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This article is part of the supplement: Validation methods for functional genome annotation

Open Access Research

Genome-wide protein localization prediction strategies for gram negative bacteria

Margaret F Romine

Author Affiliations

Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA

BMC Genomics 2011, 12(Suppl 1):S1  doi:10.1186/1471-2164-12-S1-S1

Published: 15 June 2011

Additional files

Additional file 1:

Alignment of N-termini of the periplasmic [Ni-Fe] hydrogenase large subunit, HyaB. Representative N-terminal amino acid sequences from 14 different Shewanella species are shown adjacent to their corresponding locus tag. Residues found in the conserved TAT motif are shown in bold. The predicted N-termini of the mature proteins are underscored. The sequences corresponding the most N-terminal peptide identified in four of these microbes [68] using the AMT approach [69] is shown in bold and underscored.

Format: DOCX Size: 13KB Download file

Open Data

Additional file 2:

Curated ortholog grouping and location predictions for 81169 proteins predicted to be encoded in the genomes of 19 Shewanella. Pseudogenes are denoted with an asterisk in the locus tag column.

Format: XLSX Size: 2MB Download file

Open Data

Additional file 3:

FastA file of proteins predicted to be encoded in the genomes of 19 Shewanella. This file includes translations of pseudogenes, with internal stop codons assigned the value ‘X’.

Format: ZIP Size: 16.8MB Download file

Open Data