Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C644
  Reference Plasmid   NZ_CP040895.1
  Reference Plasmid Size   94635
  Reference Plasmid GC Content   0.51
  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
M0096178 PFICCDGI_00049 48455 3 Skin 0.38 protein_coding upstream_gene_variant MODIFIER -2423G>C None
M0096179 PFICCDGI_00052 48539 3 Skin 0.38 protein_coding synonymous_variant LOW 42C>T Leu14Leu
M0096180 PFICCDGI_00052 48569 3 Skin 0.38 protein_coding synonymous_variant LOW 72C>T Arg24Arg
M0096181 PFICCDGI_00052 48596 3 Skin 0.38 protein_coding synonymous_variant LOW 99A>C Ser33Ser
M0096182 PFICCDGI_00052 48605 3 Skin 0.38 protein_coding synonymous_variant LOW 108C>T Thr36Thr
M0096183 PFICCDGI_00052 48608 3 Skin 0.38 protein_coding synonymous_variant LOW 111T>C Phe37Phe
M0096184 PFICCDGI_00052 48628 3 Skin 0.38 protein_coding missense_variant MODERATE 131A>T Tyr44Phe
M0096185 PFICCDGI_00052 48630 3 Skin 0.38 protein_coding missense_variant MODERATE 133G>A Gly45Ser
M0096186 PFICCDGI_00052 48632 3 Skin 0.38 protein_coding synonymous_variant LOW 135C>T Gly45Gly
M0096187 PFICCDGI_00052 48635 3 Skin 0.38 protein_coding synonymous_variant LOW 138T>C Gly46Gly
M0096188 PFICCDGI_00052 48641 3 Skin 0.38 protein_coding synonymous_variant LOW 144G>A Glu48Glu
M0096189 PFICCDGI_00052 48644 3 Skin 0.38 protein_coding synonymous_variant LOW 147G>T Val49Val
M0096190 PFICCDGI_00052 48647 3 Skin 0.38 protein_coding synonymous_variant LOW 150C>T Pro50Pro
M0096191 PFICCDGI_00052 48653 3 Skin 0.38 protein_coding synonymous_variant LOW 156T>G Val52Val
M0096192 PFICCDGI_00053 48850 3 Skin 0.38 protein_coding synonymous_variant LOW 57T>C Ser19Ser
M0096193 PFICCDGI_00053 48861 3 Skin 0.38 protein_coding missense_variant MODERATE 68G>A Cys23Tyr
M0096194 PFICCDGI_00053 48897 3 Skin 0.38 protein_coding missense_variant MODERATE 104T>A Leu35His
M0096195 PFICCDGI_00053 48907 3 Skin 0.38 protein_coding synonymous_variant LOW 114G>T Gly38Gly
M0096196 PFICCDGI_00053 48987 3 Skin 0.38 protein_coding missense_variant MODERATE 194G>A Arg65His
M0096197 PFICCDGI_00053 49076 3 Skin 0.38 protein_coding synonymous_variant LOW 283C>A Arg95Arg
M0096198 PFICCDGI_00053 49153 3 Skin 0.38 protein_coding synonymous_variant LOW 360C>T Gly120Gly
M0096199 PFICCDGI_00053 49207 3 Skin 0.38 protein_coding synonymous_variant LOW 414G>A Thr138Thr
M0096200 PFICCDGI_00053 49214 3 Skin 0.38 protein_coding missense_variant MODERATE 421A>G Thr141Ala
M0096201 PFICCDGI_00053 49306 3 Skin 0.38 protein_coding synonymous_variant LOW 513A>G Gln171Gln
M0096202 PFICCDGI_00053 49363 3 Skin 0.38 protein_coding synonymous_variant LOW 570A>G Glu190Glu
M0096203 PFICCDGI_00053 49369 3 Skin 0.38 protein_coding synonymous_variant LOW 576T>G Arg192Arg
M0096204 PFICCDGI_00053 49373 3 Skin 0.38 protein_coding missense_variant MODERATE 580G>A Val194Ile
M0096205 PFICCDGI_00053 49392 3 Skin 0.38 protein_coding missense_variant MODERATE 599C>T Thr200Met
M0096206 PFICCDGI_00053 49507 3 Skin 0.38 protein_coding synonymous_variant LOW 714C>T Asp238Asp
M0096207 PFICCDGI_00049 49623 3 Skin 0.38 protein_coding upstream_gene_variant MODIFIER -3591A>T 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







        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
PFICCDGI_00050 ARO:3002195 100 4.7e-184 1 246 1.0000 1.0000 carbapenem IMP beta-lactamase antibiotic inactivation
PFICCDGI_00082 ARO:3002790 100 1.11e-111 1 218 1.0000 1.0000 fluoroquinolone antibiotic quinolone resistance protein (qnr) antibiotic target protection






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
PFICCDGI_00024 PHI:10387 SEN1538 91.7 1.9e-23 1 60 0.9836 1.0000 rodents salmonellosis conserved hypothetical protein reduced virulence
PFICCDGI_00049 PHI:9804 int 97.3 1.1e-13 1 37 0.1160 1.0000 rodents gastroenteritis integrase 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
PFICCDGI_00065 QDX15342.1|GH23 100 6.86e-168 1 244 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
PFICCDGI_00069 3.A.7.6.1 99 0 276 866 0.6824 1.7855 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
PFICCDGI_00070 3.A.7.6.1 85.7 2.1e-102 1 237 1.0000 0.7160 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
PFICCDGI_00072 3.A.7.6.1 92.2 4.3e-165 1 346 1.0000 1.0453 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
PFICCDGI_00073 3.A.7.6.1 98.3 1.1e-127 1 232 1.0000 0.7009 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
PFICCDGI_00074 3.A.7.6.1 98.6 3.4e-163 1 294 1.0000 0.8882 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
PFICCDGI_00075 3.A.7.6.1 97.7 1.5e-206 1 386 1.0000 1.1662 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
PFICCDGI_00076 3.A.7.6.1 99.7 3.5e-188 1 331 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family