本人手头有一基因，用TM-Pred software (cuturl('http://www.ch.embnet.org/software/TMPRED_form.html'))预测出来有4个跨膜螺旋，但是使用细胞亚定位（同pEGFPN3融合）发现在细胞核和细胞质中都有表达。
现在望高手参与讨论把：
1.存在跨膜螺旋的蛋白就一定是跨膜蛋白吗？
2.跨膜螺旋的蛋白就一定不能在细胞核和细胞质中表达吗？
3.如何自圆我说，预测的跨膜螺旋并不影响其在细胞核和细胞质中表达？
因为老外编辑紧抓此问题不放，原文如下：
Best my knowledge, there is no report that transmembrane protein can be localized everywhere including nuclei in the cells without protein processing.
想从存在跨膜螺旋的蛋白就不一定是跨膜蛋白入手，但没有合适的佐证，能有文献支持作好！作者: 箭头儿 时间: 2014-2-8 13:03
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
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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
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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
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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 ++
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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.作者: applebook=213 时间: 2014-2-8 13:16
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
Date: Wed Jul 2 13:38:31 2008
________________________________________
t ...
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作者: pengke1983 时间: 2014-2-8 13:17
It means the protein can be transmembraned, but not very stong? Am I right?
you can use chinese to write.
but I can not use chinese because not chinese input on my computer, i am sorry.
Thank you very much.作者: pengke1983 时间: 2014-2-8 13:17
But I used another software to check the protien, no transmembrane site;
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