SubtiBank SubtiBank
ykfD [2019-09-02 12:54:14]
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ykfD [2019-09-02 12:54:14]

similar to oligopeptide [SW|ABC transporter ](permease)
locus
BSU_13000
pI
9.34
mw
36.83 kDa
protein length
329 aa Sequence Blast
gene length
990 bp Sequence Blast
function
unknown
product
unknown
essential
no
synonyms
Outlinks
KEGGBsubCycSubtiListUniProtExpression Browser

Genomic Context

      

categories

  • [category|SW 1|Cellular processes] → [category|SW 1.2|Transporters] → [category|SW 1.2.1|ABC transporters] → [category|SW 1.2.1.1|Importers] → [category|SW 1.2.1.1.3|Uptake of peptides]
  • [category|SW 2|Metabolism] → [category|SW 2.3|Amino acid/ nitrogen metabolism] → [category|SW 2.3.3|Utilization of nitrogen sources other than amino acids] → [category|SW 2.3.3.4|Utilization of peptides]
  • [category|SW 6|Groups of genes] → [category|SW 6.2|Membrane proteins]

    • Gene

    Coordinates
    1,368,844 → 1,369,833

    The protein

    Protein family

  • [SW|ABC transporter superfamily] (according to UniProt)

    • Paralogous protein(s)

  • [protein|38AD697B6C9967B8BD7496E31264A21F6D0A9DEE|OppF], [protein|B88A88B4792FFFF4E1609B1FC91AAE6DBA339044|AppF]

    • Structure

  • [PDB|4FWI] (dipeptide transporter from ''Thermoanaerobacter tengcongensis'', 36% identity) [Pubmed|23385461]

    • [SW|Localization]

  • attached to the cell membrane (via [protein|062AE5FB4C778178A7F6833CB8BD9D631E461E89|DppB]-[protein|EDF8D2C49FA5552B24135E12524F9035E1E01473|DppC]) [Pubmed|10092453]

    • Expression and Regulation

    Operons

    genes
    [gene|9E922F0006DF9E84A8D5B51E9FC35B669872FF90|dppA]-[gene|062AE5FB4C778178A7F6833CB8BD9D631E461E89|dppB]-[gene|EDF8D2C49FA5552B24135E12524F9035E1E01473|dppC]-[gene|7FA72D949B930A3C7FF0391CC6CCC58EEFCA839A|dppD]-[gene|853C570CFB9382449A20BE77B44B4FE44972AA59|dppE]-[gene|C4F85F85F0C99A59145961E34B19D3AD03D2BC22|ykfA]-[gene|77EFC47449D8CC17651ED61C41AC605FCEF01270|ykfB]-[gene|D40ECAE51D9E4791C6FAAA25E2E0D0591D9FAA55|ykfC]-[gene|BB94F5388A0D1FF025E5A88A7E10AE7E4C489E5F|ykfD]
    description
    [pubmed|22383849]

    regulatory mechanism

  • [protein|90ACE0DECA58D3C1A55E135120F7A0C1C920571C|CodY]: repression, [Pubmed|12618455], in [regulon|90ACE0DECA58D3C1A55E135120F7A0C1C920571C|CodY regulon]
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    Biological materials

    Mutant

  • MGNA-A743 (ykfD::erm), available at the [https://shigen.nig.ac.jp/bsub/resource/strainGeneDisrupted/detail/743 NBRP B. subtilis, Japan]
  • BKE13000 (Δ[gene|BB94F5388A0D1FF025E5A88A7E10AE7E4C489E5F|ykfD]::erm trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKE13000 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATTTGTCTCCCTCCTTATT, downstream forward: _UP4_TAAATAAAAAGAGTGGCTCC
  • BKK13000 (Δ[gene|BB94F5388A0D1FF025E5A88A7E10AE7E4C489E5F|ykfD]::kan trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKK13000 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATTTGTCTCCCTCCTTATT, downstream forward: _UP4_TAAATAAAAAGAGTGGCTCC

    • References

  • 12618455,10092453,23385461