Detailed information    

experimental Experimentally validated

Overview

Name   comF   Type   Machinery gene
Locus tag   DSB67_RS00645 Genome accession   NZ_CP030788
Coordinates   133759..134484 (-) Length   241 a.a.
NCBI ID   WP_029388870.1    Uniprot ID   -
Organism   Vibrio campbellii strain DS40M4     
Function   ssDNA transport into the cell   
DNA binding and uptake

Function

Induction of TfoX expression resulted in upregulation of the genes required for DNA uptake and integration (comEC, comEA, comM, comF, and dprA) and pilus structure (pilABCD, pilMNOPQ, and minor pilins VC0857 to -0861) in DS40M4


Genomic Context

Location: 128759..139484
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  DSB67_RS00615 (DSB67_00615) gspL 128825..130027 (+) 1203 WP_010650508.1 type II secretion system protein GspL -
  DSB67_RS00620 (DSB67_00620) - 130035..130526 (+) 492 WP_010650509.1 type II secretion system protein M -
  DSB67_RS00625 (DSB67_00625) - 130528..131289 (+) 762 WP_010650510.1 type II secretion system protein N -
  DSB67_RS00630 (DSB67_00630) cysQ 131460..132287 (-) 828 WP_005430183.1 3'(2'),5'-bisphosphate nucleotidase CysQ -
  DSB67_RS00635 (DSB67_00635) nudE 132335..132901 (-) 567 WP_010650511.1 ADP compounds hydrolase NudE -
  DSB67_RS00640 (DSB67_00640) nfuA 133077..133661 (-) 585 WP_005430072.1 Fe-S biogenesis protein NfuA -
  DSB67_RS00645 (DSB67_00645) comF 133759..134484 (-) 726 WP_029388870.1 ComF family protein Machinery gene
  DSB67_RS00650 (DSB67_00650) bioH 134569..135333 (+) 765 WP_010650512.1 pimeloyl-ACP methyl ester esterase BioH -
  DSB67_RS00655 (DSB67_00655) - 135469..135933 (+) 465 WP_010650513.1 hypothetical protein -
  DSB67_RS00660 (DSB67_00660) - 136038..138359 (-) 2322 WP_010650514.1 Tex family protein -

Regulatory network

Positive effect      
Negative effect
Regulator Target Regulation
  tfoX comF positive effect
  tfoX pilB positive effect
  tfoX dprA positive effect
  tfoX pilC positive effect
  tfoX pilD positive effect
  tfoX pilM positive effect
  tfoX pilO positive effect
  tfoX comM positive effect
  tfoX pilA positive effect
  tfoX pilQ positive effect
  tfoX comEC positive effect
  tfoX comEA positive effect
  tfoX pilP positive effect
  tfoX pilN positive effect

Sequence

Protein


Download         Length: 241 a.a.        Molecular weight: 27684.85 Da        Isoelectric Point: 8.1508

>NTDB_id=1398 DSB67_RS00645 WP_029388870.1 133759..134484(-) (comF) [Vibrio campbellii strain DS40M4]
MLSHQWQNIMHRVLSSQCGLCRFPIPHRQTPNLMRWCDSCFDHLTPIERCMRCGLKMTEEESQAATECGECLKEPPPWRR
LYTLGDYDFPLSQQVQRFKDHGEVWHVGALTQLLAERVEQPAPVITSVPVHWQRLLKRGFNQSHILAKHLAHHLDVRYEN
KVFKRVKNVQSQRGNKKASREQNLQGAFALRGEVDFSHVAIVDDVVTTGSTVRQLCHLLLEVGVESIDIYCICRTPAPGS
L

Nucleotide


Download         Length: 726 bp        

>NTDB_id=1398 DSB67_RS00645 WP_029388870.1 133759..134484(-) (comF) [Vibrio campbellii strain DS40M4]
ATGTTATCTCATCAATGGCAAAACATCATGCATCGCGTACTCAGTAGCCAATGCGGATTATGCCGATTTCCCATACCTCA
CCGCCAAACGCCCAACCTAATGCGTTGGTGTGACAGCTGTTTTGATCACCTCACACCAATTGAGCGCTGCATGCGTTGTG
GTTTAAAAATGACAGAAGAGGAATCGCAAGCCGCCACAGAGTGTGGAGAATGCCTGAAAGAGCCACCACCATGGCGGCGT
TTGTATACCTTAGGGGATTATGACTTCCCGCTCTCTCAACAAGTACAGCGTTTTAAAGATCACGGCGAAGTCTGGCATGT
GGGCGCGCTCACTCAATTATTAGCAGAGCGAGTTGAGCAGCCTGCCCCAGTGATAACAAGTGTGCCCGTTCACTGGCAGC
GCCTCTTAAAACGAGGTTTCAACCAGAGCCACATCTTGGCCAAACACCTCGCCCATCATTTAGATGTGCGCTATGAAAAC
AAGGTATTTAAACGCGTCAAAAACGTCCAATCACAACGAGGAAACAAAAAAGCCAGTCGCGAGCAAAATTTGCAAGGGGC
ATTTGCCCTACGAGGTGAGGTGGACTTTTCCCACGTCGCGATTGTGGATGATGTGGTTACAACAGGTAGTACAGTCCGAC
AATTATGTCATTTACTACTTGAAGTTGGCGTAGAAAGCATCGATATTTACTGCATCTGCAGAACTCCTGCGCCCGGTTCG
CTCTAG

Domains

Predicted by InterProScan.

Phosphoribosyl transferase domain (Pribosyltran)

(144-237)


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
  comF Vibrio cholerae strain A1552

47.059

98.755

0.465

Multiple sequence alignment    



References

[1] Chelsea A Simpson et al. (2019) Diversity in Natural Transformation Frequencies and Regulation across Vibrio Species. MBio 10(6):e02788-19. [PMID: 31848285]