Clickable version of the Functional Landscape of the Paranome

click me!

About this figure

A visualisation of the preferentially retained duplicated genes according to their functional classes

  • [C] Energy production and conversion
  • [D] Cell cycle control, cell division, chromosome partitioning
  • [E] Amino acid transport and metabolism
  • [F] Nucleotide transport and metabolism
  • [G] Carbohydrate transport and metabolism
  • [H] Coenzyme transport and metabolism
  • [I] Lipid transport and metabolism
  • [J] Translation, ribosomal structure and biogenesis
  • [K] Transcription
  • [L] Replication, recombination and repair
  • [M] Cell wall/membrane/envelope biogenesis
  • [N] Cell motility
  • [O] Posttranslational modification, protein turnover, chaperones
  • [P] Inorganic ion transport and metabolism
  • [Q] Secondary metabolites biosynthesis, transport and catabolism
  • [R] General function prediction only
  • [S] Function unknown
  • [T] Signal transduction mechanisms
  • [U] Intracellular trafficking, secretion, and vesicular transport
  • [V] Defense mechanisms
  • [X] non of the others

How it was made

For those genomes for which a COG classification is available at NCBI), the classification was transferred to our database of the bacterial proteome on a gene by gene basis. Further, the proteome of each genome was subdivided in 2 groups, i.e. paralogous genes and singel copy genes (based on the constructed gene families), and per group a distribution over the different functional categories was calculated in terms of percentage. The Functional Landscape is than defined as the difference between the functional distribution of the paranome and the functional distribution of the single copy genes. As a result one can deduce the functional classes that have relatively more (yellow to red), or less (gradient of blue) paralogs compared to single copy genes. The genomes were listed according to the ordering of organisms in the phylogenetic tree of Fig. 1 (in the manuscript), whereas the functional classes have been ordered according to relative contribution.
By clicking a specific class:organism combination one can obtain detailed info on: (i) an overview of the number of genes per COG, (ii) a list of paralogous genes contained in the specific class:organism combination, and (iii) a list of phage- and/or transposon-related genes that correspond to this class:organism but were excluded from the analysis.

VIB / UGent
Bioinformatics & Evolutionary Genomics
Technologiepark 927
B-9052 Gent
+32 (0) 9 33 13807 (phone)
+32 (0) 9 33 13809 (fax)

Don't hesitate to contact the in case of problems with the website!