Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C263
  Reference Plasmid   LR962727.1
  Reference Plasmid Size   84625
  Reference Plasmid GC Content   0.35
  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
M0150186 CDDEPOLO_00056 51420 3 Gut 0.75 protein_coding missense_variant MODERATE 209A>T Asn70Ile
M0150187 CDDEPOLO_00056 51425 3 Gut 0.75 protein_coding synonymous_variant LOW 204C>T Val68Val
M0150188 CDDEPOLO_00056 51438 3 Gut 0.75 protein_coding missense_variant MODERATE 191A>C Asp64Ala
M0150189 CDDEPOLO_00056 51457 3 Gut 0.75 protein_coding missense_variant MODERATE 172A>G Asn58Asp
M0150190 CDDEPOLO_00056 51464 3 Gut 0.75 protein_coding synonymous_variant LOW 165T>C Asn55Asn
M0150191 CDDEPOLO_00056 51473 3 Gut 0.75 protein_coding synonymous_variant LOW 156C>T Ile52Ile
M0150192 CDDEPOLO_00056 51520 3 Gut 0.75 protein_coding missense_variant MODERATE 109A>G Lys37Glu
M0150193 CDDEPOLO_00056 51530 3 Gut 0.75 protein_coding synonymous_variant LOW 99T>C Tyr33Tyr
M0150194 CDDEPOLO_00056 51606 3 Gut 0.75 protein_coding missense_variant MODERATE 23A>C Lys8Thr
M0150195 CDDEPOLO_00056 51608 3 Gut 0.75 protein_coding synonymous_variant LOW 21G>T Pro7Pro
M0150196 CDDEPOLO_00056 51612 3 Gut 0.75 protein_coding missense_variant MODERATE 17G>A Arg6His
M0150197 CDDEPOLO_00054 51664 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -1605C>T None
M0150198 CDDEPOLO_00054 51668 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -1609T>A None
M0150199 CDDEPOLO_00057 51695 3 Gut 0.75 protein_coding synonymous_variant LOW 573A>G Val191Val
M0150200 CDDEPOLO_00057 51698 3 Gut 0.75 protein_coding synonymous_variant LOW 570A>T Ala190Ala
M0150201 CDDEPOLO_00057 51719 3 Gut 0.75 protein_coding synonymous_variant LOW 549T>C Thr183Thr
M0150202 CDDEPOLO_00057 51734 3 Gut 0.75 protein_coding synonymous_variant LOW 534C>T Arg178Arg
M0150203 CDDEPOLO_00057 51746 3 Gut 0.75 protein_coding synonymous_variant LOW 522G>A Arg174Arg
M0150204 CDDEPOLO_00057 51752 3 Gut 0.75 protein_coding synonymous_variant LOW 516A>G Ser172Ser
M0150205 CDDEPOLO_00057 51761 3 Gut 0.75 protein_coding synonymous_variant LOW 507C>T Asn169Asn
M0150206 CDDEPOLO_00057 52233 3 Gut 0.75 protein_coding missense_variant MODERATE 35T>C Val12Ala
M0150207 CDDEPOLO_00054 52426 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -2367G>T None
M0150208 CDDEPOLO_00054 52432 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -2373A>G None
M0150209 CDDEPOLO_00054 52543 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -2484G>T None
M0150210 CDDEPOLO_00054 52562 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -2503T>C None
M0150211 CDDEPOLO_00054 52666 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -2607A>T None
M0150212 CDDEPOLO_00058 52950 3 Gut 0.75 protein_coding missense_variant MODERATE 149A>G Asp50Gly
M0150213 CDDEPOLO_00059 54344 3 Gut 0.75 protein_coding synonymous_variant LOW 579A>G Ser193Ser
M0150214 CDDEPOLO_00060 55158 3 Gut 0.75 protein_coding missense_variant MODERATE 646G>A Glu216Lys
M0150215 CDDEPOLO_00060 55163 3 Gut 0.75 protein_coding missense_variant MODERATE 641A>G Asn214Ser
M0150216 CDDEPOLO_00060 55480 3 Gut 0.75 protein_coding synonymous_variant LOW 324A>C Ile108Ile






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
CDDEPOLO_00004 VFG002164 AS 97.3 0 1 1305 1.0 1 Adherence aggregation substance PrgB/Asc10 experiment
CDDEPOLO_00004 VFG002164 AS 97.3 0 1 1305 1.0 1 Adherence aggregation substance PrgB/Asc10 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
CDDEPOLO_00044 Copper (Cu) 99.3 8.2e-85 1 151 1.0000 1.0000 experiment
CDDEPOLO_00047 Copper (Cu) 100 1.4e-31 1 68 1.0000 1.0000 experiment
CDDEPOLO_00048 Copper (Cu) 99.9 0 1 710 1.0000 1.0000 experiment
CDDEPOLO_00036 Copper (Cu), Cobalt (Co) 97.9 3.6e-306 1 528 1.0000 1.0000 prediction
CDDEPOLO_00044 Copper (Cu) 100 5e-83 1 151 1.0000 1.0000 prediction
CDDEPOLO_00047 Copper (Cu) 100 3.2e-29 1 68 1.0000 1.0000 prediction
CDDEPOLO_00048 Copper (Cu) 100 0 1 710 1.0000 1.0000 prediction






        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






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






        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
CDDEPOLO_00022 3.A.7.19.1 99.3 0 1 609 1.0000 1.0856 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
CDDEPOLO_00023 3.A.7.19.1 99 0 1 719 1.0000 1.2816 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
CDDEPOLO_00026 3.A.7.19.1 86.8 1e-285 1 561 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
CDDEPOLO_00048 3.A.3.5.16 99.9 0 1 710 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.3 The P-type ATPase (P-ATPase) Superfamily