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 - 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 -