ArticleBiology direct2009
Bioinformatic flowchart and database to investigate the origins and diversity of clan AA peptidases.
Article in Biology direct, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Secreted retropepsin-like enzymes are essential for stress tolerance and biofilm formation inmBio · 2025Article
- In Silico Predictions of Ecological Plasticity Mediated by Protein Family Expansions in Early-Diverging Fungi.Journal of fungi (Basel, Switzerland) · 2022Article
- Structural-genetic insight and optimization of protease production from a novel strain of Aeromonas veronii CMF, a gut isolate of Chrysomya megacephala.Archives of microbiology · 2021Article
- LTR retrotransposons in fungi.PloS one · 2011Article
- The Gypsy Database (GyDB) of mobile genetic elements: release 2.0.Nucleic acids research · 2011Article
- Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees.Biology direct · 2009Article
- Pepsin homologues in bacteria.BMC genomics · 2009Article
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4 authors.
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Abstract
backgroundClan AA of aspartic peptidases relates the family of pepsin monomers evolutionarily with all dimeric peptidases encoded by eukaryotic LTR retroelements. Recent findings describing various pools of single-domain nonviral host peptidases, in prokaryotes and eukaryotes, indicate that the diversity of clan AA is larger than previously thought. The ensuing approach to investigate this enzyme group is by studying its phylogeny. However, clan AA is a difficult case to study due to the low similarity and different rates of evolution. This work is an ongoing attempt to investigate the different clan AA families to understand the cause of their diversity.
resultsIn this paper, we describe in-progress database and bioinformatic flowchart designed to characterize the clan AA protein domain based on all possible protein families through ancestral reconstructions, sequence logos, and hidden markov models (HMMs). The flowchart includes the characterization of a major consensus sequence based on 6 amino acid patterns with correspondence with Andreeva's model, the structural template describing the clan AA peptidase fold. The set of tools is work in progress we have organized in a database within the GyDB project, referred to as Clan AA Reference Database http://gydb.uv.es/gydb/phylogeny.php?tree=caard.
conclusionThe pre-existing classification combined with the evolutionary history of LTR retroelements permits a consistent taxonomical collection of sequence logos and HMMs. This set is useful for gene annotation but also a reference to evaluate the diversity of, and the relationships among, the different families. Comparisons among HMMs suggest a common ancestor for all dimeric clan AA peptidases that is halfway between single-domain nonviral peptidases and those coded by Ty3/Gypsy LTR retroelements. Sequence logos reveal how all clan AA families follow similar protein domain architecture related to the peptidase fold. In particular, each family nucleates a particular consensus motif in the sequence position related to the flap. The different motifs constitute a network where an alanine-asparagine-like variable motif predominates, instead of the canonical flap of the HIV-1 peptidase and closer relatives.
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