EG10367

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Author Information

Hikaru Hotta

Basic Information

  • ID: EG10367.
  • Name: gapA
  • Organism: E. coli
  • Description: Based on a EcoCyc search, this gene is primarily involved in the oxidative phosphorylation of glyceraldehyde 3-phosphate in glycolysis - "Glyceraldehyde 3-phosphate dehydrogenase A catalyzes the reversible oxidative phosphorylation of D-glyceraldehyde-3-phosphate to 1,3-bisphospho-D-glycerate in the presence of NAD+ and phosphate during glycolysis and gluconeogenesis in E. coli." Furthermore, a UniProt search outlines the reaction steps in the gene's catalytic activity - "The first reaction step involves the formation of a hemiacetal intermediate between G3P and a cysteine residue, and this hemiacetal intermediate is then oxidized to a thioester, with concomitant reduction of NAD to NADH. The reduced NADH is then exchanged with the second NAD, and the thioester is attacked by a nucleophilic inorganic phosphate to produce BPG."
  • DNA length: 1008 base pairs.
  • DNA sequence:

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

  • Amino Acid length: 336 amino acids.
  • Amino Acid sequence:

MTIKVGINGFGRIGRIVFRAAQKRSDIEIVAINDLLDADYMAYMLKYDSTHGRFDGTVEVKDGHLIVNGKKIRVTAERDPANLKWDEVGVDVVAEATGLFLTDETARKHITAGAKKVVMTGPSKDNTPMFVKGANFDKYAGQDIVSNASCTTNCLAPLAKVINDNFGIIEGLMTTVHATTATQKTVDGPSHKDWRGGRGASQNIIPSSTGAAKAVGKVLPELNGKLTGMAFRVPTPNVSVVDLTVRLEKAATYEQIKAAVKAAAEGEMKGVLGYTEDDVVSTDFNGEVCTSVFDAKAGIALNDNFVKLVSWYDNETGYSNKVLDLIAHISK

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.
    • MULTISPECIES: aldehyde dehydrogenase [Proteobacteria], Max score: 677/Query Cover: 100%/E-Value: 0.0/Ident: 100%, [1]
    • aldehyde dehydrogenase [Shigella sonnei], Max score: 677/Query Cover: 100%/E-Value: 0.0/Ident: 99%, [2]
    • MULTISPECIES: aldehyde dehydrogenase [Enterobacteriaceae], Max score: 676/Query Cover: 100%/E-Value: 0.0/Ident: 99%, [3]
  • Equivalent E. coli / JCVI functional protein: MMSYN1_0607.

Expression

  • Expression Level: high.
  • Expression Level Hypothesis: This gene is expressed highly because E.coli's gapA gene has a sequence that is more similar to that of eukaryotes than those of prokaryotes. Hence, aerobic glycolysis pathways are highly expressed.
  • Expression Level References and Description: This gene's Ecocyc page states gapA's unique similarily to eukaryotic gap genes.
  • Expression Time: right at beginning.
  • Expression Level Hypothesis: Since E.coli's gapA gene has a similar sequence in eukaryotic gap genes, we can hypothesize that that it is expressed from the early stages of the lifecycle as it is essential in glycolysis.
  • Expression Time References and Description: This gene's Ecocyc page states gapA's unique similarily to eukaryotic gap genes.

Gene Context

  • Other Components: fbaA is an enzyme 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. Despite an Ecoli equivalent version of this gene existing, a wiki page was not made for the E.coli equivalent of MMSYN1 0131
  • Possible Dependencies: Pentose phosphate pathway. It is a anabolic metabolic pathway that runs parallel to glycolysis. It is expressed by genes such as EG11960
  • Process: Oxidative phosphorylation of glyceraldehyde 3-phosphate
    • Inputs: D-glyceraldehyde 3-phosphate, phosphate, NAD+
    • Outputs: 3-phospho-D-glyceroyl phosphate, NADH

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