Question: Uniprot and UniProt.ws
0
gravatar for Juliet Hannah
5 months ago by
Juliet Hannah360
United States
Juliet Hannah360 wrote:

I would like to find the protein sequence for human APOB.

I was not able to query by "APOB" so I first looked up the Entrez ID, 338.

libraryUniProt.ws)
human <- UniProt.ws(9606)

keys <- c("338")
columns <- c("SEQUENCE","UNIPROTKB","PDB")
kt <- "ENTREZ_GENE"
res <- select(human, keys, columns, kt)

This returns the main protein, but also two variants. One variant is labeled "Apolipoprotein B variant". How can I add this label so that I am able to determine the one I want.

Also, can I search "ABOB" directly rather than going through the Entrez ID? Thanks!

James MacDonald's suggestion worked for this part.

keys <- c("APOB")
columns <- c("SEQUENCE","UNIPROTKB","PDB","GENECARDS")
kt <- "GENECARDS"
res <- select(human, keys, columns, kt)
ADD COMMENTlink modified 5 months ago • written 5 months ago by Juliet Hannah360
Answer: Uniprot and UniProt.ws
2
gravatar for James W. MacDonald
5 months ago by
United States
James W. MacDonald51k wrote:

I think you can use the GENECARDS keytype:

> select(ws, "APOB", c("SEQUENCE","UNIPROTKB","PDB"), "GENECARDS")
Getting mapping data for APOB ... and ACC
Getting mapping data for P04114 ... and PDB_ID
Getting extra data for P04114
'select()' returned 1:1 mapping between keys and columns
  GENECARDS
1      APOB
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             SEQUENCE
1 MDP<snip>KLAPGELTIIL
  UNIPROTKB  PDB
1    P04114 <NA>
> 
ADD COMMENTlink written 5 months ago by James W. MacDonald51k

Thanks James! "GENECARDS" did indeed link the name. Do you have any suggestions about adding the variant information I describe above?

ADD REPLYlink written 5 months ago by Juliet Hannah360
> z <- select(ws, "338", c("PROTEIN-NAMES","UNIPROTKB","PDB"), "ENTREZ_GENE")
Getting mapping data for 338 ... and ACC
Getting mapping data for P04114 ... and PDB_ID
Getting extra data for P04114, Q59HB3, Q7Z7Q0
'select()' returned 1:many mapping between keys and columns
> z
  ENTREZ_GENE
1         338
2         338
3         338
                                                                    PROTEIN-NAMES
1 Apolipoprotein B-100 (Apo B-100) [Cleaved into: Apolipoprotein B-48 (Apo B-48)]
2                                             Apolipoprotein B variant (Fragment)
3                                                                    APOB protein
  UNIPROTKB  PDB
1    P04114 <NA>
2    Q59HB3 <NA>
3    Q7Z7Q0 <NA>

ADD REPLYlink written 5 months ago by James W. MacDonald51k
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