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Table 3 Comparison of prediction performances

From: Refinement and prediction of protein prenylation motifs

 

FT

GGT1

 

Prosite PS00294

Beese, Casey and colleagues' rules

PrePS FT

Prosite PS00294

Beese, Casey and colleagues' rules

PrePS GGT1

Sensitivity I

85%*

72%

100%

95%*

67%

100%

Sensitivity II

NA

NA

92.6/97.9% †

NA

NA

98.6%

Probability of false positive prediction (POFP) for -CXXX motifs (GenBank sequences)

17.1%*

9.9%

6.3%

17.1%*

10.0%

1.2%

POFP -CXXX 'cytoplasmic'‡

18.2%*

8.9%

5.1%

18.2%*

8.6%

1.4%

POFP -CXXX 'nuclear'‡

13.9%*

10.5%

5.5%

13.9%*

9.6%

1.1%

POFP -CXXX 'membrane'‡

17.5%*

10.3%

3.8%

17.5%*

12.0%

0.8%

POFP --CXXX 'extracellular'$

8.6%*

7.9%

3.3%

8.6%*

9.0%

0.2%

Overall probability of false positive prediction (GenBank sequences, assuming 1.7% with -CXXX)

0.29%*

0.16%

0.11%

0.29%*

0.17%

0.02%

  1. *Prosite pattern PS00294 does not distinguish between prenylation by FT and GGT1.
  2. †Sensitivity rises to 97.9% when the exceptional motif CRPQ of hepatitis delta antigen is removed. ‡For details see Materials and methods. Sensitivity I is the rate of finding known substrates from described learning set = self-consistency. Sensitivity II is the rate of finding known substrates after their exclusion (including homologs) from the learning set = cross-validation (see Materials and methods). Probabilities of false-positive predictions (POFP) complement the specificities to 100% (Specificity = 100 - POFP). The first listed POFP estimates the rates of false positives among query proteins that have a canonical -CXXX motif (which corresponds to 1.7% of all sequences). Below are estimations of POFPs for subsets of Swiss-Prot proteins that differ in their annotated subcellular localization (see Materials and methods). The final POFP is the estimate for false-positive predictions for all sequences (for example, when analyzing complete proteomes or large databases), independent of existence of a -CXXX motif. Formatting signifies: best (bold), intermediate (plain text), worst (italic) performance.