Difference between revisions of "Sequence-based predictions TSD"
(→Signal peptides) |
(→Signal peptides) |
||
| Line 51: | Line 51: | ||
<br> |
<br> |
||
For non-secretory proteins all scores are supposed to be very low. |
For non-secretory proteins all scores are supposed to be very low. |
||
| + | |||
| + | figtable id="tbl:signalp"> |
||
| + | {| class="wikitable" style="float: right; border: 2px solid darkgray; width:600px;" cellpadding="2" |
||
| + | ! scope="row" align="left" | |
||
| + | | align="right" | [[File:Sp_P06865_HEXA_HUMAN.png|thumb|200px]] |
||
| + | | align="right" | [[File:Sp_P47863_AQP4_RAT_TSD.png|thumb|200px]] |
||
| + | |- |
||
| + | ! scope="row" align="left" | |
||
| + | | align="right" | [[File:Sp_P11279_LAMP1_HUMAN_TSD.png|thumb|200px]] |
||
| + | | align="right" | [[File:Sp_P02768_ALBU_HUMAN_TSD.png|thumb|200px]] |
||
| + | |- |
||
| + | ! scope="row" align="left" | |
||
| + | | align="left" colspan="2" |'''Table ''': Signal peptide predictions. |
||
| + | |- |
||
| + | |} |
||
| + | </figtable> |
||
| + | |||
| + | The <xr id="tbl:signalp"/> shows the identity and e-value distribution from BIG80 and BIG. |
||
== GO terms == |
== GO terms == |
||
Revision as of 15:33, 14 May 2012
Thor: He's my brother
Natasha Romanoff: He killed 80 people in 2 days
Thor: ...He's adopted
If not noted otherwise, the sequence for all predictions is the HEXA Reference sequence. A protocol for this task can be found here.
Contents
Secondary structure
Disorder
Transmembrane helices
Signal peptides
Proteins: P02768, P11279, P47863
SignalP employs 3 main scores for the prediction of signal peptides, C, S and Y. The S-score stands for the actual signal peptide prediction, with high scores indicating that the corresponding amino acid is part of a signal peptide, and low scores indicating that the amino acid is part of a mature protein.
The C-score is the cleavage score, which indicates the best cleavage cite when significantly high. (When a cleavage site position is referred to by a single number, the number indicates the first residue in the mature protein.)
Y-max is a derivative of the C-score combined with the S-score calculated to give a better cleavage site prediction than the raw C-score alone.
There are two additional scores reported in the SignalP output, namely the S-mean and the D-score. The S-mean is the average of the S-score, ranging from the N-terminal amino acid to the amino acid assigned with the highest Y-max score. The D-score is implemented as a weighted average of the S-mean and the Y-max scores.
For non-secretory proteins all scores are supposed to be very low.
figtable id="tbl:signalp">
| Table : Signal peptide predictions. | ||
</figtable>
The <xr id="tbl:signalp"/> shows the identity and e-value distribution from BIG80 and BIG.
GO terms
GOpet
<figtable id="tab:gopetgo">
| GO-Term ID | Type | Confidence | GO-Term description |
|---|---|---|---|
| GO:0003824 | Molecular function | 97% | catalytic activity |
| GO:0004563 | Molecular function | 96% | beta-N-acetylhexosaminidase activity |
| GO:0015929 | Molecular function | 96% | hexosaminidase activity |
| GO:0016787 | Molecular function | 96% | hydrolase activity |
| GO:0016798 | Molecular function | 96% | hydrolase activity acting on glycosyl bonds |
| GO:0004553 | Molecular function | 96% | hydrolase activity hydrolyzing O-glycosyl compounds |
| GO:0016799 | Molecular function | 77% | hydrolase activity hydrolyzing N-glycosyl compounds |
| GO:0046982 | Molecular function | 61% | protein heterodimerization activity |
Table TODO: </figtable>
