Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C953
  Reference Plasmid   NZ_CP083832.1
  Reference Plasmid Size   119051
  Reference Plasmid GC Content   0.54
  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
M0104969 GIFOOFNF_00084 77806 21 Skin 0.45 protein_coding synonymous_variant LOW 1119T>C Val373Val
M0104970 GIFOOFNF_00084 77815 21 Skin 0.45 protein_coding synonymous_variant LOW 1110G>T Gly370Gly
M0104971 GIFOOFNF_00084 77842 21 Skin 0.45 protein_coding synonymous_variant LOW 1083G>A Ala361Ala
M0104972 GIFOOFNF_00084 77866 21 Skin 0.45 protein_coding synonymous_variant LOW 1059T>C Asn353Asn
M0104973 GIFOOFNF_00084 77874 21 Skin 0.45 protein_coding missense_variant MODERATE 1051G>A Ala351Thr
M0104974 GIFOOFNF_00084 77895 21 Skin 0.45 protein_coding synonymous_variant LOW 1030T>C Leu344Leu
M0104975 GIFOOFNF_00084 77896 21 Skin 0.45 protein_coding synonymous_variant LOW 1029G>A Lys343Lys
M0104976 GIFOOFNF_00084 77902 21 Skin 0.45 protein_coding synonymous_variant LOW 1023T>C Ala341Ala
M0104977 GIFOOFNF_00084 77920 21 Skin 0.45 protein_coding synonymous_variant LOW 1005A>G Gly335Gly
M0104978 GIFOOFNF_00084 77921 21 Skin 0.45 protein_coding missense_variant MODERATE 1004G>C Gly335Ala
M0104979 GIFOOFNF_00084 77922 21 Skin 0.45 protein_coding missense_variant MODERATE 1003G>A Gly335Arg
M0104980 GIFOOFNF_00084 77941 21 Skin 0.45 protein_coding synonymous_variant LOW 984C>T Gly328Gly
M0104981 GIFOOFNF_00084 77946 21 Skin 0.45 protein_coding missense_variant MODERATE 979A>G Asn327Asp
M0104982 GIFOOFNF_00084 77949 21 Skin 0.45 protein_coding missense_variant MODERATE 976G>A Val326Met
M0104983 GIFOOFNF_00084 78001 20 Skin 0.43 protein_coding synonymous_variant LOW 924C>T Arg308Arg
M0104984 GIFOOFNF_00084 78019 20 Skin 0.43 protein_coding synonymous_variant LOW 906C>G Ala302Ala
M0104985 GIFOOFNF_00016 12582 4 Skin 0.09 protein_coding missense_variant MODERATE 893C>T Ala298Val
M0104986 GIFOOFNF_00016 12722 4 Skin 0.09 protein_coding synonymous_variant LOW 753C>G Gly251Gly
M0104987 GIFOOFNF_00083 76937 4 Skin 0.09 protein_coding missense_variant MODERATE 325A>C Met109Leu
M0104988 GIFOOFNF_00083 76953 4 Skin 0.09 protein_coding synonymous_variant LOW 309G>A Glu103Glu
M0104989 GIFOOFNF_00083 76995 6 Skin 0.13 protein_coding synonymous_variant LOW 267C>T Arg89Arg
M0104990 GIFOOFNF_00083 77001 6 Skin 0.13 protein_coding synonymous_variant LOW 261T>G Val87Val
M0104991 GIFOOFNF_00083 77003 6 Skin 0.13 protein_coding missense_variant MODERATE 259G>C Val87Leu
M0104992 GIFOOFNF_00083 77025 6 Skin 0.13 protein_coding synonymous_variant LOW 237T>C Asp79Asp
M0104993 GIFOOFNF_00083 77037 6 Skin 0.13 protein_coding synonymous_variant LOW 225T>G Ala75Ala
M0104994 GIFOOFNF_00083 77073 7 Skin 0.15 protein_coding synonymous_variant LOW 189G>C Leu63Leu
M0104995 GIFOOFNF_00083 77130 8 Skin 0.17 protein_coding synonymous_variant LOW 132T>C Asp44Asp
