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What is the use of Pfam database

2025-01-21 Update From: SLTechnology News&Howtos shulou NAV: SLTechnology News&Howtos > Internet Technology >

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This article will explain in detail what is the use of Pfam database for you. The editor thinks it is very practical, so I share it with you as a reference. I hope you can get something after reading this article.

In protein molecules, there are many structural-specific and functional regions, which are called domain. Domain can be regarded as the basic unit of protein function, and the function of protein is determined by multiple domain. The study of domain can better study the function of protein.

Pfam is a database of protein families. According to the results of multiple sequence alignment and hidden Markov model, proteins are divided into different families. The web address is as follows

Http://pfam.xfam.org/

In this database, the following two protein families at different levels are provided.

1. Family

Each family is uniquely identified by a PF number, as shown below

All family can be divided into the following six types

Family

A collection of related protein regions

Domain

A structural unit

Repeat

A short unit which is unstable in isolation but forms a stable structure when multiple copies are present

Motifs

A short unit found outside globular domains

Coiled-Coil

Regions that predominantly contain coiled-coil motifs, regions that typically contain alpha-helices that are coiled together in bundles of 2-7.

Disordered

Regions that are conserved, yet are either shown or predicted to contain bias sequence composition and/or are intrinsically disordered (non-globular).

2. Clan

Based on the similarity analysis of multiple family, the family with similar three-dimensional structure or the same motif can be classified as a clan, which can be regarded as the concept of superfamily. Each clan is identified by an CL number, as shown below.

In addition, it also provides the proteome information of the species, that is, the family information of all the proteins in the species, as shown below.

Take human as an example, its proteome information is as follows

It is actually a collection of Pfam corresponding to all the proteins of the species.

The latest version of the database, 31. 0, was updated in March 2017 and contains 16712 protein families. The ftp address is as follows

Ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam31.0/

The file with the suffix hmm is a hidden Markov model built by HMMER3 and can be used for sequence alignment.

This is the end of this article on "what is the use of Pfam database". I hope the above content can be helpful to you, so that you can learn more knowledge. if you think the article is good, please share it out for more people to see.

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