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Open Access Research article

Functional specialization in nucleotide sugar transporters occurred through differentiation of the gene cluster EamA (DUF6) before the radiation of Viridiplantae

Åke Västermark1*, Markus Sällman Almén1, Martin W Simmen2, Robert Fredriksson1 and Helgi B Schiöth1

Author Affiliations

1 Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24, Uppsala, Sweden

2 School of Biomedical Sciences, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh, EH8 9XD, UK

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BMC Evolutionary Biology 2011, 11:123  doi:10.1186/1471-2148-11-123

Published: 12 May 2011

Additional files

Additional file 1:

List of model organisms in study. List of name, kingdom, phylum, class, divergence time from H. sapiens, database, and reason for inclusion. The asterisk indicates that the divergence time is the average estimate in Time Tree, not the TimeTree "expert" estimate.

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Open Data

Additional file 2:

DMT families found in H. sapiens. List of DMT name, Pfam identifier, description, and status whether present in H. sapiens. DUF stands for domain unknown function, and UPF stands for unknown protein function.

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Open Data

Additional file 3:

All DMT sequences from Pfam mining (Methods) except sequences removed in alignment editing. List of all sequences in the mining after alignment editing.

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Open Data

Additional file 4:

Alignments for 19 DMT families in Jalview format. Alignments for 19 DMT families in Jalview format. The archive file contains alignment files that can be loaded in Jalview, and '.mup' files that contain Phobius TM predictions and pfam_scan domain location predictions as Jalview loadable markup language.

Format: TGZ Size: 351KB Download file

Open Data

Additional file 5:

Summary of evidence used to define alignment border. The table lists DMT families from [additional file 2: supplementary table S2], and whether alignment border can be supported by the following evidence types: symmetry, support from Jack DL, Yang NM, Saier MH, Jr. (2001), Pfam low complexity region, Jalview Quality Track (JQT), length gap, domain linker peptide SVM.

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Open Data

Additional file 6:

Unedited bipartitions tree of maximum likelihood bootstrap forest of first domain of EamA DMTs. This figure is included for comparison purpose with Figure 2. There is no lower bootrstrap support cutoff. The number of sequences is the same as in the parenthesized numbers in [Table 1].

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Open Data

Additional file 7:

Resolved dendrograms for human DMT-1, except EamA (treated in paper). The file contains the resolved dendrograms for: Cation efflux, TPT, UAA, NST, Zip, DUF914, DUF803, DUF1632, and UPF0546.

Format: TGZ Size: 15KB Download file

Open Data

Additional file 8:

Table listing number of DMT sequences in resolved maximum likelihood bootstrap forests. The table lists number of DMT sequences in resolved maximum likelihood bootstrap forests. Due to the editing necessary to achieve dendrogram resolution, the sequence numbers are reduced as compared to Table 1.

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Open Data

Additional file 9:

Table listing the number of sequences in independent branches found in resolved bootstrap forests. Summary for three of the bootstrap forests that contained independent subfamilies, showing the number of sequences in the branch system in the model organisms in [additional file 1: supplementary table S1]. The three-letter abbreviations are taken from the Latin names. The "chicken-specific branch" exists in older organisms than chicken, but does not contain any model organism sequences in M. musculus and H. sapiens. The numbers indicated can be subtracted from [Table 1] to obtain the number of sequences not members of the independent branches.

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Open Data

Additional file 10:

Table listing DMT families not present in human. The table lists the DMT name, Pfam identifier, description, and condition whether present in H. sapiens. The recommended domain border is shown, following Methods. All the DMTs not found in H. sapiens are either symmetric 5+5 or single domain DMTs.

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Open Data

Additional file 11:

Extraction of 19 DMTs in bacteria. Table lists number of bacterial full-length sequences found in Pfam species distribution for the 19 DMT families. Comparing these numbers to the numbers in plants in Table 6 shows that the distribution pattern is drastically different, where only EamA, Cation efflux and Zip families are represented in large numbers between these tables.

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Open Data

Additional file 12:

Complete listing of sequences from Pfam seed or full sequence for the DMT families not present in human. The DMTs are the non-human DMTs in [additional file 10: supplementary table S7]. The table lists DMT type, UniProt identifier, whether Bacteria, Archaea, or Eukaryota, the phylum, and full name. UniProt identifiers that are listed without species details are present in the current version of Pfam, but obsolete in UniProt. If the Pfam seed was smaller than 10, the full sequence set was used.

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Open Data

Additional file 13:

Presence of glycine constellations in TM segments in first and second DMT domains in two domain DMTs not found to be derived from EamA, excluding Cation efflux. Using the sequence conservation criteria in the methods section (>65%), the glycine constellations are found in two-domain DMTs not found to be derived from EamA. The presumed domain border of the DMTs is indicated in brackets in A+B form. N/A means that the TM does not exist in the given protein. TM(B) indicates a TM in the DMT-2 domain. The notation G(6)G indicates two glycines separated by six residues, i.e. G-X(6)-G. Cation efflux does not contain the G6G domain (see Results). SugT, RhaT, and FAE are not found in H. sapiens.

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Open Data

Additional file 14:

Archive of HMM files. The gzipped archive contains the 32 HMM files, one for each first domain of the 19 DMTs, and 2nd domains for the DMT families that have a second domain. The archive also contains 'ALL HHS.ods', a spreadsheet containing the values for all pairwise comparisons between the HMMs.

Format: TGZ Size: 243KB Download file

Open Data

Additional file 15:

Known substrates in H. sapiens of DMT nucleotide sugar transporters. The data are taken from UniProt annotation, having "reviewed" status.

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Open Data

Additional file 16:

Table listing 13 plant organisms, used in a separate extraction of DMT in plants. The table lists UniProt identifier, species name, common name, and reason for inclusion. The average divergence time, taken from TimeTree, is the average distance to the other representatives of Monocots, Dicots, Gymnosperms, Bryophytes, and Algae, from current example excluding its classification from the average.

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Open Data