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Announcing New Curated Cyanobacterial Databases in BioCyc

The microbial genome web portal contains three new, highly curated cyanobacterial Pathway/Genome Databases, in addition to one previously existing cyanobacterial database in BioCyc (for Synechococcus elongatus PCC 7942). Each database integrates a variety of information including the genome, metabolic pathways, operons, protein features, Gene Ontology terms, and orthologs. Each of these databases received extensive literature-based curation to correct annotation errors and to integrate information about experimentally determined pathways and gene functions.

"I have used BioCyc for research and teaching for over a decade. It is unquestionably one of the most useful resources for microbial metabolism and I ensure that all our microbiology students become familiar with its capabilities."
-- Prof. Louis Sherman, Purdue University

Curated cyanobacaterial databases:

These four databases will be free to access for the next few months for the community to explore them, and will then be available by subscription.

In addition, the newly curated gene functions for each of the preceding organisms were propagated via ortholog relationships among those four databases, and to the following databases. For example, gene csoS1A was newly curated as a hexameric carboxysome shell protein CsoS1A in Prochlorococcus marinus marinus CCMP1375, but orthologs of that gene are present in several of the other genomes, therefore we propagated the gene and protein names from CCMP1375 to all of the other databases in which an ortholog was present.

Curation of the three new databases involved manual removal of incorrect or irrelevant chemical compounds, reactions, and pathways; assignment of gene functions for genes with incorrect or missing annotation; construction of protein complexes; import of pathways that were not predicted due to missing/incorrect annotation; assignment of transport reactions to transporters; addition of pointers from pathways to other pathways upstream or downstream; and curation of relevant literature, including novel commentary for cyanobacterial-specific proteins and pathways. Multiple examples of corrected annotation errors are given in our blog post about these new cyanobacterial databases.

BioCyc now contains a total of 200+ cyanobacterial databases.

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