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Metabolic peculiarities of Aspergillus niger disclosed by comparative metabolic genomics

Jibin Sun1, Xin Lu1, Ursula Rinas1 and An Ping Zeng12*

Author Affiliations

1 Helmholtz Centre for Infection Research, Inhoffenstr., 38124 Braunschweig, Germany

2 Hamburg University of Technology, Institute of Bioprocess and Biosystems Engineering, Denickestr., 21071 Hamburg, Germany

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Genome Biology 2007, 8:R182  doi:10.1186/gb-2007-8-9-r182

Published: 4 September 2007

Additional files

Additional data file 1:

Methods for prediction and annotation of protein-coding sequences.

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Additional data file 2:

Orthologous groups of genes from selected fungi and their functions.

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Additional data file 3:

Strain-specific CDSs identified by cross-comparing the two A. niger strains.

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Additional data file 4:

Genome-wide metabolic network of A. niger as a reaction graph where nodes are reactions and links are common reactants (substrate or product) of two successive reactions. The color of the nodes represents different functional categories.

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Additional data file 5:

A clickable version of Figure 2 where nodes (metabolites) are linked to the KEGG Ligand database for detailed information.

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Additional data file 6:

A clickable version of Additional data file 4 where nodes (reactions) are linked to the KEGG Ligand database for detailed information.

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Additional data file 7:

All the reactions used for reconstruction of the A. niger metabolic network. The corresponding EC numbers and genes are also shown.

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Additional data file 8:

Results of a comparative assessment of the central metabolic network.

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Additional data file 9:

Enzyme-encoding genes unique to one of the two A. niger strains in comparison with the other selected fungi.

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Additional data file 10:

Enzyme-encoding genes common in both A. niger strains and unique to them in comparison with the other selected fungi.

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Additional data file 11:

Phylogenetic analysis of the S-adenosylmethionine tRNA ribosyltransferase.

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Additional data file 12:

A detailed version of Figure 3, showing a network view from glucose to citrate, including the names of all metabolites.

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Additional data file 13:

Phylogenetic analysis of citric acid synthases (CS), where 1,123 sequences from the NCBI nr protein database homologous to any of the six CSs of A. niger (cutoff E-value 1E-20, partial sequence ignored) were aligned together with the CSs from A. niger ATCC 9029 and ATCC 1015 to build the phylogenetic tree with 1,000 time bootstraps, using the software ClustalW. Part A is an overview while part B is the full phylogenetic tree with GI number, strain name, taxonomy, and bootstrap values.

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Additional data file 14:

The reaction database used for reconstruction of the metabolic network.

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Additional data file 15:

The protein database of A. niger ATCC 9029.

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