Question: ID mapping from Uniprot
0
gravatar for m.shahdoost
3.9 years ago by
m.shahdoost20
m.shahdoost20 wrote:

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

protein • 2.3k views
ADD COMMENTlink modified 3.9 years ago by Elisabeth Gasteiger1.7k • written 3.9 years ago by m.shahdoost20
0
gravatar for natasha.sernova
3.9 years ago by
natasha.sernova3.7k
natasha.sernova3.7k wrote:

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

ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by natasha.sernova3.7k
0
gravatar for Elisabeth Gasteiger
3.9 years ago by
Geneva
Elisabeth Gasteiger1.7k wrote:

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

ADD COMMENTlink written 3.9 years ago by Elisabeth Gasteiger1.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1090 users visited in the last hour