Phylogenetic analysis of condensation domains in NRPS sheds light on their functional evolution

doi:10.1186/1471-2148-7-78

BMC Evolutionary Biology

Volume 7

Viewing options:

Abstract
Full text
PDF (522KB)
Additional files

Associated material:

Related literature:

Articles citing this article
on BioMed Central
on Google Scholar
on ISI Web of Science
on PubMed Central
Other articles by authors
on Google Scholar

Rausch C
Hoof I
Weber T
Wohlleben W
Huson DH

on PubMed

Rausch C
Hoof I
Weber T
Wohlleben W
Huson DH
Related articles/pages
on Google

on Google Scholar

on PubMed

Tools:

Post to:

Research article

Phylogenetic analysis of condensation domains in NRPS sheds light on their functional evolution

Christian Rausch¹ , Ilka Hoof¹^,2 , Tilmann Weber³ , Wolfgang Wohlleben³ and Daniel H Huson¹

¹Center for Bioinformatics Tübingen (ZBIT), Eberhard-Karls-Universität Tübingen, Sand 14, 72076 Tübingen, Germany

²Center for Biological Sequence Analysis, BioCentrum, Danmarks Tekniske Universitet, Building 208, 2800 Lyngby, Denmark

³Department of Microbiology/Biotechnology, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany

author email corresponding author email

BMC Evolutionary Biology 2007, 7:78doi:10.1186/1471-2148-7-78


Published:	16 May 2007

Additional files

Additional file 1:

Phylogenetic tree of all 525 C domain sequences of this study reconstructed using phyml. Zipped Nexus file (file name extension .nex.zip, to be unpacked and opened with SplitsTree [67,71]).

Format: ZIP Size: 744KB Download file

Additional file 2:

Phylogenetic tree of all 525 C domain sequences of this study reconstructed using phyml.

Format: PDF Size: 76KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 3:

Comparison of the logos generated from the pHMMs for the 3 subtypes ^LC_L, Starter and ^DC_Ldomain using LogoMat-P [72].

Format: PDF Size: 2.1MB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 4:

HMMER outputs of glyco-NRPS: fossils in ComC and ComD. ZIP file containing two text files.

Format: ZIP Size: 17KB Download file

Additional file 5:

Profile HMMs of the 4 complete C domain subtypes (^LC_L, Starter, ^DC_L, Dual) which can be used to detect and distinguish between the subtypes. Zipped text file (file name extension .hmm to be used with the program package HMMER [49]).

Format: ZIP Size: 273KB Download file

Additional file 6:

Aligned full length condensation domains of this study. Zipped sequence file (aligned protein sequences in FASTA format).

Format: ZIP Size: 240KB Download file

Additional file 7:

Profile HMMs of all 7 motifs of all subtypes (^LC_L, Starter, ^DC_L, Dual). Zipped text file (file name extension .hmm to be used with the program package HMMER [49].

Format: ZIP Size: 42KB Download file

Additional file 8:

Listing of NRPSs from known biosynthesis clusters used in this study.

Format: PDF Size: 54KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 9:

Sequence logos of all C domain motifs created with weblogo [31]. ZIP file containing image files in the PNG file format.

Format: ZIP Size: 5.9MB Download file