Detailed information    

experimental Experimentally validated

Overview

Name   codY   Type   Regulator
Locus tag   BSU_16170 Genome accession   NC_000964
Coordinates   1690119..1690898 (+) Length   259 a.a.
NCBI ID   NP_389499.1    Uniprot ID   P39779
Organism   Bacillus subtilis subsp. subtilis str. 168     
Function   repression of comK   
Competence regulation

Function

CodY acts as a regulator of competence by influencing the expression of key competence genes. Specifically, CodY can repress the expression of comK, the master regulator of competence, thereby indirectly controlling the expression of downstream competence genes required for DNA uptake and recombination.


Genomic Context

Location: 1685119..1695898
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  BSU_16130 (BSU16130) trmFO 1685812..1687119 (+) 1308 NP_389495.1 tRNA:m(5)U-54 methyltransferase -
  BSU_16140 (BSU16140) codV 1687187..1688101 (+) 915 NP_389496.1 site-specific tyrosine recombinase for chromosome partitioning -
  BSU_16150 (BSU16150) clpQ 1688114..1688659 (+) 546 NP_389497.1 two-component ATP-dependent protease (N-terminal serine protease) -
  BSU_16160 (BSU16160) clpY 1688676..1690079 (+) 1404 NP_389498.1 two-component ATP-dependent protease (ATPase and chaperone) -
  BSU_16170 (BSU16170) codY 1690119..1690898 (+) 780 NP_389499.1 transcriptional regulator, GTP and BCAA-dependent Regulator
  BSU_16180 (BSU16180) flgB 1691278..1691667 (+) 390 NP_389500.1 flagellar component of cell-proximal portion of basal-body rod -
  BSU_16190 (BSU16190) flgC 1691667..1692119 (+) 453 NP_389501.1 flagellar component of cell-proximal portion of basal-body rod -
  BSU_16200 (BSU16200) fliE 1692130..1692450 (+) 321 NP_389502.1 flagellar basal body protein -
  BSU_16210 (BSU16210) fliF 1692496..1694106 (+) 1611 NP_389503.1 flagellar basal-body M-ring protein -
  BSU_16220 (BSU16220) fliG 1694119..1695135 (+) 1017 NP_389504.1 flagellar motor switching and energizing component -
  BSU_16230 (BSU16230) fliH 1695254..1695880 (+) 627 NP_389505.2 flagellar export apparatus subunit of cytoplasmic ATPase -

Regulatory network

Positive effect      
Negative effect
Regulator Target Regulation
  codY comK negative effect
  comK comK positive effect
  comK late competence genes positive effect
  clpP comK negative effect
  mecA comK negative effect
  kre comK negative effect
  abrB comK negative effect
  comS comK positive effect
  spo0A comK positive effect
  rok comK negative effect
  degU comK positive effect
  clpC comK negative effect
  med comK positive effect
  spo0A comK negative effect
  comK late competence genes positive effect
  clpP degU negative effect
  abrB rok negative effect
  spo0A abrB negative effect
  comA comS positive effect
  spo0A rok negative effect
  sinR spo0A negative effect
  sinR rok negative effect
  sinR degU negative effect
  degQ degU positive effect
  clpC degU negative effect
  degS degU positive effect
  rapC comA negative effect
  rapF comA negative effect
  comP comA positive effect
  sinI sinR negative effect
  phrC rapC negative effect
  phrF rapF negative effect
  comX comP positive effect
  comQ comX positive effect

Sequence

Protein


Download         Length: 259 a.a.        Molecular weight: 29013.22 Da        Isoelectric Point: 4.6514

>NTDB_id=82 BSU_16170 NP_389499.1 1690119..1690898(+) (codY) [Bacillus subtilis subsp. subtilis str. 168]
MALLQKTRIINSMLQAAAGKPVNFKEMAETLRDVIDSNIFVVSRRGKLLGYSINQQIENDRMKKMLEDRQFPEEYTKNLF
NVPETSSNLDINSEYTAFPVENRDLFQAGLTTIVPIIGGGERLGTLILSRLQDQFNDDDLILAEYGATVVGMEILREKAE
EIEEEARSKAVVQMAISSLSYSELEAIEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRSLGMKGT
YIKVLNNKFLIELENLKSH

Nucleotide


Download         Length: 780 bp        

>NTDB_id=82 BSU_16170 NP_389499.1 1690119..1690898(+) (codY) [Bacillus subtilis subsp. subtilis str. 168]
ATGGCTTTATTACAAAAAACAAGAATTATTAACTCCATGCTGCAAGCTGCGGCAGGGAAACCGGTAAACTTCAAGGAAAT
GGCGGAGACGCTGCGGGATGTAATTGATTCCAATATTTTCGTTGTAAGCCGCAGAGGGAAACTCCTTGGGTATTCAATTA
ACCAGCAAATTGAAAATGATCGTATGAAAAAAATGCTTGAGGATCGTCAATTCCCTGAAGAATATACGAAAAATCTGTTT
AATGTCCCTGAAACATCTTCTAACTTGGATATTAATAGTGAATATACTGCTTTCCCTGTTGAGAACAGAGACCTGTTTCA
AGCTGGTTTAACAACAATTGTGCCGATCATCGGAGGCGGGGAAAGATTAGGAACACTTATTCTTTCGCGTTTACAAGATC
AATTCAATGACGATGACTTAATTCTAGCTGAATACGGCGCAACAGTTGTCGGAATGGAAATCCTAAGAGAAAAAGCAGAA
GAAATTGAAGAGGAAGCAAGAAGCAAAGCTGTCGTACAAATGGCTATCAGCTCGCTTTCTTACAGTGAGCTTGAAGCAAT
TGAGCACATTTTTGAGGAGCTTGACGGAAATGAAGGTCTTCTTGTTGCAAGTAAAATTGCTGACCGTGTCGGCATTACCC
GTTCTGTTATTGTGAACGCACTCAGAAAGCTGGAGAGCGCCGGTGTTATCGAGTCTAGATCATTAGGAATGAAAGGTACT
TATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTAA

Domains

Predicted by InterproScan.

CodY helix-turn-helix domain (HTH_CodY)

(198-255)

CodY GAF-like domain (CodY)

(3-178)


Secondary structure

Protein secondary structures were predicted by S4PRED and visualized by seqviz.



3D structure

Source ID Structure
  PDB 2B0L
  PDB 2B18
  PDB 2GX5
  PDB 2HGV
  PDB 5LNH
  PDB 5LOE
  PDB 5LOJ
  PDB 5LOO

Transmembrane helices

Transmembrane helices of protein were predicted by TMHMM 2.0 and visualized by seqviz and ECharts.


Visualization of predicted probability:


Similar proteins

Only experimentally validated proteins are listed.

Protein Organism Identities (%) Coverage (%) Ha-value
  codY Lactococcus lactis subsp. lactis strain DGCC12653

47.451

98.456

0.467

Multiple sequence alignment    



References

[1] Tran Thu Hoa et al. (2002) Rok (YkuW) regulates genetic competence in Bacillus subtilis by directly repressing comK. Molecular Microbiology 43(1):15-26. [PMID: 11849533]
[2] P Serror et al. (1996) Interaction of CodY, a novel Bacillus subtilis DNA-binding protein, with the dpp promoter region. Molecular Microbiology 20(4):843-52. [PMID: 8793880]