caa a22 4500 477128556 CHVBK 20180405111657.0 cr unu---uuuuu 170330e19971101xx s 000 0 eng 10.1023/A:1012166015402 doi (NATIONALLICENCE)springer-10.1023/A:1012166015402 Evolutionary Relationships Among Proteins Probed by an Iterative Neighborhood Cluster Analysis (INCA). Alignment of Bacteriorhodopsins with the Yeast Sequence YRO2 [Elektronische Daten] [Richard Graul, Wolfgang Sadée] Purpose. Searching 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 insufficient 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. Methods. We 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, and additional lists of more distantly related sequences for each member of the cluster. Results. Bacteriorhodospins 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. Conclusions. INCA 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. Plenum Publishing Corporation, 1997 basic local alignment search tool nationallicence iterative neighborhood cluster analysis nationallicence bacteriorhodopsins nationallicence protein sequences nationallicence Graul Richard Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, University of California San Francisco, 94143-0446, San Francisco, California aut Sadée Wolfgang Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, University of California San Francisco, 94143-0446, San Francisco, California aut Pharmaceutical Research Kluwer Academic Publishers-Plenum Publishers 14/11(1997-11-01), 1533-1541 0724-8741 14:11<1533 1997 14 11095 https://doi.org/10.1023/A:1012166015402 text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1023/A:1012166015402 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Graul Richard Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, University of California San Francisco, 94143-0446, San Francisco, California aut NATIONALLICENCE 700 1- Sadée Wolfgang Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, University of California San Francisco, 94143-0446, San Francisco, California aut NATIONALLICENCE 773 0- Pharmaceutical Research Kluwer Academic Publishers-Plenum Publishers 14/11(1997-11-01), 1533-1541 0724-8741 14:11<1533 1997 14 11095 Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer