Figure 1.
Homology based annotation transfer: Problems.
(A) Paralogy problem: Paralogs are more likely to diverge functionally with respect to orthologs. If our putative template is a paralog, the probability that the query has similar function decreases. (B) Moonlighting problem: If the template performs multiple functions, the query could have retained only some of them (and vice-versa, if the query were a moonlighting protein, using a non-moonlighting template would result in an incomplete annotation of the query). (C) Multi-domain proteins problem: If the template is annotated based on the function of a domain that is not aligned to the query, annotation transfer is not possible. (D) Database mis-annotations problem: Database entries may have been mis-annotated; the risk is especially high if annotation was performed automatically via homology transfer.
Table 1.
Do's and Don'ts of annotation transfer by homology.
Table 2.
Do's and Don'ts of annotation transfer by homology.
Figure 2.
Using structure to predict function.
The protein represented here is PDBid: 2eve. All figures are derived from the Northeast Structural Genomics Consortium structure gallery (http://nmr.cabm.rutgers.edu:9090/gallery/jsp/Gallery.jsp). AstexViewer 2.0 [49] is used for visualization. (A) Superposition of 2eve structure (gray) and of the structure of a homolog (blue, PDBid: 2ar1), using Skan [59]. 2eve hosts three co-crystallized small non-functional ligands (green; ball and stick). Three structurally aligned residues of 2eve and 2ar1 are also shown (red and yellow; ball and stick). (B) Surface residue conservation: Conserved residues (mauve) versus variable residues (cyan). Conservation is calculated as follows: homologs of 2eve are collected using three iterations of PSI-BLAST [15] retaining all homologs with E-value<10−3 and reducing redundancy at 80% sequence identity with CD-HIT [85]. Then, a multiple sequence alignment is created using CLUSTALW [86]. Finally, the multiple sequence alignment is used as input to ConSurf [54], which uses it to calculate residue conservation. (C) Residue conservation within the protein largest cavity (as defined by SCREEN [87]). (D) 2eve surface electrostatic potential (using GRASP2 [59]) (positive in blue, negative in red).