dbCAN: a web resource for automated carbohydrate-active enzyme annotation

Abstract

Carbohydrate-active enzymes (CAZymes) are very important to the biotech industry, particularly the emerging biofuel industry because CAZymes are responsible for the synthesis, degradation and modification of all the carbohydrates on Earth. We have developed a web resource, dbCAN (http://csbl.bmb.uga.edu/dbCAN/annotate.php), to provide a capability for automated CAZyme signature domain-based annotation for any given protein data set (e.g. proteins from a newly sequenced genome) submitted to our server. To accomplish this, we have explicitly defined a signature domain for every CAZyme family, derived based on the CDD (conserved domain database) search and literature curation. We have also constructed a hidden Markov model to represent the signature domain of each CAZyme family. These CAZyme family-specific HMMs are our key contribution and the foundation for the automated CAZyme annotation.

Figure 1.

Flowchart of our procedure for identifying and defining signature domain models for an example CAZyme family. Here this family contains four full-length proteins with different lengths. The red box is the signature domain regions defining the CAZyme family. It could be either identified by searching against annotated functional domain models in the CDD database or retrieved from literature curation. Boxes in other colors are non-overlapped domain regions annotated by other CDD models. The CDD search is done by RPS-BLAST, the multiple sequence alignment is done by MAFFT (default parameters), the building of HMM is done by hmmbuild and all other processes are done by self-developed perl scripts.

Figure 2.

Snapshots of dbCAN annotation server. (A) The query page, where users can paste some FASTA format protein sequences in the text box or upload a text file containing the FASTA sequences. Clicking on ‘submit’ will invoke the hmmscan program in the backend server to search the queried sequences against the dbCAN HMMs. (B) The result page, where users can download the raw output from the hmmscan run and view the processed tabular format output (if alignment length >80 amino acids, use E-value < 1e − 5, otherwise use E-value < 1e − 3). A diagram is shown in the bottom to illustrate the CAZyme domain architecture according to the positional information in the tabular output.