Detailed information    

experimental Experimentally validated

Overview

Name   comD   Type   Regulator
Locus tag   SM12261_RS09375 Genome accession   NZ_CP028414
Coordinates   1864387..1865712 (-) Length   441 a.a.
NCBI ID   WP_020902616.1    Uniprot ID   -
Organism   Streptococcus mitis NCTC 12261     
Function   phosphorylation of ComE   
Competence regulation

Function

Upregulated in response to CSP as measured by RNA-seq.


Genomic Context

Location: 1859387..1870712
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SM12261_RS09350 (SM12261_1804) - 1860083..1862725 (-) 2643 WP_000472064.1 YhgE/Pip domain-containing protein -
  SM12261_RS09355 (SM12261_1805) - 1862853..1863395 (+) 543 WP_001158274.1 TetR/AcrR family transcriptional regulator -
  SM12261_RS09370 (SM12261_1808) comE 1863638..1864390 (-) 753 WP_000866073.1 competence system response regulator transcription factor ComE Regulator
  SM12261_RS09375 (SM12261_1809) comD 1864387..1865712 (-) 1326 WP_020902616.1 competence system sensor histidine kinase ComD Regulator
  SM12261_RS09380 (SM12261_1810) comC 1865725..1865847 (-) 123 WP_004238992.1 competence-stimulating peptide ComC Regulator
  SM12261_RS09390 (SM12261_1812) rlmH 1866130..1866609 (-) 480 WP_000695934.1 23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH -
  SM12261_RS09395 (SM12261_1813) htrA 1866792..1867973 (+) 1182 WP_000681587.1 S1C family serine protease Regulator
  SM12261_RS09400 (SM12261_1814) spo0J 1868031..1868789 (+) 759 WP_000410370.1 ParB/RepB/Spo0J family partition protein Regulator

Regulatory network

Positive effect      
Negative effect
Regulator Target Regulation
  comD comE positive effect
  comE comX/sigX/comX2/sigX2 positive effect
  comX/sigX/comX2/sigX2 late competence genes positive effect
  comX/sigX/comX2/sigX2 late competence genes positive effect
  comW comX/sigX/comX2/sigX2 positive effect
  comX/sigX/comX1/sigX1 late competence genes positive effect
  comX/sigX/comX1/sigX1 late competence genes positive effect
  comW comX/sigX/comX1/sigX1 positive effect
  comE comX/sigX/comX1/sigX1 positive effect
  comE comD positive effect
  comC comD positive effect
  comE comE positive effect
  comE comB positive effect
  comE comC positive effect
  comE comM positive effect
  comE comW positive effect
  comE comA positive effect
  comB comC positive effect
  comA comC positive effect
  comM cbpD negative effect

Sequence

Protein


Download         Length: 441 a.a.        Molecular weight: 51152.92 Da        Isoelectric Point: 7.5225

>NTDB_id=486 SM12261_RS09375 WP_020902616.1 1864387..1865712(-) (comD) [Streptococcus mitis NCTC 12261]
MDFLAVLVVILHIFIISKSYYLICKNKINIKELCFFGGYTFLVESVFELSFYFIYLDGLGIEKFLFPLVLYSYFRFIKKY
EKYRGVFLSLLLSLLYNSTHTFLSVTLSSIIGDDTALQYHSLFFLVVVALTYVVIVTIIRYFHLELNYFDKDYLYPFLKK
VFFALLLLHVVSFISDMVSTIKHLNSFGSILSSIVFISLLLTFFAMNSHKEKMEKEIALKQKKFEQKHLQNYTDEIVGLY
NEIRGFRHDYAGMLVSMQMAIDSGDLQEIDRVYNEVLVKANHKLRSDKYTYFDLNNIEDSALRSLVAQSIVYARNNGVEF
TLEVKDKITKLPIELLDLVRIMSVLLNNAVEGSADSYKKQMEVAVIKMETETVIVIQNSCKMTMTPSGDLFALGFSTKGR
NRGVGLNNVKELLDKYNNIILETEMEGSTFRQIIRFKREFE

