Building a Metabolic Reconstruction

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It is useful to group the recognized genes into the recognized

pathways, complexes, and nonmetabolic molecular machines. Here is how

we view this process:

1. Our annotation team has constructed sets of functional roles

that are annotated simultaneously because the functional roles

are related. The roles may be distinct subunits of a complex

(e.g., the subunits of the ATP synthase or the ribosomal

proteins), a set of functional roles that constitute a pathway

(e.g., Histidine Degradation) or the genes may make up a

nonmetabolic molecular machine (e.g., a repair machine, a

transport cassette, or a 2-component regulatory system). We

call each of these sets of roles a "subsystem". Our annotators

have carefully assembled the functional roles that make up a

subsystem and for each one constructed a spreadsheet in which

each row is a genome and each column is a distinct functional

role. The cells of the spreadsheet contain the genes from the

specific genome that implement the specific functional role.

For example (SEE POWERPOINT PICTURES OF HISTIDINE DEGRADATION).

2. We automatically, using the examples contained in the manually

curated set of subsystems, try to locate the appropriate genes

within the newly-sequenced genome and identify a new instance

(i.e., a new row in the spreadsheet) of the subsystem. When we

can identify all of the genes needed to implement an operational

version of the subsystem, it substantially increases the

confidence we have in the assigned functions, and it forms a

critical piece of information needed to support the generation

of metabolic models.

3. Where we recognize a portion of a subsystem, we may have failed

to accurately identify some genes, we may have misannotated

genes, or we may have a new variant of the subsystem (e.g., a

new variant of a common pathway),

4. We consider a metabolic reconstruction to simply be the set of

recognized, operational instances of our subsystem collection.

This is distinct from an actual initial estimate of the

metabolic network (which we provide, as well). The metabolic

reconstruction includes information about the nonmetabolic

machinery supported by the genome. We are not completely happy

with the term "metabolic reconstruction", but that is the term

that has stuck and the one in common usage within our group.