I scaned some protein sequences for transmembrane and nucleotide-binding domain organisation on ScanProsite and I don't quite understand some results?

16 July 2016 1 9K Report

Looking at the image I attached, is the domain organisation (TMD-NBD)2 or TMD-NBD-TMD-TMD-NBD.

Hi Charles,

I've checked common topologies of ABC transporters at http://www.ncbi.nlm.nih.gov/pubmed/16337630 (there's a PDF at http://www.enzim.hu/data/pdf/16337630.pdf) and it looks like your protein is a ABCB or ABCC topology, depending on sequence length. Is it possible that ScanProsite might have broken TMD2 in two fragments, as these domains are less conserved (http://www.ebi.ac.uk/interpro/entry/IPR003439)?

Hope this helps, Bruno

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