Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C622
  Reference Plasmid   NZ_CP037947.1
  Reference Plasmid Size   73152
  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
M0169888 PHECCOGN_00081 66638 3 Gut 0.15 protein_coding synonymous_variant LOW 4395G>T Thr1465Thr
M0169889 PHECCOGN_00081 66656 3 Gut 0.15 protein_coding synonymous_variant LOW 4413A>G Glu1471Glu
M0169890 PHECCOGN_00081 66761 3 Gut 0.15 protein_coding synonymous_variant LOW 4518T>G Leu1506Leu
M0169891 PHECCOGN_00081 66762 3 Gut 0.15 protein_coding missense_variant MODERATE 4519G>T Ala1507Ser
M0169892 PHECCOGN_00081 66794 3 Gut 0.15 protein_coding synonymous_variant LOW 4551A>T Ala1517Ala
M0169893 PHECCOGN_00081 66797 3 Gut 0.15 protein_coding synonymous_variant LOW 4554C>G Pro1518Pro
M0169894 PHECCOGN_00081 66800 3 Gut 0.15 protein_coding synonymous_variant LOW 4557G>A Gly1519Gly
M0169895 PHECCOGN_00081 66803 3 Gut 0.15 protein_coding synonymous_variant LOW 4560C>T Arg1520Arg
M0169896 PHECCOGN_00081 66812 3 Gut 0.15 protein_coding synonymous_variant LOW 4569G>A Pro1523Pro
M0169897 PHECCOGN_00081 66850 3 Gut 0.15 protein_coding missense_variant MODERATE 4607G>C Gly1536Ala
M0169898 PHECCOGN_00081 66853 3 Gut 0.15 protein_coding missense_variant MODERATE 4610A>G Lys1537Arg
M0169899 PHECCOGN_00081 66857 3 Gut 0.15 protein_coding synonymous_variant LOW 4614A>C Ser1538Ser
M0169900 PHECCOGN_00081 66860 3 Gut 0.15 protein_coding synonymous_variant LOW 4617A>C Ala1539Ala
M0169901 PHECCOGN_00081 67218 3 Gut 0.15 protein_coding missense_variant MODERATE 4975T>C Cys1659Arg
M0169902 PHECCOGN_00081 67313 3 Gut 0.15 protein_coding missense_variant MODERATE 5070G>T Glu1690Asp
M0169903 PHECCOGN_00082 67581 3 Gut 0.15 protein_coding synonymous_variant LOW 48C>A Ala16Ala
M0169904 PHECCOGN_00082 67605 3 Gut 0.15 protein_coding synonymous_variant LOW 72G>A Ser24Ser
M0169905 PHECCOGN_00082 67608 3 Gut 0.15 protein_coding missense_variant MODERATE 75G>T Leu25Phe
M0169906 PHECCOGN_00082 67741 3 Gut 0.15 protein_coding synonymous_variant LOW 208C>T Leu70Leu






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
PHECCOGN_00046 VFG001445 TraJ 100 6e-116 1 200 0.8772 0.995 Invasion unknown protein experiment
PHECCOGN_00046 VFG001445 TraJ 100 4.5e-115 1 200 0.8772 0.995 Invasion unknown protein 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
PHECCOGN_00005 ARO:3002660 99.3 4.37e-205 1 278 1.0000 1.0000 aminoglycoside antibiotic APH(6) antibiotic inactivation
PHECCOGN_00006 ARO:3002639 99.6 5.98e-202 1 267 1.0000 1.0000 aminoglycoside antibiotic APH(3'') antibiotic inactivation
PHECCOGN_00007 ARO:3000412 100 4.11e-186 1 271 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
PHECCOGN_00011 ARO:3000873 100 5.12e-208 1 286 1.0000 1.0000 monobactam TEM beta-lactamase antibiotic inactivation
PHECCOGN_00013 ARO:3002863 100 3.34e-121 1 169 1.0000 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
PHECCOGN_00030 ARO:3000166 99.3 3.06e-283 1 401 1.0000 1.0000 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
PHECCOGN_00031 ARO:3003479 100 1.46e-152 1 207 1.0000 0.9952 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump 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






        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
PHECCOGN_00044 QBO43050.1|GH23 100 3.33e-156 1 215 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
PHECCOGN_00030 2.A.1.2.68 99.8 6.4e-221 1 401 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)