Here is an example:
# COX2_BACSU Length: 278
# COX2_BACSU Number of predicted TMHs: 3
# COX2_BACSU Exp number of AAs in TMHs: 68.6888999999999
# COX2_BACSU Exp number, first 60 AAs: 39.8875
# COX2_BACSU Total prob of N-in:
0.99950
# COX2_BACSU POSSIBLE N-term signal sequence
COX2_BACSU TMHMM2.0
inside 1 6
COX2_BACSU TMHMM2.0
TMhelix 7 29
COX2_BACSU TMHMM2.0
outside 30 43
COX2_BACSU TMHMM2.0
TMhelix 44 66
COX2_BACSU TMHMM2.0
inside 67 86
COX2_BACSU TMHMM2.0
TMhelix 87 109
COX2_BACSU TMHMM2.0
outside 110 278
If the whole sequence is labeled as inside or outside, the prediction
is that it contains no membrane
helices. It is probably not wise to interpret it as a prediction
of location. The prediction gives the most probable location and orientation
of transmembrane helices in the sequence. It is found by an algorithm called
N-best (or 1-best in this case) that sums over all paths through the model
with the same location and direction of the helices.
The first few lines gives some statistics:
Length: the length of the protein sequence. Number of predicted TMHs: The number of predicted transmembrane helices. Exp number of AAs in TMHs: The expected number of amino acids intransmembrane helices. If this number is larger than 18 it is very likely to be a transmembrane protein (OR have a signal peptide). Exp number, first 60 AAs: The expected number of amino acids in transmembrane helices in the first 60 amino acids of the protein. If this number more than a few, you should be warned that a predicted transmembrane helix in the N-term could be a signal peptide. Total prob of N-in: The total probability that the N-term is on the cytoplasmic side of the membrane. POSSIBLE N-term signal sequence: a warning that is produced when "Exp number, first 60 AAs" is larger than 10.