Algorithm for Predicting Functionally Equivalent Proteins from BLAST and HMMER Searches

Dong, Yu; Lee, Dong Hoon; Kim, Seong Keun; Lee, Choong Hoon; Song, Ju Yeon; Kong, Eun Bae; Kim, Jihyun F.

doi:10.4014/jmb.1203.03050

Cited by 10 publications

(7 citation statements)

References 25 publications

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“…A common assumption made in such sequence comparisons is that significant shifts in protein function will correspond to large differences in sequence, but at the molecular level even changes in single residues can produce drastic changes in function ( Anderson et al 2016 ). Our ability to identify orthologous genes far outpaces our ability to predict protein function based on sequence, resulting in a false positive rate of over 50% in studies that attempt to identify orthologous genes with equivalent protein functions ( Ponting 2001 ; Watson et al 2005 ; Yu et al 2012 ). Further, highly similar sequences do not necessarily indicate conservation of protein function, as is the case in the CCC, the hedgehog signaling pathway, or the glucocorticoid receptor family ( Ortlund et al 2007 ; Dickinson, Weis, et al 2011 ; Miller, Pokutta, et al 2013 ) (see supplementary table S1 , e.g., Supplementary Material online).…”

Section: Discussionmentioning

confidence: 99%

Characterization of the Cadherin–Catenin Complex of the Sea AnemoneNematostella vectensisand Implications for the Evolution of Metazoan Cell–Cell Adhesion

Clarke¹,

Miller²,

Lowe³

et al. 2016

Mol Biol Evol

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The cadherin–catenin complex (CCC) mediates cell–cell adhesion in bilaterian animals by linking extracellular cadherin-based adhesions to the actin cytoskeleton. However, it is unknown whether the basic organization of the complex is conserved across all metazoans. We tested whether protein interactions and actin-binding properties of the CCC are conserved in a nonbilaterian animal, the sea anemone Nematostella vectensis. We demonstrated that N. vectensis has a complete repertoire of cadherin–catenin proteins, including two classical cadherins, one α-catenin, and one β-catenin. Using size-exclusion chromatography and multi-angle light scattering, we showed that α-catenin and β-catenin formed a heterodimer that bound N. vectensis Cadherin-1 and -2. Nematostella vectensis α-catenin bound F-actin with equivalent affinity as either a monomer or an α/β-catenin heterodimer, and its affinity for F-actin was, in part, regulated by a novel insert between the N- and C-terminal domains. Nematostella vectensis α-catenin inhibited Arp2/3 complex-mediated nucleation of actin filaments, a regulatory property previously thought to be unique to mammalian αE-catenin. Thus, despite significant differences in sequence, the key interactions of the CCC are conserved between bilaterians and cnidarians, indicating that the core function of the CCC as a link between cell adhesions and the actin cytoskeleton is ancestral in the eumetazoans.

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Section: Discussionmentioning

confidence: 99%

Characterization of the Cadherin–Catenin Complex of the Sea AnemoneNematostella vectensisand Implications for the Evolution of Metazoan Cell–Cell Adhesion

Clarke¹,

Miller²,

Lowe³

et al. 2016

Mol Biol Evol

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“…BLAST software was utilized to compare the Unigene sequence with NR, Swiss-Prot, GO, COG, KOG, and KEGG databases; HMMER software was employed to compare the Unigene sequence with Pfam database after predicting the amino acid sequence of Unigene; and the annotation information of Unigene was obtained [ 59 ]. By selecting BLAST parameter E-value less than 1 × 10 −5 and HMMER parameter E-value less than 1 × 10 −10 , Unigene with annotation information was finally acquired.…”

Section: Methodsmentioning

confidence: 99%

Chemical Constituents and Molecular Mechanism of the Yellow Phenotype of Yellow Mushroom (Floccularia luteovirens)

