Detailed information    

experimental Experimentally validated

Overview

Name   comF   Type   Machinery gene
Locus tag   DR_RS07135 Genome accession   NC_001263
Coordinates   1395054..1395674 (+) Length   206 a.a.
NCBI ID   WP_027480036.1    Uniprot ID   -
Organism   Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539     
Function   ssDNA transport into the cell   
DNA binding and uptake

Function

We identified the factors (PilQ, PilD, type IV pilins, PilB, PilT, ComEC-ComEA, and ComF) involved in DNA uptake and DNA translocation across the external and cytoplasmic membranes and showed that the DNA-uptake machinery is similar to that described in the Gram negative bacterium Vibrio cholerae.


Genomic Context

Location: 1390054..1400674
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  DR_RS07110 (DR_1384) - 1390186..1390737 (-) 552 WP_027480035.1 TetR/AcrR family transcriptional regulator -
  DR_RS07115 (DR_1385) - 1390917..1391408 (+) 492 WP_010888024.1 DUF4142 domain-containing protein -
  DR_RS07120 (DR_1386) ychF 1391767..1392864 (+) 1098 WP_010888025.1 redox-regulated ATPase YchF -
  DR_RS07125 (DR_1387) - 1392928..1394043 (-) 1116 WP_010888026.1 N-acetylmuramoyl-L-alanine amidase family protein -
  DR_RS07130 (DR_1388) - 1394218..1394871 (+) 654 WP_010888027.1 hypothetical protein -
  DR_RS07135 (DR_1389) comF 1395054..1395674 (+) 621 WP_027480036.1 ComF family protein Machinery gene
  DR_RS07140 (DR_1390) - 1395685..1396233 (-) 549 WP_010888029.1 DUF1684 domain-containing protein -
  DR_RS07145 (DR_1391) - 1396230..1396451 (-) 222 WP_027480037.1 RNA-binding S4 domain-containing protein -
  DR_RS07150 (DR_1392) - 1396664..1397599 (+) 936 WP_027480038.1 hypothetical protein -
  DR_RS07155 (DR_1393) - 1397656..1398369 (-) 714 WP_010888032.1 histidine phosphatase family protein -
  DR_RS07160 (DR_1394) purM 1398366..1399427 (-) 1062 WP_162177712.1 phosphoribosylformylglycinamidine cyclo-ligase -
  DR_RS07165 (DR_1395) crtE 1399495..1400484 (+) 990 WP_010888034.1 geranylgeranyl diphosphate synthase CrtE -

Sequence

Protein


Download         Length: 206 a.a.        Molecular weight: 21651.22 Da        Isoelectric Point: 10.9813

>NTDB_id=1312 DR_RS07135 WP_027480036.1 1395054..1395674(+) (comF) [Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539]
MIDLLRVLLPRACPGCGAQLGRAAGLCDRCRAELRPRVERHSPLSAQATPHLVTLGRYQGVPRRAVRALKYGGARDVAGP
LGRALAAGVPASWQIAAVVPVPLHPSRQRERGYNQAELLAQAMAAELGVPCLPLLTRTRATAQQAKLHASERSSNLAGAF
AVRGAVPPGTLLILDDVLTTGSTLLACRDALHAAGVTDLKYAAVAR

Nucleotide


Download         Length: 621 bp        

>NTDB_id=1312 DR_RS07135 WP_027480036.1 1395054..1395674(+) (comF) [Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539]
ATGATCGACCTGCTGCGAGTGCTGCTGCCCCGCGCCTGCCCCGGCTGCGGCGCCCAGCTGGGCCGCGCCGCCGGGCTGTG
TGACCGCTGCCGCGCGGAGCTTCGACCCCGGGTGGAGCGGCACTCGCCCCTCTCGGCGCAGGCCACGCCGCATCTGGTCA
CGCTGGGGCGGTACCAGGGCGTCCCCCGCCGGGCGGTACGGGCGCTGAAATACGGCGGGGCGCGGGACGTGGCCGGGCCG
CTGGGGCGGGCGCTCGCAGCGGGGGTTCCGGCGAGCTGGCAAATAGCCGCTGTGGTGCCGGTGCCGCTGCATCCTTCGCG
CCAGCGTGAGCGCGGGTACAACCAGGCCGAGTTGCTGGCGCAGGCGATGGCCGCTGAGCTGGGGGTGCCTTGCCTGCCGC
TCCTCACCCGCACCCGCGCCACCGCTCAGCAGGCCAAGTTGCACGCCAGCGAGCGCAGCAGCAATCTGGCGGGGGCTTTC
GCGGTGCGCGGCGCCGTGCCGCCAGGCACCCTCCTCATTCTGGACGATGTGCTGACGACCGGCAGCACGCTCCTGGCCTG
CCGGGACGCCCTGCACGCGGCGGGCGTGACCGACCTGAAATACGCGGCGGTAGCGCGCTAA

Domains

Predicted by InterproScan.

Double zinc ribbon domain (DZR_2)

(4-38)

Phosphoribosyl transferase domain (Pribosyltran)

(116-205)


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] Solenne Ithurbide et al. (2020) Natural Transformation in Deinococcus radiodurans: A Genetic Analysis Reveals the Major Roles of DprA, DdrB, RecA, RecF, and RecO Proteins. Frontiers in Microbiology 11:1253. [PMID: 32625182]