GPI Lipid Anchor Project

Occurence of potentially GPI modified proteins in kingdoms of life:
Eukaryota / Saccharomyces cerevisiae:
Comparison with the data from L.H.P. Caro et al., YEAST, Vol.13, 1477-1489 (1997)

Contact:
Birgit Eisenhaber (MDC/IMP)
Peer Bork (MDC/EMBL)
Frank Eisenhaber (IMP)

With the help of the Von Heijne algorithm L.H.P. Caro et al. have identified 686 open reading frames in the genome of Saccharomyces cerevisiae that encode proteins with a potential N-terminal signal sequence for entering the secretory pathway. 51 of these proteins and 7 additional ORFs have been proposed to contain a potential GPI attachment signal. Asparagine and glycine have been considered as the only suitable amino acid types for the GPI attachment site.

We have tested the data set of L.H.P. Caro with our prediction program with the following results:

1. 15 proteins have been predicted as GPI anchored with the same GPI attachment site proposed in the paper of Caro et al.

   Gene name	ID	Length	predicted GPI site	proposed GPI site
   YCL048w	gi|5313	463	440 (N)	440 (N)
   YDR077w	gi|577804	338	318 (N)	318 (N)
   YER150w	gi|603390	148	127 (N)	127 (N)
   YIR019c	gi|557822	1367	1346 (G)	1346 (G)
   YJR151c	gi|1015903	1161	1137 (N)	1137 (N)
   YKL096w	gi|486159	239	217 (N)	217 (N)
   YLR040c	gi|1360368	224	203 (N)	203 (N)
   YLR110c	gi|1360502	133	112 (G)	112 (G)
   YLR121c	gi|1360524	508	483 (N)	483 (N)
   YLR194c	gi|544510	254	236 (N)	236 (N)
   YNL322c	gi|1302436	313	288 (N)	288 (N)
   YNL327w	gi|1302445	1041	1020 (G)	1020 (G)
   YOR009w	gi|1420104	487	465 (N)	465 (N)
   YOR214c	gi|1420499	236	212 (N)	212 (N)
   YPL130w	gi|1244784	223	198 (N)	198 (N)

2. 13 proteins have been predicted as GPI anchored with a GPI attachment site differing from the site proposed in the paper of Caro et al.

   Gene name	ID	Length	predicted GPI site	proposed GPI site
   YAL063c	gi|758410	1322	1302 (N)	1299 (G)
   YAR050w	gi|694125	1537	1517 (N)	1514 (G)
   YBR067c	gi|536314	210	186 (N)	192 (N)
   YDR349c	gi|849178	596	573 (D)	559 (G)
   YER011w	gi|603603	254	233 (N)	234 (G)
   YHR126c	gi|500678	159	138 (A)	137 (G)
   YHR211w	gi|458919	1075	1055 (N)	1052 (G)
   YJL078c	gi|1008238	881	864 (N)	853 (G)
   YLR120c	gi|1360522	569	542 (S)	548 (N)
   YLR343w	gi|609384	555	531 (D)	530 (N)
   YLR391w-a	gi|2580460	238	217 (G)	220 (N)
   YMR006c	gi|728653	706	681 (A)	680 (N)
   YOR382w	gi|1420823	153	124 (S)	130 (G)

3. In 30 proteins described in the paper we could not predict a GPI-anchor signal.
   The GPI attachment signal of yeast slightly differs from metazoan and protozoan cells for which our prediction function parameters were defined. The C-terminal sequences of 11 proteins do not fit well to the profile-dependent part of the prediction function:
   YDR055w
   YDR522c
   YGR189c
   YJR004c
   YKL046c
   YLR042c
   YMR008c
   YMR307w
   YNL190w
   YNR044w
   YOL030w
   Probably, these proteins would be predicted as GPI-anchored by using a fungal-specific prediction function.
   For further 8 proteins we could not detect a suitable omega-site:
   YDR261c
   YDR534c
   YIL011w
   YJR150c
   YKR102w
   YMR200w
   YMR215w
   YOL132w
   8 proteins lack an appropriately constructed hydrophobic tail:
   YCR089w
   YDR144c
   YJL171c
   YKL096w-a
   YNL300w
   YOR010c
   YOR383c
   YPL261c
   The protein YEL040w has a relatively large volume of the spacer region.
   The protein YOL155c has an extraordinarily hydrophobic spacer.
   The sequence of YBR078 is non-compatible with our prediction function at all.
   

Author: Birgit.Eisenhaber@nt.imp.univie.ac.at

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Last modified: 13th June 2002