Detailed information    

experimental Experimentally validated

Overview

Name   ylbF   Type   Regulator
Locus tag   BSU_14990 Genome accession   NC_000964
Coordinates   1568420..1568869 (+) Length   149 a.a.
NCBI ID   NP_389382.1    Uniprot ID   -
Organism   Bacillus subtilis subsp. subtilis str. 168     
Function   accelerate the production of Spo0A~P   
Competence regulation

Function

YmcA and YlbF interact with a third protein, YaaT to form a tripartite complex. The YmcA-YlbF-YaaT complex affects the phosphotransfer between Spo0F and Spo0B, thus accelerating the production of Spo0A~P.


Genomic Context

Location: 1563420..1573869
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  BSU_14910 (BSU14910) ctaE 1563437..1564060 (+) 624 NP_389374.1 cytochrome caa3 oxidase (subunit III) -
  BSU_14920 (BSU14920) ctaF 1564063..1564395 (+) 333 NP_389375.1 cytochrome caa3 oxidase (subunit IV) -
  BSU_14930 (BSU14930) ctaG 1564422..1565315 (+) 894 NP_389376.1 cytochrome aa(3) assembly factor -
  BSU_14940 (BSU14940) ylbA 1565347..1565709 (-) 363 NP_389377.1 hypothetical protein -
  BSU_14950 (BSU14950) ylbB 1565849..1566295 (+) 447 NP_389378.2 putative enzyme -
  BSU_14960 (BSU14960) ylbC 1566379..1567419 (+) 1041 NP_389379.1 hypothetical protein -
  BSU_14970 (BSU14970) ylbD 1567651..1568049 (+) 399 NP_389380.1 sporulation-related protein (coat) -
  BSU_14980 (BSU14980) ylbE 1568065..1568304 (+) 240 NP_389381.1 hypothetical protein -
  BSU_14990 (BSU14990) ylbF 1568420..1568869 (+) 450 NP_389382.1 subunit of a sporulation, competence and biofilm formation regulatory complex controlling RNase Y (RicAFT complex / FAD / two [4Fe-4S]2+) Regulator
  BSU_15000 (BSU15000) ylbG 1568924..1569196 (+) 273 NP_389383.1 hypothetical protein -
  BSU_15010 (BSU15010) rsmD 1569519..1570073 (+) 555 NP_389384.2 16S rRNA m2G966 methyltransferase -
  BSU_15020 (BSU15020) coaD 1570078..1570563 (+) 486 NP_389385.1 phosphopantetheine adenylyltransferase -
  BSU_15030 (BSU15030) spoVV 1570574..1571800 (-) 1227 NP_389386.1 dipicolinic acid transporter (to the spore) -
  BSU_15040 (BSU15040) ylbK 1571981..1572763 (+) 783 NP_389387.1 putative hydrolase -
  BSU_15050 (BSU15050) sepM 1572765..1573790 (+) 1026 NP_389388.2 putative degradative enzyme Regulator

Regulatory network

Positive effect      
Negative effect
Regulator Target Regulation
  ylbF spo0A positive effect
  spo0A comK negative effect
  comK comK positive effect
  comK late competence genes positive effect
  codY comK negative 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
  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
  ymcA spo0A positive effect
  sinR spo0A negative effect
  yaaT spo0A positive 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: 149 a.a.        Molecular weight: 16913.96 Da        Isoelectric Point: 4.9284

>NTDB_id=665 BSU_14990 NP_389382.1 1568420..1568869(+) (ylbF) [Bacillus subtilis subsp. subtilis str. 168]
MYATMESVRLQSEAQQLAEMILQSETAENYRNCYKRLQEDEEAGRIIRSFIKIKEQYEDVQRFGKYHPDYREISRKMREI
KRELDLNDKVADFKRAENELQSILDEVSVEIGTAVSEHVKVPTGNPYFDGLSSCGGGCGSGGSCGCKVS

Nucleotide


Download         Length: 450 bp        

>NTDB_id=665 BSU_14990 NP_389382.1 1568420..1568869(+) (ylbF) [Bacillus subtilis subsp. subtilis str. 168]
ATGTATGCGACGATGGAATCCGTGCGGCTTCAAAGTGAAGCTCAGCAGCTTGCCGAGATGATTCTGCAGTCGGAGACGGC
TGAGAACTACCGCAATTGTTACAAGCGTCTCCAGGAAGATGAAGAGGCAGGTCGGATTATTCGTTCTTTTATCAAAATAA
AAGAGCAGTATGAGGATGTACAGCGTTTTGGCAAATATCATCCTGACTATAGAGAAATATCCCGGAAAATGAGGGAGATC
AAACGTGAGCTGGACCTGAACGATAAGGTGGCTGACTTCAAGAGAGCTGAAAATGAGCTCCAGTCCATTCTTGATGAGGT
CAGCGTTGAGATTGGGACAGCTGTTTCGGAGCATGTGAAAGTTCCGACTGGGAACCCTTATTTTGACGGTTTGTCTTCAT
GCGGAGGCGGCTGCGGTTCAGGCGGAAGCTGCGGATGTAAAGTGTCCTGA

Domains

Predicted by InterProScan.

Control of competence regulator ComK, YlbF/YmcA (Com_YlbF)

(12-115)


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

References

[1] Eugenie Dubnau et al. (2023) Formation of a stable RNase Y-RicT (YaaT) complex requires RicA (YmcA) and RicF (YlbF). MBio 14(4):e0126923. [PMID: 37555678]
[2] Valerie J Carabetta et al. (2013) A complex of YlbF, YmcA and YaaT regulates sporulation, competence and biofilm formation by accelerating the phosphorylation of Spo0A. Molecular Microbiology 88(2):283-300. [PMID: 23490197]
[3] P Tortosa et al. (2000) Characterization of ylbF, a new gene involved in competence development and sporulation in Bacillus subtilis. Molecular Microbiology 35(5):1110-9. [PMID: 10712692]