The COMBREX Project: Design, Methodology, and Initial Results

Anton, Brian P.; Chang, Yi-Chien; Brown, Peter Hendee; Choi, Han-Pil; Faller, Lina L.; Guleria, Jyotsna; Hu, Zhenjun; Klitgord, Niels; Levy‐Moonshine, Ami; Maksad, Almaz; Mazumdar, Varun; McGettrick, Mark; Osmani, Lais; Pokrzywa, Revonda M.; Rachlin, John; Swaminathan, Rajeswari; Allen, Benjamin; Housman, Genevieve; Monahan, Caitlin; Rochussen, Krista; Tao, Kevin; Bhagwat, Ashok S.; Brenner, Steven E.; Columbus, Linda; Crécy‐Lagard, Valérie de; Ferguson, Donald J.; Fomenkov, Alexey; Gadda, Giovanni; Morgan, Richard D.; Osterman, Andrei L.; Rodionov, Dmitry A.; Rodionova, Irina A.; Rudd, Kenneth E.; Söll, Dieter; Spain, James C.; Xu, Shuang-yong; Bateman, Alex; Blumenthal, Robert; Bollinger, J. Martin; Chang, Woo-Suk; Ferrer, Manuel; Friedberg, Iddo; Galperin, Michael Y.; Gobeill, Julien; Haft, Daniel H.; Hunt, J.F.; Karp, Peter D.; Klimke, William; Krebs, Carsten; Macelis, Dana; Madupu, Ramana; Martı́n, Marı́a Jesús; Miller, Jeffrey H; O′Donovan, Claire; Palsson, Bernhard Ø.; Ruch, Patrick; Setterdahl, Aaron T.; Sutton, Granger; Tate, John; Yakunin, Alexander F.; Tchigvintsev, Dmitri; Plata, Germán; Hu, Jie; Greiner, Russell; Horn, D.; Sjölander, Kimmen; Salzberg, Steven L.; Vitkup, Dennis; Letovsky, Stanley; Segrè, Daniel; DeLisi, Charles; Roberts, Richard J.; Steffen, Martín; Kasif, Simon

doi:10.1371/journal.pbio.1001638

Cited by 55 publications

(59 citation statements)

References 31 publications

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“…Recent advances in the efficiency and speed of gene sequencing coupled to a comparatively much slower pace of acquiring experimental evidence for protein function have given rise to a large number of hypothetical or erroneously annotated proteins in the databases (1,2). An example of a family of enzymes with a sizable amount of hypothetical proteins in the database is the nitronate monooxygenases (NMOs), with over 5000 genes in the GenBank TM currently annotated as NMO.…”

Section: Discussionmentioning

confidence: 99%

“…The discrepancy between the rapid increase in the number of sequenced genomes of prokaryotes and the slower experimental determination of protein function has resulted in the presence of a large number of hypothetical proteins in the databases, with gene function prediction often unreliable (1,2). One case of an enzyme family consisting mainly of hypothetical proteins is represented by the nitronate monooxygenases (NMOs, 2 EC 1.13.12.16), which includes Ͼ5000 genes in the GenBank TM .…”

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confidence: 99%

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Functional Annotation of a Presumed Nitronate Monoxygenase Reveals a New Class of NADH:Quinone Reductases

Ball¹,

Salvi²,

Gadda³

2016

Journal of Biological Chemistry

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The protein PA1024 from Pseudomonas aeruginosa PAO1 is currently classified as 2-nitropropane dioxygenase, the previous name for nitronate monooxygenase in the GenBank TM and PDB databases, but the enzyme was not kinetically characterized. In this study, PA1024 was purified to high levels, and the enzymatic activity was investigated by spectroscopic and polarographic techniques. Purified PA1024 did not exhibit nitronate monooxygenase activity; however, it displayed NADH:quinone reductase and a small NADH:oxidase activity. The enzyme preferred NADH to NADPH as a reducing substrate. PA1024 could reduce a broad spectrum of quinone substrates via a Ping Pong Bi Bi steady-state kinetic mechanism, generating the corresponding hydroquinones. The reductive half-reaction with NADH showed a k red value of 24 s ؊1 and an apparent K d value estimated in the low micromolar range. The enzyme was not able to reduce the azo dye methyl red, routinely used in the kinetic characterization of azoreductases. Finally, we revisited and modified the existing six conserved motifs of PA1024, which define a new class of NADH:quinone reductases and are present in more than 490 hypothetical proteins in the GenBank TM , the vast majority of which are currently misannotated as nitronate monooxygenase.

