CyanoBase, a www database containing the complete nucleotide sequence of the genome of Synechocystis sp. strain PCC6803

Abstract

CyanoBase (http://www.kazusa.or.jp/cyano/) is a database containing genomic information on the cyanobacterium Synechocystis sp. strain PCC6803. It furnishes an annotation to each of the 3168 protein genes deduced from the entire nucleotide sequence of this genome. Information on the genome can be directly accessed through three different menus: a clickable physical map of the genome, a gene classification list, and a keyword search menu, all of which are accessible from the main page of the database. The entry page for a gene annotation contains the following information: the location of the gene on the genome, the nucleotide and deduced amino acid sequence of the gene, the result of a similarity search, and the classification of the deduced gene product according to its function. This page has reverse-links to the local physical map and gene classification list so that relevant genes can be searched in terms of their location on the genome and their function. In addition, the main page of CyanoBase provides engines for similarity searches between a query sequence and the entire genome sequence and for keyword searches, in addition to numerous links to pages containing related information.

The competence gene, comF, from Synechocystis sp. strain PCC 6803 is involved in natural transformation, phototactic motility and piliation

“…strain BD413 and Pseudomonas stutzeri were compiled from the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov) and were individually compared against the Synechocystis sp. strain PCC 6803 genome using BLASTN and BLASTP (Altschul et al, 1997), accessed through CyanoBase (Nakamura et al, 1998). All potential homologues, including those with low sequence identities and similarities, were recorded and used in multiple alignments in CLUSTALW (Thompson et al, 1994), as accessed through BioManager at the Australian National Genomic Information Service (http://www.angis.org.au).…”

“…Our investigations of competence-specific factors in Synechocystis sp. strain PCC 6803 have identified a hypothetical protein, encoded by the ORF slr0388 in CyanoBase (Nakamura et al, 1998), that has limited sequence similarity (<50 %) to the ComF competence proteins of other naturally transformable bacteria. This report describes the phenotypic effects of this second competence factor found in Synechocystis sp.…”

The Metabolic Network of Synechocystis sp. PCC 6803: Systemic Properties of Autotrophic Growth

“…Our starting point is the annotated genome sequence of Synechocystis sp. PCC 6803 as obtained from the CyanoBase Web site (Nakamura et al, 1998;Nakao et al, 2010).…”

“…Main resources during the reconstruction process were the CyanoBase Web site (Nakamura et al, 1998), KEGG (Kanehisa and Goto, 2000), MetaCyc and BioCyc (Caspi et al, 2010), BRENDA (Chang et al, 2009), the CyanoMutants Web site (Nakamura et al, 1999), and to a lesser extent UniProt (UniProt Consortium, 2010). The final network is provided as a MIRIAMcompliant SBML file (Supplemental File S1) and spreadsheet (Supplemental File S2).…”

Proteomics of marine bacteria

“…The first completely sequenced genomes of marine bacteria were those of the methanogenic bacterium Methanococcus jannaschii [8] and of the cyanobacterium Synechocystis spp. [9]. Recently, the genomes of three different members of the cyanobacterium species Prochlorococcus marinus have been sequenced [10,11].…”