Gan

Bao

Liu

et al. 2022

JoF

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(1) Background: Yellow mushroom (Floccularia luteovirens) is a natural resource that is highly nutritional, has a high economic value, and is found in Northwest China. Despite its value, the chemical and molecular mechanisms of yellow phenotype formation are still unclear. (2) Methods: This study uses the combined analysis of transcriptome and metabolome to explain the molecular mechanism of the formation of yellow mushroom. Subcellular localization and transgene overexpression techniques were used to verify the function of the candidate gene. (3) Results: 112 compounds had a higher expression in yellow mushroom; riboflavin was the ninth most-expressed compound. HPLC showed that a key target peak at 23.128 min under visible light at 444 nm was Vb2. All proteins exhibited the closest relationship with Agaricus bisporus var. bisporus H97. One riboflavin transporter, CL911.Contig3_All (FlMCH5), was highly expressed in yellow mushrooms with a different value (log2 fold change) of −12.98, whereas it was not detected in white mushrooms. FlMCH5 was homologous to the riboflavin transporter MCH5 or MFS transporter in other strains, and the FlMCH5-GFP fusion protein was mainly located in the cell membrane. Overexpression of FlMCH5 in tobacco increased the content of riboflavin in three transgenic plants to 26 μg/g, 26.52 μg/g, and 36.94 μg/g, respectively. (4) Conclusions: In this study, it is clear that riboflavin is the main coloring compound of yellow mushrooms, and FlMCH5 is the key transport regulatory gene that produces the yellow phenotype.

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“…Pfam domains, signal peptide cleavage sites and transmembrane helices were also identified and integrated into the database. These were predicted using HMMER [ 64 ], signal [ 65 ] and tmHMM [ 66 ] respectively with default parameters. Finally, Gene Ontology (GO) and eggNOG information were obtained from the Swiss-Prot database [ 63 ], whereas associated KEGG pathways were identified by a BLASTP search with an E-value cutoff 10e-10.…”

Section: Construction and Contentmentioning

confidence: 99%

PdumBase: a transcriptome database and research tool for Platynereis dumerilii and early development of other metazoans

et al. 2018

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BackgroundThe marine polychaete annelid Platynereis dumerilii has recently emerged as a prominent organism for the study of development, evolution, stem cells, regeneration, marine ecology, chronobiology and neurobiology within metazoans. Its phylogenetic position within the spiralian/ lophotrochozoan clade, the comparatively high conservation of ancestral features in the Platynereis genome, and experimental access to any stage within its life cycle, make Platynereis an important model for elucidating the complex regulatory and functional molecular mechanisms governing early development, later organogenesis, and various features of its larval and adult life. High resolution RNA-seq gene expression data obtained from specific developmental stages can be used to dissect early developmental mechanisms. However, the potential for discovery of these mechanisms relies on tools to search, retrieve, and compare genome-wide information within Platynereis, and across other metazoan taxa.ResultsTo facilitate exploration and discovery by the broader scientific community, we have developed a web-based, searchable online research tool, PdumBase, featuring the first comprehensive transcriptome database for Platynereis dumerilii during early stages of development (2 h ~ 14 h). Our database also includes additional stages over the P. dumerilii life cycle and provides access to the expression data of 17,213 genes (31,806 transcripts) along with annotation information sourced from Swiss-Prot, Gene Ontology, KEGG pathways, Pfam domains, TmHMM, SingleP, and EggNOG orthology. Expression data for each gene includes the stage, the normalized FPKM, the raw read counts, and information that can be leveraged for statistical analyses of differential gene expression and the construction of genome-wide co-expression networks. In addition, PdumBase offers early stage transcriptome expression data from five further species as a valuable resource for investigators interested in comparing early development in different organisms. To understand conservation of Platynereis gene models and to validate gene annotation, most Platynereis gene models include a comprehensive phylogenetic analysis across 18 species representing diverse metazoan taxa.ConclusionsPdumBase represents the first online resource for the early developmental transcriptome of Platynereis dumerilii. It serves as a research platform for discovery and exploration of gene expression during early stages, throughout the Platynereis life cycle, and enables comparison to other model organisms. PdumBase is freely available at http://pdumbase.gdcb.iastate.edu.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4987-0) contains supplementary material, which is available to authorized users.

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Algorithm for Predicting Functionally Equivalent Proteins from BLAST and HMMER Searches

Cited by 10 publications

References 25 publications

Characterization of the Cadherin–Catenin Complex of the Sea AnemoneNematostella vectensisand Implications for the Evolution of Metazoan Cell–Cell Adhesion

Characterization of the Cadherin–Catenin Complex of the Sea AnemoneNematostella vectensisand Implications for the Evolution of Metazoan Cell–Cell Adhesion

Chemical Constituents and Molecular Mechanism of the Yellow Phenotype of Yellow Mushroom (Floccularia luteovirens)

PdumBase: a transcriptome database and research tool for Platynereis dumerilii and early development of other metazoans

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