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. 2006 Jul 1;34(Web Server issue):W99-103.
doi: 10.1093/nar/gkl351.

Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information

Sunghoon Lee  1 , Byungwook Lee, Insoo Jang, Sangsoo Kim, Jong Bhak
Affiliations

Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information

Sunghoon Lee et al. Nucleic Acids Res. .

Abstract

The Localizome server predicts the transmembrane (TM) helix number and TM topology of a user-supplied eukaryotic protein and presents the result as an intuitive graphic representation. It utilizes hmmpfam to detect the presence of Pfam domains and a prediction algorithm, Phobius, to predict the TM helices. The results are combined and checked against the TM topology rules stored in a protein domain database called LocaloDom. LocaloDom is a curated database that contains TM topologies and TM helix numbers of known protein domains. It was constructed from Pfam domains combined with Swiss-Prot annotations and Phobius predictions. The Localizome server corrects the combined results of the user sequence to conform to the rules stored in LocaloDom. Compared with other programs, this server showed the highest accuracy for TM topology prediction: for soluble proteins, the accuracy and coverage were 99 and 75%, respectively, while for TM protein domain regions, they were 96 and 68%, respectively. With a graphical representation of TM topology and TM helix positions with the domain units, the Localizome server is a highly accurate and comprehensive information source for subcellular localization for soluble proteins as well as membrane proteins. The Localizome server can be found at http://localizome.org/.

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Figures

Figure 1
Figure 1
The procedure overview of determining TM topology and TM helix numbers of a query protein sequence. Long gray lines are proteins, vertical bold lines are TM helices, rectangles are various PfamA domains, and ‘in’ and ‘out’ represent the TM topology. The shaded types of rectangles represent the domain type. A curved line in the box represents the cell membrane.
Figure 2
Figure 2
Screenshots of the output page of the Localizome server: (A) protein image, (B) falsely predicted TM topology by Phobius, (C) corrected TM topology by LocaloDom and (D) domain table containing domains and their TM topology information.
See this image and copyright information in PMC

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