Dam/dcm Methylation in GCG

Peter Rice pmr at sanger.ac.uk
Wed Sep 15 06:01:01 EST 1999


Harry Mangalam <mangalam at home.com> writes:

> Is there an easy way to mask enzymes for possible Dam or Dcm methylase
> interference in 'map' or 'mapplot' or any other GCG app?

You would need to know the sensitivity of each enzyme to each specific
methylation. REBASE has the corresponding methylases for the enzymes
(where known), but if the Dam or Dcm sites overlap another enzyme
target, or if the correspoonding methylase makes a different
modification, there is no guide to what effect this could have.

You could check REBASE for methylases with the exact same target as
Dam and Dcm but it would not be complete. For example, EcoRII should
be inhibited by Dcm as the EcoRII methylase has the same product as
Dcm. Similarly, MboI should be inhibited by Dam.

We have a restrict program in EMBOSS which we would be happy to modify
if anyone can provide data for interference by other methylations.


Examples (REBASE in bairoch format):

Dcm methylase:
==============

ID   M.EcoDcm
ET   M
AC   RB00004;
OS   Escherichia coli K-12
PT   EcoRII
RS   CCWGG, ?;
MS   2(5mC);
//

MboI and methylase:
===================

ID   MboI
ET   R2
AC   RB00095;
OS   Moraxella bovis
PT   MboI
RS   GATC, 0;
//
ID   M.MboIA
ET   M2
AC   RB03283;
OS   Moraxella bovis
PT   MboI
RS   GATC, ?;
MS   2(6mA);
//
ID   M.MboIB
ET   M2
AC   RB03284;
OS   Moraxella bovis
PT   MboI
RS   GATC, ?;
MS   2(6mA);
//

Dam methylase:
==============

ID   M.EcoDam
ET   M
AC   RB00014;
OS   Escherichia coli K-12
PT   MboI
RS   GATC, ?;
MS   2(6mA);
//

EcoRII and methylase:
=====================

ID   EcoRII
ET   R2
AC   RB00006;
OS   Escherichia coli R245
PT   EcoRII
RS   CCWGG, 0;
//
ID   M.EcoRII
ET   M2
AC   RB0000
OS   Escherichia coli R245
PT   EcoRII
RS   CCWGG, ?;
MS   2(5mC);
//

-- 
----------------------------------------------------------------------
Peter Rice                | Informatics Division, The Sanger Centre,
E-mail: pmr at sanger.ac.uk  | Wellcome Trust Genome Campus,
Tel: (44) 1223 494967     | Hinxton, Cambridge, CB10 1SA, England
Fax: (44) 1223 494919     | URL: http://www.sanger.ac.uk/Users/pmr/




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