Protein alignment agains all known databases

[kryblykrably]

Hello,
I want to find out, whether my protein contains a certain binding domain. What is the easiest way to align it against all known databases?
Thanks!

[JackBean]

NCBI is not large enough? They have specialized search for domains, you can look onto SwissProt, they could have some other tools too. Also you can search against PDB (e.g. on NCBI) or look for Dali search, I think. The proteins are highly redundant, you don't ave to look necesarily to all of them

[kryblykrably]

NCBI is not large enough? They have specialized search for domains, you can look onto SwissProt, they could have some other tools too.

Well, I tried it, but no success. What it gives are mostly different variations of the same protein or its parts submitted under different names in the database. What I need is actually to look for other domains. Is there a tool somewhere that can look for all known domains within a given sequence?

[JackBean]

if you have detected some domains, you can't have other domains in the same sequence!

[kryblykrably]

if you have detected some domains, you can't have other domains in the same sequence!

Why not, why can't a protein have several different domains. E.g. catalytic domain, localization domain, dimerization domain... In my case, the catalytic domain is known, and I want to find out about the other domains, if any.

[JackBean]

but not on the same sequence. So, the your identified domain is spanning whole sequence or not?

[kryblykrably]

but not on the same sequence. So, the your identified domain is spanning whole sequence or not?

no. say, a protein is ~300 residues; one domain is known - it spans about 70 residues. So about 230 residues are still available, and I want to look for other domains

[JackBean]

OK, I see now But still, NCBI blast should tell you, whether there are any domains. As I said before, you could try DALI search, but I think, you need structure for that.
Or try this
http://expasy.org/tools/#pattern

[mith]

You could try substrings of the original sequence?

[fcs]

Take a look at Interproscan:

http://www.ebi.ac.uk/Tools/InterProScan/

This is a very nice tool that I used to use to find domains for a given sequence.

[AMM]

Yes, if I have understood your question right, there is a way you can see the domains, hydophobic, hydrophilic points in a given sequence.
1. Go to http://www.uniprot.org/
2. Click on Blast
3. Enter the protein sequence, click Blast
4. Click on one of the Acession in the list below
5. Scroll down and you will see the different domians in the sequence, if that sequence contains a specific sequence for a domain.

Thanks

[verginov]

You can investigate your sequence using several methods, based on different type of searches and databases. Start with with the NCBI's RPS-Blast (so called Domain search), then run the InterProScan algorithm and do not forget to check the applications, included in the program - check them all. Alternatively you can run the HMMscan program that searches a protein hidden Markov model (HMM) database and remains one of the best ways to find remote domain structures. Some more algorithms for domains and motifs searches are: BLIMPS, PrintScan and PrositeScan. If you look for some signals as cleavage sites and postranslational modifications or wonder if your protein contains trans-membrane helices, try the applications on: http://www.cbs.dtu.dk/services/