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Clustal omega

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Clustal Omega is a multiple sequence alignment program. It aligns protein or nucleotide sequences and produces a visual representation of the alignment.

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Lab products found in correlation

3 protocols using clustal omega

1

Structural Insights into WaaA Enzyme

Cited 1 time
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Protein Data Bank (PDB) was used to conduct homology search (Rose et al., 2015 (link)). For WaaA, the structure of membrane-embedded monofunctional glycosyltransferase WaaA from Aquifex aeolicus (PDB code: 2XCI.A) was used as the template based on the quality of models produced. Multiple sequence alignment was performed using Clustal Omega from UniProt (Yip et al., 2008 (link)). The ESPript server was used to predict the secondary structure of WaaA (Robert and Gouet, 2014 (link)). The Alphafold v2.3.1 monomer_casp14 model was used to predict the structures of WaaA and WaaA* (Jumper et al., 2021 (link)). The biological and functional insights derived from the predicted models were verified by matching the models with the protein function database.
Xiao L., Qi Z., Song K., Lv R., Chen R., Zhao H., Wu H., Li C., Xin Y., Jin Y., Li X., Xu X., Tan Y., Du Z., Cui Y., Zhang X., Yang R., Zhao X, & Song Y. (2023). Interplays of mutations in waaA, cmk, and ail contribute to phage resistance in Yersinia pestis. Frontiers in Cellular and Infection Microbiology, 13, 1174510.
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2

Alignment Analysis of NAD+ Synthetases

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An alignment ana­lysis was performed using the Clustal Omega program at the Uniprot Align site (https://www.uniprot.org/align). The microbial sources of the deduced amino acid sequences of NAD+ synthetases in the alignment are shown in Table S1.
Kucho K.I., Asukai K, & Nguyen T.V. (2023). NAD+ Synthetase is Required for Free-living and Symbiotic Nitrogen Fixation in the Actinobacterium Frankia casuarinae. Microbes and Environments, 38(1), ME22093.
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3

Comparative Analysis of BUB-1 and BubR1 SLiMs

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All sequence alignments were performed using Clustal Omega (Sievers et al., 2011) The short linear motifs (SLiMs) of C. elegans BUB-1 (R279-D292;UniProtKB Q21776), human BubR1 (I666-A679;UniProtKB O60566-1) and RepoMan (K587-P600; UniProtKB (Waterhouse et al., 2009) .
Borja L.B., Soubigou F., Taylor S.J., Bringas C.F., Budrewicz J., Lara-González P., Turpin C.G.S., Bembenek J.N., Cheerambathur D.K., & Pelisch F. (2020). BUB-1 targets PP2A:B56 to regulate chromosome congression during meiosis I in C. elegans oocytes.
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