Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C355
  Reference Plasmid   NZ_AP018397.1
  Reference Plasmid Size   201884
  Reference Plasmid GC Content   0.52
  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
M0153452 IEBAHDHJ_00138 115753 3 Gut 0.15 protein_coding missense_variant MODERATE 383A>G Glu128Gly
M0153453 IEBAHDHJ_00149 124740 4 Gut 0.20 protein_coding synonymous_variant LOW 438G>A Lys146Lys
M0153454 IEBAHDHJ_00149 125109 3 Gut 0.15 protein_coding synonymous_variant LOW 807T>C Asn269Asn
M0153455 IEBAHDHJ_00149 125160 3 Gut 0.15 protein_coding synonymous_variant LOW 858G>A Pro286Pro
M0153456 IEBAHDHJ_00149 125505 3 Gut 0.15 protein_coding synonymous_variant LOW 1203T>G Val401Val
M0153457 IEBAHDHJ_00149 125532 3 Gut 0.15 protein_coding missense_variant MODERATE 1230C>A Asn410Lys
M0153458 IEBAHDHJ_00149 125547 3 Gut 0.15 protein_coding synonymous_variant LOW 1245C>T Asp415Asp
M0153459 IEBAHDHJ_00149 125766 3 Gut 0.15 protein_coding synonymous_variant LOW 1464T>A Ala488Ala
M0153460 IEBAHDHJ_00152 134715 4 Gut 0.20 protein_coding upstream_gene_variant MODIFIER -3645T>A 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
IEBAHDHJ_00069 VFG043568 OmpD 77 2e-160 8 370 0.9811 1.0028 Adherence phosphoporin PhoE 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
IEBAHDHJ_00039 Arsenic (As), Antimony (Sb), Bismuth (Bi) 100 8.1e-64 1 117 1.0000 1.0000 experiment
IEBAHDHJ_00040 Arsenic (As), Antimony (Sb) 98.3 1.9e-67 20 139 0.8633 1.0000 experiment
IEBAHDHJ_00041 Arsenic (As), Antimony (Sb) 99 0 1 583 1.0000 1.0000 experiment
IEBAHDHJ_00042 Arsenic (As), Antimony (Sb) 99.3 1.7e-231 1 429 1.0000 1.0000 experiment
IEBAHDHJ_00043 Arsenic (As), Antimony (Sb) 99.3 3.5e-77 1 141 1.0000 1.0000 experiment
IEBAHDHJ_00051 Magnesium (Mg), Cobalt (Co), Nickel (Ni), Manganese (Mn) 99.4 5.9e-178 1 316 1.0000 1.0000 experiment
IEBAHDHJ_00069 Methyl Viologen [class: Paraquat] 77 4.1e-162 8 370 1.0000 1.0221 experiment
IEBAHDHJ_00039 Arsenic (As) 100 1.9e-61 1 117 1.0000 1.0000 prediction
IEBAHDHJ_00040 Arsenic (As) 100 5.1e-66 20 139 0.8633 1.0000 prediction
IEBAHDHJ_00041 Arsenic (As), Antimony (Sb) 100 0 1 583 1.0000 1.0000 prediction
IEBAHDHJ_00042 Arsenic (As), Antimony (Sb) 100 6.9e-231 1 429 1.0000 1.0000 prediction
IEBAHDHJ_00043 Arsenic (As) 100 1.6e-75 1 141 1.0000 1.0000 prediction
IEBAHDHJ_00051 Magnesium (Mg), Cobalt (Co), Nickel (Ni), Manganese (Mn) 100 2.1e-176 1 316 1.0000 1.0000 prediction
IEBAHDHJ_00069 Methyl Viologen [class: Paraquat] 95.7 4.3e-205 1 370 1.0054 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
IEBAHDHJ_00051 PHI:2479 corA 88 1.7e-160 1 316 1.0000 1.0000 eudicots soft rot magnesium/nickel/cobalt transporter reduced virulence
IEBAHDHJ_00069 PHI:123435 ompD 77 6.9e-161 8 370 0.9811 0.9890 rodents salmonellosis porin OmpD unaffected pathogenicity
IEBAHDHJ_00151 PHI:3317 hsdR 73 0 1 1038 1.0000 1.0000 rodents Glasser's disease involved in pathogenicity 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
IEBAHDHJ_00021 AUV34601.1|GH32 100 0 1 452 1 0.97





        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
IEBAHDHJ_00022 4.A.1.2.1 97.4 5.9e-247 1 456 1.0000 1.0000 4 Group Translocators 4.A Phosphotransfer-driven Group Translocators (PTS) 4.A.1 The PTS Glucose-Glucoside (Glc) Family
IEBAHDHJ_00023 1.B.3.1.2 89.7 9.8e-267 1 505 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.3 The Sugar Porin (SP) Family
IEBAHDHJ_00041 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
IEBAHDHJ_00042 3.A.4.1.1 93.7 1.3e-219 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
IEBAHDHJ_00051 1.A.35.1.1 99.4 2.2e-176 1 316 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.35 The CorA Metal Ion Transporter (MIT) Family
IEBAHDHJ_00069 1.B.1.1.4 80.9 4.2e-174 1 370 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.1 The General Bacterial Porin (GBP) Family
IEBAHDHJ_00074 1.E.4.1.1 100 1.1e-51 1 106 0.1386 0.9725 1 Channels/Pores 1.E Holins 1.E.4 The LydA Holin (LydA Holin) Family
IEBAHDHJ_00075 1.E.4.1.2 97.8 4.1e-46 1 93 1.0000 1.0000 1 Channels/Pores 1.E Holins 1.E.4 The LydA Holin (LydA Holin) Family
IEBAHDHJ_00114 1.E.53.1.7 81.7 3e-28 1 71 1.0000 1.0000 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family