Announcing New Curated Cyanobacterial Databases in BioCyc
The BioCyc.org 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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