MMSYN1 0607

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Author Information

Hikaru Hotta

Basic Information

  • ID: MMSYN1_0607
  • Name: gap
  • Organism: JCVI-Syn3.0
  • Description: This gene is involved in glucose transport and catabolism. Based on a Conserved Domain Search, this gene plays a central role in glycolysis and gluconeogenesis - the blurb mentions that the gene encodes for "the enzyme responsible for the interconversion of 1,3-diphosphoglycerate and glyceraldehyde-3-phosphate." According to the relevant wikipedia page, other than catalyzing the sixth step of glycolysis in the cytosol of the cell, this gene can activate transcription as it is contained in the OCA-S transcriptional coactivator complex. This gene is also involved in cell apoptosis as outlined by the relevant wikipedia page - the gene "is S-nitrosylated by NO in response to cell stress, which causes it to bind to the protein SIAH1, a ubiquitin ligase. The complex moves into the nucleus where Siah1 targets nuclear proteins for degradation, thus initiating controlled cell shutdown." Other functions of the gene include acting as a metabolic switch under oxidative stress, assist vesicle transport from the endoplasmic reticulum to the Golgi apparatus. As we can see, this gene has one main function in glycolysis but has multiple secondary functions.
  • DNA Length: 1014 base pairs.
  • DNA sequence:

ATG TCA AAG AAA GTC GCC ATT AAT GGA TTT GGA CGT ATT GGT CGC CTT ACT TTC CGC CAA TTG TTC GAG AAA GAC ATC GAG ATT GTC GCA ATT AAC GAT TTG ACT GAC ACG AAG ACT CTT GCG TAT TTG TTG GAG TTT GAT ACC GCA CAA GGT ATC TTT TGT GAA GGT GAG ATT TCA CAC ACA GAC AAC AGC ATC ATC GTC AAG GGG AAG GAA GTA AAA GTC TTC GCC GAA AAA GAC GCC AGT AAT TTA CCC TGG TCT GAG TTA AAA GTT GAT CTT GTT ATC GAA AGC ACA GGA TTC TAC ACA GAT AAA GAA AAA GCC AGT GCA CAC ATC AAA GCC GGA GCG AAA AAA GTC GTC ATC AGC GCT CCT GCA ACT GGA GAC TTA AAA ACG GTC GTC TAC GGA GTG AAT CAT AAA TCA TTG ACA AGC GAT GAT GTC ATT ATC TCG GGT GCA TCT TGT ACG ACA AAT TGT TTA ACA CCT TTC ACG AAA GCC CTG GAT GAT GCC TTC ACG ATT AAG AAG GGC TTC ATG ACC ACT GTA CAC GCA GTA ACG AAT GAC CAA CGC CTG CTT GAC CTG AAC CAT AAA GAC GTT CGT CGT GGC CGC GCC GCT GCA TGG AAC ATC GTA CCT TCA ACC ACT GGT GCA GCT AAG GCA GTA AGC CTT GTC TTA CCG CAT CTT AAA GGC AAA CTT GAT GGA TAT GCC TTG CGT GTC CCA ACG ATC ACA GGA TCT ATC ACA GAC TTA ACA GTC GAA TTT GAA AAC CAA GAG TTA ACA GTG GAA CAA ATC AAT AAC GCT GTG AAG AAA GCG CTT GAA GCG GAT GCC GAT CTG GCG AAG GCA ATG AAG TAT GAA ACT CGC CCC ATT GTT TCA TCA GAT ATC ATT GGC AGT AAA TAC GGT TCC ATT TTC GAC GCC ACC TTA ACC AAG GTG ATG AAC GTC GAC GGC AAG CAA CTG GTG AAA GTT TGC TCG TGG TAC GAC AAT GAA TCT AGC TAC GTG TCG CAA CTT GTT CGC ACA ACC ATT TAT TTC ATG AGC TTA

  • Amino Acid length: 338 amino acids.
  • Amino Acid sequence:

MSKKVAINGFGRIGRLTFRQLFEKDIEIVAINDLTDTKTLAYLLEFDTAQGIFCEGEISHTDNSIIVKGKEVKVFAEKDASNLPWSELKVDLVIESTGFYTDKEKASAHIKAGAKKVVISAPATGDLKTVVYGVNHKSLTSDDVIISGASCTTNCLTPFTKALDDAFTIKKGFMTTVHAVTNDQRLLDLNHKDVRRGRAAAWNIVPSTTGAAKAVSLVLPHLKGKLDGYALRVPTITGSITDLTVEFENQELTVEQINNAVKKALEADADLAKAMKYETRPIVSSDIIGSKYGSIFDATLTKVMNVDGKQLVKVCSWYDNESSYVSQLVRTTIYFMSL

Function and Homologs

  • Product: Glyceraldehyde 3-phosphate dehydrogenase
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • Name: type I glyceraldehyde-3-phosphate dehydrogenase [Mycoplasma capricolum], Max score: 656/Query Cover: 100%/E-Value: 0.0/Ident: 93%, [1]
    • Name: type I glyceraldehyde-3-phosphate dehydrogenase [Mycoplasma feriruminatoris], Max score: 655/Query Cover: 100%/E-Value: 0.0/Ident: 93%, [2]
    • Name: type I glyceraldehyde-3-phosphate dehydrogenase [Mycoplasma feriruminatoris], Max score: 655/Query Cover: 100%/E-Value: 0.0/Ident: 93%, [3]
  • Equivalent E. coli / JCVI functional protein: EG10367.

Expression

  • Expression Level: low.
  • Expression Level Hypothesis: This gene catalyzes the sixth step of glycolysis. Because JCVI Syn3.0 is a facultative anaerobe, not all the steps of glycolysis occur and therefore, the sixth step is not vital in its metabolic functioning.
  • Expression Level References and Description: According to open anesthesia aerobic and anaerobic glycolysis follow different catabolic pathways suggesting low expression level.
  • Expression Time: late.
  • Expression Level Hypothesis: Though its function in anaerobic glycolysis may be limited, this gene is also involved in cell apoptosis which would come late in the lifecycle of the organism when it will start to disintegrate.
  • Expression Time References and Description: Information was gathered from the relevant wikipedia page on Glyceraldehyde 3-phosphate dehydrogenase.

Gene Context

  • Other Components: MMSYN1 0131. fbaA2 is an enzyme that splits fructose 1,6-bisphosphate, into dihydroxyacetone phosphate (DHAP) and glyceraldehyde 3-phosphate (G3P). It is on the same pathway in glycolysis as gapA to make glyceraldehyde-3P.
  • Possible Dependencies: Pentose phosphate pathway. It is a anabolic metabolic pathway that runs parallel to glycolysis. It is expressed by genes such as MMSYN1 0262.
  • Process: Two-step conversion of G3P
    • Inputs: Glyceraldehyde 3-phosphate, NAD+, Pi
    • Outputs: D-glycerate 1,3-bisphosphate, NADH, H+

Construct

We will handle this - not part of your assignment

  • Synthesis Score: The synthesis score: 1,2,3
  • Predicted Translation Rate: Prediction of construct translation rate from the RBS calculator
  • Design Notes and Details:
  • GenBank File: A link to the GenBank file. file