Open Access Research article

Insights into the evolution of sorbitol metabolism: phylogenetic analysis of SDR196C family

Agustín Sola-Carvajal, María I García-García, Francisco García-Carmona and Álvaro Sánchez-Ferrer*

  • * Corresponding author: Álvaro Sánchez-Ferrer alvaro@um.es

Author Affiliations

Department of Biochemistry and Molecular Biology-A, Faculty of Biology, Regional Campus of International Excellence “Campus Mare Nostrum”, University of Murcia Campus Espinardo, Murcia, E-30100, Spain

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BMC Evolutionary Biology 2012, 12:147  doi:10.1186/1471-2148-12-147

Published: 16 August 2012

Additional files

Additional file 1:

Distribution of SDH gene among bacteria. The table indicates the bacterial species that encode a SDH gene, its taxonomy, ecology and niche.

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Additional file 2:

GC content differences between SDH genes and genome. The table indicates the differences in GC content between the SDH gene and the core genome of the bacterium, where it is encoded.

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Additional file 3:

Structure of the SDH clusters among bacterial groups. SDH gene was placed in the middle to facilitate cluster visualization. Variants of the cluster among taxonomic groups are represented by numbers (1–21).

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Additional file 4:

Multiple sequence alignments (MSAs) obtained with GUIDANCE and their corresponding Guidance scores [[25,26]. The file shows the result obtained for the MSA of the 6 lineages, 3 sublineages and 16S rRNA. In all cases, an overall quality assessment (Guidance score) of above 0.97 was obtained with the MSA algorithm PRANK [27].

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Additional file 5:

Phylogenetic trees of bacteria containing SDH gene. The file shows two phylogenetic trees of SDH gene using Bayesian and Maximun Likelihood, as tree building methods.

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Additional file 6:

Phylogenetic trees (16S rRNA) of bacteria containing the SDH gene. The file contained two phylogenetic trees of 16S rRNA of bacteria containing SDH gene, using Bayesian and Maximum Likelihood, as tree building methods.

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Additional file 7:

Molecular modeling of SDH enzymes from the six lineages described in bacterial SDH. The proteins were modeled with Geno3D [49] and rendered by PyMol [50]. Selected proteins were Uniprot codes: lineage 1, A3MHB9; lineage 2, A1WMN; lineage 3 E1VCL7; lineage 4, A5FVQ; lineage 5, A9CES4; lineage 6.1, O68112; lineage 6.2, A3K129; lineage 6.3, A3PKH5.

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Additional file 8:

Multiple sequence alignment of bacterial SDH proteins. ESPript [37] output was obtained with the aligned sequences from Additional file 1. Strictly conserved residues have a solid background. Symbols above sequences represent the secondary structure. Conserved structural blocks (I-XI) are shown below the sequences. Circles represent the divergent amino acids according to the following color code: Grey; conserved amino acids in Lineage I and divergent in Lineage V, Red; conserved amino acids in Lineage I and divergent in Lineage VI, Orange; conserved amino acids in Lineage II and divergent in Lineage I, Black; conserved amino acids in Lineage II and divergent in Lineage VI, Pink; conserved amino acids in Lineage V and divergent in Lineage I, Purple; conserved amino acids in Lineage V and divergent in Lineage VI, Green; conserved amino acids in Lineage VI and divergent in Lineage I, Blue; conserved amino acids in Lineage VI and divergent in Lineage II.

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Additional file 9:

Predicted critical amino acid sites responsible for functional divergence. The table represents the values of Qk of all pair analyses. Values with a Qk > 0.75 are indicated with a red background.

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Additional file 10:

Candidates for amino acid sites related with functional divergence. The numbering used corresponds with that of the alignment implemented by DIVERGE. Cat. I refers to Category I and Cat. II refers to Category II. A: Cat. II; conserved tandem in Lineage II and variable in Linage I. B: Cat. I; Conserved tandem in Lineage I and variable in Lineage V and Cat. II; conserved tandem in Lineage V and variable in Lineage I. C: Cat. I; conserved tandem in Lineage V and variable in Lineage VI. D: Cat. I; conserved tandem in Lineage I and variable in Lineage VI and Cat. II; conserved tandem in Lineage VI and variable in Lineage I. E: Cat. I; conserved tandem in Lineage II and variable in Lineage VI and Cat. II; conserved tandem in Lineage VI and variable in Lineage II. Critical amino acids responsible for functional divergence are shown in the R. sphaeroides SDH crystal structure (pdb:1k2w). Divergent residues of category I are depicted in red and those of category II are depicted in blue.

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Additional file 11:

Alignment of SDH family in ClustalW format (.aln) used in the DIVERGE analysis.

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Additional file 12:

Phylogenetic tree in PhylM (.ph) used in the DIVERGE analysis.

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