SPEPLIP
A signal peptide is predicted in 204 proteins
CYSPRED
The bonding state of Cysteines has been predicted after removing the signal peptide predicted with SPEPLIP
No. of Bonded Cys 1940 in 205 proteins
No. of FreeCys 7749 in 923 proteins
No. of proteins with both Free and Bonded Cys: 108
TRANSMEBRANE HELICES
Predictions were made after removing the signal peptide.
ENSEMBLE predicted transmembrane helices in 275 proteins (84 have also a Signal Pep, 71 have at least two Bonded Cys)
MEMSAT predicted transmembrane helices in 395 proteins (96 have also a Signal Pep, 107 have at least two Bonded Cys)
TMHMM predicted transmembrane helices in 247 proteins (74 have also a Signal Pep, 60 have at least two Bonded Cys )
TMHMMdomfix predicted transmembrane helices in 264 proteins (74 have also a Signal Pep, 63 have at least two Bonded Cys)
PRODIV predicted transmembrane helices in 254 proteins (75 have also a Signal Pep, 65 have at least two Bonded Cys)
The union of these sets gives 424 proteins
The Intersection gives 218 proteins
7 proteins are predicted as transmembrane by ENSEMBLE alone
115 proteins are predicted as transmembrane by MEMSAT alone
0 proteins are predicted as transmembrane by TMHMM alone
11 proteins are predicted as transmembrane by TMHMMdomfix alone
0 proteins are predicted as transmembrane by PRODIV alone
GENE VARIANTS
The 1097 proteins come from 434 genes.
252 genes are listed with variants (from 2 up to 17)
Analysing the ENSEMBLE results:
76 of these 252 genes have a TM-helix in at least one variant
58 of these genes are predicted with a different number of TMHs in different variants
32 of these are predicted or not as Transmembrane depending on the variant
Analysing the MEMSAT results:
122 of these 252 genes have a TM-helix in at least one variant
84 of these genes are predicted with a different number of TMHs in different variants
63 of these are predicted or not as Transmembrane depending on the variant
Analysing the TMHMM results:
64 of these 252 genes have a TM-helix in at least one variant
43 of these genes are predicted with a different number of TMHs in different variants
25 of these are predicted or not as Transmembrane depending on the variant
Analysing the TMHMMdomfix results:
73 of these 252 genes have a TM-helix in at least one variant
51 of these genes are predicted with a different number of TMHs in different variants
33 of these are predicted or not as Transmembrane depending on the variant
Analysing the PRODIV results:
70 of these 252 genes have a TM-helix in at least one variant
51 of these genes are predicted with a different number of TMHs in different variants
31 of these are predicted or not as Transmembrane depending on the variant
METHODS
CYSPRED
Martelli PL, Fariselli P, Malaguti L, Casadio R. -Prediction of the disulfide bonding state of cysteines in proteins with hidden neural networks- Protein Eng. 15:951-953 (2002)
SPEPLIP
Fariselli P, Finocchiaro G, Casadio R -SPEPlip: the detection of signal peptide and lipoprotein cleavage sites- Bioinformatics 19:2498-2499 (2003)
ENSEMBLE 1.0
Martelli PL, Fariselli P, Casadio R -An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins- Bioinformatics 19:I205-I211 (2003)
MEMSAT
McGuffin LJ, Bryson K, Jones DT -The PSIPRED protein structure prediction server- Bioinformatics 16:404-405 (2000)
TMHMM 2.0
Krogh A, Larsson B, von Heijne G, Sonnhammer EL -Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes- J Mol Biol 19;305:567-580 (2001)
TMHMMdomfix
Bernsel A, Von Heijne G -Improved membrane protein topology prediction by domain assignments.
Protein Sci 14:1723-1728 (2005)
PRODIV
Viklund H, Elofsson A -Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information- Protein Sci 13: 1908-1917 (2004)