# Copyright © SRI International 1996,1999-2002, Marine Biological Laboratory 1996-2001, DoubleTwist Inc. 1997-1999. All Rights Reserved. # Please see the license agreement regarding the use of and distribution of this file. # The format of this file is defined at http://bioinformatics.ai.sri.com/ptools/flatfile-format.html . # # Species: E. coli K-12 # Database: EcoCyc # Version: 11.5 # File Name: classes.dat # Date and time generated: August 6, 2007, 17:31:52 # UNIQUE-ID - Regulation TYPES - FRAMES COMMENT - This class describes most forms of protein, RNA or activity regulation. Regulation can be either by a direct influence on the protein's activity /(e.g. allosteric inhibition of an enzyme) or by influencing the quantity of active protein available (e.g. by inducing or blocking its transcription /or translation). The one form of regulation that is not covered by this class is when the quantity of a protein is regulated as a result of chemical /or binding reactions that either produce or consume the active form of a protein -- these are represented as Reactions instead. There can be /some ambiguity as to what should be represented as a reaction and what should be represented as a regulation event. In general, an event that /can be represented as a reaction should be when a) there is sufficiently detailed information known to model it as a reaction, b) both reactants /and products exist as stable, independent entities, and c) our schema supports referring to both reactant and product of the reaction independently /and there is some justification for wanting to go down to that level of detail. For example, a transcription factor bound to a small molecule will /generally have a different activity than the unbound transcription factor. This could be represented either as the reaction TF + x -> TF-x or as /a regulation event in which x activates or inhibits the activity of TF. However, because both TF and TF-x are stable molecules which can /potentially regulate different transcription units (not all will, but some do), or TF could bind another small molecule y and regulate yet another set /of transcription units, we prefer to model this kind of interaction as a reaction when the data is available. On the other hand, an enzyme binding to /some inhibitor could also be represented as a reaction, but since there is rarely any reason to refer to the enzyme-inhibitor complex outside of /the context of the reaction the enzyme catalyzes, we choose instead to model these events as regulation events in which the inhibitor regulates the /activity of the enzyme. / /Instances of this class represent a one-to-one mapping between regulator and regulated-entity (i.e. an entity may regulate many processes, or a /process may be regulated by many entities, but each one requires its own instance of Regulation to represent it) // UNIQUE-ID - Publications TYPES - FRAMES COMMENT - Instances of this class are publications, usually those cited within a PGDB. // UNIQUE-ID - Protein-Features TYPES - FRAMES COMMENT - Instances of of this class define a region of interest on a polypeptide, plus, /optionally, one or more states associated with the region. Different subclasses are used to specify /points, linear regions, and regions involving noncontiguous segments of an amino-acid chain. / /For example, an instance F of this class could define an amino-acid residue that /can be phorphorylated, plus the fact that this residue can take on two possible /states: PHOSPHORYLATED and UNPHOSPHORYLATED. The feature instance /itself does not describe the state of a particular protein. Instead, we would /represent the phosphorylated and unphosphorylated forms of a protein by /creating two instances of class Proteins. Both of those instances, in their /FEATURES slot, would contain the value F, linking to the same feature /instance. However, in the two proteins, F would be annotated differently /to indicate the state of that feature. One protein would use an /annotation label STATE with a value PHOSPHORYLATED to denote /that the residue is phosphorylated. / / // UNIQUE-ID - Polymer-Segments TYPES - FRAMES COMMENT - Describes a linear region of a polymer, such a a segment of a DNA /molecule or of an amino-acid chain. //