update/ecYeastGEM/v8.6.0/2022 07 03 20 48 59

[automator-metatlas]

update ecYeastGEM based on v8.6.0

MATLAB is selecting SOFTWARE OPENGL rendering.

***************************************************************
   GECKO: Adding enzyme constraints to a genome-scale model
***************************************************************

Getting genome-scale model ready... Done!

==================
Generating ecModel:
==================
Retrieving EC numbers............................................ Done!
Matching kcats............................................ Done!
Adding enzymes to reactions............................................................... Done!
Improving model with curated data....................................................................................... Done!
Removing repeated rxn: r_0226No2 & r_0226No3
Removing repeated rxn: r_0438No1 & r_0438No2
Removing repeated rxn: r_0438No1 & r_0438No3
Removing repeated rxn: r_0438No1 & r_0438No4
Removing repeated rxn: r_0438No2 & r_0438No3
Removing repeated rxn: r_0438No2 & r_0438No4
Removing repeated rxn: r_0438No3 & r_0438No4
Removing repeated rxn: r_0439No1 & r_0439No2
Merging reactions: arm_r_0439 & r_0439No1
Merging reactions: arm_r_0543 & r_0543No1
Merging reactions: arm_r_1838 & r_1838No1
Removing unused protein: P00424
Removing unused protein: P18496
Removing unused protein: P22135
Removing unused protein: P32453
Removing unused protein: Q3E7B6
Removing incorrect pathways... Done!

==============================================================
Generating ecModel with shared pool assumption (ecModel_batch):
==============================================================
Calculating total abundance.................................................................... Done!
WARNING: Reaction r_1663 is not present in the reaction list

WARNING: Reaction r_4062 is not present in the reaction list

WARNING: Reaction r_4064 is not present in the reaction list

Matching data to enzymes in model... Done!
Estimating GAM.............................................................. Done!
Fitted GAM = 22.6 -> Error = 0.19501
[�Warning: MATLAB has disabled some advanced graphics rendering features by switching to software OpenGL. For more information, click <a href="matlab:opengl('problems')">here</a>.]� 
Total protein amount measured = 0 g/gDW
Total enzymes measured = 0 enzymes
Enzymes in model with 0 g/gDW = 0 enzymes
Total protein amount not measured = 0.5 g/gDW
Total enzymes not measured = 968 enzymes
Total protein in model = 0.5 g/gDW
The ECmodel is overconstrained!
******************* Limiting Kcats curation *******************
*Iteration #1
 Automatic search // EC#: 5.4.99.7
  Protein:P38604 Rxn#:3764 name: lanosterol synthase (No1)
  prev_Kcat:0.0019367 new_Kcat:4.0763 CC:0.64044 Err:-60.8152%
*Iteration #2
 Automatic search // EC#: 6.3.5.3
  Protein:P38972 Rxn#:3004 name: 5'-phosphoribosylformyl glycinamidine synthetase (No1)
  prev_Kcat:0.05 new_Kcat:5.0675 CC:0.36473 Err:-46.6957%
*Iteration #3
 Automatic search // EC#: 4.2.1.20
  Protein:P00931 Rxn#:4168 name: tryptophan synthase (indoleglycerol phosphate) (No1)
  prev_Kcat:0.022301 new_Kcat:775.75 CC:0.41649 Err:-24.4645%
*Iteration #4
 Automatic search // EC#: 6.3.4.- 6.3.4.9 6.3.4.10 6.3.4.11 6.3.4.15
  Protein:P48445 Rxn#:3044 name: acetyl-CoA carboxylase, reaction (No1)
  prev_Kcat:1.23 new_Kcat:450000 CC:0.060583 Err:-19.8836%
*Iteration #5
 Automatic search // EC#: 2.1.1.14
  Protein:P05694 Rxn#:3794 name: methionine synthase (No1)
  prev_Kcat:0.33 new_Kcat:3.5 CC:0.047003 Err:-16.4844%
*Iteration #6
 Automatic search // EC#: 2.7.6.1
  Protein:P32895 Rxn#:3997 name: phosphoribosylpyrophosphate synthetase (No1)
  prev_Kcat:0.65999 new_Kcat:1170 CC:0.045044 Err:-12.7209%
*Iteration #7
 Automatic search // EC#: 4.1.1.65
  Protein:P39006 Rxn#:4685 name: PS decarboxylase (1-16:1, 2-16:1), mitochondrial membrane (No1)
  prev_Kcat:0.053334 new_Kcat:366.6667 CC:0.042325 Err:-9.0232%
***************************************************************
Fitting sigma factor....................... Done!
Saving simulation results files...
File successfully saved.
Sigma factor (fitted for growth on glucose): 0.51

=============
Saving models:
=============
Saving ecYeastGEMv8.6.0:
Converting RAVEN structure to COBRA..
Each model.subSystems{x} is a character array, and this format is retained.
Document written
Each model.subSystems{x} is a character array, and this format is retained.
Saving ecYeastGEM_batchv8.6.0:
Converting RAVEN structure to COBRA..
Each model.subSystems{x} is a character array, and this format is retained.
Document written
Each model.subSystems{x} is a character array, and this format is retained.