Amylase, α-

Dissociation constant

Administrative data

Endpoint:

dissociation constant

Data waiving:

study technically not feasible

Justification for data waiving:

other:

Justification for type of information:

JUSTIFICATION FOR DATA WAIVING
Alpha-amylase belongs to the group of UVCB’s and due to the fact that individual alpha-amylase molecules differ in the amount of ionisable components the pKa will depend on the composition of the individual alpha-amylase. However, the pKa values can be estimated based on the below approach described below. The isoelectric point (pI) of a protein is the pH at which a particular protein carries no net electrical charge in the statistical mean. The pI can be calculated as the average of the pKa’s in the protein.

UniProt was search for “alpha-amylase” and the pI was calculated (EMBOSS) for the predicted mature enzyme (SignalP). For the 1734 found sequences, the range of the pI was 4.2 to 7.2 [5%;95%] percentile with a median of 5.3.

The median alpha-amylase pKa is 5.3.

UniProt
The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data.
The UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc). UniProt is a collaboration between the European Bioinformatics Institute (EMBL-EBI), the SIB Swiss Institute of Bioinformatics and the Protein Information Resource (PIR). Across the three institutes more than 100 people are involved through different tasks such as database curation, software development and support.

EMBOSS
EMBOSS is "The European Molecular Biology Open Software Suite".
EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages.

For citing:
EMBOSS: The European Molecular Biology Open Software Suite (2000) Rice,P. Longden,I. and Bleasby,A. Trends in Genetics 16, (6) pp276—277

SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks.

For citing:
Improved prediction of signal peptides: SignalP 3.0. Jannick Dyrløv Bendtsen, Henrik Nielsen, Gunnar von Heijne and Søren Brunak. J. Mol. Biol., 340:783-795, 200