Open Access Research article

Identification of the type II cytochrome c maturation pathway in anammox bacteria by comparative genomics

Christina Ferousi1, Daan R Speth1, Joachim Reimann1, Huub JM Op den Camp1, James WA Allen2, Jan TM Keltjens1 and Mike SM Jetten1*

Author Affiliations

1 Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Heyendaalseweg 135, 6525, AJ, Nijmegen, the Netherlands

2 Department of Biochemistry, University of Oxford, South Parks Road, OX13QU Oxford, UK

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BMC Microbiology 2013, 13:265  doi:10.1186/1471-2180-13-265

Published: 23 November 2013

Additional files

Additional file 1:

Reference protein datasets for cytochrome c maturation Systems (I-III) and thioredoxin dataset for System II.

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Additional file 2:

Cytochrome c maturation System biomarkers. For each cytochrome c maturation System (I-III), essential protein components that can be used as suitable biomarkers for annotation purposes were selected (for details see Additional file 3) and their defining characteristics are listed herein.

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Additional file 3:

Selection criteria for cytochrome c maturation System biomarkers.

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Additional file 4:

CcsA and CcsB homologs identified in four anammox genera using blastP. Homology identification was performed with blastP as implemented in CLC genomics workbench (v6.5.1, CLCbio, Aarhus, Denmark). Whole anammox genomes are used as queries against a reference database that comprises all reviewed entries for CcsA and CcsB available at UNIPROT. An E-value of 10-6 was set as cut off to prevent ambiguity.

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Open Data

Additional file 5:

CcsA and CcsB homologs identified in four anammox genera using HHpred and HMMER. Homology identification was performed with blastP as implemented in CLC genomics workbench (v6.5.1, CLCbio, Aarhus, Denmark). Whole anammox genomes are used as queries against a reference database that comprises all reviewed entries for CcsA and CcsB available at UNIPROT. Intra- and intergenome searches with the significant hits from Kuenenia as queries were also performed (Additional file 4). Retrieved results were further analyzed with HHpred and HMMER. An E-value of 10-3 was set as cut off to prevent ambiguity.

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Open Data

Additional file 6:

CcsX and DsbD homologs identified in four anammox genera using blastP, HHpred and HMMER. Homology identification was performed with blastP as implemented in CLC genomics workbench (v6.5.1, CLCbio, Aarhus, Denmark). Whole anammox genomes are used as queries against a reference database that comprises all reviewed entries for CcsX and DsbD available at UNIPROT. Retrieved results were further analyzed with HHpred and HMMER. (*): E-value cut off set at 10-6; (**): E-value cut off set at 10-3.

Format: XLSX Size: 14KB Download file

Open Data