limits.yaml

- reaction: NGAM
  fixed: 2.344
  comment: NGAM calibration based on Kengen 1994
#- reaction: R00965
#  fixed: 0
#  pmid: 21317259
#  comment: pyrF knockout, if present

### below are the limits in physiological condition based on the literature
- reaction: R01061
  lower: 0
  upper: 1000
  pmid: 12921536, 21409597, 21736643
  comment: This is the NAD version of GAPDH. GAPDH/PGK play a major
    role only in gluconeogenesis in Thermococcales. [pmid:21736643] So here limit the direction from G13P2 => GAP.
- reaction: R01063
  lower: 0
  upper: 1000
  pmid: 12921536, 21409597, 21736643
  comment: This is the NADP version of GAPDH. GAPDH/PGK play a major
    role only in gluconeogenesis in Thermococcales. [pmid:21736643] So here limit the direction from G13P2 => GAP.
- reaction: R00700
  lower: 0
  upper: 1000
  comment: SHI and SHII are 'uptake' hydrogenases - they can be deleted without significantly affecting the H2 production (pmid:22557999); MBH is responsible for almost all H2 production (or MBS if sulfur is present) and SHI and SHII are primarily H2 consuming, so constraining to H2 consuming direction
- reaction: R07181
  lower: 0
  upper: 1000
  comment: SHI and SHII are 'uptake' hydrogenases - they can be deleted without significantly affecting the H2 production (pmid:22557999); MBH is responsible for almost all H2 production (or MBS if sulfur is present) and SHI and SHII are primarily H2 consuming, so constraining to H2 consuming direction
- reaction: nfn1
  lower: 0
  upper: 1000
  comment: Nfn1 primary function seems to be maintaining a high NADPH/NADP ratio in cells favoring the forward direction [pmid:28705933], although both directions are possible [pmid:28394885]. Negative fluxes of this gene cause looping behavior in the model sh1/sh2/mbh/atps, so constraining to forward direction