Practical No.
1
SWISS PROT DATABASE
Title: Protein sequence from Swiss Prot Database
Aim: To retrieve the protein Kerarin from the Protein Sequence Database, Swiss Prot
TREMBL
Theory:
Protein: Proteins are essential nutrients for the human body. They are one of the building
blocks of body tissue and can also serve as a fuel source. As a fuel, proteins provide as much
energy density as carbohydrates. The most important aspect and defining characteristic of
protein from a nutritional standpoint is its amino acid composition. Amino acids are the
building blocks of protein.
Database: A biological database is a large, organized body of persistent data, usually
associated with computerized software designed to update, query, and retrieve components of
the data stored within the system. A simple database might be a single file containing many
records, each of which includes the same set of information.
Swiss Prot: Swiss-Prot is the expertly curated component of UniProtKB (produced by the
UniProt consortium). It contains hundreds of thousands of protein descriptions, including
function, domain structure, subcellular location, post-translational modifications and
functionally characterized variants. UniProt is one of the most widely used protein information
resources in the world.
Sequence: A biological sequence is a single, continuous molecule of nucleic acid or protein.
It can be thought of as a multiple inheritance class hierarchy. One hierarchy is that of the
underlying molecule type: DNA, RNA, or protein. It could be a physical or genetic map, an
actual sequence of amino acids or nucleic acids, or some more complicated data structure
building a composite view from other entries.
Procedure:
1. Open the Swiss prot webpage www.expasy.org
2. Type in the protein name Keratin in the search field text to retrieve its sequence.
3. Out of the numerous entries any desired sequence of any organism is clicked.
4. The webpage is saved and protein sequence in the FASTA format is retrieved this sequence
is saved as a txt file.
Result:
Thus, the protein Keratin sequence was successfully retrieved. The detailed procedure how
the various screen on the webpage look like is shown below.
>sp|Q14533|KRT81_HUMAN Keratin, type II cuticular Hb1 OS=Homo sapiens
OX=9606 GN=KRT81 PE=1 SV=3
MTCGSGFGGRAFSCISACGPRPGRCCITAAPYRGISCYRGLTGGFGSHSVCGGFRAGSCG
RSFGYRSGGVCGPSPPCITTVSVNESLLTPLNLEIDPNAQCVKQEEKEQIKSLNSRFAAF
IDKVRFLEQQNKLLETKLQFYQNRECCQSNLEPLFEGYIETLRREAECVEADSGRLASEL
NHVQEVLEGYKKKYEEEVSLRATAENEFVALKKDVDCAYLRKSDLEANVEALIQEIDFLR
RLYEEEILILQSHISDTSVVVKLDNSRDLNMDCIIAEIKAQYDDIVTRSRAEAESWYRSK
CEEMKATVIRHGETLRRTKEEINELNRMIQRLTAEVENAKCQNSKLEAAVAQSEQQGEAA
LSDARCKLAELEGALQKAKQDMACLIREYQEVMNSKLGLDIEIATYRRLLEGEEQRLCEG
IGAVNVCVSSSRGGVVCGDLCVSGSRPVTGSVCSAPCNGNVAVSTGLCAPCGQLNTTCGG
GSCGVGSCGISSLGVGSCGSSCRKC
