Table 2 Comparison of prediction of helix orientation for structure-based and computationally predicted helices in Leu transporter LeuTAa from Aquifex aeolicus (PDB ID: 2A65).
From: Prediction of transmembrane helix orientation in polytopic membrane proteins
TM Helix | Source | First Residue Number | TM helix sequence | LIPS prediction |
|---|---|---|---|---|
1 | Struct | 15 | ILAMAGNAVGLGNF LRFPVQ | Buried |
| Â | TMHMM | 7 | HWATRLGL ILAMAGNAVGLGNF | Â |
2 | Struct | 41 | GAFMIPYIIAFLLVGIPLMW | Correct |
| Â | TMHMM | 39 | GG GAFMIPYIIAFLLVGIPLMW I | Correct |
3 | Struct | 92 | ILGVFGLWIPLVVAIYYVYI ESWTLGFAIK | Correct |
| Â | TMHMM | 89 | FAK ILGVFGLWIPLVVAIYYVYI | Correct |
4 | Struct | 166 | LFAYIVFLITMFINVSILI | Correct |
| Â | TMHMM | 165 | SLFAYIVFLITMFINVSILI RGI | 2nd best |
5 | Struct | 193 | R FAKIAMPTLFILAVFLVIR | Wrong |
| Â | TMHMM | 194 | FAKIAMPTLFILAVFLVIR VFLL | Wrong |
6 | Struct | 241 | PGVWIAAVGQIFFTLSLGFGAI | Buried |
| Â | TMHMM | 243 | VWIAAVGQIFFTLSLGFGAI ITY | Â |
7 | Struct | 279 | GLTAATLNEKAEVI LGGSI | Correct |
| Â | TMHMM | 293 | LGGSI SIPAAVAFFGVANAVAIA | * |
8 | Struct | 342 | FLWFFLLFFAGLTSSI AIMQPMI | Correct |
| Â | TMHMM | 335 | AGGTFLG FLWFFLLFFAGLTSSI | Correct |
9 | Struct | 379 | VLWTAAIVFFSAHLVMF L | Wrong |
| Â | TMHMM | 378 | A VLWTAAIVFFSAHLVMF | Correct |
10 | Struct | 398 | KSLDEMD FWAGTIGVVFFGLTELI | Correct |
| Â | TMHMM | 405 | FWAGTIGVVFFGLTELI IFFWIF | Correct |
11 | Struct | 450 | YVMRYITPAFLAVLLVVWAR EYI | Correct |
| Â | TMHMM | 447 | IYY YVMRYITPAFLAVLLVVWAR | Correct |
12 | Struct | 482 | TV WITRFYIIGLFLFLTF | 2nd best |
| Â | TMHMM | 484 | WITRFYIIGLFLFLTF LVFL | 2nd best |