ArticlePharmaceutical research1997
Evolutionary relationships among proteins probed by an iterative neighborhood cluster analysis (INCA). Alignment of bacteriorhodopsins with the yeast sequence YRO2.
Article in Pharmaceutical research, 1997. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 21 citations in OpenAlex.
- Protein Activity of the Fusarium fujikuroi Rhodopsins CarO and OpsA and Their Relation to Fungus-Plant Interaction.International journal of molecular sciences · 2018Article
- Are Synonymous Sites in Primates and Rodents Functionally Constrained?Journal of molecular evolution · 2016Article
- Microbial rhodopsins: wide distribution, rich diversity and great potential.Biophysics and physicobiology · 2015Review
- Light-promoted rhodopsin expression and starvation survival in the marine dinoflagellate Oxyrrhis marina.PloS one · 2014Article
- Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism.Microbiology and molecular biology reviews : MMBR · 2004Review
- Making sense of EST sequences by CLOBBing them.BMC bioinformatics · 2002Article
- Evolutionary relationships among G protein-coupled receptors using a clustered database approach.AAPS pharmSci · 2001Article
- Human proton/oligopeptide transporter (POT) genes: identification of putative human genes using bioinformatics.AAPS pharmSci · 2000Article
- The nop-1 gene of Neurospora crassa encodes a seven transmembrane helix retinal-binding protein homologous to archaeal rhodopsins.Proceedings of the National Academy of Sciences of the United States of America · 1999Article
- The Venus flytrap of periplasmic binding proteins: an ancient protein module present in multiple drug receptors.AAPS pharmSci · 1999Review
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
purposeSearching the existing databases for homologous sequences is essential to understanding a protein's structure and function. For a query sequence, its nearest neighbors can be identified by BLAST (basic local alignment search tool). However, a single query sequence is sufficient to define the entire neighborhood of related sequences, and multiple BLAST queries are needed. We describe here a program which permits automated and iterative BLAST analysis of an entire neighborhood of sequences and apply this to search for homologs of the bacteriorhodopsins outside the archaea phylum.
methodsWe have developed a Java program, 'Iterative Neighborhood Cluster Analysis' (INCA), which performs iterative BLAST searches, beginning with a single starter sequence, and proceeding with any other sequence achieving a predefined minimum alignment score. This results in a cluster of sequences where each sequence is related to at least one other sequence by the cutoff score, additional lists of more distantly related sequences for each member of cluster.
resultsBacteriorhodopsins had not been previously aligned with any other protein family with scores indicative of probable homology. Using INCA, we identified a probable homolog in yeast, YRO2_YEAST, also containing seven putative transmembrane domains. A finding of probable homology was supported by additional alignment strategies.
conclusionsINCA is a useful tool to assess complete protein neighborhoods. With an increasing database, INCA can serve to detect the emergence of evolutionary links between even the most distantly related protein families. Identifying a homolog of the bacteriorhodopsins in yeast illustrates this approach but at the same time highlights the vast evolutionary distances between polytopic membrane proteins, such as the bacteriorhodopsins.
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