Nucleotide


Download         Length: 1326 bp        

>NTDB_id=486 SM12261_RS09375 WP_020902616.1 1864387..1865712(-) (comD) [Streptococcus mitis NCTC 12261]
ATGGATTTTCTTGCAGTATTAGTTGTGATATTACATATTTTTATTATTAGTAAAAGTTACTATTTAATATGTAAAAATAA
AATAAATATAAAAGAACTATGCTTTTTTGGTGGTTATACATTCCTAGTAGAATCAGTATTTGAACTTTCCTTTTATTTTA
TATACTTAGATGGATTAGGAATTGAAAAATTTTTATTTCCTTTGGTATTATATTCATATTTTAGATTTATTAAAAAGTAT
GAGAAGTATAGAGGAGTATTCTTAAGTTTACTACTATCCCTTTTATATAATAGCACTCATACCTTTCTATCCGTAACTTT
ATCCTCTATAATAGGAGATGATACTGCCCTACAATATCATAGTCTATTCTTTTTAGTTGTAGTGGCGTTGACTTATGTTG
TTATCGTAACAATCATTCGTTATTTCCATTTGGAACTAAACTATTTTGACAAAGATTATCTCTATCCTTTCTTGAAAAAA
GTCTTTTTTGCTTTACTACTTCTACATGTTGTATCTTTCATTTCAGATATGGTAAGTACGATTAAACATTTGAATAGTTT
TGGAAGTATTTTATCATCTATTGTCTTTATCTCTTTACTTTTGACCTTTTTTGCAATGAATTCGCATAAAGAAAAAATGG
AGAAAGAGATTGCTTTGAAGCAGAAGAAATTTGAACAGAAACATTTACAGAATTATACAGATGAAATTGTCGGACTGTAT
AATGAAATCCGTGGTTTTCGACATGACTATGCCGGGATGCTTGTCAGCATGCAGATGGCAATTGATAGTGGTGATTTACA
GGAAATTGACAGAGTTTACAATGAAGTTTTGGTCAAAGCAAATCACAAACTGCGTTCAGATAAGTATACTTACTTTGACT
TGAACAACATAGAAGATTCAGCTTTACGAAGTTTGGTTGCTCAGTCAATTGTCTATGCTCGAAATAATGGTGTAGAGTTT
ACACTGGAAGTAAAAGATAAGATTACCAAGCTCCCAATTGAACTATTGGATTTGGTTCGTATCATGAGTGTTTTATTGAA
CAATGCTGTAGAAGGATCAGCTGATAGCTATAAAAAACAAATGGAAGTAGCAGTTATTAAGATGGAAACCGAAACAGTTA
TTGTGATTCAGAATTCATGTAAAATGACGATGACTCCTTCAGGAGATCTATTTGCCTTAGGATTCTCCACTAAGGGAAGA
AATCGCGGAGTAGGCTTAAATAATGTGAAAGAACTACTAGATAAATACAACAATATTATTTTAGAAACAGAGATGGAAGG
CAGTACATTTAGACAAATTATTAGGTTTAAGAGGGAATTTGAATGA

Domains

Predicted by InterproScan.

GHKL domain (HATPase_c_5)

(334-434)


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
  comD/comD2 Streptococcus pneumoniae TIGR4

86.621

100

0.866
  comD/comD1 Streptococcus pneumoniae R6

86.168

100

0.862
  comD/comD1 Streptococcus pneumoniae D39

86.168

100

0.862
  comD/comD1 Streptococcus pneumoniae Rx1

86.168

100

0.862
  comD Streptococcus mitis SK321

85.261

100

0.853
  comD/comD1 Streptococcus gordonii str. Challis substr. CH1

45.647

93.819

0.428
  comD/comD2 Streptococcus gordonii strain NCTC7865

47.044

88.209

0.415

Multiple sequence alignment    



References

[1] G Salvadori et al. (2018) High-resolution profiles of the Streptococcus mitis CSP signaling pathway reveal core and strain-specific regulated genes. BMC Genomics 19(1):453. [PMID: 29898666]