Detailed information    

experimental Experimentally validated

Overview

Name   sigH   Type   Regulator
Locus tag   LCA_RS08360 Genome accession   NC_007576
Coordinates   1658326..1658886 (-) Length   186 a.a.
NCBI ID   WP_011375367.1    Uniprot ID   Q38V00
Organism   Latilactobacillus sakei subsp. sakei 23K     
Function   promote expression of competence genes   
Competence regulation

Function

Twenty-five genes potentially regulated by σ(H) in L. sakei 23 K were revealed by genome-wide transcriptomic profiling of sigH overexpression and/or quantitative PCR analysis. More than half of them are involved in the synthesis of a DNA uptake machinery linked to genetic competence, and in DNA metabolism.


Genomic Context

Location: 1653326..1663886
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  LCA_RS08330 (LCA_1671) rplA 1654677..1655366 (-) 690 WP_004270847.1 50S ribosomal protein L1 -
  LCA_RS08335 (LCA_1672) rplK 1655465..1655890 (-) 426 WP_004270859.1 50S ribosomal protein L11 -
  LCA_RS08340 (LCA_1673) - 1656016..1656879 (-) 864 WP_101494624.1 alpha/beta fold hydrolase -
  LCA_RS08345 (LCA_1674) nusG 1657216..1657764 (-) 549 WP_011375364.1 transcription termination/antitermination protein NusG -
  LCA_RS08350 (LCA_1675) secE 1657862..1658041 (-) 180 WP_011375365.1 preprotein translocase subunit SecE -
  LCA_RS08355 (LCA_1676) rpmG 1658051..1658200 (-) 150 WP_011375366.1 50S ribosomal protein L33 -
  LCA_RS08360 (LCA_1677) sigH 1658326..1658886 (-) 561 WP_011375367.1 sigma-70 family RNA polymerase sigma factor Regulator
  LCA_RS08365 (LCA_1678) - 1658964..1659497 (-) 534 WP_011375368.1 NYN domain-containing protein -
  LCA_RS08370 (LCA_1679) rlmB 1659501..1660388 (-) 888 WP_011375369.1 23S rRNA (guanosine(2251)-2'-O)-methyltransferase RlmB -
  LCA_RS08375 (LCA_1680) - 1660375..1660782 (-) 408 WP_004265086.1 Mini-ribonuclease 3 -
  LCA_RS08380 (LCA_1681) cysS 1660779..1662185 (-) 1407 WP_011375371.1 cysteine--tRNA ligase -

Regulatory network

Positive effect      
Negative effect
Regulator Target Regulation
  sigH comEC positive effect
  sigH comFC positive effect
  sigH comGE positive effect
  sigH recA positive effect
  sigH comGA positive effect
  sigH ssb positive effect
  sigH comEA positive effect
  sigH comFA positive effect
  sigH comGB positive effect
  sigH comGC positive effect
  sigH dprA positive effect
  sigH comGD positive effect
  sigH comGF positive effect
  sigH comC positive effect

Sequence

Protein


Download         Length: 186 a.a.        Molecular weight: 22089.20 Da        Isoelectric Point: 6.9905

>NTDB_id=612 LCA_RS08360 WP_011375367.1 1658326..1658886(-) (sigH) [Latilactobacillus sakei subsp. sakei 23K]
MEQTKRDELLISAVAQNDSQALDVLFKAYLPMVYHTLAPYYIRLFDEDDWLQEARIVCYETCQCYDCQKGKSFGSFYKLR
FKNHILNLLRRELAQKRRGDRQAVLIAERPERDAISEDTVTYYQSQFELRCYLETLSPFELVSFRVLTGQLSIDEACCQL
DCTIDQLKRGQSRCQTKLKRYYQENR

Nucleotide


Download         Length: 561 bp        

>NTDB_id=612 LCA_RS08360 WP_011375367.1 1658326..1658886(-) (sigH) [Latilactobacillus sakei subsp. sakei 23K]
ATGGAACAAACAAAGCGCGACGAACTGCTGATTTCAGCAGTGGCTCAGAATGATTCACAAGCATTAGATGTATTATTCAA
GGCGTATTTGCCGATGGTGTATCACACCCTGGCGCCATATTATATCCGGTTATTCGATGAAGACGATTGGTTACAAGAAG
CCCGGATTGTTTGTTACGAAACTTGCCAGTGTTACGATTGTCAAAAAGGCAAAAGTTTTGGAAGTTTCTATAAATTACGG
TTTAAAAACCACATTTTAAATTTACTGCGCCGAGAACTCGCGCAAAAACGGCGAGGTGATCGTCAGGCAGTATTGATTGC
GGAACGACCAGAACGTGACGCGATTTCAGAAGATACGGTCACTTATTATCAATCGCAGTTTGAATTGCGATGTTATCTTG
AAACGCTGTCGCCATTTGAATTAGTGTCGTTTCGGGTGCTGACCGGGCAGCTTTCAATTGATGAAGCTTGTTGCCAACTC
GATTGTACGATTGATCAGTTGAAACGGGGCCAATCAAGGTGTCAGACTAAGTTAAAACGGTATTATCAAGAGAATCGTTA
A

Domains

Predicted by InterproScan.

Sigma-70 region 2 (Sigma70_r2)

(25-92)


Secondary structure

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



3D structure

Source ID Structure
  AlphaFold DB Q38V00

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

References

[1] Solveig Schmid et al. (2012) Alternative sigma factor σH activates competence gene expression in Lactobacillus sakei. BMC Microbiology 12:32. [PMID: 22409597]