Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C287
  Reference Plasmid   NC_008460.1
  Reference Plasmid Size   120730
  Reference Plasmid GC Content   0.49
  Reference Plasmid Mobility Type   conjugative





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
M0151293 AKNPKNPE_00003 7013 13 Gut 0.62 protein_coding upstream_gene_variant MODIFIER -3886A>C None
M0151294 AKNPKNPE_00009 7826 3 Gut 0.14 protein_coding synonymous_variant LOW 276T>C Tyr92Tyr
M0151295 AKNPKNPE_00009 7833 3 Gut 0.14 protein_coding stop_gained HIGH 283G>T Gly95*
M0151296 AKNPKNPE_00009 7835 3 Gut 0.14 protein_coding synonymous_variant LOW 285A>G Gly95Gly
M0151297 AKNPKNPE_00009 7838 3 Gut 0.14 protein_coding stop_gained HIGH 288G>A Trp96*
M0151298 AKNPKNPE_00009 7841 3 Gut 0.14 protein_coding synonymous_variant LOW 291G>A Arg97Arg
M0151299 AKNPKNPE_00009 7853 3 Gut 0.14 protein_coding synonymous_variant LOW 303C>T Ser101Ser
M0151300 AKNPKNPE_00009 7880 3 Gut 0.14 protein_coding synonymous_variant LOW 330G>A Ala110Ala
M0151301 AKNPKNPE_00009 7890 3 Gut 0.14 protein_coding missense_variant MODERATE 340T>G Ser114Ala
M0151302 AKNPKNPE_00009 7901 3 Gut 0.14 protein_coding synonymous_variant LOW 351A>C Ala117Ala
M0151303 AKNPKNPE_00009 7910 3 Gut 0.14 protein_coding synonymous_variant LOW 360T>G Pro120Pro
M0151304 AKNPKNPE_00009 7913 3 Gut 0.14 protein_coding synonymous_variant LOW 363C>T Ser121Ser
M0151305 AKNPKNPE_00009 7966 3 Gut 0.14 protein_coding missense_variant MODERATE 416C>A Thr139Lys
M0151306 AKNPKNPE_00009 7969 3 Gut 0.14 protein_coding missense_variant MODERATE 419A>C Glu140Ala
M0151307 AKNPKNPE_00138 114484 7 Gut 0.33 protein_coding missense_variant MODERATE 173T>G Ile58Arg
M0151308 AKNPKNPE_00007 7264 4 Gut 0.19 protein_coding synonymous_variant LOW 186G>A Glu62Glu
M0151309 AKNPKNPE_00007 7280 4 Gut 0.19 protein_coding missense_variant MODERATE 202T>C Cys68Arg
M0151310 AKNPKNPE_00003 7007 3 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -3880G>A None
M0151311 AKNPKNPE_00008 7407 3 Gut 0.14 protein_coding synonymous_variant LOW 54T>C Ser18Ser






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
AKNPKNPE_00026 VFG035902 Dispersin 95.2 1.7e-190 17 392 0.9592 1 Others permease AatP experiment
AKNPKNPE_00027 VFG035909 Dispersin 93.4 6e-215 1 412 1.0 1 Others outer membrane protein AatA experiment
AKNPKNPE_00028 VFG035916 Dispersin 95.3 1.2e-107 1 212 1.0 0.7766 Others AatB experiment
AKNPKNPE_00029 VFG035923 Dispersin 97.1 1.3e-109 1 209 1.0 1 Others ATP-binding protein AatC experiment
AKNPKNPE_00030 VFG035929 Dispersin 88.9 1.2e-204 1 402 1.0 0.995 Others AatD experiment
AKNPKNPE_00130 VFG034574 Dispersin 94.8 4e-60 1 116 1.0 1 Others dispersin experiment
AKNPKNPE_00001 VFG013084 MsbB2 96.1 3.3e-160 1 279 1.0 0.8885 Others lauroyl-Kdo(2)-lipid IV(A) myristoyltransferase prediction
AKNPKNPE_00002 VFG020186 VirK 99.3 1.3e-167 1 282 1.0 0.8924 Others virulence factor VirK prediction
AKNPKNPE_00006 VFG036086 AggR 97 4e-139 1 265 1.0 1 Regulation aggregative adherence transcriptional regulator AggR prediction
AKNPKNPE_00012 VFG033809 Vat 99.8 0 1 1364 1.0 1 Effector delivery system vacuolating autotransporter toxin prediction
AKNPKNPE_00016 VFG042451 Hda adhesin 99.6 1.4e-133 26 252 0.9008 1 Adherence HdaD prediction
AKNPKNPE_00017 VFG042452 Hda adhesin 99.5 0 1 800 1.0 0.9501 Adherence HdaC prediction
AKNPKNPE_00018 VFG042453 Hda adhesin 98.6 2.1e-78 1 142 1.0 1 Adherence HdaB prediction
AKNPKNPE_00019 VFG042454 Hda adhesin 90.6 1.7e-87 1 170 1.0 1 Adherence HdaA prediction
AKNPKNPE_00026 VFG035902 Dispersin 95.2 1.2e-189 17 392 0.9592 1 Others permease AatP prediction
AKNPKNPE_00027 VFG035909 Dispersin 93.4 4.5e-214 1 412 1.0 1 Others outer membrane protein AatA prediction
AKNPKNPE_00028 VFG035915 Dispersin 97.2 3.4e-109 1 212 1.0 0.7766 Others AatB prediction
AKNPKNPE_00029 VFG035919 Dispersin 98.6 5.2e-110 1 209 1.0 1 Others ATP-binding protein AatC prediction
AKNPKNPE_00030 VFG035925 Dispersin 90.3 4.4e-206 1 402 1.0 0.9975 Others AatD prediction
AKNPKNPE_00130 VFG034574 Dispersin 94.8 3e-59 1 116 1.0 1 Others dispersin 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
AKNPKNPE_00140 ARO:3002644 100 1.78e-197 1 264 1.0000 1.0000 aminoglycoside antibiotic APH(3') 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
AKNPKNPE_00003 PHI:10400 Sfgtr4 (ORF186) 96.1 6.6e-209 1 362 1.0000 1.0000 primates shigellosis putative lipopolysaccharides (LPS) glycosyltransferase (Gtr) reduced virulence
AKNPKNPE_00006 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
AKNPKNPE_00003 CBG27776.1|GT4 100 3.79e-272 1 362 1 1
AKNPKNPE_00079 BAF33961.1|GH23 100 2.02e-123 1 169 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