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Open Access Highly Accessed Research article

The diversity of cyanobacterial metabolism: genome analysis of multiple phototrophic microorganisms

Christian Beck1, Henning Knoop2, Ilka M Axmann1 and Ralf Steuer2*

Author Affiliations

1 Institute for Theoretical Biology, Charité-Universitätsmedizin, Invalidenstr. 43, D-10115 Berlin, Germany

2 Institute for Theoretical Biology, Humboldt-University of Berlin, Invalidenstr. 43, D-10115 Berlin, Germany

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BMC Genomics 2012, 13:56  doi:10.1186/1471-2164-13-56

Published: 2 February 2012

Additional files

Additional file 1:

Text file of CLOGs. Tab separated text file containing all CLOGs found by our methodes. Each line represents one CLOG, the entries for each strain are separated by tabs. Genes are annotated with the respective EC number, is applicable. If one strain has more than one entry in a CLOG, the genes are separated by a tilde. The last column summarizes all EC numbers denoted to genes in this CLOG and the frequency of appearance. Multiple ECs in one CLOG are separated by a hash.

Format: TXT Size: 1MB Download file

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Additional file 2:

Table of strains assigned to CLOGs of different sizes. The table provides the number of CLOGs assigned to each strain. The fraction of CLOGs associated with one or more EC number is given in brackets. The size of a CLOG is determined by the number of strains that it is associated with.

Format: DOC Size: 74KB Download file

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Additional file 3:

Table of enriched Gene Onthology terms. An excel file which contains the list of enriched GO terms for genes of the core CLOGs as well as for genes of the unique CLOGs. For each enriched term the table gives: the GO specific ID; the term in clear text; the total number of CLOGs annotated with the term across all clusters; the number of CLOGs in the particular set annotated with the term; the expected number of CLOGs in the current set annotated with the term, given an uniform distribution; the significance level of the enrichment, calculated with fisher's exact test. Only results with a p-value below 1e-3 are shown. Each list is divided into the three GO domains "biological process", "cellular component", and "molecular function".

Format: XLS Size: 53KB Download file

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Additional file 4:

Table of differential codon usage. The table shows the differences in codon usage of core and unique genes across all 16 cyanobacterial strains. Each number indicates the difference in codon usage of the core genes of one strain (row) compared to the core or unique genes of one strain (columns) and is calculated as described in Methods.

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Additional file 5:

Differences in EC annotation. The pdf contains a list of EC numbers corresponding to groups A and D in Figure 7, respectively.

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Additional file 6:

Tables of CLOGs related to key enzymes of central metabolism. The table provides the CLOGs associated to enzymes involved in the storage metabolism, glycolysis, Calvin Benson cycle, PPP, pyruvate metabolism and TCA cycle. For each strain a dot is representing a strain specific gene which can be found in the CLOG with the corresponding enzymatic function. Bracketed dots represent genes, which are assigned to that CLOG, but differ in annotation and most likely in function.

Format: XLS Size: 132KB Download file

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Additional file 7:

Annotated phylogenetic tree. Shown is a maximum-likelihood distance tree for sequenced cyanobacteria reproduced from Gupta et al. 2010 [9]. Strains chosen for analysis are indicated by red arrows.

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