Supplemenal - Model Gaps Filled and Extant.doc

Supplemental - Model Gaps Filled and Extant
Like any metabolic reconstruction, the presented reconstruction of Methanosarcina acetivorans contains gaps in the genome annotation due to an plete knowledge about its metabolism. Many of the pathways in the Bacteria domain differ from those in the Archaea, and much progress has been made illuminating those differences. However, as this supplemental shows, there is clearly more work to be done pletely understand metabolism in the Archaea, and particularly in M. acetivorans.
Presented here are two lists. First we present a list of gaps found in the previously-published M. barkeri reconstruction that have been filled or partially filled in the presented reconstruction. Second, we present a list of known gaps in the work of M. acetivorans as of the time of publication of our model. The names of the metabolites in the plots below correspond to the metabolite IDs in the metabolic model. Some of the pathways described here have other biochemical evidence such as carbon labeling, but the evidence was described in anisms and no genes have been identified to carry out the proposed functions. Other pathways or reactions have known genes in anisms but they have no significant sequence homology with any genes in M. acetivorans.
The genome of Methanosarcina acetivorans contains over 1000 ORFs annotated as hypothetical proteins. It is our hope that this list will be useful for assigning functions to some of them and furthering the general knowledge of archaeal metabolic functions.
Figure Key
The key to the figures in this section is shown in table below. If a gene product in anism has been verified to perform the reaction, the gene locus is shown in parenthesis (. (MJ_0001) ). Any genes in M. acetivorans predicted to perform the same reaction are shown adjacent (no M. acetivorans gene is shown if there was no sequence similarity with the verified genes).
Table . Key to model gap figures.
Color
Pattern
Meaning
Red
i