HumanPRENbase
Database of Prenylated Human
Proteins and their Orthologues

Protein CaaX Farnesylation, CaaX Geranylgeranylation and Rab Geranylgeranylation


List only  CLUSTERS  with the following features:
 
 Modification Status:
KNOWN
(experimentally verified
cluster members)
 
LIKELY
(experimentally verified
homologues)
 
NEW
(no clear experimentally
verified homologues)
 
OUT-OF-CONTEXT 
     
 Minimum
 clustersize:


 Modifying Enzyme:
FT 
GGT1 
GGT2 
  exclude allow require
 
 Eukaryotic selection:  (overruled by kingdom selection)
Mammalia
Aves
Amphibia
Ray-finned Fishes
Insecta
Nematoda
Fungi
Plants
Other
exclude allow require

 Kingdoms of Life:
Viruses
Eukaryota
(fine-tuning on the right)
Synthetic
  exclude allow require

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List only  SEQUENCES  with the following features:
 
 Modifying Enzyme:
FT 
GGT1 
GGT2 
exclude allow require
 
 Eukaryotic selection:
Mammalia
Aves
Amphibia
Ray-finned Fishes
Insecta
Nematoda
Fungi
Plants
Other
exclude include
 NON-Eukaryotic 
 Selection:
Viruses
Synthetic
  exclude include
Overrule above TAX selection and only list HUMAN sequences
 Rank results by:
size of full cluster
size of cluster after selection
evOluation of full cluster
evOluation of cluster after selection
phylogenic complexity of full cluster
phylogenic complexity of cluster after selection




Want to check your own sequences for prenylation? Click here for the Prenylation Prediction Suite (PrePS) submission form.

Paste querycode below to recover a previous query:

(Selections in form above will be ignored if valid querycode is entered)

HumanPRENbase is a derivate of PRENbase with focus on human prenylated proteins. In PRENbase, paralogous proteins are clustered together in their respective larger family when they are highly similar to each other. This happens, for example, with the different Ras proteins H-Ras, K-Ras, N-ras, etc. Paralogues can nevertheless have different functions or often similar but more specialized roles. Especially in the light of the importance of prenylation of several members of the Ras, Rab and Rho GTPase families, we sought a solution to investigate the prenylation status of individual human proteins rather than larger families they are part of. Therefore, we employed a scheme of reciprocal BLASTs in order to identify the true orthologues of a set of prenylated human proteins (see accompanying publication for details). 238 individual human proteins and their orthologues form the clusters in HumanPRENbase.

Click here to go back to PRENbase!

This search interface is designed to allow sophisticated queries for the experimental status of the modification (known/predicted...), exclusive or shared types of modifying enzymes (FT, GGT1, GGT2) as well as for evolutionary conservation by constraining the taxonomic distribution within these clusters or for single sequences.

The listed status annotation is taken from the general PRENbase cluster. Therefore, "+" means that at least one member of the larger protein family has been experimentally verified to be prenylated. This is the case, for example, for the large Ras, Rab and Rho families of GTPases, where the prenylation of each individual member has not been shown directly but often can be safely inferred if a valid prenylation motif exists.

To start with, the default settings will give access to the collection of both known and predicted prenylated proteins clustered around individual human proteins, which can then be browsed. Below we have listed a series of standard queries that you might find useful or are particularly biologically important:

  • Review of previous knowledge of prenylated proteins:

List the clusters including KNOWN prenylated proteins.

  • LIKELY prenylation candidates for experimental validation (close homologue already verified):

List the clusters including LIKELY prenylated proteins.

  • Targets for experimental validation of NEW predicted prenylation:

List the clusters including NEWLY PREDICTED prenylated proteins.

As above but require conservation between Mammalia and Insecta.
As above but require conservation between Mammalia and Nematoda.
As above but require conservation between Mammalia and Fungi.
As above but require conservation between Mammalia and Plants.

  • Possible targets for FTI (FT inhibition, see accompanying publications for details):

List only proteins that are unique substrates to FT and not GGT1 or GGT2.

List the clusters of proteins containing unique substrates to FT and not GGT1 or GGT2 and conserved between Human and Insecta.

List the clusters of proteins containing unique substrates to FT and not GGT1 or GGT2 and conserved between Human and Nematoda.

List the clusters of proteins containing unique substrates to FT and not GGT1 or GGT2 and conserved between Human and Fungi.

List the clusters of proteins containing unique substrates to FT and not GGT1 or GGT2 and conserved between Human and Plants.

  • FT substrates less affected by FT inhibition or with altered anchor type under FTI:

List FT substrates that can be alternatively prenylated by GGT1.

  • Predicted prenylation in Viruses:

List the number of viral proteins with capacity to be prenylated if the biological context would allow processing by eukaryotic host enzymes.

  • Possible importance of specific farnesyl anchor length:

List clusters that only include FT but not GGT1 or GGT2 substrates.

  • Evolutionary exchangeability of different prenyl anchors:

List clusters that include both FT and GGT1 substrates.