update/eciML1515/2022 07 03 23 05/2022 07 03 23 06 07

[automator-metatlas]

update eciML1515 based on 2022-07-03-23-05

MATLAB is selecting SOFTWARE OPENGL rendering.
WARNING: Potentially problematic ") AND (" in the grRules for reaction(s): 
	PFL
	RNDR1
	RNDR3
	RNDR4
	CITL
	NO3R1bpp
	NO3R2bpp
	ATPS4rpp
	CPGNtonex
	...and 19 more

WARNING: The following metabolite names begin with a number directly followed by space:
	2doxg6p_c
	3amp_p
	3cmp_p
	2dglc_p
	3cmp_e
	3ump_e
	2dglc_e
	3amp_e
	3ump_p
	2dglc_c


***************************************************************
   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...Improving model with curated data
............................................................. Done!
Removing repeated rxn: THMDt2pp_copy1 & THMDt2pp_copy2
Removing repeated rxn: URIt2pp_copy1 & URIt2pp_copy2
Removing repeated rxn: ADNt2pp_copy1 & ADNt2pp_copy2
Removing repeated rxn: GLCtex_copy1 & GLCtex_copy2
Removing repeated rxn: CYTDt2pp_copy1 & CYTDt2pp_copy2

==============================================================
Generating ecModel with shared pool assumption (ecModel_batch):
==============================================================
Calculating total abundance............................................Matching data to enzymes in model... Done!
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 = 0.5793 g/gDW
Total enzymes not measured = 1259 enzymes
Total protein in model = 0.5793 g/gDW
The ECmodel is overconstrained!
******************* Limiting Kcats curation *******************
*Iteration #1
 Automatic search // EC#: 6.3.5.3
  Protein:P15254 Rxn#:2574 name: Phosphoribosylformylglycinamidine synthase (No1)
  prev_Kcat:0.05 new_Kcat:5.0675 CC:2.3159 Err:21.2491%
***************************************************************
Fitting sigma factor....................... Done!
[�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>.]� 
Saving simulation results files...
File successfully saved.
Sigma factor (fitted for growth on glucose): 0.41

=============
Saving models:
=============
Saving eciML15152022-07-03-23-05:
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 eciML1515_batch2022-07-03-23-05:
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.