about protein domains in pfam - (Aug/24/2006 )
Hello to all. I've been following this forum for about a year and got useful answers most of the time, so this is my first post.
I'm new to bioinformatics tools, and I need to find if there is a way to see the smaller/ sub domains in a defined domain in pfam or NCBI's Conserved Domain Database. My entry gives two hexokinase domains as answer but what I want to see is things like Glucose binding domain, ATP binding domain (parts related to phosphate and adenosine). In literature I see everybody gives those domains and I have the main reference paper but I'm sure there is a way to find those domains using the softwares on the pfam, ncbi or somewhere else.
So if anyone can reply and suggest a database (even a help file is useful), method or anything else I will be glad. thanks in advance.. 
Asli
Asli
Hi,
You can try using the following servers to get information on protein families and domains:
1) PRINTS - Protein Motif fingerprint db
2) ProDom - Protein domain db (Automatically generated)
3) Prosite - db of families and domains. Just cut and paste your sequence and you'll get a graphical view of your domain/families. contains 1440 documentation entries that describe 1331 patterns, 4 rules and 644 profiles/matrices
4) InterProScan - Scan a sequence against all the motif databases in InterPro
Hope this helps.
Good luck!
Ermm are you sure you are looking at domains? Ot seems to me like you are looking a specific motifs, specific sequence that carry a distinct function, whereas a domain is more of a large structural fragment with a known function(s).
thanks for your replies, I'll try to have a look at the reference databases you (sara) gave..
and (I told you that I'm new to this field, and I may have some confusions about the terms) but, is it correct to say "ATP binding sequence" instead of ATP binding domain? so how should I interpret the result of pfam search when it says "hexokinase domain"? I am searching for some conserved sequences that lead to structural and functional similarities among genes of similar(?) organisms, like if we know the sequence belongign to yeast, than I may look for a similar sequence+structure in another fungi... am I so confused??? thanks..
I was not 'having a go'. From a structural biology point of view a domain is a large structure... have a look at the astral domain database. These domains may carry several distinct functional motifs. Features such as ATP binding have specific sequences maybe something like GGG[L/I]XXX[L/I]GGG (I just made that up so don't have a go at me). So in an ATP binding domain, you will be looking for a specific motif - indeed one of the databases Sara pointed out to you has this information (sorry I can't remember which)
Again, please don't take my post as hostile, I just wanted to clarify what, exactly, you meant.