小中大
Could you tell me what can I get from the result of TM-Pred software . The name of the gene is sly-9.
TMpred output for sly-9
[ISREC-Server] Date: Wed Jul 2 13:38:31 2008
________________________________________
tmpred -par=matrix.tab -html -min=17 -max=33 -def -in=wwwtmp/.TMPRED.1276.4779.seq -out=wwwtmp/.TMPRED.1276.4779.out -out2=wwwtmp/.TMPRED.1276.4779.out2 -out3=wwwtmp/.TMPRED.1276.4779.txt >wwwtmp/.TMPRED.1276.4779.err
Sequence: SDS...FVN, length: 148
Prediction parameters: TM-helix length between 17 and 33
________________________________________
1.) Possible transmembrane helices
The sequence positions in brackets denominate the core region.
Only scores above 500 are considered significant.
Inside to outside helices : 2 found
from to score center
58 ( 62) 82 ( 82) 798 71
95 ( 95) 114 ( 114) 104 104
Outside to inside helices : 2 found
from to score center
55 ( 62) 82 ( 82) 952 71
94 ( 94) 114 ( 114) 663 104
________________________________________
2.) Table of correspondences
Here is shown, which of the inside->outside helices correspond to which of the outside->inside helices.
Helices shown in brackets are considered insignificant.
A "+"-symbol indicates a preference of this orientation.
A "++"-symbol indicates a strong preference of this orientation.
inside->outside | outside->inside
58- 82 (25) 798 | 55- 82 (28) 952 +
( 95- 114 (20) 104 ) | 94- 114 (21) 663 ++
________________________________________
3.) Suggested models for transmembrane topology
These suggestions are purely speculative and should be used with extreme caution since they are based on the assumption that all transmembrane helices have been found.
In most cases, the Correspondence Table shown above or the prediction plot that is also created should be used for the topology assignment of unknown proteins.
2 possible models considered, only significant TM-segments used
*** the models differ in the number of TM-helices ! ***
-----> STRONGLY prefered model: N-terminus inside
2 strong transmembrane helices, total score : 1461
# from to length score orientation
1 58 82 (25) 798 i-o
2 94 114 (21) 663 o-i
------> alternative model
1 strong transmembrane helices, total score : 952
# from to length score orientation
1 55 82 (28) 952 o-i
Thank you very much.
