Detailed information    

experimental Experimentally validated

Overview

Name   comB2   Type   Machinery gene
Locus tag   C694_RS00095 Genome accession   NC_018939
Coordinates   13702..13983 (+) Length   93 a.a.
NCBI ID   WP_001272690.1    Uniprot ID   -
Organism   Helicobacter pylori 26695     
Function   transformation-associated type IV transport system   
DNA binding and uptake

Function

By combining computer prediction modeling, experimental topology determination, generation of knockout strains, and genetic complementation studies we identified ComB2, ComB3, and ComB6 as essential components of the transformation apparatus, structurally and functionally homologous to VirB2, VirB3, and VirB6, respectively.


Genomic Context

Location: 8702..18983
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  C694_RS00075 (C694_00050) groES 9268..9624 (-) 357 WP_000671934.1 co-chaperone GroES -
  C694_RS00080 (C694_00055) dnaG 9911..11590 (+) 1680 WP_000601638.1 DNA primase -
  C694_RS00085 (C694_00060) - 11587..12639 (+) 1053 WP_000721203.1 MnmA/TRMU family protein -
  C694_RS00090 (C694_00065) - 12728..13555 (+) 828 WP_001154906.1 DUF5718 family protein -
  C694_RS00095 (C694_00070) comB2 13702..13983 (+) 282 WP_001272690.1 TrbC/VirB2 family protein Machinery gene
  C694_RS00100 (C694_00075) comB3 13983..14246 (+) 264 WP_000584956.1 hypothetical protein Machinery gene
  C694_RS00105 (C694_00080) comB4 14248..16611 (+) 2364 WP_000890508.1 VirB4 family type IV secretion/conjugal transfer ATPase Machinery gene
  C694_RS00110 (C694_00085) - 16932..18272 (+) 1341 WP_015056018.1 COG3014 family protein -

Sequence

Protein


Download         Length: 93 a.a.        Molecular weight: 10525.78 Da        Isoelectric Point: 9.1450

>NTDB_id=1209 C694_RS00095 WP_001272690.1 13702..13983(+) (comB2) [Helicobacter pylori 26695]
MSAHFLKIVFLVGMCVSSLFAEGLEGFFNALEAQLKSPIAKGILMVIFIGIAIYVWRNLDRWKEILFTILGVVFGIFLFF
KAPSLANWFMGIF

Nucleotide


Download         Length: 282 bp        

>NTDB_id=1209 C694_RS00095 WP_001272690.1 13702..13983(+) (comB2) [Helicobacter pylori 26695]
ATGTCCGCTCATTTTTTAAAAATCGTTTTTTTAGTAGGCATGTGCGTTTCAAGTTTGTTCGCTGAAGGTTTAGAGGGGTT
TTTTAACGCCCTAGAAGCCCAGCTCAAAAGCCCCATCGCTAAGGGGATTTTAATGGTGATTTTCATAGGGATCGCTATTT
ATGTGTGGAGGAATTTGGACCGGTGGAAAGAGATCTTATTCACGATCCTTGGCGTGGTGTTTGGGATTTTTTTATTCTTT
AAAGCTCCGAGTTTAGCGAATTGGTTTATGGGAATTTTTTAA

Domains

Predicted by InterproScan.

TrbC/VIRB2 pilin (TrbC)

(7-89)


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] Prashant P Damke et al. (2019) Identification of the periplasmic DNA receptor for natural transformation of Helicobacter pylori. Nature Communications 10(1):5357. [PMID: 31767852]
[2] Arno Karnholz et al. (2006) Functional and topological characterization of novel components of the comB DNA transformation competence system in Helicobacter pylori. Journal of Bacteriology 188(3):882-93. [PMID: 16428391]
[3] Tzu-Lung Lin et al. (2006) Isolation and characterization of a competence operon associated with transformation and adhesion in Helicobacter pylori. Microbes And Infection 8(12-13):2756-65. [PMID: 17045509]