ArticleProceedings of the National Academy of Sciences of the United States of America2005
Sequence signatures and the probabilistic identification of proteins in the Myc-Max-Mad network.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 30 citations in OpenAlex.
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- Identification and characterization of tyrosine kinases in anole lizard indicate the conserved tyrosine kinase repertoire in vertebrates.Molecular genetics and genomics : MGG · 2017Article
- Venom Insulins of Cone Snails Diversify Rapidly and Track Prey Taxa.Molecular biology and evolution · 2016Article
- Genome-wide identification and analysis of basic helix-loop-helix domains in dog, Canis lupus familiaris.Molecular genetics and genomics : MGG · 2015Article
- Classification and evolutionary analysis of the basic helix-loop-helix gene family in the green anole lizard, Anolis carolinensis.Molecular genetics and genomics : MGG · 2013Article
- Accurate discrimination of bHLH domains in plants, animals, and fungi using biologically meaningful sites.BMC evolutionary biology · 2012Article
- Phylogenetic analysis and classification of the fungal bHLH domain.Molecular biology and evolution · 2012Article
- Premetazoan ancestry of the Myc-Max network.Molecular biology and evolution · 2011Article
- NClassG+: A classifier for non-classically secreted Gram-positive bacterial proteins.BMC bioinformatics · 2011Article
- Evolution of the Max and Mlx networks in animals.Genome biology and evolution · 2011Article
- ProCoS: Protein composition server.Bioinformation · 2010Article
- Site-specific evolutionary rates in proteins are better modeled as non-independent and strictly relative.Bioinformatics (Oxford, England) · 2008Article
- Biochemical and functional evidence of p53 homology is inconsistent with molecular phylogenetics for distant sequences.Journal of molecular evolution · 2008Article
- Background frequencies for residue variability estimates: BLOSUM revisited.BMC bioinformatics · 2007Article
- Spectral analysis of sequence variability in basic-helix-loop-helix (bHLH) protein domains.Evolutionary bioinformatics online · 2007Article
- Proteomic discovery of Max as a novel interacting partner of C/EBPalpha: a Myc/Max/Mad link.Leukemia · 2006Article
- Solving the protein sequence metric problem.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
Abstract
Accurate identification of specific groups of proteins by their amino acid sequence is an important goal in genome research. Here we combine information theory with fuzzy logic search procedures to identify sequence signatures or predictive motifs for members of the Myc-Max-Mad transcription factor network. Myc is a well known oncoprotein, and this family is involved in cell proliferation, apoptosis, and differentiation. We describe a small set of amino acid sites from the N-terminal portion of the basic helix-loop-helix (bHLH) domain that provide very accurate sequence signatures for the Myc-Max-Mad transcription factor network and three of its member proteins. A predictive motif involving 28 contiguous bHLH sequence elements found 337 network proteins in the GenBank NR database with no mismatches or misidentifications. This motif also identifies at least one previously unknown fungal protein with strong affinity to the Myc-Max-Mad network. Another motif found 96% of known Myc protein sequences with only a single mismatch, including sequences from genomes previously not thought to contain Myc proteins. The predictive motif for Myc is very similar to the ancestral sequence for the Myc group estimated from phylogenetic analyses. Based on available crystal structure studies, this motif is discussed in terms of its functional consequences. Our results provide insight into evolutionary diversification of DNA binding and dimerization in a well characterized family of regulatory proteins and provide a method of identifying signature motifs in protein families.
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