The Clustal Omega Multiple Alignment Package

Sievers, Fabian; Higgins, Desmond G.

doi:10.1007/978-1-0716-1036-7_1

Cited by 220 publications

(166 citation statements)

References 13 publications

Supporting

Mentioning

136

Contrasting

Unclassified

Order By: Relevance

“…We have upgraded the multiple-sequence alignment tools available for EcoCyc to use Clustal Omega ( Sievers and Higgins, 2021 ) to compute alignments and MSA Viewer ( Yachdav et al, 2016 ) to display the alignments (website command Analysis → Multiple Sequence Alignment).…”

Section: Resultsmentioning

confidence: 99%

The EcoCyc Database in 2021

et al. 2021

View full text Add to dashboard Cite

The EcoCyc model-organism database collects and summarizes experimental data for Escherichia coli K-12. EcoCyc is regularly updated by the manual curation of individual database entries, such as genes, proteins, and metabolic pathways, and by the programmatic addition of results from select high-throughput analyses. Updates to the Pathway Tools software that supports EcoCyc and to the web interface that enables user access have continuously improved its usability and expanded its functionality. This article highlights recent improvements to the curated data in the areas of metabolism, transport, DNA repair, and regulation of gene expression. New and revised data analysis and visualization tools include an interactive metabolic network explorer, a circular genome viewer, and various improvements to the speed and usability of existing tools.

show abstract

Section: Resultsmentioning

confidence: 99%

The EcoCyc Database in 2021

et al. 2021

View full text Add to dashboard Cite

show abstract

“…Starting from 24 pairs of manually curated QS synthases and receptors ( Supplementary file 1A ), we searched for homologs in complete bacterial genomes using BLAST (e-value <0.01) ( Altschul et al, 1990 ). We filtered the BLAST hits by sequence identity (>30%) to the query and the alignment coverage (query coverage >0.75 and hit coverage >0.75), and the filtered hits were aligned by Clustal Omega ( Sievers and Higgins, 2021 ). We selected the LasI/R system from P. aeruginosa PAO1 as the target and mapped the multiple sequence alignments (MSA) to the target system.…”

Section: Methodsmentioning

confidence: 99%

A covariation analysis reveals elements of selectivity in quorum sensing systems

Miranda

Cong

Schaefer

et al. 2021

eLife

View full text Add to dashboard Cite

Many bacteria communicate with kin and coordinate group behaviors through a form of cell-cell signaling called acyl-homoserine lactone (AHL) quorum sensing (QS). In these systems, a signal synthase produces an AHL to which its paired receptor selectively responds. Selectivity is fundamental to cell signaling. Despite its importance, it has been challenging to determine how this selectivity is achieved and how AHL QS systems evolve and diversify. We hypothesized that we could use covariation within the protein sequences of AHL synthases and receptors to identify selectivity residues. We began by identifying about 6,000 unique synthase-receptor pairs. We then used the protein sequences of these pairs to identify covariation patterns and mapped the patterns onto the LasI/R system from Pseudomonas aeruginosa PAO1. The covarying residues in both proteins cluster around the ligand-binding sites. We demonstrate that these residues are involved in system selectivity toward the cognate signal and go on to engineer the Las system to both produce and respond to an alternate AHL signal. We have thus demonstrated that covariation methods provide a powerful approach for investigating selectivity in protein-small molecule interactions and have deepened our understanding of how communication systems evolve and diversify.

show abstract

“…Initial analysis for the compliance with expected result was performed by searching the sequence in the NCBI [11] database using BLAST [12]. The obtained DNA and protein sequences were aligned using standard parameters in the ClustalO program [13], VIENNA formats (for aligning in fasta format) [14]. Aligned sequences were analyzed using the MView interface.…”

Section: Methodsmentioning

confidence: 99%

Study of the VvMybA1 gene allele state of some colored and uncolored grapevine varieties

et al. 2021

View full text Add to dashboard Cite

As a result of the work, genetic markers were created that were used to identify alleles of the VvMybA1 genes, which control the anthocyanin color of berries in grape varieties. Using these markers, alleles were identified in grape varieties belonging to different ecologicalgeographical groups. In the process of work, alleles were sequenced and compared with the NCBI database in order to identify their state and their belonging to a specific type of structure. In addition, these sequences were compared with each other to reveal the structural features of varieties with and without color of berries. Single nucleotide polymorphisms, structural features, and deletions in the structure of alleles were revealed.

show abstract

The Clustal Omega Multiple Alignment Package

Cited by 220 publications

References 13 publications

The EcoCyc Database in 2021

The EcoCyc Database in 2021

A covariation analysis reveals elements of selectivity in quorum sensing systems

Study of the VvMybA1 gene allele state of some colored and uncolored grapevine varieties

Contact Info

Product

Resources

About