TMexpo help

INPUT

• SEQUENCE FORMAT
  Please input the protein sequence in FASTA format. Single-letter representation of 20 amino acids is accepted. Check your sequence before submitting to the program. The word following the character ">" is the identifier of the sequence.

  Here is an example:
  

  >1xio_A
  MNLESLLHWIYVAGMTIGALHFWSLSRNPRGVPQYEYLVAMFIPIWSGLAYMAMAIDQGKVEAAGQIAHYARYIDWMVTT
  PLLLLSLSWTAMQFIKKDWTLIGFLMSTQIVVITSGLIADLSERDWVRYLWYICGVCAFLIILWGIWNPLRAKTRTQSSE
  LANLYDKLVTYFTVLWIGYPIVWIIGPSGFGWINQTIDTFLFCLLPFFSKVGFSFLDLHGLRNLNDSRQTTGDRFAENTL
  QFVENITLFANSRRQQSRRRV
  

• LOCATION OF TM HELICES
  TMexpo needs the location of TMHs as input for prediction. This information can be obtained from a real structure or topology prediction programs. Once the location of TMH is given, TMexpo will predict the exposure for each residue and additionally predict the rotational angles for each TMH. Provide the label (TM-helix: H or M; Loop: L, I, O, 1, or 2) for each residue along the entire sequence. Pay attention to the length of the residue labels which must be equal to the sequence length given in FASTA.

• HOW TO SUBMIT
  Click on SUBMIT to send your request and a confirmation page will appear. The page will refresh itself every 15 seconds and display the result when prediction is finished. The prediction results will be stored online for 30 days and discarded thereafter.

OUTPUT (example)

• PREDICTED HELICAL ROTATIONAL ANGLES:
  Predicted helical rotational angle for each defined TMH is shown in a helical wheel, with each residue color-coded by the predicted relative lipid exposure values. By default, the first TMH is shown. For example, predicted fully buried residues (predicted rASA value 0.00~0.05) is colored in RED. The first residue of the helical wheel is encircled in BLACK, and labeled with sequence position. All helical wheels are shown in a left-handed configuration (clock-wise rotation). In the helical wheel, the predicted membrane(lipid)-facing moment is shown in a BROWN arrow, with respect to reference which is shown in a dashed line (0°). Change the helical wheel from the menu to retrieve the results for other TMHs.
  
  

• DETAIL OF PREDICTION RESULTS:
  The detail of prediction results of each residue is shown in a table. The fields in the table from left to right is Position, Residue, Topology, Predicted accessible surface area (ASA), Predicted relative ASA (rASA), Predicted state given by Support Vector Regression (SVR), and Predicted state given by Support Vector Machine (SVM). The results can be downloaded via the link. The explanation is listed below:

  1. Topology: H:helix or L:Loop based on the location of TMH defined.
  2. Predicted ASA: the predicted real number ASA of each residue, which is obtained by multiplying the predicted rASA with a reference value in a Gly-X-Gly tripeptide (Samanta et al., 2002).
  3. Predicted rASA: the predicted real number rASA of each residue.

REFERENCE

1. Samanta U. et al. (2002) Quantifying the accessible surface area of protein residues in their local environment. Protein Eng. 15(8):659-67.