Clustal Omega, Accurate Alignment of Very Large Numbers of Sequences

Sievers, Fabian; Higgins, Desmond G.

doi:10.1007/978-1-62703-646-7_6

Cited by 1,047 publications

(828 citation statements)

References 8 publications

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“…Conserved residues in the active site of BSS are in bold. The alignment was performed in Clustal Omega (43). HPD, 4-hydroxyphenylacetate decarboxylase from Clostridium difficile; PFL2, pyruvate formate lyase-like protein from Archeoglobus fulgidus; GDH, glycerol dehydratase from Clostridium butyricum; CutC, choline trimethylamine lyase from Desulfovibrio alaskensis; PFL, pyruvate formate lyase from Escherichia coli.…”

Section: Discussionmentioning

confidence: 99%

Substrate-bound Structures of Benzylsuccinate Synthase Reveal How Toluene Is Activated in Anaerobic Hydrocarbon Degradation

Funk

Marsh

Drennan

2015

Journal of Biological Chemistry

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Background: Benzylsuccinate synthase (BSS) catalyzes the formation of a COC bond between toluene and fumarate by a radical mechanism. Results: BSS binds substrates in a buried active site and uses conformational changes to gate access. Conclusion: BSS and related enzymes precisely position substrates for chemistry. Significance: These structures reveal the molecular basis for BSS radical chemistry and substrate specificity.

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Section: Discussionmentioning

confidence: 99%

Substrate-bound Structures of Benzylsuccinate Synthase Reveal How Toluene Is Activated in Anaerobic Hydrocarbon Degradation

Funk

Marsh

Drennan

2015

Journal of Biological Chemistry

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“…Sequences were edited in BioEdit 7.2.5 software [24] to trim the non-overlapping 5 and 3 regions for the purpose of restricting the multiple sequence alignment within the minimum common region. Those edited sequences were aligned using Clustal omega [25]. The unrooted phylogenetic tree was constructed using the neighbor-joining (NJ) method [26]] and Kimura's two-parameter algorithm [27], as implemented within the MEGA 6.06 software [28].…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Isolation and Characterization of Native Microalgae from the Peruvian Amazon with Potential for Biodiesel Production

et al. 2017

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Biodiesel production from microalgae triacylglycerols is growing, because this feedstock is a more sustainable and advantageous alternative. In this study, we isolated and identified fourteen strains of native microalgae from the Peruvian Amazon. These strains showed great heterogeneity in biomass productivity, lipid productivity and lipid content, and thus, three of them (Acutodesmus obliquus, Ankistrodesmus sp. and Chlorella lewinii) were selected for further evaluation under culture of nitrogen-sufficient (+N) and nitrogen-deficient (−N) Chu medium No. 10. These microalgae species showed modifications in biomolecule content (protein, lipid and carbohydrate) with a pronounced increase of lipids and carbohydrate and a decrease of protein content under stress culture. Furthermore, the fatty acid profile was peculiar for each species, and these patterns showed evident changes, particularly in the proportion of saturated and monounsaturated fatty acids. The results of this research suggest that the isolated native microalgae, from the Peruvian Amazon, could be suitable candidates for biodiesel production.

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“…Multiple alignments were performed with the program Clustal Omega (Sievers and Higgins 2013) to ensure that all sequences of COI marker gene provide a homologous fragment and to detect the percentage of similarity found between COI rRNA gene sequences underlining a possible genetic divergence between them (Ward 2012). COI rRNA gene sequences were translated into amino acids with the online program ExPASy translation tool (http://web.…”

Section: Sequence Alignment and Analysismentioning

confidence: 99%

Fisheries and biodiversity along Mediterranean Sea: Italian and Egyptian coast overview

Guerriero

Rabbito

Alwany

et al. 2017

Euro-Mediterr J Environ Integr

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Mediterranean fish species living along Italian (Gaeta) and Egyptian (Alexandria) coasts were analyzed using DNA barcodes for molecular identification. Mitochondrial Cytochrome c Oxidase subunit 1 (COI) gene was sequenced from 31 different marine species to test whether the morphology-based assignment of individuals into 19 families, 6 orders was supported by DNA-based species delimitation and Neighbour Joining cladogram. All COI rRNA gene barcodes were matched with reference sequences of expected species, according to morphological identification. Neighbour joining tree was drawn based on COI rRNA gene and the majority of specimens clustered in agreement with their taxonomic classification. Our results updated Mediterranean edible fish knowledge providing graphical resources, taxonomical and bioinformatics references, improving the genetic fish database and the basic molecular information to strengthen the science-policy interface for biodiversity and ecosystem services as conservation, blue economy, and long-term human well-being.

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Clustal Omega, Accurate Alignment of Very Large Numbers of Sequences

Cited by 1,047 publications

References 8 publications

Substrate-bound Structures of Benzylsuccinate Synthase Reveal How Toluene Is Activated in Anaerobic Hydrocarbon Degradation

Substrate-bound Structures of Benzylsuccinate Synthase Reveal How Toluene Is Activated in Anaerobic Hydrocarbon Degradation

Isolation and Characterization of Native Microalgae from the Peruvian Amazon with Potential for Biodiesel Production

Fisheries and biodiversity along Mediterranean Sea: Italian and Egyptian coast overview

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