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.
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.
The sequences can be input in the following two ways:
- Paste a single sequence (just the amino acids) or a number of sequences inFASTAformat into the upper window of the main server page.
- Select a FASTAfile on your local disk, either by typing the file name into the lower windowor by browsing the disk.
Both ways can be employed at the same time: all the specified sequences willbe processed. However, there may be not more than 5,000 sequences in one submission.
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. | |
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
The S-score for the signal peptide prediction is reported for every single amino acid position in the submitted sequence, with high scores indicating that the corresponding amino acid is part of a signal peptide, and low scores indicating that the amino acid is part of a mature protein.
How does SignalP work? ›
SignalP 6.0 is based on a protein language model, which makes it capable of understanding the phylogenomic context of a protein from its amino acid sequence directly. The model does no longer require the organism information for prediction.
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.
What is an example of a signal peptide? ›
Signal peptides
One example of a signal peptide in cosmeceutical products is valine-glycine-valine-alanine-proline-glycine (VGVAPG). This amino acid sequence has been shown to stimulate human skin fibroblast production, downregulate elastin expression, and promote the chemotaxis of fibroblasts in vitro.
What are the scores in SignalP? ›
A weighted average of the mean S and the max. Y scores. This is the score that is used to discriminate signal peptides from non-signal peptides. For non-secretory proteins all the scores represented in the SignalP output should ideally be very low (close to the negative target value of 0.1).
How to interpret antibody results? ›
A positive antibody test means the test has detected high levels of antibodies (above a certain amount) in your blood. It does NOT mean you are currently infected with COVID-19. The nucleocapsid antibody test detects antibodies that are produced by the immune system in response to COVID-19.
How do you identify a signal peptide? ›
In eukaryotes, signal peptide length ranges from approximately 12 to 40 amino acid residues with an average length of about 23 residues. Due to their N-terminal location and their tripartite structure, many signal peptides can be identified at first sight from the primary sequences of the proteins.
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.
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.
Why is the signal peptide important? ›
Signal peptides function to prompt a cell to translocate the protein, usually to the cellular membrane. In prokaryotes, signal peptides direct the newly synthesized protein to the SecYEG protein-conducting channel, which is present in the plasma membrane.
Signal peptides: For firmness
“These work by sending a message to the skin to stimulate production of collagen, elastin, and other proteins,” explains Marisa Garshick, M.D., a board-certified dermatologist at Manhattan Dermatology & Cosmetic Surgery in New York City.
How to remove signal peptides? ›
The signal peptides were removed in situ by carrying out cell-free protein synthesis in the presence of different concentrations of Triton X-100 (0.01%–0.5%, w/v) from the start of incubation in order for the N-terminal signal peptide to be cleaved-off immediately after its translation in the reaction mixture.
How do you interpret protein gel electrophoresis results? ›
Interpret Results
Simply draw a horizontal line across from the marker bands and estimate the size of the DNA in your sample based on the closest match. To accurately determine the size of DNA fragments in base pairs, you need to calculate the relative mobility of each band.
How do you interpret cell signal strength? ›
Cell phone signal strength is measured in decibels (dBm). Signal strengths can range from approximately -30 dBm to -110 dBm. The closer that number is to 0, the stronger the cell signal. In general, anything better than -85 decibels is considered a usable signal.
How do you read a protein marker? ›
A “protein molecular weight marker” (also called a “ladder”) is typically included on either of the two sides. The marker contains a mixture of proteins, each with a known molecular weight. This allows the user to determine the molecular weight of each protein in the sample.
How to interpret Blastp results? ›
Interpreting BLAST Results. BLAST results show all of the taxa that share sequence similarity with the query sequence based on the selected database. The results page includes a search summary, hit description table, graphic summary, and alignments that can help determine the quality or accuracy of a given hit.
