MaxAlign: maximizing usable data in an alignment

Gouveia-Oliveira, Rodrigo; Sackett, Peter Wad; Pedersen, Anders Gorm

doi:10.1186/1471-2105-8-312

Cited by 111 publications

(82 citation statements)

References 16 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The original dataset was reduced to 598 sequences by removing redundant sequences and increasing gap-free sites using CD-HIT [32] and MaxAlign [33] within the MAFFT online alignment tool [34] (http://mafft.cbrc.jp/alignment/server/). The tree was built using 100 iterations and a 60% threshold value for bootstraps.…”

Section: Methodsmentioning

confidence: 99%

Exploring Bacterial Carboxylate Reductases for the Reduction of Bifunctional Carboxylic Acids

Khusnutdinova

Flick

Popović

et al. 2017

Biotechnology Journal

View full text Add to dashboard Cite

Carboxylic acid reductases (CARs) selectively reduce carboxylic acids to aldehydes using ATP and NADPH as cofactors under mild conditions. Although CARs have attracted significant interest, only a few enzymes have been characterized to date, whereas the vast majority of CARs have yet to be examined. Herein we report that 12 bacterial CARs reduced a broad range of bifunctional carboxylic acids containing oxo-, hydroxy-, amino-, or second carboxyl groups with several enzymes showing activity toward 4-hydroxybutanoic (4-HB) and adipic acids. These CARs exhibited significant reductase activity against substrates whose second functional group is separated from the carboxylate by at least three carbons with both carboxylate groups being reduced in dicarboxylic acids. Purified CARs supplemented with cofactor regenerating systems (for ATP and NADPH), an inorganic pyrophosphatase, and an aldo-keto reductase catalyzed a high conversion (50–76%) of 4-HB to 1,4-butanediol (1,4-BDO) and adipic acid to 1,6-hexanediol (1,6-HDO). Likewise, Escherichia coli strains expressing eight different CARs efficiently reduced 4-HB to 1,4-BDO with 50–95% conversion, whereas adipic acid was reduced to a mixture of 6-hydroxyhexanoic acid (6-HHA) and 1,6-HDO. Thus, our results illustrate the broad biochemical diversity of bacterial CARs and their compatibility with other enzymes for applications in biocatalysis.

show abstract

Section: Methodsmentioning

confidence: 99%

Exploring Bacterial Carboxylate Reductases for the Reduction of Bifunctional Carboxylic Acids

Khusnutdinova

Flick

Popović

et al. 2017

Biotechnology Journal

View full text Add to dashboard Cite

show abstract

“…After sequence retrieval, multiple alignments were prepared using MAFFT 6.956 85 , and ambiguous codons were removed using trimAl 57 implemented in Phylogears2-2.0.2013.03.15 (http://www.fifthdimension.jp/products/phylogears/) with the 'gappyout' option. Poorly aligned sequences were removed using MaxAlign 86 . Phylogenetic trees were reconstructed by the maximum-likelihood method using RAxML v8.0.26 51 with the general time-reversible (GTR) model of nucleotide substitution and four discrete gamma categories of rate heterogeneity ('GTRGAMMA' option).…”

Section: Go Enrichment Analysis Supplementarymentioning

confidence: 99%

Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory

et al. 2017

View full text Add to dashboard Cite

Carnivorous plants exploit animals as a nutritional source and have inspired long-standing questions about the origin and evolution of carnivory-related traits. To investigate the molecular bases of carnivory, we sequenced the genome of the heterophyllous pitcher plant Cephalotus follicularis, in which we succeeded in regulating the developmental switch between carnivorous and non-carnivorous leaves. Transcriptome comparison of the two leaf types and gene repertoire analysis identified genetic changes associated with prey attraction, capture, digestion and nutrient absorption. Analysis of digestive fluid proteins from C. follicularis and three other carnivorous plants with independent carnivorous origins revealed repeated co-options of stress-responsive protein lineages coupled with convergent amino acid substitutions to acquire digestive physiology. These results imply constraints on the available routes to evolve plant carnivory.

show abstract

“…Sequences less than 250 or more than 650 amino acids in length were discarded. The resulting list was trimmed using MaxAlign [67], which removes sequences creating significant gaps in a multiple sequence alignment. This is designed to remove truncated or incorrectly annotated sequences, but in this case also removed several proteins that appear to have a sequence swap similar to OpuAC of Bacillus subtilis [39,40].…”

Section: Sequence and Structure Analysismentioning

confidence: 99%

Crystal Structure of the Substrate-Binding Domain from Listeria monocytogenes Bile-Resistance Determinant BilE

2016

View full text Add to dashboard Cite

BilE has been reported as a bile resistance determinant that plays an important role in colonization of the gastrointestinal tract by Listeria monocytogenes, the causative agent of listeriosis. The mechanism(s) by which BilE mediates bile resistance are unknown. BilE shares significant sequence similarity with ATP-binding cassette (ABC) importers that contribute to virulence and stress responses by importing quaternary ammonium compounds that act as compatible solutes. Assays using related compounds have failed to demonstrate transport mediated by BilE. The putative substrate-binding domain (SBD) of BilE was expressed in isolation and the crystal structure solved at 1.5 Å. Although the overall fold is characteristic of SBDs, the binding site varies considerably relative to the well-characterized homologs ProX from Archaeoglobus fulgidus and OpuBC and OpuCC from Bacillus subtilis. This suggests that BilE may bind an as-yet unknown ligand. Elucidation of the natural substrate of BilE could reveal a novel bile resistance mechanism.

show abstract

MaxAlign: maximizing usable data in an alignment

Abstract: Background: The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. In phylogenetic and other analyses, for instance, gapped columns are often discarded entirely from the alignment.

Cited by 111 publications

References 16 publications

Exploring Bacterial Carboxylate Reductases for the Reduction of Bifunctional Carboxylic Acids

Exploring Bacterial Carboxylate Reductases for the Reduction of Bifunctional Carboxylic Acids

Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory

Crystal Structure of the Substrate-Binding Domain from Listeria monocytogenes Bile-Resistance Determinant BilE

Contact Info

Product

Resources

About