6-Phosphogluconolactonase

Further details of the analysis

The T. brucei 6PGL was compared with the SwissProt release 39 / TrEMBL release 17 database indexed at European Bioinformatics Institute (EBI, Hinxton UK), containing 671,000 protein sequences, using the NCBI BLASTP program and the BLOSUM 62 matrix (http://www2.ebi.ac.uk/blastall/) . Click here to inspect the BLASTP output file.

The best E values (e-150) were obtained with itself (Q9GRG6) and with the sequence of the cyanobacterium Synechocystis sp (6PGL_SYNY3) (E value 3e-23), with whom it shared 35% identical positions (according to the BlastP algorithm).

All sequences from the BlastP output with E values of e-10 or smaller were selected for the creation of a multiple alignment in Clustal. The T. brucei sequence shared (after removal of gaps) the highest percentage of identical residues with the Synechocystis sequence (40.1%). The percentages of identity with the other taxa ranged from 40 - 29%.

The alignment was freed from gaps and converted to Phylip format. This final alignment containing 30 sequences and 162 sites was used for likelihood mapping as implemented in PUZZLE version 4.0.1. The result indicated that the dataset contained only a weak phylogenetic signal (with 15% star-like quartets). As a consequence the maximum likelihood tree created by Puzzle was highly star-like and did not allow to determine the branching order of most of the taxa.

(To test a possible monophyly of the trypanosomatids with the cyanobacteria a four-cluster likelihood mapping was carried out. The result revealed that only 4.6% of the quartets supported such monophyly, while 63.5% of quartets were unresolved star-like trees.)

When some long branching taxa such as the Treponema, Thermotoga and C. elegans were removed from the dataset in an NJ analysis the T. brucei sequence started to become monophyletic with the cyanobacteria although with little bootstrap support (44%) and paraphyletic with the cyanobacteria in a MP analysis. This new dataset, containing 27 taxa and 162 sites, was saved to disk for further analysis. Likelihood mapping showed that the phylogenetic signal in the dataset had slightly increased (from 15 to 12% starlike quartets trees). To test a possible monophyly of the trypanosomatids with the cyanobacteria a four-cluster likelihood mapping was carried out. The result revealed that only 17.2% of the quartet trees supported such monophyly, while 58% of quartets were unresolved star-like trees.

The maximum likelihood analysis showed that the tree remained very star-like with little resolution in the order of branching in the procaryotic clade. Smallest ML distances of the T. brucei sequence were found with the two cyanobacteria (1.29 and 1.31) while distances with the other taxa ranged from 1.39-1.77

Conclusion