Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2865
  Reference Plasmid   DP1807004503_bin.5__NODE_104_length_13232_cov_4.669230
  Reference Plasmid Size   13232
  Reference Plasmid GC Content   0.59
  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
M0064490 JPIHCGKF_00003 362 6 Skin 0.21 protein_coding upstream_gene_variant MODIFIER -2202A>G None
M0064491 JPIHCGKF_00003 486 3 Skin 0.11 protein_coding upstream_gene_variant MODIFIER -2078G>A None
M0064492 JPIHCGKF_00002 2322 8 Skin 0.29 protein_coding synonymous_variant LOW 189A>G Gln63Gln
M0064493 JPIHCGKF_00003 3626 11 Skin 0.39 protein_coding missense_variant MODERATE 1063T>C Phe355Leu
M0064494 JPIHCGKF_00004 4789 12 Skin 0.43 protein_coding synonymous_variant LOW 426T>C Asn142Asn
M0064495 JPIHCGKF_00004 5097 12 Skin 0.43 protein_coding missense_variant MODERATE 734A>G His245Arg
M0064496 JPIHCGKF_00004 5265 21 Skin 0.75 protein_coding missense_variant MODERATE 902C>T Ala301Val
M0064497 JPIHCGKF_00004 5359 5 Skin 0.18 protein_coding synonymous_variant LOW 996C>T Asn332Asn
M0064498 JPIHCGKF_00004 6094 12 Skin 0.43 protein_coding synonymous_variant LOW 1731T>C Asp577Asp
M0064499 JPIHCGKF_00002 6496 14 Skin 0.50 protein_coding upstream_gene_variant MODIFIER -3986T>C None
M0064500 JPIHCGKF_00005 7185 27 Skin 0.96 protein_coding synonymous_variant LOW 573T>C Gly191Gly
M0064501 JPIHCGKF_00003 3274 3 Skin 0.11 protein_coding synonymous_variant LOW 711A>G Glu237Glu
M0064502 JPIHCGKF_00003 3313 3 Skin 0.11 protein_coding synonymous_variant LOW 750C>T Ser250Ser
M0064503 JPIHCGKF_00003 3317 3 Skin 0.11 protein_coding synonymous_variant LOW 754T>C Leu252Leu
M0064504 JPIHCGKF_00003 3322 3 Skin 0.11 protein_coding synonymous_variant LOW 759T>C Pro253Pro
M0064505 JPIHCGKF_00007 9844 7 Skin 0.25 protein_coding missense_variant MODERATE 1825T>C Ser609Pro
M0064506 JPIHCGKF_00001 4263 3 Skin 0.11 protein_coding upstream_gene_variant MODIFIER -3246G>A None
M0064507 JPIHCGKF_00001 4269 3 Skin 0.11 protein_coding upstream_gene_variant MODIFIER -3252C>T None
M0064508 JPIHCGKF_00001 4298 3 Skin 0.11 protein_coding upstream_gene_variant MODIFIER -3281A>G None
M0064509 JPIHCGKF_00001 4353 3 Skin 0.11 protein_coding upstream_gene_variant MODIFIER -3336T>C None
M0064510 JPIHCGKF_00001 4357 3 Skin 0.11 protein_coding upstream_gene_variant MODIFIER -3340C>T None
M0064511 JPIHCGKF_00004 4389 3 Skin 0.11 protein_coding missense_variant MODERATE 26A>G Asn9Ser
M0064512 JPIHCGKF_00004 4409 3 Skin 0.11 protein_coding synonymous_variant LOW 46C>T Leu16Leu
M0064513 JPIHCGKF_00004 4436 3 Skin 0.11 protein_coding missense_variant MODERATE 73A>G Thr25Ala
M0064514 JPIHCGKF_00004 4460 3 Skin 0.11 protein_coding missense_variant MODERATE 97C>T Leu33Phe
M0064515 JPIHCGKF_00004 4473 3 Skin 0.11 protein_coding missense_variant MODERATE 110C>T Thr37Ile
M0064516 JPIHCGKF_00004 4475 3 Skin 0.11 protein_coding missense_variant MODERATE 112T>C Ser38Pro
M0064517 JPIHCGKF_00004 4496 3 Skin 0.11 protein_coding missense_variant MODERATE 133T>C Phe45Leu
M0064518 JPIHCGKF_00004 4513 3 Skin 0.11 protein_coding synonymous_variant LOW 150A>C Leu50Leu






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
JPIHCGKF_00006 VFG046465 EF-Tu 70.8 2.6e-167 1 397 1.0 1.0076 Adherence elongation factor Tu experiment
JPIHCGKF_00006 VFG046458 EF-Tu 70.8 1.5e-166 1 397 1.0 1.0076 Adherence elongation factor Tu 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
JPIHCGKF_00006 ARO:3003361 79.1 1.88e-236 1 397 1.0000 1.0000 elfamycin antibiotic elfamycin resistant EF-Tu antibiotic target alteration






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
JPIHCGKF_00006 PHI:10282 tufA 71.3 5.3e-167 1 397 1.0000 1.0000 primates skin infection; food poisoning; respiratory disease elongation factor Tu increased virulence (hypervirulence)






        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





        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