ID mapping from Uniprot

Question

[m.shahdoost]

Hi my friends I have a huge nunber of prob id codes. and I need their gene names and also their protein. I use Annotation for find the genes name and also uniprot codes seperatly to determine the protein . But some of probs id do not have uniprot codes.please help me to find the protein name of those which do not have uniprot id. thanks

Answer 1

[natasha.sernova]

see the following post for proteins with id:

How to get a fastA file with amino acid sequences from a list of accession numbers

try to use blast against UniProtKB or any other DB within UniProt If some protein doesn't have uniprot ID

http://www.uniprot.org/blast/

I’ve checked this approach for some fragment of Aspergillus protein:

APGHRDFIKNMITGTSQADCAILIIASGTGEFEAGISKDGQTREHALLAFTLGVRQLIVALNKMDTCKWS EDRYNEIVKETSNFIKKVGYNPKAVPFVPISGFNGDNMLEPSPNCP

and got this:

http://www.uniprot.org/blast/uniprot/B2016043046C5QFYU9R

I repeated the same for bacterial protein:

gi|85676342|dbj|BAE77592.1| chromosomal replication initiator protein DnaA, DNA-binding transcriptional dual regulator [Escherichia coli str. K-12 substr. W3110] MSLSLWQQCLARLQDELPATEFSMWIRPLQAELSDNTLALYAPNRFVLDWVRDKYLNNINGLLTSFCGAD APQLRFEVGTKPVTQTPQAAVTSNVAAPAQVAQTQPQRAAPSTRSGWDNVPAPAEPTYRSNVNVKHTFDN FVEGKSNQLARAAARQVADNPGGAYNPLFLYGGTGLGKTHLLHAVGNGIMARKPNAKVVYMHSERFVQDM VKALQNNAIEEFKRYYRSVDALLIDDIQFFANKERSQEEFFHTFNALLEGNQQIILTSDRYPKEINGVED RLKSRFGWGLTVAIEPPELETRVAILMKKADENDIRLPGEVAFFIAKRLRSNVRELEGALNRVIANANFT GRAITIDFVREALRDLLALQEKLVTIDNIQKTVAEYYKIKVADLLSKRRSRSVARPRQMAMALAKELTNH SLPEIGDAFGGRDHTTVLHACRKIEQLREESHDIKEDFSNLIRTLSS

I got the following with DnaA from E.coli:

http://www.uniprot.org/blast/uniprot/B2016050146C7CIW2VV

Answer 2

[Elisabeth Gasteiger]

Do you have examples of the codes you have? Have you tried UniProt's ID mapping service? http://www.uniprot.org/uploadlists