PhosphaBase

PhosphaBase Search Tutorial

Quick Search
Advanced Search
Sequence Classification
Search Tips

FingerPRINTScan Tutorial

Search PRINTS with FingerPRINTScan

Quick Search

This is a basic keyword search. You may enter a gene or protein name, Swiss-Prot/TrEMBL identifier (e.g. "P60484"), organism, function (e.g. "cell cycle") or a tissue location (e.g. "heart"). This search is case-insensitive and partial keywords can also be entered.

The results table contains the family colour-code for each protein, their PhosphaBase ID (PhbID), gene and protein names and the organism they are from. These are ordered by subfamily and then by PhbID within each family. The results in the table can be reordered by clicking on the column headings.

Advanced Search

Four types of search are provided. All of these may be performed with or without an organism entered as well:

1) Gene name/Protein Name
2) Family
3) Function
4) Tissue

With the Gene/Protein or Family search the results table shows the same fields as the quick search; family colour, PhbID, gene, protein and organism. In addition, the Function and Tissue searches also return function or tissue information, respectively. The Gene/Protein, Function and Tissue results are ordered by subfamily and the Family results are ordered by organism. Sequences are ordered by PhbID within the subfamilies. As with the Quick search, the results in the table can be reordered by clicking on the column headings.

The results tables from both a quick and an advanced search contain PhbIDs, which are links to a detailed page about each particular protein. Here there is a summary section, containing the information shown in the results list, and also a list of external database links. Some, or all, of the following information can be provided: Swiss-Prot/TrEMBL identifier, InterPro domain matches, PDB links, IntAct links and OMIM disease links.

Sequence Classification

All phosphatases within this database have been placed into one of 5 phosphatase families or into an "unclassified" group:

PTP	Protein tyrosine phosphatases and Low Molecular Weight PTPs (LMW-PTPs)
DUSP	Dual-specificity phosphatases including cdc25
PTEN/MTM	PTEN and Myotubularins
Ser/Thr	Serine/threonine phosphatases; PPP, PPM (PP2C) and FCP subtypes
Histidine	Histidine phosphatases
Unclassified	Unclassified Serine/threonine and tyrosine phosphatases

This colour code is visible on all search and results pages as a reminder.

Unclassified phosphatase sequences are those that match a parent domain for a family, which is the more general match. They do not contain any other domains to help place them in a more detailed category. For example, there is an InterPro domain (IPR000387), which is a more general identifier of proteins belonging to the tyrosine phosphatase family. If this domain, but no others, is matched by a protein then it cannot be placed in the PTP, DUSP or Lipid phosphatase classes. Many proteins matching only IPR000387 will be false positives (not phosphatases but they match the pattern) and some may truly be phosphatases but are not similar enough to the more specific domains to be picked up.

Search Tips

It is often more useful to use the Quick Search to start with (located at the top right of the page) to locate your particular protein. This searches against several fields of information and will return anything related to your query.
When using the "By Name" search on the Advanced Search page, be aware that gene and protein names for the same sequence often differ, for example, PTPRR is the gene expressing the protein sometimes called PTP-SL. To make it easier to find your sequence of interest, try entering your term as both a gene name and a protein name.
If you cannot find your protein it may be helpful to try an alternative protein or gene name. If you have tried several searches and think your protein may be missing then please contact us to let us know of the problem.

FingerPRINTScan Tutorial

Searching the PRINTS database using FingerPRINTScan

FingerPRINTScan can be found here and information about the program can be found on the FingerPRINTScan homepage.

There are four areas you can play with. Although you can change the values of various parameters, the default should be good enough. Briefly, the E-value is the statistical calculation of the possible occurance of your sequence in the database. You then have the choice between various versions of the FingerPRINTScan database (the latest is the highest number, in our example "Prints38_1").

In order to scan the database with our sequence, we'll have to submit the sequence to the database. You can paste a sequence directly, or submit an ID code from the UNIPROT, UNIPROT_SWISSPROT or UNIPROT_TREMBL databases.

Once you have entered a sequence or ID number, you can screen the database using the

button. If there is a match to your sequence, tables illustrating the results will be displayed. In the represented example, the pasted sequence most probably fits with a KIM PTPase domain, as indicated by the first result in the table. Note here that the E-value is very low for this result, indicating high homology for the submitted sequence with a fingerprint in the database.

You can then access further details or view the graphical display for the results. Motif3D can be used to visualise a 3D representation of the fingerprint your sequence matches in a solved structure.