Using the Structure‐Function Linkage Database to Characterize Functional Domains in Enzymes
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- Abstract
- Table of Contents
- Figures
- Literature Cited
Abstract
The Structure?Function Linkage Database (SFLD; http://sfld.rbvi.ucsf.edu/) is a Web?accessible database designed to link enzyme sequence, structure, and functional information. This unit describes the protocols by which a user may query the database to predict the function of newly sequenced enzymes and to correct misannotated functional assignments for enzymes currently in public databases. It is especially useful in helping a user discriminate functional capabilities of a sequence that is only distantly related to characterized sequences in publicly available databases.
Keywords: superfamily analysis; sequence analysis; structure?function relationships; function prediction; annotation transfer
Table of Contents
- Basic Protocol 1: Using the SFLD to Predict the Function of an Uncharacterized Enzyme
- Basic Protocol 2: Using the SFLD to Correct Misannotated Functional Assignments
- Guidelines for Understanding Results
- Commentary
- Literature Cited
- Figures
Materials
Figures
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Figure 2.10.1 The SFLD homepage. View Image -
Figure 2.10.2 The SFLD Search by Enzyme page with a protein sequence pasted into the Protein Sequence box. View Image -
Figure 2.10.3 SFLD sequence search results. Results are displayed in tabular format, sorted by HMMER E‐value. View Image -
Figure 2.10.4 Alignment of a query sequence with the SFLD galactonate dehydratase family. The query sequence is the top sequence in the alignment. View Image -
Figure 2.10.5 Alignment of a query sequence with the SFLD galactonate dehydratase family. Family‐specific catalytic residues are automatically highlighted. Note that the catalytic residue position numbering given in the table below the alignment is keyed to an alignment without a query sequence, and therefore may not correspond to the numbering on alignments that include query sequences. View Image -
Figure 2.10.6 A dendrogram of the SFLD galactonate dehydratase family, plus a query sequence. View Image -
Figure 2.10.7 The SFLD family page for the galactonate dehydratase family. View Image -
Figure 2.10.8 The SFLD family page for the muconate cycloisomerase family. Note the second display panel, which provides a pictorial view of the active site for a representative family member with a solved crystal structure. View Image -
Figure 2.10.9 The NCBI homepage with Protein selected in the Search listbox and gi number 23100420 specified as the protein sequence for which to search. View Image -
Figure 2.10.10 NCBI summary protein search results for gi number 23100420. View Image -
Figure 2.10.11 The SFLD Browse by Reaction page. View Image -
Figure 2.10.12 Alignment of a query sequence with the SFLD muconate cycloisomerase family. Family‐specific catalytic residues are automatically highlighted. View Image
Videos
Literature Cited
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Key References | |
Pegg et al., 2005. See above. | |
Describes the SFLD. | |
Gerlt and Babbitt, 2001. See above. | |
Describes various mechanisms of enzyme evolution, including chemistry‐driven evolution of mechanistically diverse superfamilies. Several mechanistically diverse superfamilies are discussed in detail. | |
Babbitt et al., 1995. See above. | |
Describes the use of superfamily analysis to elucidate the function of an uncharacterized ORF in Escherichia coli. | |
Internet Resources | |
http://sfld.rbvi.ucsf.edu/ | |
The Structure‐Function Linkage Database. | |
http://theseed.uchicago.edu/FIG/index.cgi | |
Get operon context information for a specific gene. | |
http://modbase.compbio.ucsf.edu/modbase‐cgi‐new/search_form.cgi | |
View modeled 3‐D structures for a specific protein. |