Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1451
  Reference Plasmid   NZ_PP261912.1
  Reference Plasmid Size   71206
  Reference Plasmid GC Content   0.46
  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
M0211051 JNJPONKL_00015 11632 4 Gut 0.50 protein_coding missense_variant MODERATE 200G>T Gly67Val
M0211052 JNJPONKL_00016 11957 4 Gut 0.50 protein_coding synonymous_variant LOW 72C>G Pro24Pro
M0211053 JNJPONKL_00011 12369 4 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4116T>G None
M0211054 JNJPONKL_00001 538 3 Gut 0.38 protein_coding upstream_gene_variant MODIFIER -428T>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
JNJPONKL_00010 VFG034574 Dispersin 94.8 4e-60 1 116 1.0 1 Others dispersin experiment
JNJPONKL_00040 VFG035902 Dispersin 95.2 1.7e-190 17 392 0.9592 1 Others permease AatP experiment
JNJPONKL_00041 VFG035909 Dispersin 93.4 2.1e-215 1 412 1.0 1 Others outer membrane protein AatA experiment
JNJPONKL_00042 VFG035916 Dispersin 94.8 3.6e-107 1 212 1.0 0.7766 Others AatB experiment
JNJPONKL_00043 VFG035923 Dispersin 97.1 1.3e-109 1 209 1.0 1 Others ATP-binding protein AatC experiment
JNJPONKL_00044 VFG035929 Dispersin 89.6 1e-206 1 402 1.0 0.995 Others AatD experiment
JNJPONKL_00010 VFG034574 Dispersin 94.8 3e-59 1 116 1.0 1 Others dispersin prediction
JNJPONKL_00018 VFG013084 MsbB2 96.2 2.9e-181 1 314 1.0 1 Others lauroyl-Kdo(2)-lipid IV(A) myristoyltransferase prediction
JNJPONKL_00019 VFG020186 VirK 99.1 3.2e-188 1 316 1.0 1 Others virulence factor VirK prediction
JNJPONKL_00024 VFG036086 AggR 97 4e-139 1 265 1.0 1 Regulation aggregative adherence transcriptional regulator AggR prediction
JNJPONKL_00033 VFG042451 Hda adhesin 100 3.6e-134 26 252 0.9008 1 Adherence HdaD prediction
JNJPONKL_00034 VFG042452 Hda adhesin 99.8 0 1 800 1.0 0.9501 Adherence HdaC prediction
JNJPONKL_00035 VFG042453 Hda adhesin 100 5e-80 1 142 1.0 1 Adherence HdaB prediction
JNJPONKL_00036 VFG042454 Hda adhesin 99.4 1.5e-94 1 170 1.0 1 Adherence HdaA prediction
JNJPONKL_00040 VFG035902 Dispersin 95.2 1.2e-189 17 392 0.9592 1 Others permease AatP prediction
JNJPONKL_00041 VFG035909 Dispersin 93.4 1.5e-214 1 412 1.0 1 Others outer membrane protein AatA prediction
JNJPONKL_00042 VFG035915 Dispersin 96.7 9.9e-109 1 212 1.0 0.7766 Others AatB prediction
JNJPONKL_00043 VFG035919 Dispersin 98.6 5.2e-110 1 209 1.0 1 Others ATP-binding protein AatC prediction
JNJPONKL_00044 VFG035925 Dispersin 91.1 3.6e-208 1 402 1.0 0.9975 Others AatD 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
JNJPONKL_00029 ARO:3002683 100 3.08e-171 1 219 1.0000 1.0000 phenicol antibiotic chloramphenicol acetyltransferase (CAT) 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
JNJPONKL_00020 PHI:10400 Sfgtr4 (ORF186) 96.1 6.6e-209 1 362 1.0000 1.0000 primates shigellosis putative lipopolysaccharides (LPS) glycosyltransferase (Gtr) reduced virulence
JNJPONKL_00024 PHI:9507 aggR 97 1.4e-139 1 265 1.0000 1.0000 moths diarrhea transcriptional activator 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
JNJPONKL_00020 CBG27776.1|GT4 100 3.79e-272 1 362 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