QuickTree: building huge Neighbour-Joining trees of protein sequences
ABSTRACT We have written a fast implementation of the popular Neighbor-Joining tree building algorithm. QuickTree allows the reconstruction of phylogenies for very large protein families (including the largest Pfam alignment containing 27000 HIV GP120 glycoprotein sequences) that would be infeasible using other popular methods.
Full-textDOI: · Available from: Alex Bateman, Jun 06, 2014
- SourceAvailable from: Shradha Khater
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- "Multiple sequence alignment (MSA) for each family was built using ClustalW. For phylogenetic analysis, bootstrapped trees were built and visualized using QuickTree (Howe et al. 2002) tool of PHYLIP package and iTOL, respectively. The phylogenetic trees can be accessed using the URL http://itol.embl.de/shared/shradha "
ABSTRACT: Bacterial phosphothreonine lyases catalyze a novel post-translational modification involving formation of dehydrobutyrine/dehyroalanine by β elimination of the phosphate group of phosphothreonine or phosphoserine residues in their substrate proteins. Though there is experimental evidence for presence of dehydro amino acids in human proteins, no eukaryotic homologs of these lyases have been identified as of today. A comprehensive genome wide search for identifying phosphothreonine lyase homologs in eukaryotes was carried out. Our fold based search revealed structural and catalytic site similarity between bacterial phosphothreonine lyases and BLES03, a human protein with unknown function. Ligand induced conformational changes similar to bacterial phosphothreonine lyases, and movement of crucial arginines in the loop region to the catalytic pocket upon binding of phosphothreonine containing peptides was seen during docking and molecular dynamics studies. Genome wide search for BLES03 homologs using sensitive profile based methods revealed their presence not only in eukaryotic classes like chordata and fungi, but also in bacterial and archaebacterial classes. The synteny of these archaebacterial BLES03 like proteins was remarkably similar to that of type IV lantibiotic synthetases which harbor LanL like phosphothreonine lyase domains. Hence, context based analysis reinforced our earlier sequence/structure based prediction of phosphothreonine lyase catalytic function for BLES03. Our in silico analysis has revealed that BLES03 like proteins with previously unknown function are novel eukaryotic phosphothreonine lyases involved in biosynthesis of dehydro amino acids, while their bacterial and archaebacterial counterparts might be involved in biosynthesis of natural products similar to lantibiotics.Genome Biology and Evolution 07/2014; 6(8). DOI:10.1093/gbe/evu161 · 4.53 Impact Factor
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- "Thus, we used a method to filter the potential non-targets based on the preliminary phylogenetic analysis of all sequences matching the HMM profile. Firstly, full sequence dataset were aligned by ClustalW-MPI (Li, 2003), and subjected to neighbor-joining tree reconstruction by Quick- Tree (Howe et al., 2002). Secondly, all protein sequences were clustered based on the pairwise distance (60.3). "
ABSTRACT: Despite intense scrutiny from researchers in the fields of biochemistry and metabolism, our understanding of the evolutionary history of the key anabolic shikimate pathway remains limited. To shed light on the early evolutionary events leading to the assembly of the pathway, we investigated the distributions, domain architectures and phylogenies of component enzymes using a bioinformatic procedure based on Hidden Markov Model profiles. The aro genes for the canonical shikimate pathway had most wider distribution in prokaryotes; and the variant pathway coordinated by 2-amino-3,7- dideoxy-D-threo-hept-6-ulosonic acid (ADH) synthase and type II 3-dehydroquinate (DHQ) synthase could be identified in most of archaeal species. In addition, the ancient bidirectional horizontal gene transfer events had happened between two prokaryotic domains: Bacteria and Archaea. Besides 3- deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase, the phylogenetically distinct subfamilies of 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase and chorismate synthase had ever emerged in the evolutionary history of shikimate pathway. These findings provide new insight into the early evolution of the shikimate pathway and advance our understanding of the evolution of metabolic pathways.Molecular Phylogenetics and Evolution 02/2014; 75:154-164. DOI:10.1016/j.ympev.2014.02.015 · 4.02 Impact Factor
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- "Thus, we filtered the potential nontargets based on a preliminary phylogenetic analysis of all sequences matching the HMM profile. First, the complete sequence data set was aligned with ClustalW- MPI (Li 2003) and subjected to neighbor-joining tree reconstruction with QuickTree (Howe et al. 2002). Second, all protein sequences were clustered based on their pairwise distances ( 0.3). "
ABSTRACT: Menaquinone (MK) is an important component of the electron transfer system in prokaryotes. One of its precursors, 1,4-dihydroxy-2-naphthoate, can be synthesized from chorismate by the classical MK pathway. Interestingly, in some bacteria, chorismate can also be converted to 1,4-dihydroxy-6-naphthoate by four enzymes encoded by mqnABCD in an alternative futalosine pathway. In this study, six crucial enzymes belonging to these two independent nonhomologous pathways were identified in the predicted proteomes of prokaryotes representing a broad phylogenetic distribution. Although the classical MK pathway was found in 32.1% of the proteomes, more than twice the proportion containing the futalosine pathway, the latter was found in a broader taxonomic range of organisms (18 of 31 phyla). The prokaryotes equipped with the classical MK pathway were almost all aerobic or facultatively anaerobic, but those with the futalosine pathway were not only aerobic or facultatively anaerobic but also anaerobic. Phylogenies of enzymes of the classical MK pathway indicated that its genes in Archaea were probably acquired by an ancient horizontal gene transfer from bacterial donors. Therefore, the organization of the futalosine pathway likely predated that of the classical MK pathway in the evolutionary history of prokaryotes.Genome Biology and Evolution 01/2014; 6(1). DOI:10.1093/gbe/evu007 · 4.53 Impact Factor