The Putative Secondary Structure of the putative coronavirus nsp3
 
1.氨基酸组成:(%)
%A: 7.6 %C: 4.1 %D: 2.4 %E: 1.4 %F: 6.5 %M: 4.8 %N: 3.1 %P: 2.4 %Q: 2.4 %R: 3.1
%G: 4.8 %H: 1.4 %I: 5.9 %K: 4.5 %L: 15.5 %S: 5.5 %T: 6.9 %V: 9.0 %W: 2.1 %Y: 6.5
 
2.Helix,Sheet等的预测结果:
方法:向The PredictProtein server提交多肽序列.预测实现方法参见Rost B(1996)
结果:结果包括两个部分,Fig1为图象化以后的结果图,直接的预测结果请参看这里
Fig1.Helix,Strand预测结果
 
3.Motif预测:
方法:在prosit中通过序列比对,找到蛋白中可能含有的序列的motif.
结果:下表中列出了改序列中可能含有的motif.其中,数字表示motif的第一个氨基酸在整个序列中的位置,后面的字母表示氨基酸序列.
 
N-glycosylation site
Protein kinase C phosphorylation site
Prokaryotic membrane lipoprotein lipid attachment site
174 NYSG
 127 TAR

45 FTLGIMAIAAC
N-myristoylation site
Casein kinase II phosphorylation site
Tyrosine kinase phosphorylation site
177 GVVTTI
279 GGKPCI


96 TWLE
130 TVYD
247 STQE
264 SSID

109 RLKDCVMY
 
4.穿膜片断预测结果
这是用The PredictProtein Server预测二阶结构的结果之一,下表列出了可能的穿膜片断以及整个肽链在膜内和膜外的分布情况.由于以下是序列扫描以后的结果,所有有些非膜蛋白也有可能被预测为有穿膜序列.
Positions Segments Explain
1- 16 i1 inside region 1
17- 41 M1 membrane helix 1
42- 45 o1 outside region 1
46- 70 M2 membrane helix 2
71- 74 i2 inside region 2
75- 93 M3 membrane helix 3
94- 109 o2 outside region 2
110- 128 M4 membrane helix 4
129- 137 i3 inside region 3
138- 155 M5 membrane helix 5
156- 160 o3 outside region 3
161- 185 M6 membrane helix 6
186- 189 i4 inside region 4
190- 214 M7 membrane helix 7
215- 218 o4 outside region 4
219- 237 M8 membrane helix 8
238- 264 i5 inside region 5
265- 282 M9 membrane helix 9
283- 290 o5 outside region 5
具体的预测结果请参看这里
 
参考文献:
1.PHD: predicting one-dimensional protein structure by profile-based neural networks.
2.Prediction of protein secondary structure at better than 70% accuracy
3.Topology prediction for helical transmembrane proteins at 86% accuracy
4.The PROSITE database, its status in 1999.