id.features()

Description

Obtains features related to the provided id

Usage

id.features(id, features = “”)

Arguments

id the UniProt identifier of the protein of interest.

features a string identifying the features (comma separated) to be recovered.

Value

Returns a named list with the requested features. By default the the function provides info regarding the following features: id, reviewed, entry name and organism. If wished, this list of features can be expanded using the argument ‘features’.

Details

The ptm package offers a set of functions aimed to assist us to download and handle sequences from different databases:

Herein we illustrate the use of id.features() using the UniProt ID P35557, which corresponds to the human glucokinase (hexokinase-4)

gk <- id.features('P35557')
gk

## $Entry
## [1] "P35557"
## 
## $Status
## [1] "reviewed"
## 
## $Entry_name
## [1] "HXK4_HUMAN"
## 
## $Organism
## [1] "Homo sapiens (Human)"

By default we only recover information regarding a few basic features, but we can expand the information retrieved by this function using the argument features. For instance,

gk <- id.features('P35557', features = 'ec,keywords,database(PDB)')

Note, that we have requested three additional features:

The Enzyme Commission number for this enzyme

gk$EC

## [1] "2.7.1.1"

Keywords linked to this protein

gk$Keywords

## [1] "3D-structure;ATP-binding;Allosteric enzyme;Alternative splicing;Cytoplasm;Diabetes mellitus;Disease mutation;Glycolysis;Kinase;Mitochondrion;Nucleotide-binding;Nucleus;Polymorphism;Reference proteome;Transferase"

gk`Cross-reference_(PDB)`

## [1] "1GLK;1V4S;1V4T;3A0I;3F9M;3FGU;3FR0;3GOI;3H1V;3ID8;3IDH;3IMX;3QIC;3S41;3VEV;3VEY;3VF6;4DCH;4DHY;4ISE;4ISF;4ISG;4IWV;4IXC;4L3Q;4LC9;4MLE;4MLH;4NO7;4RCH;5V4W;5V4X;6E0E;6E0I;"

There is a larga list of features that can be retrieved. You can look up your relevant feature’s name in the full list of UniProtKB found herein.

Finally, one last example. Let’s find the subcellular locations for this protein:

gk <- id.features('P35557', features = 'comment(SUBCELLULAR LOCATION)')
gk

## [1] "SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:10456334, ECO:0000269|PubMed:24187134}. Nucleus {ECO:0000269|PubMed:10456334, ECO:0000269|PubMed:24187134}. Mitochondrion {ECO:0000250|UniProtKB:P17712}. Note=Under low glucose concentrations, GCK associates with GCKR and the inactive complex is recruited to the hepatocyte nucleus. {ECO:0000269|PubMed:10456334}."