M0104996 GIFOOFNF_00083 77141 8 Skin 0.17 protein_coding synonymous_variant LOW 121C>T Leu41Leu
M0104997 GIFOOFNF_00083 77145 8 Skin 0.17 protein_coding synonymous_variant LOW 117T>C Tyr39Tyr
M0104998 GIFOOFNF_00083 77154 8 Skin 0.17 protein_coding synonymous_variant LOW 108G>A Pro36Pro
M0104999 GIFOOFNF_00083 77157 8 Skin 0.17 protein_coding synonymous_variant LOW 105C>A Thr35Thr
M0105000 GIFOOFNF_00083 77172 8 Skin 0.17 protein_coding synonymous_variant LOW 90T>C Arg30Arg
M0105001 GIFOOFNF_00083 77232 8 Skin 0.17 protein_coding synonymous_variant LOW 30C>T Ala10Ala
M0105002 GIFOOFNF_00083 77247 8 Skin 0.17 protein_coding synonymous_variant LOW 15C>G Thr5Thr
M0105003 GIFOOFNF_00083 77257 8 Skin 0.17 protein_coding missense_variant MODERATE 5G>A Ser2Asn
M0105004 GIFOOFNF_00082 77266 8 Skin 0.17 protein_coding upstream_gene_variant MODIFIER -367T>G None
M0105005 GIFOOFNF_00084 77279 8 Skin 0.17 protein_coding splice_region_variant&stop_retained_variant LOW 1646A>G Ter549Ter
M0105006 GIFOOFNF_00084 77281 8 Skin 0.17 protein_coding synonymous_variant LOW 1644A>G Gly548Gly
M0105007 GIFOOFNF_00084 77284 8 Skin 0.17 protein_coding synonymous_variant LOW 1641T>C Ala547Ala
M0105008 GIFOOFNF_00084 77308 8 Skin 0.17 protein_coding synonymous_variant LOW 1617C>T Asp539Asp
M0105009 GIFOOFNF_00084 77332 8 Skin 0.17 protein_coding synonymous_variant LOW 1593T>C Leu531Leu
M0105010 GIFOOFNF_00113 94639 4 Skin 0.09 protein_coding missense_variant MODERATE 140T>C Val47Ala






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
GIFOOFNF_00014 Mercury (Hg) 96.2 2.7e-39 1 78 1.0000 1.0000 experiment
GIFOOFNF_00015 Mercury (Hg) 90.1 1.6e-54 1 121 1.0000 1.0000 experiment
GIFOOFNF_00016 Mercury (Hg) 92.5 8.4e-292 1 561 1.0000 1.0000 experiment
GIFOOFNF_00017 Mercury (Hg) 80.1 1.6e-61 1 141 1.0000 1.0000 experiment
GIFOOFNF_00018 Mercury (Hg) 85.7 4.5e-38 1 91 1.0000 1.0000 experiment
GIFOOFNF_00019 Mercury (Hg) 99.1 8.5e-62 17 131 0.8779 0.9914 experiment
GIFOOFNF_00020 Arsenic (As), Antimony (Sb), Bismuth (Bi) 100 8.1e-64 1 117 1.0000 1.0000 experiment
GIFOOFNF_00021 Arsenic (As), Antimony (Sb) 98.3 1.6e-67 1 120 1.0000 1.0000 experiment
GIFOOFNF_00022 Arsenic (As), Antimony (Sb) 99 0 1 583 1.0000 1.0000 experiment
GIFOOFNF_00023 Arsenic (As), Antimony (Sb) 99.5 2e-232 1 429 1.0000 1.0000 experiment
GIFOOFNF_00024 Arsenic (As), Antimony (Sb) 99.3 3.5e-77 1 141 1.0000 1.0000 experiment
GIFOOFNF_00082 Mercury (Hg) 100 2.9e-41 1 78 1.0000 1.0000 experiment
GIFOOFNF_00083 Mercury (Hg) 98.3 1.6e-62 1 121 1.0000 1.0000 experiment
GIFOOFNF_00084 Mercury (Hg) 85.4 1.6e-266 1 548 1.0237 1.0000 experiment
GIFOOFNF_00085 Mercury (Hg) 100 3.3e-40 1 81 1.0000 1.0000 experiment
GIFOOFNF_00086 Mercury (Hg) 93.3 4.9e-40 1 90 0.9890 0.9890 experiment
GIFOOFNF_00087 Mercury (Hg) 94 4.1e-60 1 116 1.0000 1.0000 experiment
GIFOOFNF_00088 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 94.4 1.5e-75 1 144 1.0000 1.0000 experiment
