Detailed information    

experimental Experimentally validated

Overview

Name   codY   Type   Regulator
Locus tag   V4T04_RS08565 Genome accession   NZ_JAZICS010000006
Coordinates   82051..82839 (+) Length   262 a.a.
NCBI ID   WP_003129722.1    Uniprot ID   -
Organism   Lactococcus lactis subsp. lactis strain DGCC12653     
Function   repress the expression of comX   
Competence regulation

Function

The nitrogen global regulator CodY is a direct repressor of comX.


Genomic Context

Location: 77051..87839
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  V4T04_RS08540 - 77417..78208 (+) 792 WP_349651904.1 DNA/RNA non-specific endonuclease -
  V4T04_RS08545 - 78374..78583 (+) 210 WP_010905160.1 hypothetical protein -
  V4T04_RS08550 - 78595..78834 (+) 240 WP_003129719.1 hypothetical protein -
  V4T04_RS08555 - 79031..80614 (+) 1584 WP_033899174.1 APC family permease -
  V4T04_RS08560 - 80683..81897 (+) 1215 WP_349651905.1 pyridoxal phosphate-dependent aminotransferase -
  V4T04_RS08565 codY 82051..82839 (+) 789 WP_003129722.1 GTP-sensing pleiotropic transcriptional regulator CodY Regulator
  V4T04_RS08570 gatC 83681..83986 (+) 306 WP_010905163.1 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatC -
  V4T04_RS08575 gatA 83986..85446 (+) 1461 WP_031559095.1 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA -
  V4T04_RS08580 - 85450..86052 (+) 603 WP_058202908.1 NUDIX hydrolase -
  V4T04_RS08585 gatB 86092..87525 (+) 1434 WP_003129725.1 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB -

Regulatory network

Positive effect      
Negative effect
Regulator Target Regulation
  codY comX negative effect
  clpP comX negative effect
  mecA comX negative effect
  ccpA comX negative effect
  covR comX negative effect
  covS comX negative effect
  clpC comX negative effect

Sequence

Protein


Download         Length: 262 a.a.        Molecular weight: 29128.46 Da        Isoelectric Point: 4.5254

>NTDB_id=605 V4T04_RS08565 WP_003129722.1 82051..82839(+) (codY) [Lactococcus lactis subsp. lactis strain DGCC12653]
MATLLEKTRKITAILQDGVTDLQQELPYNSMTERLANVIDCNACVINTKGELLGYSLPYNTNNDRVDQFFYDRKLPDEYV
RAAVRIYDTMANVPVDRPLAIFPEESLGDFPKGVTTLAPIYGSGMRLGTFIMWREDGEFTDDDLVLVELATTVIGVQLSN
LKLEQMEENIRKDTMATMAVNTLSYSEMKAVKAIIEELDGEEGHVIASVIADKIGITRSVIVNALRKLESAGVIESRSLG
MKGTYLKVLNTGLFDKLAGRNF

Nucleotide


Download         Length: 789 bp        

>NTDB_id=605 V4T04_RS08565 WP_003129722.1 82051..82839(+) (codY) [Lactococcus lactis subsp. lactis strain DGCC12653]
GTGGCTACATTACTTGAAAAAACACGTAAAATCACCGCGATTTTGCAAGATGGAGTGACCGATTTGCAACAAGAGTTGCC
ATATAACAGTATGACTGAACGCTTGGCAAACGTCATTGATTGCAATGCATGTGTGATTAATACGAAGGGCGAGTTGCTTG
GTTACTCATTGCCTTATAATACAAACAATGACCGTGTTGACCAATTTTTCTATGATCGTAAATTGCCTGATGAATATGTT
CGTGCGGCAGTACGTATCTACGATACAATGGCAAACGTTCCTGTTGACCGTCCATTAGCAATCTTCCCAGAAGAAAGCCT
TGGCGATTTTCCAAAAGGTGTGACAACTTTAGCACCTATTTATGGTTCTGGAATGCGTTTGGGAACATTTATCATGTGGC
GTGAAGACGGCGAATTCACTGATGATGATTTGGTCTTAGTTGAACTTGCAACAACAGTAATTGGTGTTCAACTCTCAAAT
CTTAAACTTGAACAAATGGAAGAAAATATCCGTAAAGACACCATGGCAACTATGGCTGTTAACACACTTTCATATTCAGA
AATGAAAGCTGTTAAAGCAATCATTGAAGAGCTTGATGGTGAAGAAGGGCATGTTATCGCTTCTGTCATTGCTGACAAGA
TTGGGATTACACGTTCAGTCATCGTTAACGCATTGCGTAAACTCGAATCTGCTGGTGTAATTGAATCACGTTCACTTGGT
ATGAAAGGAACTTATCTTAAAGTTCTTAATACTGGTTTATTTGATAAACTTGCAGGACGTAATTTCTAA

Domains

Predicted by InterproScan.

CodY helix-turn-helix domain (HTH_CodY)

(201-258)

CodY GAF-like domain (CodY)

(3-182)


Secondary structure

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



3D structure

Source ID Structure

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 Bacillus subtilis subsp. subtilis str. 168

47.451

98.456

0.467

Multiple sequence alignment    



References

[1] Frédéric Toussaint et al. (2024) Unveiling the regulatory network controlling natural transformation in lactococci. PLoS Genetics 20(7):e1011340. [PMID: 38950059]