Detailed information    

experimental Experimentally validated

Overview

Name   comF   Type   Machinery gene
Locus tag   A1552VC_RS20525 Genome accession   NZ_CP028894
Coordinates   2669899..2670759 (+) Length   286 a.a.
NCBI ID   WP_001884047.1    Uniprot ID   Q9KNL3
Organism   Vibrio cholerae strain A1552     
Function   ssDNA transport into the cell   
DNA binding and uptake

Function

ComEA shuttles the transforming DNA through the periplasm and toward the inner membrane aqueous channel ComEC, which, potentially in concert with ComF, transports a single DNA strand into the cytoplasm.


Genomic Context

Location: 2664899..2675759
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  A1552VC_RS12500 (A1552VC_02469) greB 2665427..2665912 (-) 486 WP_000850496.1 transcription elongation factor GreB -
  A1552VC_RS12505 (A1552VC_02470) - 2666157..2668478 (+) 2322 WP_000030087.1 Tex family protein -
  A1552VC_RS12510 (A1552VC_02471) - 2668570..2669040 (-) 471 WP_000961392.1 hypothetical protein -
  A1552VC_RS12515 (A1552VC_02472) bioH 2669202..2669963 (-) 762 WP_001240449.1 pimeloyl-ACP methyl ester esterase BioH -
  A1552VC_RS20525 comF 2669899..2670759 (+) 861 WP_001884047.1 ComF family protein Machinery gene
  A1552VC_RS12525 (A1552VC_02474) nfuA 2670847..2671434 (+) 588 WP_000070178.1 Fe-S biogenesis protein NfuA -
  A1552VC_RS12530 (A1552VC_02475) nudE 2671573..2672121 (+) 549 WP_000095812.1 ADP compounds hydrolase NudE -
  A1552VC_RS12535 (A1552VC_02476) cysQ 2672144..2672971 (+) 828 WP_000106799.1 3'(2'),5'-bisphosphate nucleotidase CysQ -
  A1552VC_RS12540 (A1552VC_02477) - 2673023..2673781 (-) 759 WP_000817146.1 type II secretion system protein N -
  A1552VC_RS12545 (A1552VC_02478) gspM 2673783..2674280 (-) 498 WP_000661339.1 type II secretion system protein GspM -
  A1552VC_RS12550 (A1552VC_02479) gspL 2674290..2675501 (-) 1212 WP_001288747.1 type II secretion system protein GspL -

Regulatory network

Positive effect      
Negative effect
Regulator Target Regulation
  qstR comF positive effect
  qstR comEC positive effect
  tfoX comEC positive effect
  hapR comEC positive effect
  qstR comEA positive effect
  tfoX comEA positive effect
  hapR comEA positive effect
  crp comEA positive effect
  qstR comM positive effect
  crp qstR positive effect
  tfoX qstR positive effect
  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 pilQ positive effect
  tfoX pilC positive effect
  chiS tfoX positive effect
  hapR qstR positive effect
  hapR dns negative effect

Sequence

Protein


Download         Length: 286 a.a.        Molecular weight: 32545.47 Da        Isoelectric Point: 8.0588

>NTDB_id=1154 A1552VC_RS20525 WP_001884047.1 2669899..2670759(+) (comF) [Vibrio cholerae strain A1552]
MPQPCTNTRSCPCPLTCQYNAMVTVSPSISIFIHSANWQDEAHYPDSWLAMLTHWLRKTTAPLLTPECHLCRLALDTNSP
FGVCSACQAWLEHGYRCARCGLPTLTPVDQCGQCLGQPPPWRKLMCVGDYRFPLSDAVHQLKYQRQFWQAPRLAKLLATQ
INEPAPLLCSVPLHWRRRWQRGFNQSDLLARELANMLNVEYDHQLFARRRATPHQQGLSKAQRIHNLRDAFVLNHPPNQP
HVAIVDDVVTTGSTIRHLCDLLLDVGVQSIDIYCICRTPEPKDSHG

Nucleotide


Download         Length: 861 bp        

>NTDB_id=1154 A1552VC_RS20525 WP_001884047.1 2669899..2670759(+) (comF) [Vibrio cholerae strain A1552]
ATGCCCCAGCCGTGTACCAATACCAGATCTTGCCCTTGTCCACTGACTTGCCAATACAACGCCATGGTCACAGTTTCTCC
GTCTATTTCCATCTTCATCCACTCTGCCAATTGGCAAGATGAAGCACATTACCCCGATTCTTGGCTCGCTATGTTAACCC
ATTGGCTCAGAAAAACTACCGCACCACTGCTGACTCCGGAATGTCATCTCTGTCGACTGGCGCTAGATACAAATTCGCCG
TTTGGCGTCTGCTCTGCCTGCCAAGCTTGGCTTGAGCACGGTTATCGCTGCGCACGCTGCGGTTTACCGACTCTTACCCC
AGTTGATCAGTGCGGGCAGTGTTTGGGTCAGCCTCCGCCGTGGCGAAAACTGATGTGTGTCGGCGATTACCGCTTTCCAC
TTAGTGATGCGGTGCATCAACTCAAATACCAACGCCAGTTTTGGCAAGCGCCGCGCTTGGCTAAGCTACTCGCCACCCAG
ATTAACGAGCCAGCCCCGTTGCTGTGCAGCGTGCCACTGCATTGGCGGCGACGCTGGCAACGCGGCTTTAATCAAAGCGA
TCTGCTGGCGCGCGAGTTAGCCAATATGCTGAACGTTGAATATGACCACCAACTCTTTGCACGCCGCCGAGCGACACCGC
ATCAACAAGGACTCAGCAAGGCGCAGCGAATCCACAACCTACGCGATGCGTTTGTGCTGAATCATCCGCCAAACCAACCA
CATGTTGCGATTGTGGACGATGTGGTGACCACAGGCAGTACGATCCGACATTTATGCGATTTACTGCTTGATGTCGGTGT
GCAAAGCATTGATATTTACTGCATATGCCGCACTCCCGAGCCGAAAGATAGCCACGGTTGA

Domains

Predicted by InterproScan.

Phosphoribosyl transferase domain (Pribosyltran)

(189-281)


Secondary structure

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



3D structure

Source ID Structure
  AlphaFold DB Q9KNL3

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 campbellii strain DS40M4

47.059

98.755

0.465

Multiple sequence alignment    



References

[1] Milena Jaskólska et al. (2018) QstR-dependent regulation of natural competence and type VI secretion in Vibrio cholerae. Nucleic Acids Research 46(20):10619-10634. [PMID: 30102403]
[2] Patrick Seitz et al. (2013) DNA-uptake machinery of naturally competent Vibrio cholerae. Proceedings of The National Academy of Sciences of The United States of America 110(44):17987-92. [PMID: 24127573]