Information Technology Reference
In-Depth Information
tryptophane residues. This amino acid is a large molecule, that does not fit to a very
ordered structure like D-helise forming the middle of the spectrin molecule (triple helical
repeats). It probably forms the links between the consecutive repeats in the triple helical
repeat chain. The fragment including residues: 2160-2490 concerns 100% non-homologous
and non-identical positions. The rate of variety in this area is very high - this fragment (330
amino acid residues) is dominated by deletions. The diversity of this area suggests that it is
not a crucial fragment for the main protein (E-spectrin) functions and the amino acid
composition of this segment depends on the localization and functions characteristic for an
individual protein. The C-terminal part of the E-spectrin molecule begins with the residue
2490. The homology within this fragment is moderate; definitely lower than the homology
within the N-terminal fragment. It concerns plenty of deletions, the rate of identity is
minimal.
Apart from changes of similarity of comparing sequences characteristic for whole
regions, there are sporadic, single point mutations noticed within the sequences. Probably
these are results of defensive processes because of lethal mutations caused by appearing of
STOP codons. Those codons must be removed - by putting a single deletion. This situation
takes place especially in positions rich in amino acid residues, that have codons similar to
STOP codons: Leu and Ser (position 342 - those codons are semihomologous to codons:
UAA, UAG and UGA). Presence of such a type of deletions in proteins suggests their
taxonomic similarity.
2.3 The consensus sequence
The consensus sequence5 is a peculiar summary all the positions in the global multiple
alignment of E-spectrin protein family, concerns a piece of information about general
structure of a given family. The consensus sequence (Fig. 3.) is composed of three types of
signs: letter amino acid symbols (in conservative positions) - in the E-spectrin family
consensus sequence, when a position was occupied by one type of amino acid residue in at
least 54,55%. The “X” sign means a position with indefinite amino acid residue - there are
genetic relations among amino acids occupying this position, but there is no amino acid
residue, that would occur in this place very often. The rate of semihomologous residues in
this position must be at least 29,09%. The “-“ sign means a deletion - in case of exceeding
the limit of 49,09% deletions in occurring position.
Figure 3.
A fragment of E-spectrin consensus sequence (positions: 1-480). The
residues in bold occupy their positions in at least 89,09% (extremely conservative).
After construction the E-spectrin consensus sequence, basic parameters that
characterize the whole E-spectrin family were calculated (Tab. 1.).
