TY - JOUR
T1 - Discovery of new enzymatic functions and metabolic pathways using genomic enzymology web tools
AU - Zallot, Remi
AU - Oberg, Nils
AU - Gerlt, John A.
N1 - Funding Information:
The web resource that provides ‘democratized’ community access to EFI-EST and EFI-GNT was originally developed with support from National Institutes of Health U54GM093342 and currently is supported by NIH P01GM118303 . R.Z. is currently supported by the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie Individual Fellowships Grant agreement H2020-MSCA-IF-2018 839116 deCrYPtion.
Funding Information:
The web resource that provides ‘democratized’ community access to EFI-EST and EFI-GNT was originally developed with support from National Institutes of HealthU54GM093342 and currently is supported by NIH P01GM118303. R.Z. is currently supported by the European Union's Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie Individual Fellowships Grant agreement H2020-MSCA-IF-2018 839116 deCrYPtion.
Publisher Copyright:
© 2020 Elsevier Ltd
PY - 2021/6
Y1 - 2021/6
N2 - The continuing expansion of protein and genome sequence databases is an opportunity to identify novel enzymes with biotechnological applications. Whether applied to enzymology, chemical biology, systems biology, and microbiology, database mining must be ‘user-friendly’ so that experimentalists can devise focused strategies to discover the in vitro activities and in vivo functions of uncharacterized enzymes. We developed a suite of genomic enzymology tools (https://efi.igb.illinois.edu/) to (1) generate sequence similarity networks (SSNs) for exploration of sequence-function space in protein families (EFI-EST) and (2) provide genome context for members of protein families (EFI-GNT). Integrated analysis of this complementary information allows to generate testable hypotheses about new functions. After a brief overview of EFI-EST and EFI-GNT, we describe applications that illustrate their use.
AB - The continuing expansion of protein and genome sequence databases is an opportunity to identify novel enzymes with biotechnological applications. Whether applied to enzymology, chemical biology, systems biology, and microbiology, database mining must be ‘user-friendly’ so that experimentalists can devise focused strategies to discover the in vitro activities and in vivo functions of uncharacterized enzymes. We developed a suite of genomic enzymology tools (https://efi.igb.illinois.edu/) to (1) generate sequence similarity networks (SSNs) for exploration of sequence-function space in protein families (EFI-EST) and (2) provide genome context for members of protein families (EFI-GNT). Integrated analysis of this complementary information allows to generate testable hypotheses about new functions. After a brief overview of EFI-EST and EFI-GNT, we describe applications that illustrate their use.
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U2 - 10.1016/j.copbio.2020.12.004
DO - 10.1016/j.copbio.2020.12.004
M3 - Review article
C2 - 33418450
AN - SCOPUS:85098862678
SN - 0958-1669
VL - 69
SP - 77
EP - 90
JO - Current Opinion in Biotechnology
JF - Current Opinion in Biotechnology
ER -