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Functional Annotation of a Presumed Nitronate Monoxygenase Reveals a New Class of NADH:Quinone Reductases

Ball¹,

Salvi²,

Gadda³

2016

Journal of Biological Chemistry

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“…Over 99 % of all annotations are created in this manner, and they are applied to approximately 76 % of all genes [ 6 ]-the remaining 24 % of genes typically have no annotation or are listed as "hypothetical protein." With the exponential growth of biological databases and the labor-intensive nature of manual curation, it is inevitable that automated computational predictions will provide the vast majority of annotations populating current and future databases.…”

Section: Sources Of Gene Ontology Annotations: Curated and Computatiomentioning

confidence: 99%

“…One such attempt at community building is focused on bacterial proteins: COMBREX ( COM putational BR idge to Ex periments), along with additional efforts such as the Enzyme Function Initiative [ 19 ]. The database ( http://combrex.bu.edu ) classifi es the gene function status of 3.3 million bacterial genes, including 13,665 proteins that have experimentally determined functions [ 6 ]. The database contains traceable statements to experimentally characterized proteins, thereby providing support for a given annotation in a clear and transparent manner.…”

Section: Approaches To Test Computational Predictions With Experimentmentioning

confidence: 99%

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Evaluating Computational Gene Ontology Annotations

Škunca

Roberts

Steffen

2016

Methods in Molecular Biology

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Two avenues to understanding gene function are complementary and often overlapping: experimental work and computational prediction. While experimental annotation generally produces high-quality annotations, it is low throughput. Conversely, computational annotations have broad coverage, but the quality of annotations may be variable, and therefore evaluating the quality of computational annotations is a critical concern.In this chapter, we provide an overview of strategies to evaluate the quality of computational annotations. First, we discuss why evaluating quality in this setting is not trivial. We highlight the various issues that threaten to bias the evaluation of computational annotations, most of which stem from the incompleteness of biological databases. Second, we discuss solutions that address these issues, for example, targeted selection of new experimental annotations and leveraging the existing experimental annotations.

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Accurate Microbial Genome Annotation Using an Integrated and User-Friendly Environment for Community Expertise of Gene Functions: The MicroScope Platform

Vallenet¹,

Médigue²

2015

Springer Protocols Handbooks

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The overwhelming list of new bacterial genomes becoming available on a daily basis makes accurate genome annotation an essential step that ultimately determines the relevance of the thousands of genomes stored in public databanks. The reference databases and computational methods that constitute the basis of automatic genome annotation pipelines are constantly evolving: firstly, the annotation of single genomes can now be performed through simultaneous analysis of multiple genomes in a comparative context; secondly, the focus of genome annotation has been extended to the reconstruction of genome-scale metabolic networks that allow for a more comprehensive overview of the functional capabilities of the organism under study. Starting from the results of structural, functional and relational annotation pipelines, MicroScope provides an integrated environment for the annotation and comparative analysis of prokaryotic genomes, by combining tools and graphical interfaces for genome analysis and manual curation of gene annotations in a comparative genomics context. In the present chapter, we discuss the different stages of annotation using the MicroScope platform, and, through examples of degradation pathways in bacterial species, we illustrate some of the functionalities that are useful for improving the quality of automatic genome annotations. Thus, we demonstrate that integrated environments such as MicroScope clearly contribute to maintaining accurate resources, through the help of the user community.

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The COMBREX Project: Design, Methodology, and Initial Results

Abstract: Experimental data exists for only a vanishingly small fraction of sequenced microbial genes. This community page discusses the progress made by the COMBREX project to address this important issue using both computational and experimental resources.

Cited by 55 publications

References 31 publications

Functional Annotation of a Presumed Nitronate Monoxygenase Reveals a New Class of NADH:Quinone Reductases

Functional Annotation of a Presumed Nitronate Monoxygenase Reveals a New Class of NADH:Quinone Reductases

Evaluating Computational Gene Ontology Annotations

Accurate Microbial Genome Annotation Using an Integrated and User-Friendly Environment for Community Expertise of Gene Functions: The MicroScope Platform

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