TargetP 2.0 - DTU Health Tech (2024)

Subcellular location of proteins: mitochondrial, chloroplastic, secretory pathway, or other

TargetP-2.0 server predicts the presence of N-terminal presequences: signal peptide (SP), mitochondrial transit peptide (mTP), chloroplast transit peptide (cTP) or thylakoid luminal transit peptide (lTP). For the sequences predicted to contain an N-terminal presequence a potential cleavage site is also predicted.

Submit data

Instructions

1. Specify the input sequences

All the input sequences must be in one-letter amino acidcode. The allowed alphabet (not case sensitive) is as follows:

A C D E F G H I K L M N P Q R S T V W Y and X (unknown)

All the alphabetic symbols not in the allowed alphabetwill be converted to X before processing. All the non-alphabeticsymbols, including white space and digits, will be ignored.

2. Customize your run

Organism group:
Choose Plant for any organism with chloroplasts/plastids and Non-plant otherwise.
Output format:
You can choose between two output formats:

Long

Shows one plot and one summary per sequence.

Short

Convenient if you submit lots of sequences. Shows only one line of output per sequence and no graphics.

3. Submit the job

Click on the "Submit" button. The status of your job (either 'queued'or 'running') will be displayed and constantly updated until it terminates andthe server output appears in the browser window.

At any time during the wait you may enter your e-mail address and simply leavethe window. Your job will continue; you will be notified by e-mail when it hasterminated. The e-mail message will contain the URL under which the results arestored; they will remain on the server for 24 hours for you to collect them.

Example Outputs

To appear...

Training and testing data set

The dataset used for training, validating, and testing TargetP 2.0 (using nested cross-validation) can be found here.

The sequences are in FASTA format with the UniProt AC as sequence name: Download

The annotations are in a tab-separated file where each line contains three fields: The UniProt AC, the type of targeting peptide,and the length of the targeting peptide.
The type can be

"SP" for signal peptide,
"MT" for mitochondrial transit peptide (mTP),
"CH" for chloroplast transit peptide (cTP),
"TH" for thylakoidal lumen composite transit peptide (lTP),
"Other" for no targeting peptide (in this case, the length is given as 0).

Download

Predictions on proteomes

Results from TargetP predictions on whole proteomes from UniProt (gzipped text files):

Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
hom*o sapiens
Mus musculus
Xenopus laevis
Xenopus tropicalis
Arabidopsis thaliana
Brachypodium distachyon
Oryza sativa
Solanum lycopersicum
Vitis vinifera
Saccharomyces cerevisiae
Schizosaccharomyces pombe

Please cite:

Detecting Sequence Signals in Targeting Peptides Using Deep Learning
José Juan Almagro Armenteros, Marco Salvatore, Ole Winther, Olof Emanuelsson, Gunnar von Heijne, Arne Elofsson, and Henrik Nielsen
Life Science Alliance 2 (5), e201900429. doi:10.26508/lsa.201900429(Open access)

The source code for training and running TargetP 2.0 is available under the creativecommons CC BY-NC-SA license from Github.

Version history

2.0

The current server. New in this version:

Deep learning: TargetP 2.0 is based on convolutional and recurrent (LSTM) neural networks with a multi-attention layer. The deep recurrent neural network architecture is better suited to recognizing sequence motifs of varying length, such as signal or transit peptides, than traditional feed-forward neural networks (as used in TargetP 1).
Thylakoid lumen proteins: TargetP 2.0 is now able to predict thylakoid luminal transit peptides (luTPs), which are composed of a chloroplast transit peptide (cTP) followed by a second peptide similar to a bacterial signal peptide.

1.1

The original server. Based on feed-forward neural networks.

Software Downloads

Version 2.0

Linux
Darwin

Version 1.1b

SunOS
OSF1
Linux
IRIX
AIX

GETTING HELP

If you need help regarding technical issues (e.g. errors or missing results) contact Technical Support. Please include the name of the service and version (e.g. NetPhos-4.0) and the options you have selected. If the error occurs after the job has started running, please include the JOB ID (the long code that you see while the job is running).

If you have scientific questions (e.g. how the method works or how to interpret results), contact Correspondence.

Correspondence: Technical Support:

FAQs

How do signal peptides work? ›

The signal peptide is a peptide segment of about 20–40 amino acids, which is fused to a protein for secretion and is an essential element in the process of transporting a protein out of the cell membrane (Zhou et al., 2016).

Discover More Details ›

What is the signal peptide of the chloroplast? ›

The transit peptide (TP) is a signal sequence in chloroplast interior proteins. In the cytosol, the TP is recognized by cytosolic chaperones such as Hsp70, Hsp90, or factors yet to be identified, which leads to the targeting of preproteins to the chloroplast.

See Details ›

How long does it take to see results from peptides? ›

Typically, you can expect to start seeing some results within a few weeks. From there, you will notice improvement until around three to six months into the treatment. At that point, the full effects will be more noticeable.

Keep Reading ›

Is taking peptides good for you? ›

Peptides are smaller versions of proteins. They may provide pro-aging support, anti-inflammatory, or muscle-building properties. Recent research indicates that some types of peptides could have a beneficial role in slowing down the aging process, reducing inflammation, and destroying microbes.

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What is the function of the signal recognition peptide? ›

The signal recognition particle (SRP) is a highly expressed and conserved RNP that is essential for the co-translational targeting of secretory and membrane proteins to the endoplasmic reticulum by facilitating the proper localization of translating ribosomes to this compartment in eukaryotic cells.

Keep Reading ›

What cleaves the signal peptide? ›

In eukaryotes, signal sequences direct the insertion of proteins into the membrane of the endoplasmic reticulum and are usually cleaved off by signal peptidase. The resulting signal peptides are presumably rapidly degraded, but some still have functions on their own.

Know More ›

What is the function of the signal peptide in insulin? ›

The signal peptide is cleaved in the lumen of the rER by a signal peptidase (located on the lumenal side of the rER membrane). Within the cisternae of the rER, proinsulin undergoes rapid folding and disulfide bond formation to generate the native tertiary structure, the direct precursor of insulin.

How do signal proteins work? ›

The signaling proteins can process information from their immediate environment (outside the cells) or from integration of several simultaneous signals from close or distant cells to produce an action.

Tell Me More ›

What is the prediction of signal peptides? ›

Annotation of predicted signal peptides

We annotate signal peptides which are predicted by the application of the predictive tools Phobius, Predotar, SignalP and TargetP. At least two methods must return a positive signal peptide prediction in order for the prediction to be annotated in UniProtKB.

Get More Info ›

Do signal peptides get cleaved? ›

In eukaryotes, signal sequences direct the insertion of proteins into the membrane of the endoplasmic reticulum and are usually cleaved off by signal peptidase. The resulting signal peptides are presumably rapidly degraded, but some still have functions on their own.

Read The Full Story ›