Detailed information    

experimental Experimentally validated

Overview

Name   comGD   Type   Machinery gene
Locus tag   LCA_RS06465 Genome accession   NC_007576
Coordinates   1278323..1278775 (-) Length   150 a.a.
NCBI ID   WP_041820876.1    Uniprot ID   -
Organism   Latilactobacillus sakei subsp. sakei 23K     
Function   dsDNA binding to the cell surface; assembly of the pseudopilus   
DNA binding and uptake

Function

All the late competence (com) operons encoding structural elements of the DNA uptake machinery were highly activated by sigHLsa overexpression.


Genomic Context

Location: 1273323..1283775
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  LCA_RS06430 (LCA_1296) - 1273470..1273835 (+) 366 WP_011374991.1 DUF805 domain-containing protein -
  LCA_RS06435 - 1274378..1274836 (-) 459 WP_011374992.1 hypothetical protein -
  LCA_RS06440 (LCA_1298) - 1274891..1276087 (-) 1197 WP_011374993.1 acetate/propionate family kinase -
  LCA_RS06445 (LCA_1299) - 1276109..1277119 (-) 1011 WP_011374994.1 class I SAM-dependent methyltransferase -
  LCA_RS06450 (LCA_1300) - 1277243..1277581 (-) 339 WP_011374995.1 hypothetical protein -
  LCA_RS06455 (LCA_1301) comGF 1277544..1278056 (-) 513 WP_041820873.1 competence type IV pilus minor pilin ComGF Machinery gene
  LCA_RS06460 (LCA_1302) comGE 1278031..1278336 (-) 306 WP_011374997.1 hypothetical protein Machinery gene
  LCA_RS06465 (LCA_1303) comGD 1278323..1278775 (-) 453 WP_041820876.1 competence type IV pilus minor pilin ComGD Machinery gene
  LCA_RS06470 (LCA_1304) comGC 1278747..1279046 (-) 300 WP_011374999.1 prepilin-type N-terminal cleavage/methylation domain-containing protein Machinery gene
  LCA_RS06475 (LCA_1305) comGB 1279043..1280050 (-) 1008 WP_011375000.1 type II secretion system F family protein Machinery gene
  LCA_RS06480 (LCA_1306) comGA 1280043..1280933 (-) 891 WP_011375001.1 competence type IV pilus ATPase ComGA Machinery gene
  LCA_RS06485 (LCA_1307) - 1281049..1281780 (-) 732 WP_011375002.1 YebC/PmpR family DNA-binding transcriptional regulator -
  LCA_RS06490 (LCA_1308) - 1281871..1282371 (-) 501 WP_011375003.1 VanZ family protein -
  LCA_RS06495 (LCA_1309) - 1282468..1282842 (+) 375 WP_011375004.1 hypothetical protein -

Regulatory network

Positive effect      
Negative effect
Regulator Target Regulation
  sigH comGD positive effect
  sigH comEC positive effect
  sigH comFC positive effect
  sigH comGE positive effect
  sigH recA positive effect
  sigH comGA positive effect
  sigH ssb positive effect
  sigH comEA positive effect
  sigH comFA positive effect
  sigH comGB positive effect
  sigH comGC positive effect
  sigH dprA positive effect
  sigH comGF positive effect
  sigH comC positive effect

Sequence

Protein


Download         Length: 150 a.a.        Molecular weight: 17376.23 Da        Isoelectric Point: 10.0735

>NTDB_id=620 LCA_RS06465 WP_041820876.1 1278323..1278775(-) (comGD) [Latilactobacillus sakei subsp. sakei 23K]
MKAARLSKNEGFTLIEMCVVLAIVSLLSWLPIYQIKQYRAQQAEQLFLHQFETSWDAARQYVAIEPRAVGVMWDAPTHTI
TFKGAGESFRNHQLVLPETLTVSNPAEWHLINITHNKGIKPRTLKLKSTLNNREYQYKVQMMWGVLHVQK

Nucleotide


Download         Length: 453 bp        

>NTDB_id=620 LCA_RS06465 WP_041820876.1 1278323..1278775(-) (comGD) [Latilactobacillus sakei subsp. sakei 23K]
TTGAAGGCGGCACGGTTAAGCAAAAATGAAGGTTTTACGTTGATTGAAATGTGCGTGGTCTTAGCGATTGTAAGCTTATT
AAGCTGGTTGCCGATTTATCAGATTAAGCAATATCGTGCGCAACAGGCTGAGCAGTTGTTTCTACATCAATTTGAAACGA
GTTGGGATGCAGCTCGTCAATATGTGGCAATTGAACCGCGTGCCGTCGGTGTGATGTGGGATGCACCAACACATACGATC
ACATTTAAAGGTGCTGGTGAGTCATTTAGAAATCATCAACTCGTATTACCAGAAACTTTAACAGTGAGTAACCCAGCCGA
ATGGCATTTAATTAATATTACTCATAATAAGGGTATTAAACCGCGCACCTTAAAGTTAAAATCAACGCTTAATAATCGTG
AATATCAGTATAAAGTCCAGATGATGTGGGGGGTATTACATGTTCAGAAGTAG

Domains

Predicted by InterproScan.

Prokaryotic N-terminal methylation motif (N_methyl)

(7-28)


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] Solveig Schmid et al. (2012) Alternative sigma factor σH activates competence gene expression in Lactobacillus sakei. BMC Microbiology 12:32. [PMID: 22409597]