Detailed information    

experimental Experimentally validated

Overview

Name   comGA   Type   Machinery gene
Locus tag   LCA_RS06480 Genome accession   NC_007576
Coordinates   1280043..1280933 (-) Length   296 a.a.
NCBI ID   WP_011375001.1    Uniprot ID   Q38W23
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: 1275043..1285933
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  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 -
  LCA_RS06505 (LCA_1310) - 1283072..1284163 (-) 1092 WP_011375005.1 zinc ribbon domain-containing protein -
  LCA_RS06510 (LCA_1311) - 1284403..1284642 (+) 240 WP_011375006.1 cytochrome b5 domain-containing protein -
  LCA_RS06515 (LCA_1312) - 1284708..1285721 (-) 1014 WP_011375007.1 YeiH family protein -

Regulatory network

Positive effect      
Negative effect
Regulator Target Regulation
  sigH comGA positive effect
  sigH comEC positive effect
  sigH comFC positive effect
  sigH comGE positive effect
  sigH recA 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 comGD positive effect
  sigH comGF positive effect
  sigH comC positive effect

Sequence

Protein


Download         Length: 296 a.a.        Molecular weight: 32956.78 Da        Isoelectric Point: 6.4932

>NTDB_id=617 LCA_RS06480 WP_011375001.1 1280043..1280933(-) (comGA) [Latilactobacillus sakei subsp. sakei 23K]
MSTEEKLTTLLKHCAKQRVQDLYFTPTIGGWRLTERRQSDLVTNQELDKPTGTRYLNRLKYMAGMDISETRRAQTGRSEL
QLADQTIYLRLATVGDFLNRESLVIRFIYPIGAIYHCDDQQILAQLTQMSRQSGLILFAGPTGSGKTTSLYHLAQQSMSA
KMVVAIEDPIEIVAPEFLQLQVNDNAGLSYAELLKISLRLRPDTLIIGEIRDLETAQYVVSAALSGHLVLSTIHARSTQG
VVARLLDLGISELQLRACLTGIAYQSLVTKDDVVQAHYELLTGSDYFSKKEGGCDV

Nucleotide


Download         Length: 891 bp        

>NTDB_id=617 LCA_RS06480 WP_011375001.1 1280043..1280933(-) (comGA) [Latilactobacillus sakei subsp. sakei 23K]
ATGTCAACTGAAGAAAAGCTAACAACTTTATTAAAGCATTGTGCTAAACAACGTGTTCAAGATCTTTATTTTACACCGAC
AATAGGTGGCTGGCGCTTGACGGAACGTCGTCAGAGCGATTTGGTCACCAATCAAGAATTGGATAAACCGACTGGAACGC
GTTATTTAAATCGACTGAAGTATATGGCGGGGATGGATATCAGCGAGACTCGGCGTGCGCAAACCGGCCGCTCGGAATTA
CAGCTAGCCGATCAAACAATTTATTTACGCCTAGCGACGGTCGGGGATTTTTTAAACCGCGAAAGCTTGGTCATTCGGTT
TATCTATCCAATTGGTGCCATCTATCATTGTGATGATCAACAGATCTTGGCGCAATTAACGCAGATGAGTCGACAGTCGG
GCTTAATTCTTTTCGCTGGGCCGACTGGTTCTGGTAAAACGACTAGTCTCTATCATCTGGCCCAACAATCAATGAGTGCC
AAGATGGTGGTTGCTATTGAAGATCCGATTGAAATTGTTGCACCTGAGTTTTTGCAACTGCAGGTCAACGATAATGCGGG
ATTGAGCTACGCCGAGCTATTAAAAATTAGTTTACGACTGCGACCGGATACGCTGATTATCGGTGAGATTCGCGATTTAG
AGACAGCCCAATACGTGGTTTCTGCGGCCTTAAGTGGCCACCTGGTATTGAGTACTATTCACGCTCGGAGTACACAGGGC
GTGGTCGCGCGCTTATTAGATCTTGGTATTTCTGAGCTGCAGTTGCGGGCCTGTCTAACGGGAATTGCCTACCAATCGTT
GGTGACAAAAGACGACGTTGTGCAAGCCCATTATGAATTATTAACTGGTTCAGATTATTTCTCAAAAAAAGAAGGTGGTT
GCGATGTATAA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(12-269)


Secondary structure

Protein secondary structures were predicted by S4PRED and visualized by seqviz.



3D structure

Source ID Structure
  AlphaFold DB Q38W23

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
  comGA/cglA/cilD Streptococcus pneumoniae TIGR4

41.912

91.892

0.385
  comGA/cglA/cilD Streptococcus pneumoniae D39

41.912

91.892

0.385
  comGA/cglA/cilD Streptococcus pneumoniae Rx1

41.912

91.892

0.385
  comGA/cglA/cilD Streptococcus pneumoniae R6

41.912

91.892

0.385
  comGA/cglA/cilD Streptococcus mitis NCTC 12261

43.019

89.527

0.385
  comGA Lactococcus lactis subsp. cremoris KW2

37.793

100

0.382
  comGA/cglA Streptococcus sobrinus strain NIDR 6715-7

41.241

92.568

0.382
  comYA Streptococcus gordonii str. Challis substr. CH1

40.809

91.892

0.375
  comYA Streptococcus mutans UA159

38.909

92.905

0.361
  comYA Streptococcus mutans UA140

38.909

92.905

0.361

Multiple sequence alignment    



References

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