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Expediting topology data gathering for the TOPDB database.

Dobson L, Langó T, Reményi I, Tusnády GE - Nucleic Acids Res. (2014)

Bottom Line: Results of global topology analysis of various organisms as well as topology data generated by high throughput techniques, like the sequential positions of N- or O-glycosylations were incorporated into the TOPDB database.We show that reliability values highly correlate with the per protein topology accuracy of the utilized prediction method.Altogether, more than 52,000 new topology data and more than 2600 new transmembrane proteins have been collected since the last public release of the TOPDB database.

View Article: PubMed Central - PubMed

Affiliation: 'Momentum' Membrane Protein Bioinformatics Research Group, Institute of Enzymology, RCNS, HAS, Budapest PO Box 7, H-1518, Hungary.

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Distribution of proteins with different number of transmembrane segments in the TOPDB database.
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Figure 1: Distribution of proteins with different number of transmembrane segments in the TOPDB database.

Mentions: The distribution of the number of transmembrane segments among the TOPDB entries is shown in Figure 1. The most prevalent class is the bitopic TMP class; about 40% of α-helical TMPs belong to this class. We have found similar distribution in the HTP (http://htp.enzim.hu) (37), which indicates that the α-helical bitopic TMPs are not over-represented in the TOPDB database. However, we have to note that while in the HTP database (37) the second more abundant class of proteins contain 7 TM segments, in the TOPDB the second and third most prevalent classes of TMPs are those that contain 2 or 12 TM segments. This difference is probably due to the different organism sources in the two databases. The TOPDB database contains several bacterial TMPs, and it was shown that bacterial transmembrane proteomes contains less 7 TM proteins than eukaryote proteomes (41).


Expediting topology data gathering for the TOPDB database.

Dobson L, Langó T, Reményi I, Tusnády GE - Nucleic Acids Res. (2014)

Distribution of proteins with different number of transmembrane segments in the TOPDB database.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383934&req=5

Figure 1: Distribution of proteins with different number of transmembrane segments in the TOPDB database.
Mentions: The distribution of the number of transmembrane segments among the TOPDB entries is shown in Figure 1. The most prevalent class is the bitopic TMP class; about 40% of α-helical TMPs belong to this class. We have found similar distribution in the HTP (http://htp.enzim.hu) (37), which indicates that the α-helical bitopic TMPs are not over-represented in the TOPDB database. However, we have to note that while in the HTP database (37) the second more abundant class of proteins contain 7 TM segments, in the TOPDB the second and third most prevalent classes of TMPs are those that contain 2 or 12 TM segments. This difference is probably due to the different organism sources in the two databases. The TOPDB database contains several bacterial TMPs, and it was shown that bacterial transmembrane proteomes contains less 7 TM proteins than eukaryote proteomes (41).

Bottom Line: Results of global topology analysis of various organisms as well as topology data generated by high throughput techniques, like the sequential positions of N- or O-glycosylations were incorporated into the TOPDB database.We show that reliability values highly correlate with the per protein topology accuracy of the utilized prediction method.Altogether, more than 52,000 new topology data and more than 2600 new transmembrane proteins have been collected since the last public release of the TOPDB database.

View Article: PubMed Central - PubMed

Affiliation: 'Momentum' Membrane Protein Bioinformatics Research Group, Institute of Enzymology, RCNS, HAS, Budapest PO Box 7, H-1518, Hungary.

Show MeSH