Locating Motif Within A Protein Sequence

Question

[Elmo]

Hi,

I don't really know how to put this in words but as I am having a protein sequence, I viewed its conserved domains detected using CD Search at NCBI and then I obtained its superfamily with description that this protein contains two copies of motif, say HXXHH, however, I only found one within the sequence. What does this infer? I'm quite of a beginner to this field, so sorry if the question does not make much sense. :(

Please advice. Thank you in advance!

[Neilfws]

This question is not very clear. You're confused because one resource states that your sequence should have 2 copies of a motif, but you "found" (how?) only one? It might help to state what the protein is so we can look for ourselves.

[Elmo]

Thank you for your reply. The protein belongs to the FAD superfamily and it is stated that there are two copies of the motif HXHH. I actually looked through the sequence manually to find that motif. (Is there a tool to scan for it?) But I'm positive that there is only one. Thank you for your time.

Answer 1

[Pablacious]

Hi,

You can use EMBOSS package "preg" program to find a motif (written as a regular expression) within a sequence. You can try EMBOSS through a web interface here.

There are a few other tools in emboss that help you on this kind of motif search, so take a look at the other programs of the package as well.

Good luck ;->.

Answer 2

[Larry_Parnell]

ELM is also good for identifying the occurrence of short motifs in eukaryotic protein sequences. Under the "links" tab at ELM, a number of other specialized motif finders are listed. You can also locate other tools and databases (eg, PROSITE, ScanPROSITE) here.

Some domains, be they in DNA or protein sequence, are recognized as half-sites but would really only be considered functional when a pair of those half-sites are observed and in the right context. One cysteine residue cannot alone form a disulfide pair. Thus, the annotation of the domain you're looking at may describe the need to have two sites to form a functional unit. ELM and PROSITE do provide such annotation.