I think that depends on what the depositor considered complete. Just as an example the construct you cloned say from residue 20 - 380 would you consider that complete or would you consider only the sequence complete if it contained the first 20residues ? Regarding the gaps in terms of missing residues in the structure because they were not observed you shouldn't be worried as they are included in the FASTA sequence. 3TGH just as an example, would you consider that complete ?
Jürgen On Mar 26, 2012, at 10:54 PM, Francois Berenger wrote: Dear list, If I take all the fasta files for proteins in the PDB, are the sequences complete? I mean, do they have holes sometimes (missing amino acids)? Sorry for the maybe stupid question but I know that sometimes the PDB files have missing residues, I am hoping that it is not the case with the FASTA files. Regards, Francois. ...................... Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/
