Computational protocol: Identification of a dTDP-rhamnose biosynthetic pathway that oscillates with the molting cycle in Caenorhabditis elegans

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Protocol publication

[…] The protein sequences of RML-1–5 and its homologs in both free-living and parasitic nematode species were retrieved from Wormbase. MEGA6.0 was used to generate the neighbor-joining tree []. [...] Amino acid sequence alignment of RML-3 with E. coli RmlC (GenBank accession number AFC91454) was completed by using ClustalW. Modeling of the RML-4 structure was achieved via Robetta []. Streptococcus suis RmlB without substrate bound (PDB code 1OC2) and EcRmlD (PDB code 1KBZ) were used as the templates for RML-4 N-terminal (amino acids 1–344) and C-terminal domain (amino acids 345–631) modeling. Superposition of the RML-4 structure model with dTDP-Glc-bound SsRmlB (PDB code 1KER) was done using PyMol (http:://www.pymol.org). […]

Pipeline specifications

Software tools MEGA, Clustal W, Robetta, PyMOL
Databases WormBase
Applications Phylogenetics, Protein structure analysis
Organisms Caenorhabditis elegans
Chemicals Glucose, Nucleotides, Rhamnose, Uridine Diphosphate, Uridine Triphosphate