Prediction of enzyme classes in a hierarchical approach by using SPMap

Date

2010-04-01

Author

Yaman, A.
Atalay, Mehmet Volkan
Atalay, Rengül

Metadata

Show full item record

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Item Usage Stats

137
views

0
downloads

Enzymes are proteins that play important roles in biochemical reactions as catalysts. They are classified based on the reaction they catalyzed, in a hierarchical scheme by International Enzyme Commission (EC). This hierarchical scheme is expressed in four-level tree structure and a unique number is assigned to each enzyme class. There are six major classes at the top level according to the reaction they carried out and sub-classes at the lower levels are further specific reactions of these classes. The aim of this study was to build a three-level classification model based on the hierarchical structure of EC classes. ENZYME database was used to extract the information of EC classes then enzymes were assigned to these EC classes. Primary sequences of enzymes extracted from UniProtKB/Swiss-Prot database were used to extract features. A subsequence based feature extraction method, Subsequence Profile Map (SPMap) was used in this study. SPMap is a discriminative method that explicitly models the differences between positive and negative examples. SPMap considers the conserved subsequences of protein sequences in the same class. SPMap generates the feature vector of each sample protein as a probability of fixed-length subsequences of this protein with respect to a probabilistic profile matrix calculated by clustering similar subsequences in the training data set. In our case, positive and negative training datasets were prepared for each class, at each level of the tree structure. SPMap was used for feature extraction and Support Vector Machines (SVMs) were used for classification. Five-fold cross validation was used to test the performance of the system. The overall sensitivity, specificity and AUC values for the six major EC classes are 93.08%, 98.95% and 0.993, respectively. The results at the second and third levels were also comparable to those of six major classes.

Subject Keywords

Biochemical research methods, Biotechnology, Applied microbiology

URI

https://hdl.handle.net/11511/32291

Journal

NEW BIOTECHNOLOGY

DOI

https://doi.org/10.1016/j.nbt.2010.01.023

Collections

Graduate School of Informatics, Article

Suggestions

OpenMETU
Core

Understanding the biotechnological potential of bifunctional enzyme: catalase-phenol oxidase YÜZÜGÜLLÜ, YONCA; Chi Trinh, Chi Trinh; Smith, Mark; Pearson, Arwen; Ögel, Zümrüt Begüm; Mc Pherson, Michael J. (2012-09-23) Catalases are common enzymes in all aerobic and many anaerobic organisms. Their main function is the decomposition of hydrogen peroxide into oxygen and water. Four classes of catalases have been defined including monofunctional heme-containing catalases, catalase–peroxidases, manganese catalases, and minor catalases. Although they have been studied for many years, a secondary peroxide-independent oxidative function of catalase is regarded as a new term discovery in the literature. Catalase–phenol oxidase (C...
Prediction of enzyme classes in a hierarchical approach by using spmap Yaman, Ayşe Gül; Atalay, Mehmet Volkan; Department of Computer Engineering (2009) Enzymes are proteins that play an important role in biochemical reactions as catalysts. They are classified based on the reaction they catalyzed, in a hierarchical scheme by International Enzyme Commission (EC). This hierarchical scheme is expressed as a four-level tree structure and a unique number is assigned to each enzyme class. There are six major classes at the top level according to the reaction they carried out and sub-classes at the lower levels are further specific reactions of these classes. The ...
Targeted disruption of homoserine dehydrogenase gene and its effect on cephamycin C production in Streptomyces clavuligerus Yilmaz, Ebru I.; Caydasi, Ayse K.; Özcengiz, Gülay (Springer Science and Business Media LLC, 2008-01-01) The aspartate pathway of Streptomyces clavuligerus is an important primary metabolic pathway which provides substrates for beta-lactam synthesis. In this study, the hom gene which encodes homoserine dehydrogenase was cloned from the cephamycin C producer S. clavuligerus NRRL 3585 and characterized. The fully sequenced open reading frame encodes 433 amino acids with a deduced M (r) of 44.9 kDa. The gene was heterologously expressed in the auxotroph mutant Escherichia coli CGSC 5075 and the recombinant protei...
Analysis of acyl CoA ester intermediates of the mevalonate pathway in Saccharomyces cerevisiae. Şeker, Tamay; Nielsen, J (Springer Science and Business Media LLC, 2005-04-01) The mevalonate pathway plays an important role in providing the cell with a number of essential precursors for the synthesis of biomass constituents. With respect to their chemical structure, the metabolites of this pathway can be divided into two groups: acyl esters [acetoacetyl CoA, acetyl CoA, hydroxymethylglutaryl (HMG) CoA] and phosphorylated metabolites (isopentenyl pyrophosphate, dimethylallyl pyrophosphate, geranyl pyrophosphate, farnesyl pyrophosphate). In this study, we developed a method for the ...
Determination and metabolic engineering of rate limiting reactions in aromatic amino acid pathway in Bacillus subtilis for L-phenylaianine production Guzide, Calik; Yasemin, Demirci; Pinar, Calik; Ozdamar, Tuncer H. (2007-09-01) Rate limiting reactions in the aromatic-group amino acid pathway (AAAP) in Bacillus subtilis for l-phenylalanine (Phe) production were determined as reported elsewhere (Özçelik-Şenver et al., 2004). The biochemical reactions in the AAAP start with the reaction using phosphoenolpyruvate (PEP) and erythrose 4-phosphate (E4P) synthesised in the glycolysis pathway and the PPP, respectively, leading to the formation of Phe via chorismate by branching at prephenate. The branch-point metabolites E4P supplied in vi...

Citation Formats

A. Yaman, M. V. Atalay, and R. Atalay, “Prediction of enzyme classes in a hierarchical approach by using SPMap,” NEW BIOTECHNOLOGY, pp. 0–0, 2010, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/32291.