Detailed information    

experimental Experimentally validated

Overview

Name   tfoX   Type   Regulator
Locus tag   A1552VC_RS04550 Genome accession   NZ_CP028894
Coordinates   952889..953476 (+) Length   195 a.a.
NCBI ID   WP_001005366.1    Uniprot ID   A0A0K9UTP3
Organism   Vibrio cholerae strain A1552     
Function   master regulator of natural competence   
Competence regulation

Function

TfoX is the master regulator of natural transformation in V. cholerae, activating competence genes in response to chitin. TfoX is also shown to invlove in the induction of T6SS.


Genomic Context

Location: 947889..958476
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  A1552VC_RS04530 (A1552VC_00896) panP 948211..949857 (-) 1647 WP_000253201.1 pyridoxal-dependent aspartate 1-decarboxylase PanP -
  A1552VC_RS04535 (A1552VC_00897) - 949967..950476 (-) 510 WP_000826868.1 hypothetical protein -
  A1552VC_RS04540 (A1552VC_00898) - 950665..951570 (-) 906 WP_000948497.1 lysine exporter LysO family protein -
  A1552VC_RS04545 (A1552VC_00899) - 951591..952511 (-) 921 WP_000019000.1 HDOD domain-containing protein -
  A1552VC_RS04550 (A1552VC_00900) tfoX 952889..953476 (+) 588 WP_001005366.1 TfoX/Sxy family DNA transformation protein Regulator
  A1552VC_RS04555 (A1552VC_00901) - 953572..954120 (-) 549 WP_001232641.1 hypothetical protein -
  A1552VC_RS04560 (A1552VC_00902) - 954311..954808 (-) 498 WP_001031964.1 response regulator -
  A1552VC_RS04565 (A1552VC_00903) - 954805..956760 (-) 1956 WP_001082992.1 ATP-binding protein -
  A1552VC_RS04570 (A1552VC_00904) - 956983..958248 (+) 1266 WP_000835928.1 YdgA family protein -

Regulatory network

Positive effect      
Negative effect
Regulator Target Regulation
  tfoX pilO positive effect
  tfoX pilB positive effect
  tfoX pilP positive effect
  tfoX pilA positive effect
  tfoX pilD positive effect
  tfoX dprA positive effect
  tfoX pilM positive effect
  tfoX pilN positive effect
  tfoX comEA positive effect
  tfoX pilQ positive effect
  tfoX qstR positive effect
  tfoX comEC positive effect
  tfoX pilC positive effect
  chiS tfoX positive effect
  hapR comEA positive effect
  hapR qstR positive effect
  hapR dns negative effect
  hapR comEC positive effect
  crp comEA positive effect
  crp qstR positive effect
  qstR comEA positive effect
  qstR comEC positive effect
  qstR comF positive effect
  qstR comM positive effect

Sequence

Protein


Download         Length: 195 a.a.        Molecular weight: 22816.03 Da        Isoelectric Point: 6.9718

>NTDB_id=1144 A1552VC_RS04550 WP_001005366.1 952889..953476(+) (tfoX) [Vibrio cholerae strain A1552]
MNEQQFFDYVTKFGAYQKRSMFGGIGLFQHDAMYVLVSEDRIFVRGGEELDPELLALGCEKYRHVKKQTTATVNYYDITE
LYEQHHPELDSIIERSIQFSVNQREFQRSAASRRLRDLPNMQLTLERMVKKAGIDDVETFMSLGAPEVFNKVRQAYGSDV
DVKLLWKFAGAIEGIHWKLLQEPRKRQLLESCQQR

Nucleotide


Download         Length: 588 bp        

>NTDB_id=1144 A1552VC_RS04550 WP_001005366.1 952889..953476(+) (tfoX) [Vibrio cholerae strain A1552]
ATGAATGAGCAACAGTTTTTCGACTACGTAACTAAGTTTGGCGCCTACCAAAAACGCTCGATGTTTGGTGGTATTGGCTT
GTTTCAACACGACGCTATGTATGTGTTGGTCAGTGAAGACCGCATTTTTGTGCGTGGTGGAGAAGAGCTCGACCCTGAGC
TCTTGGCCTTAGGGTGCGAGAAATATCGCCATGTTAAAAAACAGACAACGGCAACCGTAAACTATTACGACATCACTGAA
CTGTATGAGCAACATCACCCTGAGCTAGACTCGATTATTGAACGCTCGATTCAGTTTTCTGTGAATCAGCGGGAATTTCA
ACGCTCAGCAGCCAGTCGTCGTCTACGGGATTTACCCAATATGCAACTGACTTTGGAGCGTATGGTAAAAAAAGCGGGCA
TTGACGATGTGGAAACTTTTATGAGCCTCGGTGCGCCAGAAGTGTTTAATAAGGTGCGTCAAGCTTATGGAAGTGATGTC
GATGTAAAACTACTGTGGAAGTTTGCGGGTGCGATTGAAGGCATTCACTGGAAACTGCTGCAAGAGCCGCGTAAGCGCCA
ACTGTTAGAAAGTTGTCAGCAGCGTTAA

Domains

Predicted by InterproScan.

TfoX C-terminal domain (TfoX_C)

(112-190)

TfoX N-terminal domain (TfoX_N)

(9-99)


Secondary structure

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



3D structure

Source ID Structure
  AlphaFold DB A0A0K9UTP3

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
  tfoX Vibrio cholerae O1 biovar El Tor strain DRC-193A

100

100

1
  tfoX Vibrio cholerae O1 biovar El Tor strain P27459

100

100

1
  tfoX Vibrio cholerae O1 biovar El Tor strain E7946

100

100

1
  tfoX Vibrio cholerae O1 biovar El Tor str. N16961

100

100

1
  tfoX Vibrio campbellii strain DS40M4

69.43

98.974

0.687
  tfoX Vibrio parahaemolyticus RIMD 2210633

68.394

98.974

0.677
  tfoX Aliivibrio fischeri ES114

59.043

96.41

0.569

Multiple sequence alignment    



References

[1] Lisa C Metzger et al. (2019) Ecological implications of gene regulation by TfoX and TfoY among diverse Vibrio species. Environmental Microbiology 21(7):2231-2247. [PMID: 30761714]
[2] Sandrine Borgeaud et al. (2015) The type VI secretion system of Vibrio cholerae fosters horizontal gene transfer. Science (New York, N.Y.) 347(6217):63-7. [PMID: 25554784]
[3] Mirella Lo Scrudato et al. (2012) The regulatory network of natural competence and transformation of Vibrio cholerae. PLoS Genetics 8(6):e1002778. [PMID: 22737089]
[4] Karin L Meibom et al. (2005) Chitin induces natural competence in Vibrio cholerae. Science (New York, N.Y.) 310(5755):1824-7. [PMID: 16357262]