PhyloFacts::
Innate Immunity Phylogenomic Explorer

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Innate Immunity Phylogenomic Explorer v. 2.0.   7 November 2009: 194 families; 4,627 Hidden Markov Models (family and subfamilies).

We combine evolutionary tree construction with structure analysis to reconstruct the phylogeny of Innate Immunity proteins and provide subfamily classifications. The molecular evolution of these complex proteins involves gene duplication and domain shuffling, to produce a vast and challenging superfamily of biological macromolecules.

Trans-kingdom Innate Immunity
We collaborate with several groups in the structural and functional characterization of proteins involved in innate immunity. Many of the protein domains that have been shown experimentally to be involved in mammalian innate immunity (e.g., Toll Interleukin Receptor, or TIR, domains) are also involved in disease resistance processes in plants.

See the UC Berkeley Trans-kingdom Innate Immunity Group.

This work is funded by grant number R01 HG002769 from the National Human Genome Research Institute of the NIH.

Please cite the following paper in references to this resource: Nandini Krishnamurthy, Duncan Brown, Dan Kirshner and Kimmen Sjölander, "PhyloFacts: An online structural phylogenomic encyclopedia for protein functional and structural classification," Genome Biology.

Protein Search

Submit sequences for classification against the HMM library. This library is designed to help biologists do the following:

  • Predict molecular function by phylogenomic analysis, using the phylogenetic tree for the family.
  • Classify novel sequences to functional subtypes, using the subfamily HMMs for the family.
  • Predict specificity positions, using the alignment analysis plots for each family.

Browse Books in our library

Each "book" in the HMM library corresponds roughly to a (whole-chain) protein family or domain, and contains the following data (generally downloadable, in different formats):

  • A cluster of homologs, typically from many species
  • One or more phylogenetic trees.
  • A decomposition of the tree into subtrees, to identify functional subfamilies.
  • A multiple sequence alignment for the family, as well as for individual subfamilies.
  • GO (Gene Ontology) annotations and evidence codes.
  • Other annotations and experimental data.
  • Hyperlinks to papers and online resources.
  • An analysis of the family's multiple sequence alignment using the subfamily decomposition to predict specificity positions defining the individual subtypes.
  • A predicted structure, including construction of comparative models for some families.
  • A predicted cellular localization (i.e., membrane-localized, secreted, cytoplasmic, nuclear, etc.