Comments (3)
List of remaining missing biomass compounds:
- cpd15817 3hdpgpe 2-O-(3'-hydroxy)phytanyl-3-O-phytanyl-sn-glycero-l-phosphoethanolamine
- cpd15818 3hdpgpg 2-O-(3'-hydroxy)phytanyl-3-O-phytanyl-sn-glycerol-1-phospho-3'-sn-glycerol
- cpd15819 3hdpgpi 2-O-(3'-hydroxyl)phytanyl-3-O-phytanyl-sn-glycero-1-phospho-myo-inositol
- cpd15820 3hdpgps 2-O-(3'-hydroxy)phytanyl-3-O-phytanyl-sn-glycero-l-phosphoserine
- cpd15834 adocblhbi Adenosylcobalamin-HBI
- cpd15858 dpgpe 2,3-O-phytanyl-sn-glycero-1-phosphoethanolamine
- cpd15859 dpgpg 2,3-di-O-phytanyl-sn-glycerol-1-phospho-3'-sn-glycerol
- cpd15860 dpgpi 2,3-O-phytanyl-sn-glycero-1-phospho-myo-inositol
- cpd15861 dpgps 2,3-O-phytanyl-sn-glycero-1-phosphoserine
- cpd15880 gdpgpi glucosaminyl archaetidyl-myo-inositol
- cpd15884 h4spt tetrahydrosarcinapterin
from gapseq.
cpd15834 (adocblhbi – Adenosylcobalamin-HBI) is replaced with the new metabolite entry cpd33626 (adenosyl factor III), which denotes the same metabolite but whose biosynthesis pathways are based on MetaCyc (PWY-7969). It can new be produced with the gapseq reaction database.
cpd15884 (h4spt – tetrahydrosarcinapterin) can now also be produced.
List of remaining missing archaea biomass compounds, that cannot be produced:
- cpd15817 (3hdpgpe – 2-O-(3'-hydroxy)phytanyl-3-O-phytanyl-sn-glycero-l-phosphoethanolamine)
- cpd15818 (3hdpgpg – 2-O-(3'-hydroxy)phytanyl-3-O-phytanyl-sn-glycerol-1-phospho-3'-sn-glycerol)
- cpd15819 (3hdpgpi – 2-O-(3'-hydroxyl)phytanyl-3-O-phytanyl-sn-glycero-1-phospho-myo-inositol)
- cpd15820 (3hdpgps – 2-O-(3'-hydroxy)phytanyl-3-O-phytanyl-sn-glycero-l-phosphoserine)
- cpd15858 (dpgpe – 2,3-O-phytanyl-sn-glycero-1-phosphoethanolamine)
- cpd15859 (dpgpg – 2,3-di-O-phytanyl-sn-glycerol-1-phospho-3'-sn-glycerol)
- cpd15860 (dpgpi – 2,3-O-phytanyl-sn-glycero-1-phospho-myo-inositol)
- cpd15861 (dpgps – 2,3-O-phytanyl-sn-glycero-1-phosphoserine)
- cpd15880 (gdpgpi – glucosaminyl archaetidyl-myo-inositol)
from gapseq.
Following the recent commit 39ab2cb , also all remaining biomass components can now be produced.
from gapseq.
Related Issues (20)
- How was dat/media/gut.csv formulated?
- stat: cannot stat '/scratch/users/nus/e0512805/gapseq/src/../dat/seq/Bacteria/rev/sequences.tar.gz': No such file or directory HOT 8
- Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached: [rest.uniprot.org] SSL connection timeout HOT 4
- Issue with options when calling subcommand for "gapseq doall". HOT 3
- Download sequences fails HOT 2
- HTML entities for special characters in reaction name causes incorrect uniprot queries HOT 1
- libsbml and libglpk not found while installed using conda HOT 4
- Question: GapSeq includes a protein as being present when it got a bad blast? HOT 14
- Reaction inferred from pseudogene regions when using gapseq on genome fasta file.
- CHNOSZ NOT FOUND HOT 1
- [Request Update] [Tutorial] For anyone who intend to use CPLEX in gapseq HOT 3
- Diamond not used for the transport-find command HOT 2
- Could not use find-transport function using '-m' option for specific metabolite. HOT 8
- subex.tbl issue HOT 1
- Any plans on updating MetaCyc database? HOT 2
- Using seed reaction database in Adapt function HOT 8
- adding pathways| Error: No model reactions found and Error: Error in !opt$sbml.no.output : invalid argument type HOT 5
- Inquiry on instllation HOT 2
- Inquiry on error HOT 5
- Missing exchange reactions are not being added in the "adapt" module HOT 3
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