We have isolated metagenome from seawater. The whole metagenome was sequenced using NGS platform. The sequencing reads were assembled and whole metageomic sequence obtained. Genes were predicted in assembled metagenome sequence (Contigs). The genes coding CAZymes were identified by analyzing the genes against CAZy database. Now wee need to assign the original taxa to the each CAZyme gene. Your suggestions are welcome.
You may take the NCBI approach...
Choose the lowest clade you can be sure about. This is usually below Subphylum, but it may be difficult to get much deeper. The you classify your sequence as unclassified "clade". Check for instance this entry at the taxonomy browser inside NCBI portal:
https://www.ncbi.nlm.nih.gov/nuccore/45219921
you will notice it does not have complete taxonomical information, and under taxonomy the entry corresponds to:
https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=232235&lvl=3&lin=f&keep=1&srchmode=1&unlock
Best wishes,
Rogelio
Dear Md Imran ,
After getting contigs we need to organize and orient them into scaffolds. these scaffolds are the input for PRODIGAL to predict coding DNA and putative ID assignment is done by Blastp vs NR proteins. Taxonomy Browser tool gives the taxa of each enzyme.
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