GIFOOFNF_00014 Mercury (Hg) 98.7 5.1e-39 1 78 1.0000 1.0000 prediction
GIFOOFNF_00015 Mercury (Hg) 100 3.1e-59 1 121 1.0000 1.0000 prediction
GIFOOFNF_00016 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 99.8 0 1 561 1.0000 1.0000 prediction
GIFOOFNF_00017 Mercury (Hg) 80.9 3.2e-60 1 141 1.0000 1.0000 prediction
GIFOOFNF_00018 Mercury (Hg) 94.5 9.1e-40 1 91 1.0000 1.0000 prediction
GIFOOFNF_00019 Mercury (Hg) 99.2 2.5e-67 1 131 1.0000 1.0000 prediction
GIFOOFNF_00020 Arsenic (As) 100 1.9e-61 1 117 1.0000 1.0000 prediction
GIFOOFNF_00021 Arsenic (As) 100 4.4e-66 1 120 1.0000 1.0000 prediction
GIFOOFNF_00022 Arsenic (As), Antimony (Sb) 100 0 1 583 1.0000 1.0000 prediction
GIFOOFNF_00023 Arsenic (As), Antimony (Sb) 99.8 6.9e-231 1 428 0.9977 1.0000 prediction
GIFOOFNF_00024 Arsenic (As) 100 1.6e-75 1 141 1.0000 1.0000 prediction
GIFOOFNF_00082 Mercury (Hg) 100 6.6e-39 1 78 1.0000 1.0000 prediction
GIFOOFNF_00083 Mercury (Hg) 100 7.3e-61 1 121 1.0000 1.0000 prediction
GIFOOFNF_00084 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 100 1.7e-306 1 548 1.0000 1.0000 prediction
GIFOOFNF_00085 Mercury (Hg) 100 7.6e-38 1 81 1.0000 1.0000 prediction
GIFOOFNF_00086 Mercury (Hg) 100 8.2e-41 1 91 1.0000 0.9785 prediction
GIFOOFNF_00087 Mercury (Hg) 100 7e-61 1 116 1.0000 1.0000 prediction
GIFOOFNF_00088 Mercury (Hg) 100 6.6e-77 1 144 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






        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
GIFOOFNF_00034 AWF77827.1|GT4 100 5.21e-274 1 370 1 1
GIFOOFNF_00035 AWF77828.1|GT4 100 1.34e-295 1 403 1 1
GIFOOFNF_00036 AWF77829.1|GT2 100 1.11e-236 1 329 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
GIFOOFNF_00007 2.A.33.1.2 97.1 4e-204 1 382 0.9974 0.9974 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.33 The NhaA Na+:H+ Antiporter (NhaA) Family
GIFOOFNF_00014 1.A.72.5.1 80.8 7.5e-33 1 78 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
GIFOOFNF_00018 1.A.72.3.1 85.7 1.7e-36 1 91 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
GIFOOFNF_00019 1.A.72.3.1 93 6.2e-56 17 131 0.8779 1.2637 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
GIFOOFNF_00022 3.A.4.1.1 85.5 1.5e-282 1 581 0.9966 1.3543 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.4 The Arsenite-Antimonite (ArsAB) Efflux Family
GIFOOFNF_00023 3.A.4.1.1 93.9 1.5e-220 1 429 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.4 The Arsenite-Antimonite (ArsAB) Efflux Family
GIFOOFNF_00082 1.A.72.5.1 78.2 1.1e-31 1 78 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
GIFOOFNF_00085 1.A.72.1.1 100 1.2e-38 1 81 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
GIFOOFNF_00086 1.A.72.3.1 93.3 3.1e-38 1 90 0.9890 0.9890 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
GIFOOFNF_00087 1.A.72.3.1 93.1 1.1e-56 1 116 1.0000 1.2747 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily