MMSYN1 0729

From BioE80 Boot
Jump to: navigation, search

Author Information

Name: Sanura N'Jaka | SUID: sanura

Basic Information

  • ID: MMSYN1_0729
  • Name: gpmI
  • Organism: JCVI 3.0 - Mycoplasma mycoides
  • Description: This gene is involved in step 3 of a subpathway of glycolysis that synthesizes pyruvate from D-glyceraldehyde 3-phosphate. Specifically, it catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate. gpmI
  • DNA Length: 1,593 base pairs.
  • DNA sequence:

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

  • Amino Acid length: 531 amino acids.
  • Amino Acid sequence:

MKVKRPVLLAILDGWGISEPDKGNAVDNANMVFVEYLKKTYPWLKAHASGKWVGLPDNQMGNSEVGHIHLGAGRINLESLAKLNHETKTNNIAKNEEIVKSFEYVKNNNSALHLMGLFSNGGVHSHFDHMIAIYKAAIDYGITNIKFDLITDGRDTKPKLAYDFVKDLLELIKQNNNIGVISSISGRYYAMDRDKRFDRSRIAYNAITNRNNVRSFTNILDYIQQEYMINHDDEMIIPAFNQDDLNGNLKANDAIIMTNFRPDRAIQISSILTNKNYIAWQSEAFSDAEFIGDKIRFVSMMKYSDSITSPHIAYPPKPLTNTLGQYLSKLGLKQLRIAETEKIAHVTFFFDGGNDYFKNGLAKNDEITLANAYIDLIPSAKVATYDLKPQMSAVEITDKLLEEIKKDEFDFIVLNFANCDMVGHTGNNKATEIACKTLDEQLKRIHEEFVLRHNGIMIITADHGNAEIMIDKDGQVNKKHTTSLVPIIITDLNIKLKQNDPAIAKVAPTILDLMNIEIPKEMELESMIDHN

Function and Homologs

  • Product: 2,3-diphosphoglycerate-independent
  • Module: phosphoglycerate mutase
  • Closest homologous proteins:
    • Name: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase, Max score: 2,735/Query Cover: 531/E-Value: 0.0/Ident: 98.9%, E4PSI5
    • Name: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase, Max score: 2,718/Query Cover: 531/E-Value: 0.0/Ident: 97.7%, C7LL54
    • Name: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase, Max score: 2,715/Query Cover: 531/E-Valu: 0.0/Ident: 97.6%, F4MQU3
  • Equivalent E. coli / JCVI functional protein: Link to the identified E. coli functional analog of the protein encoded by the gene: EG12296

Expression

  • Expression Level: high
  • Expression Level Hypothesis: Because it catalyzes an interconversion, this interconversion may happen an unlimited amount of times and we would therefore want as much of the gene as possible so that the transition runs smoothly.
  • Expression Level References and Description: I was able to find my gene in the database. M. genitalium database
  • Expression Time: At which time should the gene be expressed in the lifecycle of our organism? right at the beginning
  • Expression Level Hypothesis: Because there is no way of knowing when or how often the interconversion will need to take place, it is best to express right at the beginning to insure that the transition is able to continually run smoothly.
  • Expression Time References and Description: I used known functions and descriptions of the gene to come up with my own hypothesis of the expression time.

Gene Context

  • Other Components: This module only has one component.
  • Possible Dependencies: Phosphoglycerate kinase MMSYN1_0606 is a dependent of this module because it is necessary for the interconversion to take place, as it is the step before this module in a sub pathway of glycolysis that synthesizes pyruvate. gpmI
  • Process: This module is a step in a sub pathway of glycolysis that catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate.
    • Inputs: 2-phospho-D-glycerate
    • Outputs: 3-phospho-D-glycerate

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