Login

Join for Free!
112435 members
table of contents table of contents

This paper will provide some examples of misleading annotations with regard to …


Biology Articles » Bioinformatics » Bioinformatics as a critical prerequisite to transcriptome and proteome studies » Proteins containing several functional domains

Proteins containing several functional domains
- Bioinformatics as a critical prerequisite to transcriptome and proteome studies

Proteins containing several functional domains may be a problem when results of sequence comparison or functional domain search are not carefully interpreted. A first example is the protein encoded by At3g22060. It is presently annotated as a receptor protein kinase related in the NCBI, TAIR, and TIGR databases because it contains a PFAM profile named Domain of Unknown Function DUF 26 (PF01657) usually associated with the protein kinase domain PFAM (PF00069) not present in this protein. The protein has therefore no predictable function at the moment. A second example is that of proteins belonging to a family of curculin-like (mannose-binding) lectins (At1g78850, At1g78860, and At1g16900). It is mentioned in the NCBI, TAIR, TIGR, and MIPS databases that they show low similarity to a Ser/Thr protein kinase of Zea mays (GI: 2598067). This similarity does exist with the curculin-like (mannose-binding) lectin domain (PF01453), but not with the protein kinase domain (PF00069) of the Z. mays protein absent in many members of the lectin family. The same is true for At1g53070 that is annotated as protein kinase related. The encoded protein has a legume lectin beta domain (PF00139) and no protein kinase domain. The annotation of genes At1g78850 and At1g53070 misled the authors of a proteomic study discussing the presence of putative protein kinases in cell wall preparations (Chivasa et al., 2002Go; Ndimba et al., 2003Go). They actually found putative lectins with completely different biological functions.

 


rating: 1.00 from 2 votes | updated on: 31 Oct 2006 | views: 3614 |

Rate article:







excellent!bad…