Swiss-Prot identifier

Each protein is identified by its SWISS-PROT identifier (Ref 52). 

Sequences are submitted to PredictProtein either by sending an E-mail message or by using a Web front end. Several options are available for sequence submission the query sequences can be submitted as single-letter amino acid code or by its SWISS-PROT identifier. In addition, a multiple sequence alignment in PASTA format or as a PIR alignment can also be submitted for secondary structure prediction. 

Bacterial proteins from MALDI FTMS experiments are identifiable using the Swiss-Prot database.53 In order to identify any microorganism, it is neces-... 

The version number changes only when the protein sequence coded by the CDS changes, and the stable part remains unchanged. The "STATUS IDENTIFIER" provides information about the relationship between the sequence in the SWISS-PROT entry and the CDS in the corresponding EMBL entry. 

High-speed identification from either PMF or MS/MS data can be achieved from non-redundant protein databases (Mann ef a/., 2001). These often include valuable annotations giving insight into functions of isolated and identified proteins. Many of these databases, such as NCBInr (National Centre for Biotechnology Information) and Swiss Prot (ExPASy Molecular Biology Server), can be used for protein identification. 

Rather than using an amino acid sequence to search SWISS-PROT, AACompI-dent of ExPASy Proteomic tools (http //www.expasy.ch/tools/) uses the amino acid composition of an unknown protein to identify known proteins of the same composition. The program requires the desired amino acid composition, the pi and molecular weight of the protein (if known), the appropriate taxonomic class, and any special keywords. The user must select from one of six amino acid constellations that influence how the analysis is performed. For each sequence in the database, the algorithm computes a score based on the difference in compositions between the sequence and the query composition. The results, returned by e-mail, are organized as three ranked lists. Because the computed scores are a measure of difference, a score of zero implies that there is exact correspondence between the query compo-... 

The known functional sites are described in the FEATURE lines of the annotated sequence hies such as PIR, GenPept, and Swiss-Prot. The PRO SITE database (http //www.expasy.ch/sprot/prosite.html) consists of biologically significant patterns/prohles/signatures that may aid in identifying the query sequence to the known family of proteins (Hofmann et al., 2000). The database that is composed of two ascii (text) hies, PROSITE.dat and PROSITE.doc, can be downloaded using FTP from ExPASy (ftp //www.expasy.ch/databases/prosite/) or Swiss Institute for... 

A variety of protein/DNA databases, such as GenBank, EMBL, NCBI, GenPept, Swiss-Prot, TrEMBL, PIR, OWL, IPI, and dbEST, are maintained by independent research groups for use by the public for proteome analysis. Databases have links to other databases and also provide vital information related to the identified proteins such as functions, any PTMs, domain and sites, 3D structures, homology to other proteins, associated diseases, sequence conflicts, and variants. 

Apart from text searches, both SWISS-PROT and TrEMBL can be queried by sequence analysis tools as well as protein identification and characterization tools. Tools like Peptldent or FindMod (see Section 4.4) take advantage of the annotation of SWISS-PROT/TrEMBL to improve their capacities of identifying and characterizing active chains and proteins annotated to be post-translationally modified. This is better than basing their computations and predictions merely on the precursor protein sequences. 

Figure 8.13. Increased sensitivity using PSI-BLAST. The human histidine triad (HIT) protein (SWISS-PROT P49789) was used as the query in a BLASTP search with the PSI-BLAST functionality enabled. Definition lines, scores, and values are shown for all statistically significant matches newly identified in each iteration.

Rather than using an amino acid sequence to search SWISS-PROT, AACompIdent uses the amino acid composition of an imknown protein to identify known proteins of the same composition (Wilkins et al., 1996). As inputs, the program requires the desired amino acid composition, the isoelectric point (pi) and molecular weight of... 

---