Identification of cyclic nucleotide gated channels using regular expressions
KAUST DepartmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Computational Bioscience Research Center (CBRC)
Permanent link to this recordhttp://hdl.handle.net/10754/562962
MetadataShow full item record
AbstractCyclic nucleotide-gated channels (CNGCs) are nonselective cation channels found in plants, animals, and some bacteria. They have a six-transmembrane/one- pore structure, a cytosolic cyclic nucleotide-binding domain, and a cytosolic calmodulin-binding domain. Despite their functional similarities, the plant CNGC family members appear to have different conserved amino acid motifs within corresponding functional domains than animal and bacterial CNGCs do. Here we describe the development and application of methods employing plant CNGC-specific sequence motifs as diagnostic tools to identify novel candidate channels in different plants. These methods are used to evaluate the validity of annotations of putative orthologs of CNGCs from plant genomes. The methods detail how to employ regular expressions of conserved amino acids in functional domains of annotated CNGCs and together with Web tools such as PHI-BLAST and ScanProsite to identify novel candidate CNGCs in species including Physcomitrella patens. © Springer Science+Business Media New York 2013.
JournalMethods in Molecular Biology
- Phylogeny and evolution of plant cyclic nucleotide-gated ion channel (CNGC) gene family and functional analyses of tomato CNGCs.
- Authors: Saand MA, Xu YP, Munyampundu JP, Li W, Zhang XR, Cai XZ
- Issue date: 2015 Dec
- Importance of the alphaC-helix in the cyclic nucleotide binding domain for the stable channel regulation and function of cyclic nucleotide gated ion channels in Arabidopsis.
- Authors: Chin K, Moeder W, Abdel-Hamid H, Shahinas D, Gupta D, Yoshioka K
- Issue date: 2010 May
- Calmodulin binding to Arabidopsis cyclic nucleotide gated ion channels.
- Authors: Abdel-Hamid H, Chin K, Shahinas D, Moeder W, Yoshioka K
- Issue date: 2010 Sep
- Cyclic nucleotide-gated ion channel gene family in rice, identification, characterization and experimental analysis of expression response to plant hormones, biotic and abiotic stresses.
- Authors: Nawaz Z, Kakar KU, Saand MA, Shu QY
- Issue date: 2014 Oct 4
- Identification of a functionally essential amino acid for Arabidopsis cyclic nucleotide gated ion channels using the chimeric AtCNGC11/12 gene.
- Authors: Baxter J, Moeder W, Urquhart W, Shahinas D, Chin K, Christendat D, Kang HG, Angelova M, Kato N, Yoshioka K
- Issue date: 2008 Nov