Which are the protein classes

Question

[carlos_marchi]

Hi,

I'd like to know if there is a list of universal protein classes and there is a protein database in which each one has its corresponding protein class. I haven't found this classification in Uniprot database, for example.

Here is an example of protein classes that I find:

https://www.proteinatlas.org/humanproteome/proteinclasses

https://cambridgeproteinarrays.com/ProteinClassCoverage.php

Can anyone help me, please?

Thanks

[Kevin Blighe]

Boa tarde Carlos, o que significa 'universal protein classes'?

[carlos_marchi]

Hi Kevin! In fact, I'd like to know if there is a functional classification of proteins that is used in any biological protein databases. For example, DrugBank uses 4 classes of drug targets: Enzymes, Transporters, Carries and Receptors. However, I read in some articles using other classes, including GPCR, Nuclear Receptors, Transcriptor Factors and much others. So, I would like to know if there is a list that has all classes of protein functions and whether it is possible to search proteins based on a functional class in the UniProt or another protein database, for example: I would like to get all the proteins in UniProt whose protein function is the GPRC class.

[carlos_marchi]

Olá Kevin! Eu vi no site do drugbank uma classificação de proteínas alvos de drogas, podendo ser Target, Enzyme, Carrie e Transporter. Em alguns artigos que li, eles utilizaram alvos de drogas relacionadas a GPRC, Transcriptor Factor, Nuclear receptor, dentre outros. Gostaria de saber se há uma lista/classificação para todos os tipos de proteínas relacionadas a drogas e se consigo obter informação de uma proteína específica com base na classe funcional da proteína. Por exemplo, gostaria de obter todas as proteínas no site UniProt ou algum outro site de proteínas em elas sejam do tipo GPRC.

Answer 1

[Elisabeth Gasteiger]

In the UniProt Knowledgebase entries, and in particular in Swiss-Prot, the reviewed section of UniProtKB, you can find a section "Sequence similarities" which contains information about sequence-based protein families to which a protein belongs. See also

• https://www.uniprot.org/help/sequence_similarities
• https://www.uniprot.org/docs/similar
• https://www.uniprot.org/help/family_membership
• https://www.uniprot.org/help/list_specific_proteins

You may also be able to use UniProtKB keywords (https://www.uniprot.org/keywords/) and/or Gene Ontology annotation to help you with your classification (https://www.uniprot.org/help/sequence_similarities). Feel free to contact the UniProt helpdesk if you have any more specific questions.