Detailed information NTG0000388

Experimentally validated

Overview

• Name: comYD
• Type: Machinery gene
• Locus tag: SMU_RS09020
• Genome accession: NC_004350
• Coordinates: 1853553..1853957 (-)
• Length: 134 a.a.
• NCBI ID: WP_002263438.1
• Uniprot ID: -
• Organism: Streptococcus mutans UA159
• 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: 1848553..1858957

Locus tag	Gene name	Coordinates (strand)	Size (bp)	Protein ID	Product	Description
SMU_RS08985 (SMU.1976c)	-	1849011..1849451 (-)	441	WP_002263445.1	hypothetical protein	-
SMU_RS08990 (SMU.1977c)	-	1849420..1849665 (-)	246	WP_002263444.1	helix-turn-helix transcriptional regulator	-
SMU_RS08995 (SMU.1978)	comYI	1850234..1851433 (-)	1200	WP_002263443.1	acetate kinase	Machinery gene
SMU_RS09000 (SMU.1979c)	comYH	1851492..1852445 (-)	954	WP_002263442.1	class I SAM-dependent methyltransferase	Machinery gene
SMU_RS09005 (SMU.1980c)	comYG	1852500..1852889 (-)	390	WP_002263441.1	competence type IV pilus minor pilin ComGG	Machinery gene
SMU_RS09010 (SMU.1981c)	comYF	1852867..1853301 (-)	435	WP_002263440.1	competence type IV pilus minor pilin ComGF	Machinery gene
SMU_RS09015 (SMU.1982c)	comYE	1853288..1853581 (-)	294	WP_002263439.1	competence type IV pilus minor pilin ComGE	Machinery gene
SMU_RS09020 (SMU.1983)	comYD	1853553..1853957 (-)	405	WP_002263438.1	competence type IV pilus minor pilin ComGD	Machinery gene
SMU_RS09025 (SMU.1984)	comYC	1853944..1854258 (-)	315	WP_002263437.1	competence type IV pilus major pilin ComGC	Machinery gene
SMU_RS09030 (SMU.1985)	comYB	1854258..1855289 (-)	1032	WP_255262721.1	competence type IV pilus assembly protein ComGB	Machinery gene
SMU_RS09035 (SMU.1987)	comYA	1855225..1856166 (-)	942	WP_002263435.1	competence type IV pilus ATPase ComGA	Machinery gene
SMU_RS09040 (SMU.1988c)	-	1856296..1856679 (-)	384	WP_002263434.1	DUF1033 family protein	-

Regulatory network

Positive effect      

Negative effect

Regulator	Target	Regulation
irvR	comYD	negative effect
irvR	comYC	negative effect
irvR	comYF	negative effect
irvR	comYG	negative effect
irvR		negative effect
irvR	dprA	negative effect
irvR	comYB	negative effect
irvR	comYE	negative effect
irvR	comYH	negative effect
irvR	comYI	negative effect
irvR	comYA	negative effect

Sequence

Protein

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

>NTDB_id=388 SMU_RS09020 WP_002263438.1 1853553..1853957(-) (comYD) [Streptococcus mutans UA159]
MSRIKAFTLIESLVTLAITSFLILSFSGSITQTFAKVEERLFFLSFEHLYRDTQKLSVYQRQDMTLILKSEYISNGVEVL
KIPKDVKLERNKTLHFDQAGGNSSLEKLVFQTSDEKRVTYQLYIGSGQYKKTES

Nucleotide

• Length: 405 bp

>NTDB_id=388 SMU_RS09020 WP_002263438.1 1853553..1853957(-) (comYD) [Streptococcus mutans UA159]
ATGTCGCGAATTAAAGCTTTTACGCTTATAGAAAGTTTAGTGACTTTGGCAATTACTAGTTTTTTGATTTTAAGCTTTTC
AGGTAGTATAACTCAAACGTTTGCCAAAGTAGAAGAGCGTCTCTTTTTTCTTTCTTTTGAACATCTTTACCGTGACACGC
AAAAACTTAGTGTTTATCAAAGACAAGATATGACTTTAATATTAAAAAGCGAATATATCTCAAATGGTGTTGAAGTACTT
AAAATCCCTAAGGATGTCAAACTAGAGAGGAATAAAACTTTGCACTTTGATCAGGCAGGAGGAAATTCTTCTTTAGAAAA
ACTTGTTTTTCAAACATCTGATGAAAAAAGAGTTACTTATCAATTATATATAGGAAGTGGTCAGTATAAAAAAACAGAAA
GTTAA

Domains

Predicted by InterproScan.

• Prokaryotic N-terminal methylation motif (N_methyl) (1-25)

Similar proteins

Only experimentally validated proteins are listed.

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
comYD	Streptococcus mutans UA140	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

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]