Detailed information    

experimental Experimentally validated

Overview

Name   comYD   Type   Machinery gene
Locus tag   FSA28_RS09390 Genome accession   NZ_CP044495
Coordinates   1859327..1859731 (-) Length   134 a.a.
NCBI ID   WP_002263438.1    Uniprot ID   -
Organism   Streptococcus mutans UA140     
Function   dsDNA binding to the cell surface; assembly of the pseudopilus   
DNA binding and uptake

Function

RT-PCR analysis of the orf junctions confirmed that all nine orfs of comY operon were present in a single transcript, while real-time RT-PCR analysis demonstrated that these orfs were expressed at a level very similar to that of the first orf in the operon. Mutations were constructed in all nine putative orfs. The first seven genes (comYA-G) were found to be essential for natural competence, while comYH and comYI had reduced and normal natural competence ability, respectively.


Genomic Context

Location: 1854327..1864731
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  FSA28_RS09350 (FSA28_1633) - 1854466..1854711 (-) 246 WP_002265894.1 helix-turn-helix transcriptional regulator -
  FSA28_RS09360 (FSA28_1634) tnpA 1855331..1855794 (-) 464 Protein_1743 IS200/IS605 family transposase -
  FSA28_RS09365 (FSA28_1635) comYI 1856008..1857207 (-) 1200 WP_002263443.1 acetate kinase Machinery gene
  FSA28_RS09370 (FSA28_1636) comYH 1857266..1858219 (-) 954 WP_002291646.1 class I SAM-dependent methyltransferase Machinery gene
  FSA28_RS09375 (FSA28_1637) comYG 1858274..1858663 (-) 390 WP_002263441.1 competence type IV pilus minor pilin ComGG Machinery gene
  FSA28_RS09380 (FSA28_1638) comYF 1858641..1859075 (-) 435 WP_002264245.1 competence type IV pilus minor pilin ComGF Machinery gene
  FSA28_RS09385 (FSA28_1639) comYE 1859062..1859355 (-) 294 WP_002263439.1 competence type IV pilus minor pilin ComGE Machinery gene
  FSA28_RS09390 (FSA28_1640) comYD 1859327..1859731 (-) 405 WP_002263438.1 competence type IV pilus minor pilin ComGD Machinery gene
  FSA28_RS09395 (FSA28_1641) comYC 1859718..1860032 (-) 315 WP_002263437.1 competence type IV pilus major pilin ComGC Machinery gene
  FSA28_RS09400 (FSA28_1642) comYB 1860032..1861063 (-) 1032 WP_257638827.1 competence type IV pilus assembly protein ComGB Machinery gene
  FSA28_RS09405 (FSA28_1643) comYA 1860999..1861940 (-) 942 WP_002291652.1 competence type IV pilus ATPase ComGA Machinery gene
  FSA28_RS09410 (FSA28_1644) - 1862071..1862454 (-) 384 WP_002263434.1 DUF1033 family protein -

Sequence

Protein


Download         Length: 134 a.a.        Molecular weight: 15444.77 Da        Isoelectric Point: 9.5619

>NTDB_id=397 FSA28_RS09390 WP_002263438.1 1859327..1859731(-) (comYD) [Streptococcus mutans UA140]
MSRIKAFTLIESLVTLAITSFLILSFSGSITQTFAKVEERLFFLSFEHLYRDTQKLSVYQRQDMTLILKSEYISNGVEVL
KIPKDVKLERNKTLHFDQAGGNSSLEKLVFQTSDEKRVTYQLYIGSGQYKKTES

Nucleotide


Download         Length: 405 bp        

>NTDB_id=397 FSA28_RS09390 WP_002263438.1 1859327..1859731(-) (comYD) [Streptococcus mutans UA140]
ATGTCGCGAATTAAAGCTTTTACGCTTATAGAAAGTTTAGTGACTTTGGCAATTACTAGTTTTTTGATTTTAAGCTTTTC
AGGTAGTATAACTCAAACGTTTGCCAAAGTAGAAGAGCGTCTCTTTTTTCTTTCTTTTGAACATCTTTACCGTGACACGC
AAAAACTTAGTGTTTATCAAAGACAAGATATGACTTTAATATTAAAAAGCGAATATATCTCAAATGGTGTTGAAGTACTT
AAAATCCCTAAGGATGTCAAACTAGAGAGGAATAAAACTTTGCACTTTGATCAGGCAGGAGGAAATTCTTCTTTAGAAAA
ACTTGTTTTTCAAACATCTGATGAAAAAAGAGTTACTTATCAATTATATATAGGAAGTGGTCAGTATAAAAAAACAGAAA
GTTAA

Domains

Predicted by InterproScan.

Prokaryotic N-terminal methylation motif (N_methyl)

(1-25)


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
  comYD Streptococcus mutans UA159

100

100

1
  comYD Streptococcus gordonii str. Challis substr. CH1

50.388

96.269

0.485
  comGD/cglD Streptococcus mitis NCTC 12261

49.612

96.269

0.478
  comGD/cglD Streptococcus pneumoniae R6

49.219

95.522

0.47
  comGD/cglD Streptococcus pneumoniae D39

49.219

95.522

0.47
  comGD/cglD Streptococcus pneumoniae Rx1

49.219

95.522

0.47
  comGD/cglD Streptococcus mitis SK321

48.438

95.522

0.463
  comGD/cglD Streptococcus pneumoniae TIGR4

48.438

95.522

0.463
  comGD Lactococcus lactis subsp. cremoris KW2

39.394

98.507

0.388

Multiple sequence alignment    



References

[1] Justin Merritt et al. (2005) A unique nine-gene comY operon in Streptococcus mutans. Microbiology (Reading, England) 151(Pt 1):157-166. [PMID: 15632435]