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Missing direction information in reactions.dat file

asked 2020-06-16 06:04:23 -0500

BorisGorelik gravatar image

updated 2020-06-23 01:26:20 -0500

The reactions.dat files list various known reactions. For each reaction, a list of "LEFT" and "RIGHT" compounds is provided. Many reactions also specify their REACTION-DIRECTION which can be one of the following: 'LEFT-TO-RIGHT', 'RIGHT-TO-LEFT', 'PHYSIOL-RIGHT-TO-LEFT', 'PHYSIOL-LEFT-TO-RIGHT', 'REVERSIBLE', 'IRREVERSIBLE-LEFT-TO-RIGHT'

The problem is that many reactions don't have this field. Is it safe to assume that when REACTION-DIRECTION isn't listed, the direction is left-to-right? .

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answered 2020-06-16 18:32:45 -0500

Suzanne Paley gravatar image

No, if no reaction direction is listed, it is not safe to make any assumption about it. In general, reactions are defined in a direction (i.e. the left and right slots) according to EC conventions, which may have little bearing on the physiological direction. When we specify a reaction direction, it is either because our curators have specifically curated that direction based on the literature or on chemical knowledge, or because the software can infer a direction based on the direction it goes within some pathway or when catalyzed by some enzyme. If we don't have the information to make an inference, and a curator has not specifically examined the reaction, we don't assign one. This doesn't necessarily mean the direction is unknown -- some of the reactions imported from the EC have comments that make the direction clear, but that info is not in a form that is interpretable by our software.

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Asked: 2020-06-16 06:04:23 -0500

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Last updated: Jun 23 '20