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Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
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Updated: Jun 2, 2026

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances

Published on: October 11, 2018

A bioinformatics classifier and database for heme-copper oxygen reductases.

Filipa L Sousa¹, Renato J Alves, José B Pereira-Leal

¹Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal.

|May 12, 2011

Summary

A new bioinformatics tool classifies Heme-Copper Oxygen Reductases (HCOs) and Nitric Oxide Reductases (NORs), revealing three main functional groups and their evolutionary relationships. This advances our understanding of aerobic respiration enzymes.

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Area of Science:

Biochemistry
Bioinformatics
Evolutionary Biology

Background:

Heme-copper oxygen reductases (HCOs) are crucial enzymes in aerobic respiration, catalyzing dioxygen reduction to water and proton translocation.
The expanding genomic data necessitates a robust classification system for HCOs, as previous classifications have been challenged.

Purpose of the Study:

To re-evaluate and refine the classification of Heme-Copper Oxygen Reductases (HCOs) and Nitric Oxide Reductases (NORs).
To develop and validate a precise bioinformatics tool for classifying these enzyme families.

Main Methods:

A novel bioinformatics classifier was developed for HCO and Nitric Oxide Reductase (NOR) sequences, specifically targeting subunit I.
The classifier was benchmarked against a gold standard set, achieving 99.8% global recall and precision.
The tool was applied to classify HCOs and NORs across 552 completely sequenced genomes.

Main Results:

The analysis of an expanded dataset confirmed three primary functional and evolutionary groups of HCOs.
Significant homology was identified between NORs and HCOs.
A close evolutionary relationship was demonstrated between NORs and C-type HCOs.

Conclusions:

The study supports a refined classification of HCOs into three distinct groups based on new data.
Homology and evolutionary links between NORs and HCOs, particularly C-type HCOs, were established.
A publicly accessible classification web tool and integrated database for HCOs and NORs were created.