EG12386

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Author Information

Trina Sarkar

Basic Information

  • ID: EG12386
  • Name: csiR
  • Organism: E. coli
  • Description: ABC transporters utilize the energy of ATP binding and hydrolysis to transport various substrates across cellular membranes. An effluxer (or exporter) is a specific ABC transporter that is present in both prokaryotes and eukaryotes and pumps toxins and drugs out of the cell using active transport [1]. Additionally, permeases are transmembrane proteins that use a proton gradient to diffuse molecules out of the cell [2].
  • DNA Length: 663 base pairs.
  • DNA sequence:

ACCATTA CGTCTCTGGA TGGCTATCGC TGGCTGAAGA ACGATATTAT TCGCGGTAAT TTTCAACCGG ATGAAAAATT ACGAATGAGT TTGCTGACAT CGCGTTATGC ACTTGGCGTT GGGCCGTTAC GGGAAGCTCT TTCGCAACTG GTGGCGGAAC GGCTGGTCAC GGTGGTGAAT CAAAAAGGGT ATCGGGTGGC GTCTATGTCA GAGCAGGAGC TGCTCGATAT TTTCGACGCC CGCGCCAATA TGGAAGCGAT GTTAGTGAGT CTGGCGATTG CCCGCGGTGG CGATGAGTGG GAGGCAGACG TTCTCGCAAA AGCGCATCTG CTGAGTAAGC TTGAGGCCTG TGACGCCAGC GAGAAAATGC TTGATGAGTG GGATCTGCGT CATCAGGCGT TTCATACGGC AATTGTGGCG GGCTGTGGTT CTCACTATTT GCTGCAAATG CGTGAACGGT TGTTTGATCT GGCGGCGCGT TATCGATTTA TCTGGCTGCG GCGAACGGTG CTTTCGGTGG AAATGCTGGA GGATAAACAC GATCAGCACC AGACCCTGAC TGCGGCGGTA CTGGCGCGAG ATACCGCGCG CGCCAGTGAG TTAATGCGCC AGCATTTACT GACGCCAATT CCCATTATCC AGCAGGCGAT GGCTGGCAAT

  • Amino Acid length: 220 amino acids.
  • Amino Acid sequence:

MTITSLDGYR WLKNDIIRGN FQPDEKLRMS LLTSRYALGV GPLREALSQL VAERLVTVVN QKGYRVASMS EQELLDIFDA RANMEAMLVS LAIARGGDEW EADVLAKAHL LSKLEACDAS EKMLDEWDLR HQAFHTAIVA GCGSHYLLQM RERLFDLAAR YRFIWLRRTV LSVEMLEDKH DQHQTLTAAV LARDTARASE LMRQHLLTPI PIIQQAMAGN

Function and Homologs

  • Product: Efflux ABC transporter permease
  • Module: ATP-binding cassette (ABC) transporter
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • putative transcriptional regulator [Escherichia coli O157:H7 str. EDL933], 451 / 100% / 4e-162 / 100%, AAG57772.1
    • MULTISPECIES: transcriptional regulator [Proteobacteria], 450 / 100% / 4e-162 / 100%, WP_000156811.1
    • transcriptional regulator [Escherichia coli], 449 / 100% / 7e-162 / 99%, WP_001560421.1
  • Equivalent E. coli / JCVI functional protein: MMSYN1_0639

Expression

  • Expression Level: low
    • Expression Level Hypothesis: I hypothesize that the protein's expression level is low because it uses active transport to remove excess waste and can thus be reused.
    • Expression Level References and Description: To determine the protein expression le9vel, I looked at the expression level for the close relative MMSYN1_0531, another efflux ABC transporter permease. It also had pertinent information regarding the expression level hypothesis which I then later corroborated with Boundless Microbiology. The gene sheet was linked in the M.Genitalium dataset, found at File:MgenitaliumSimProteinCounts.xlsx.
  • Expression Time: late
    • Expression Level Hypothesis: Since this protein is responsible for removing waste, I hypothesize that it is expressed later in a cell life cycle, after the cell has accumulated waste.
    • Expression Time References and Description: Again, I looked at the expression time for the close relative MMSYN1_0531 which was linked in the "M.Genitalium" dataset.

Gene Context

  • Other Components in the functional module: ybbA. According to the e.coli gene specification sheet, ybbA is the ATP binding component and ybbB is the membrane component.
  • Possible Dependencies: ATP
  • Process: Metabolite uptake transport
    • Inputs: ATP, molecule/substrate being transported
    • Outputs: ADP, phosphate, same molecule/substrate that has now been transported to other side of the membrane

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
  • https://en.wikipedia.org/wiki/ATP-binding_cassette_transporter
  • https://en.wikipedia.org/wiki/Permease
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