 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
GAHJGFOD_00182 ARO:3000802 71.5 2.71e-206 19 465 0.9413 0.9374 macrolide antibiotic resistance-nodulation-cell division (RND) antibiotic efflux pump antibiotic efflux
GAHJGFOD_00183 ARO:3000801 76.6 0 1 1032 0.9981 0.9990 macrolide antibiotic resistance-nodulation-cell division (RND) antibiotic efflux pump antibiotic efflux






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
GAHJGFOD_00085 PHI:9804 int 100 3e-14 1 37 0.1098 1.0000 rodents gastroenteritis integrase reduced virulence
GAHJGFOD_00170 PHI:9804 int 100 3e-14 1 37 0.1098 1.0000 rodents gastroenteritis integrase 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
GAHJGFOD_00143 QGZ33004.1|GH23 100 1.61e-132 1 189 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
GAHJGFOD_00182 2.A.6.2.15 71.1 5.8e-168 14 467 0.9518 1.1692 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily
GAHJGFOD_00183 2.A.6.2.15 76.7 0 1 1032 0.9885 2.6462 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily
GAHJGFOD_00184 2.A.6.2.15 86.7 2e-179 1 387 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily