News

The Enzyme Function Initiative (EFI) genomic enzymology web tools have been relaunched at efi.igb.illinois.edu. With the 2.0 release, the software behind the tools has been rewritten and modernised.

The tools still support the same genomic enzymology approach, which combines sequence similarity with genome context to explore protein families. They allow users to easily create and exploit sequence similarity networks (SSNs), genome neighbourhood networks (GNNs) and genome neighbourhood diagrams (GNDs). Researchers can use them to propose new biological functions for uncharacterised proteins, and to draw on what is known about an enzyme family for biotechnological applications.

If you used the tools before, you will need to create a new account on the new website. Please do not hesitate to contact the EFI team if you have any questions. Work is led by Nils Oberg with Russell Davidson and Hunter DeMeyer. John Gerlt and I provided scientific guidance. The work was funded by the National Institutes of Health/National Institute of General Medical Sciences (grant R24GM141196 to John A. Gerlt).

The CD-HIT web server has been unavailable since 2022. As an alternative, I have released CD-HIT in Google Colab, a notebook that builds CD-HIT from source and clusters your sequences in the browser. You don’t need to install anything.

The parameters are set through form fields with explanatory notes, and every run records its own provenance (CD-HIT version, command line, input checksum and timestamp), so results are easy to reproduce and report.

If you use it, please cite CD-HIT and the notebook: 10.5281/zenodo.23503573.

In October I travelled to the National University of Singapore for the opening of the Singapore National Centre for Engineering Biology (NCEB) on 5 October, followed by the Singapore Enzyme Biology Week. I am grateful to Wen Shan Yew for inviting me. Wen Shan, John Gerlt (University of Illinois Urbana-Champaign) and I work together on the ongoing development of the Enzyme Function Initiative (EFI) web tools.

On 8 October I ran a hands-on EFI workshop for graduate students who were new to the tools. We built sequence similarity networks (SSNs) to map protein families, then used genome neighbourhood networks (GNNs) and diagrams (GNDs) to look at the genomic context of their proteins of interest, with the aim of applying these approaches to their own projects.

It was a privilege to take part in the launch of the centre, and I look forward to seeing what these students discover.

Our paper “Characterization of putatively lytic bacteriophages able to infect Xanthomonas citri subsp. citri and identification of novel putative exopolysaccharide depolymerases” is out in Microbial Genomics.

Together with colleagues in Brazil, the US and the UK, we isolated and sequenced 72 bacteriophages that infect Xanthomonas citri, the bacterium that causes Asiatic citrus canker. Almost all of them are closely related, like the bacterial population they infect. Using structure-based annotation (HHsearch and AlphaFold), we found conserved tail-fibre proteins that may be depolymerases, able to break down the bacterium’s xanthan gum capsule. In greenhouse trials, one phage cut canker lesions by 60%. This makes phages a promising, sustainable alternative to copper sprays.

Read the paper: 10.1099/mgen.0.001821

Our paper “A cloaked glutamate decarboxylase sustains the GABA shunt in Mycobacterium tuberculosis” is out in Proceedings of the National Academy of Sciences.

Mycobacterium tuberculosis Rv2531c had long been annotated as a lysine/ornithine/arginine decarboxylase, a superfamily of more than 26,000 sequences. It isn’t one. Combining bioinformatics, microbiology, metabolomics and enzymology, we demonstrate that it is instead an L-glutamate decarboxylase that sustains carbon flux through the γ-aminobutyric acid (GABA) shunt in M. tuberculosis.

I contributed the creation and analysis of the sequence similarity network that placed Rv2531c in the context of its enzyme family, showing that the superfamily is composed of distinct forms with different domain organisations, and that Rv2531c belongs to a group in which no enzyme had been experimentally characterised.

A good reminder of how easily annotation bias propagates across homologous sequences, and of what network-based approaches can reveal when we look at a family as a whole rather than one sequence at a time.

Work led by Hai Minh Thai and Luiz Pedro S. de Carvalho, with Debbie M. Hunt, Yugen Miyahara, Manisha Priya and Htin L. Aung.

Read the paper: 10.1073/pnas.2619778123

The Faculty of Science and Engineering at Manchester Metropolitan University has adopted a new structure as of August 2026. I am now part of the School of Biological and Chemical Sciences.

Since July 2026, I’ve been a member of the Acid Fast Club, the UK’s mycobacteria research community.

Three papers I contributed to came out in 2024.

• “Cryptic enzymatic assembly of peptides armed with β-lactone warheads”, Nature Chemical Biology
• “Biosynthesis and function of 7-deazaguanine derivatives in bacteria and phages”, Microbiology and Molecular Biology Reviews
• “Bioinformatics-facilitated identification of novel bacterial sulfoglycosidases that hydrolyze 6-Sulfo-N-acetylglucosamine”, ACS Bio & Med Chem Au

See the full list on the Publications page.

I’ve been awarded a Springboard Award from The Academy of Medical Sciences (project SBF009\1016, £125,000, August 2024 to July 2026) for STEROSPRING, characterising an uncharted lanosterol catabolic pathway in non-tuberculous mycobacterial (NTM) species.

Details on the Funding page.

Since August 2024, I’ve been Senior Lecturer (Associate Professor) in Biochemistry in the Department of Life Sciences at Manchester Metropolitan University, having joined as Lecturer (Assistant Professor) in June 2023.