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A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases

Michelle L Green* and Peter D Karp

Author Affiliations

Bioinformatics Research Group, SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA

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BMC Bioinformatics 2004, 5:76 doi:10.1186/1471-2105-5-76

Published: 9 June 2004

Additional files

Additional File 1:

Predicted pathway hole fillers in Pathway/Genome Databases A summary of the actual changes made to the three PGDBs presented in the manuscript.

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Additional File 2:

Filled pathway holes in Cb. crescentus A list of the specific putative enzymes assigned in CauloCyc.

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Additional File 3:

Filled pathway holes in M. tuberculosis H37Rv A list of the specific putative enzymes assigned in MtbRvCyc.

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Additional File 4:

Filled pathway holes in V. cholerae A list of the specific putative enzymes assigned in MtbRvCyc.

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Additional File 5:

ClustalW alignment of query sequences and putative Caulobacter L-aspartate oxidase.

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Additional File 6:

ClustalW alignment of query sequences and putative Caulobacter nicotinate-nucleotide adenylyltransferase.

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Additional File 7:

ClustalW alignment of query sequences and putative Caulobacter NAD+ synthetase (glutamine-hydrolyzing).

Format: HTML Size: 249KB Download file

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