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    PFAM

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    Zamira Abdirassilova
    Pfam is a database of protein families that contains over 19,000 families identified using hidden Markov models. It was founded in 1995 to aid in genome annotation and each family contains a description, multiple sequence alignment, and links to other databases. Families are organized into Pfam-A, Pfam-B, and Pfam-C groups. Records can be domains, repeats, motifs, coiled coils, or disordered regions. Users can view family descriptions, alignments, structures, and links to related databases. Potential disadvantages include inconsistent use of terminology and the need to download additional software.

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    PFAM

    Uploaded by

    Zamira Abdirassilova
    46 views12 pages
    Pfam is a database of protein families that contains over 19,000 families identified using hidden Markov models. It was founded in 1995 to aid in genome annotation and each family contains a description, multiple sequence alignment, and links to other databases. Families are organized into Pfam-A, Pfam-B, and Pfam-C groups. Records can be domains, repeats, motifs, coiled coils, or disordered regions. Users can view family descriptions, alignments, structures, and links to related databases. Potential disadvantages include inconsistent use of terminology and the need to download additional software.

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    Pfam is a database of protein families that contains over 19,000 families identified using hidden Markov models. It was founded in 1995 to aid in genome annotation and each family contains a description, multiple sequence alignment, and links to other databases. Families are organized into Pfam-A, Pfam-B, and Pfam-C groups. Records can be domains, repeats, motifs, coiled coils, or disordered regions. Users can view family descriptions, alignments, structures, and links to related databases. Potential disadvantages include inconsistent use of terminology and the need to download additional software.

    Copyright:

    © All Rights Reserved
    Download as PPTX, PDF, TXT or read online from Scribd
    Download as pptx, pdf, or txt
    46 views12 pages

    PFAM

    Uploaded by

    Zamira Abdirassilova
    Pfam is a database of protein families that contains over 19,000 families identified using hidden Markov models. It was founded in 1995 to aid in genome annotation and each family contains a description, multiple sequence alignment, and links to other databases. Families are organized into Pfam-A, Pfam-B, and Pfam-C groups. Records can be domains, repeats, motifs, coiled coils, or disordered regions. Users can view family descriptions, alignments, structures, and links to related databases. Potential disadvantages include inconsistent use of terminology and the need to download additional software.

    Copyright:

    © All Rights Reserved
    Download as PPTX, PDF, TXT or read online from Scribd
    Download as pptx, pdf, or txt
    of 12

    PFAM

    PREPARED BY: ABZHAMI Z, ZHARYLKASYN A, TLEUBAYEVA D.


    CHECKED BY: YURIKOVA O.Y
    •Pfam is a database of protein families
    that includes their annotations and multiple
    sequence alignments generated using
    hidden Markov models.
    •The most recent version, Pfam 34.0,
    was released in March 2021 and contains
    19,179 families.
    HISTORY OF PFAM

    •Pfam was founded in 1995 by Erik


    Sonhammer, Sean Eddy and Richard
    Durbin as a collection of commonly
    occurring protein domains that could be
    used to annotate the protein coding genes
    of multicellular animals.
    •Major aims at inception was to aid in
    the annotation of the C. elegans genome.
    PFAM STRUCTURE
    • There are two categories of protein domain families in Pfam:
    • Pfam-A and Pfam-B. The domains do not overlap — there are no proteins in
    the database in which at least one amino acid residue belongs to two different
    domains at the same time.
    • Some families that have a common evolutionary origin and have preserved
    similarities at the level of sequences or structures are united into clans. The
    collection of clans is called Pfam-C.
    CLASSIFICATION OF RECORDS
    •A Pfam record is a set of similar sections of protein sequences. All records belong to one of six types:
    •Family— the basic type, a set of related (homologous) sites;
    •Domain is a stable structural unit, or at least a functional site, found in various protein architectures;
    •Repeat — a short section that is unstable in isolation, but forms a stable structure when several copies of
    it are present;

    •Motif — a short conservative section outside the globular domains;


    •Coiled-Coil (Superspiral block) - regions forming superspirals, i.e. bundles of 2-7 twisted
    alpha-helices;

    •Disordered (Unstructured block) — conservative areas with a displaced amino acid


    composition that do not form a stable (globular) structure.
    FEATURES

    For each family in Pfam one can:


     View a description of the family
     Domain of unknown function (YbbR)
     Look at multiple alignments
     View protein domain architectures (3D structures)
     Follow links to other databases
     View known protein structures
    DISADVANTAGES

    • Often, the term family is used, including on the Pfam website, instead of the
    term entry, which creates considerable confusion.
    • Less sensitive: more false positives and negatives
    • Its necessary to download JAVA
    http://pfam.xfam.org/

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