2D gels, E coli proteins

Peter Rice pmr at sanger.ac.uk
Wed Jul 26 13:02:22 EST 1995


In article <3v5pmo$thm at columba.udac.uu.se> dunten at onyx.bmc.uu.se (Pete Dunten) writes:
>   I know Swiss Prot provides links to 2D gels for proteins from several mammalian cell lines,
>   but not my favorite organism, lowly E coli!   Is there a web site or compilation of MW and
>   pI for E coli proteins?  

Then you have been sadly misinformed....

Swiss-Prot has links to ECO2DBASE, the E.coli 2D gel database from
F.Neidhardt. The 2D gel database itself is available by ftp from

         ncbi.nlm.nih.gov in directory repository/ECO2DBASE

and is also indexed on the SRS server (and cross-referenced to Swiss-Prot) at

               http://www.sanger.ac.uk/srs/srsc

where you will find it under "genome libraries" with the name EC2D.

We changed the database format slightly from the original distribution
(moved the column headings to be row headings so we get a neat flat file
format for an entry).

And yes, it does have MWt and pI, both calculated from sequence and
estimated from the gel.

For Swiss-Prot 31, and ECO2DBASE 6, we have 347 spots, linked to 297
Swiss-Prot entries.

For more on SRS, see the newsgroup bionet.software.srs or try our SRS
status page:

http://www.sanger.ac.uk/srs/status.html

--
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Peter Rice                           | Informatics Division
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