11 Result(s)
within
Alex Bateman
Algorithms
Bioinformatics
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Article
Open AccessStructure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis
CA_C2195 from Clostridium acetobutylicum is a protein of unknown function. Sequence analysis predicted that part of the protein contained a metallopeptidase-related domain. There are over 200 homologs of similar ...
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Article
Open AccessLUD, a new protein domain associated with lactate utilization
A novel highly conserved protein domain, DUF162 [Pfam: PF02589], can be mapped to two proteins: LutB and LutC. Both proteins are encoded by a highly conserved LutABC operon, which has been implicated in lactat...
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Article
Open AccessFilling out the structural map of the NTF2-like superfamily
The NTF2-like superfamily is a versatile group of protein domains sharing a common fold. The sequences of these domains are very diverse and they share no common sequence motif. These domains serve a range of ...
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Article
Open AccessTwo Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila
Every genome contains a large number of uncharacterized proteins that may encode entirely novel biological systems. Many of these uncharacterized proteins fall into related sequence families. By applying seque...
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Open AccessPredicting active site residue annotations in the Pfam database
Approximately 5% of Pfam families are enzymatic, but only a small fraction of the sequences within these families (<0.5%) have had the residues responsible for catalysis determined. To increase the active site...
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Open AccessReuse of structural domain–domain interactions in protein networks
Protein interactions are thought to be largely mediated by interactions between structural domains. Databases such as i Pfam relate interactions in protein structures to known domain families. Here, we investigat...
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Article
Open AccessThe Hotdog fold: wrap** up a superfamily of thioesterases and dehydratases
The Hotdog fold was initially identified in the structure of Escherichia coli FabA and subsequently in 4-hydroxybenzoyl-CoA thioesterase from Pseudomonas sp. strain CBS. Since that time structural determinations ...
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Open AccessEnhanced protein domain discovery using taxonomy
It is well known that different species have different protein domain repertoires, and indeed that some protein domains are kingdom specific. This information has not yet been incorporated into statistical met...
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Article
Open AccessThe TROVE module: A common element in Telomerase, Ro and Vault ribonucleoproteins
Ribonucleoproteins carry out a variety of important tasks in the cell. In this study we show that a number of these contain a novel module, that we speculate mediates RNA-binding.
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Article
Open AccessA comparison of Pfam and MEROPS: Two databases, one comprehensive, and one specialised.
We wished to compare two databases based on sequence similarity: one that aims to be comprehensive in its coverage of known sequences, and one that specialises in a relatively small subset of known sequences. ...
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Article
Open AccessThe SGS3 protein involved in PTGS finds a family
Post transcriptional gene silencing (PTGS) is a recently discovered phenomenon that is an area of intense research interest. Components of the PTGS machinery are being discovered by genetic and bioinformatics ...
