EG12752

From BioE80 Boot
Jump to: navigation, search

Author Information

Sasha Perigo sperigo@stanford.edu

Basic Information

  • ID: EG12752
  • Name: yhaM
  • Organism: E. coli
  • Description: This gene is involved in L-cysteine detoxification. Not much else is known about it [1].
  • DNA Length: 1329 base pairs
  • DNA sequence:

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

  • Amino Acid length: 443 amino acids
  • Amino Acid sequence:

MFDSTLNPLWQRYILAVQEEVKPALGCTEPISLALAAAVAAAELEGPVERVEAWVSPNLM KNGLGVTVPGTGMVGLPIAAALGALGGNANAGLEVLKDATAQAIADAKALLAAGKVSVKI QEPCDEILFSRAKVWNGEKWACVTIVGGHTNIVHIETHDGVVFTQQACVAEGEQESPLTV LSRTTLAEILKFVNEVPFAAIRFILDSAKLNCALSQEGLSGKWGLHIGATLEKQCERGLL AKDLSSSIVIRTSAASDARMGGATLPAMSNSGSGNQGITATMPVVVVAEHFGADDERLAR ALMLSHLSAIYIHNQLPRLSALCAATTAAMGAAAGMAWLVDGRYETISMAISSMIGDVSG MICDGASNSCAMKVSTSASAAWKAVLMALDDTAVTGNEGIVAHDVEQSIANLCALASHSM QQTDRQIIEIMASKAR

Function and Homologs

  • Product: UPF0597 protein YhaM
  • Module: RNA metabolism?
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • MULTISPECIES: L-serine dehydratase alpha chain [Proteobacteria], 882/100%/0.0/100%, WP_000460499.1
    • hypothetical protein [Escherichia coli], 881/100%/0.0/99%, WP_061356137.1
    • membrane protein [Escherichia coli], 881/100%/0.0/99%, WP_032173009.1
  • Equivalent E. coli / JCVI functional protein: MMSYN1_0437

Expression

  • Expression Level: Low
  • Expression Level Hypothesis: I guessed low by looking at similar genes on the Ecoli expression data list.
  • Expression Level References and Description: [2]
  • Expression Time: unknown/impossible to tell
  • Expression Time References and Description: There's no relevant information on Uniprot or anywhere else online.

Gene Context

  • Other Components in the functional module: unknown/impossible to tell
  • Possible Dependencies: unknown/impossible to tell
  • Process: L-cysteine detoxification
    • Inputs: L-cysteine
    • Outputs: L-cysteine

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