ArticleNucleic acids research2013
CyanoLyase: a database of phycobilin lyase sequences, motifs and functions.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
22 citing papers in PubMed, 42 citations in OpenAlex.
- MARTS-DB: a database of mechanisms and reactions of terpene synthases.BMC bioinformatics · 2025Article
- Enzyme Databases in the Era of Omics and Artificial Intelligence.International journal of molecular sciences · 2023Review
- CyanoMapDB: a database integrating experimentally validated protein-protein interactions in cyanobacteria.Plant physiology · 2023Article
- Characterization of Molecular Diversity and Organization of Phycobilisomes in Thermophilic Cyanobacteria.International journal of molecular sciences · 2023Article
- A novel long-tailed myovirus represents a new T4-like cyanophage cluster.Frontiers in microbiology · 2023Article
- Diversity and Evolution of Pigment Types in Marine Synechococcus Cyanobacteria.Genome biology and evolution · 2022Article
- Crystal structure and molecular mechanism of an E/F type bilin lyase-isomerase.Structure (London, England : 1993) · 2022Article
- CyanoOmicsDB: an integrated omics database for functional genomic analysis of cyanobacteria.Nucleic acids research · 2022Article
- Phycobiliproteins: Structural aspects, functional characteristics, and biotechnological perspectives.Computational and structural biotechnology journal · 2022Review
- Molecular bases of an alternative dual-enzyme system for light color acclimation of marineProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Interplay between differentially expressed enzymes contributes to light color acclimation in marineProceedings of the National Academy of Sciences of the United States of America · 2019Article
- CpeF is the bilin lyase that ligates the doubly linked phycoerythrobilin on β-phycoerythrin in the cyanobacteriumThe Journal of biological chemistry · 2019Article
- Estimating probabilistic context-free grammars for proteins using contact map constraints.PeerJ · 2019Article
- CyanoBase: a large-scale update on its 20th anniversary.Nucleic acids research · 2017Article
- Adaptation to Blue Light in MarineFrontiers in microbiology · 2017Article
- Shedding new light on viral photosynthesis.Photosynthesis research · 2015Review
- Databases for Microbiologists.Journal of bacteriology · 2015Review
- Cyanobacterial KnowledgeBase (CKB), a Compendium of Cyanobacterial Genomes and Proteomes.PloS one · 2015Article
- Insights into the biosynthesis and assembly of cryptophycean phycobiliproteins.The Journal of biological chemistry · 2014Article
- Structure and mechanism of the phycobiliprotein lyase CpcT.The Journal of biological chemistry · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
CyanoLyase (http://cyanolyase.genouest.org/) is a manually curated sequence and motif database of phycobilin lyases and related proteins. These enzymes catalyze the covalent ligation of chromophores (phycobilins) to specific binding sites of phycobiliproteins (PBPs). The latter constitute the building bricks of phycobilisomes, the major light-harvesting systems of cyanobacteria and red algae. Phycobilin lyases sequences are poorly annotated in public databases. Sequences included in CyanoLyase were retrieved from all available genomes of these organisms and a few others by similarity searches using biochemically characterized enzyme sequences and then classified into 3 clans and 32 families. Amino acid motifs were computed for each family using Protomata learner. CyanoLyase also includes BLAST and a novel pattern matching tool (Protomatch) that allow users to rapidly retrieve and annotate lyases from any new genome. In addition, it provides phylogenetic analyses of all phycobilin lyases families, describes their function, their presence/absence in all genomes of the database (phyletic profiles) and predicts the chromophorylation of PBPs in each strain. The site also includes a thorough bibliography about phycobilin lyases and genomes included in the database. This resource should be useful to scientists and companies interested in natural or artificial PBPs, which have a number of biotechnological applications, notably as fluorescent markers.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.