Phobius

A combined transmembrane topology and signal peptide predictor

Instructions

Input

Phobius takes proteins in FASTA format. It recognises the 20 amino acids plus B, Z and X, which are all treated as unknown. Any other character is removed. Lowercase input is accepted and converted to uppercase.

This is an example (one protein):

>Q8TCT8|PSL2_HUMAN you can have comments after the ID
MGPQRRLSPAGAALLWGFLLQLTAAQEAILHASGNGTTKDYCMLYNPYWTALPSTLENAT
SISLMNLTSTPLCNLSDIPPVGIKSKAVVVPWGSCHFLEKARIAQKGGAEAMLVVNNSVL
FPPSGNRSEFPDVKILIAFISYKDFRDMNQTLGDNITVKMYSPSWPNFDYTMVVIFVIAV
FTVALGGYWSGLVELENLKAVTTEDREMRKKKEEYLTFSPLTVVIFVVICCVMMVLLYFF
YKWLVYVMIAIFCIASAMSLYNCLAALIHKIPYGQCTIACRGKNMEVRLIFLSGLCIAVA
VVWAVFRNEDRWAWILQDILGIAFCLNLIKTLKLPNFKSCVILLGLLLLYDVFFVFITPF
ITKNGESIMVELAAGPFGNNEKLPVVIRVPKLIYFSVMSVCLMPVSILGFGDIIVPGLLI
AYCRRFDVQTGSSYIYYVSSTVAYAIGMILTFVVLVLMKKGQPALLYLVPCTLITASVVA
WRRKEMKKFWKGNSYQMMDHLDCATNEENPVISGEQIVQQ

This server accepts up to 100 sequences and 50,000 residues per request; a single sequence may be at most 10,000 residues. For whole proteomes, install the standalone package.

Long output format

The long format lists the predicted transmembrane helices, the intervening loop regions and the signal peptide, as a UniProt-style feature table:

ID   MTH_DROMEa signal peptide
FT   SIGNAL        1     24
FT   REGION        1      3       N-REGION.
FT   REGION        4     19       H-REGION.
FT   REGION       20     24       C-REGION.
FT   TOPO_DOM     25    218       NON CYTOPLASMIC.
FT   TRANSMEM    219    238
FT   TOPO_DOM    239    249       CYTOPLASMIC.
//

If the whole sequence is labelled cytoplasmic or non-cytoplasmic, the prediction is that it contains no membrane helices. It is not wise to interpret that as a prediction of location. The prediction gives the most probable location and orientation of transmembrane helices, found by an algorithm called N-best (1-best in this case) that sums over all paths through the model with the same location and direction of helices.

Short output format

One line per protein: the identifier, then the number of predicted transmembrane segments, a Y/0 indicator for a signal peptide, and the topology.

SEQENCE ID                     TM SP PREDICTION
MTH_DROME                       7  Y n4-19c24/25o219-238i250-269o281-302i

Helix positions are separated by i where the loop is cytoplasmic and o where it is non-cytoplasmic. A signal peptide is given as the position of its h-region between n and c, followed by the last residue of the signal peptide and the first of the mature protein, separated by /.

Plot of probabilities

The plot shows the posterior probability that each residue is cytoplasmic, non-cytoplasmic, part of a transmembrane helix, or part of a signal peptide. Weak helices that did not make it into the prediction show up here, as does the certainty of each segment. The bar under the axis shows the one-best prediction.

Plot and prediction can look contradictory, because the plot shows per-residue probabilities whereas the prediction is the single most probable overall structure. Treat the plot as complementary information.

Constrained prediction

If you already know where part of the protein sits, fix it on the constrained prediction page and Phobius will find the most probable topology consistent with your constraints.

Homology-supported prediction

Topology is more conserved than sequence, so PolyPhobius can use an alignment of homologues to sharpen a prediction. Supply an aligned FASTA file—the prediction is reported for the first sequence. Alternatively, submit a single sequence and the server will search Swiss-Prot and build the alignment for you.

Programmatic access

See the API page for a JSON endpoint suitable for scripting.

Getting help

Please report problems via the issue tracker.