Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C49
  Reference Plasmid   AP031277.1
  Reference Plasmid Size   253975
  Reference Plasmid GC Content   0.36
  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
M0143091 OJHDIPJJ_00091 87485 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4866A>C None
M0143092 OJHDIPJJ_00091 87491 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4872A>G None
M0143093 OJHDIPJJ_00100 87543 3 Gut 1.00 protein_coding synonymous_variant LOW 3135A>G Glu1045Glu
M0143094 OJHDIPJJ_00100 87615 3 Gut 1.00 protein_coding synonymous_variant LOW 3063A>G Lys1021Lys
M0143095 OJHDIPJJ_00100 87702 3 Gut 1.00 protein_coding missense_variant MODERATE 2976G>A Met992Ile
M0143096 OJHDIPJJ_00100 87704 3 Gut 1.00 protein_coding missense_variant MODERATE 2974A>C Met992Leu
M0143097 OJHDIPJJ_00100 87763 3 Gut 1.00 protein_coding missense_variant MODERATE 2915C>T Ala972Val
M0143098 OJHDIPJJ_00100 87776 3 Gut 1.00 protein_coding missense_variant MODERATE 2902A>G Asn968Asp
M0143099 OJHDIPJJ_00100 87783 3 Gut 1.00 protein_coding synonymous_variant LOW 2895A>G Ala965Ala






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






        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
OJHDIPJJ_00221 ARO:3002597 99.8 0 1 479 1.0000 1.0000 aminoglycoside antibiotic aminoglycoside bifunctional resistance protein antibiotic inactivation






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
OJHDIPJJ_00040 PHI:5205 HMPREF0351_10118 (WxL locusC) 99.7 8.4e-226 1 392 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
OJHDIPJJ_00088 PHI:5205 HMPREF0351_10118 (WxL locusC) 71.8 1.2e-168 1 389 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
OJHDIPJJ_00112 PHI:5205 HMPREF0351_10118 (WxL locusC) 100 1e-226 1 392 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
OJHDIPJJ_00187 PHI:5205 HMPREF0351_10118 (WxL locusC) 77.6 6.3e-181 1 392 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
OJHDIPJJ_00218 PHI:5205 HMPREF0351_10118 (WxL locusC) 70.9 1.8e-153 1 367 0.9839 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
OJHDIPJJ_00224 PHI:5205 HMPREF0351_10118 (WxL locusC) 99.7 8.4e-226 1 392 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis 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
OJHDIPJJ_00006 UOO44422.1|GH1 70.3 5.95e-255 3 463 0.9746 0.985
OJHDIPJJ_00030 QMX47902.1|GH32 100 0 1 475 1 1
OJHDIPJJ_00055 AVJ42462.1|GH1 100 0 1 468 1 1
OJHDIPJJ_00060 CCO10203.2|GH1 87.9 8.11e-247 1 388 0.9949 0.9949
OJHDIPJJ_00069 AOM14759.1|GH13_18 100 0 1 486 1 1
OJHDIPJJ_00070 QQJ93880.1|GH13_31 100 1.79e-306 1 406 1 1
OJHDIPJJ_00071 QTO65065.1|GH36 100 0 1 727 1 1
OJHDIPJJ_00075 AWV59846.1|GH4 100 0 1 436 1 1
OJHDIPJJ_00086 CCO10203.2|GH1 87.9 8.11e-247 1 388 0.9949 0.9949
OJHDIPJJ_00087 CCO10203.2|GH1 87.9 8.11e-247 1 388 0.9949 0.9949
OJHDIPJJ_00124 QTO59404.1|GH1 100 0 17 484 0.9669 1
OJHDIPJJ_00139 APV52892.1|GH32 100 0 1 490 1 1
OJHDIPJJ_00276 QOJ75557.1|GH36 100 0 1 749 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
OJHDIPJJ_00054 4.A.3.1.1 71.7 4.4e-239 1 568 1.0000 0.9965 4 Group Translocators 4.A Phosphotransfer-driven Group Translocators (PTS) 4.A.3 The PTS Lactose-N,N'-Diacetylchitobiose-β-glucoside (Lac) Family
OJHDIPJJ_00072 3.A.1.1.28 75.3 5.4e-118 5 276 0.9855 0.7294 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
OJHDIPJJ_00073 3.A.1.1.28 74.1 2.8e-125 1 290 1.0000 0.7692 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily