Detailed information    

experimental Experimentally validated

Overview

Name   comFA   Type   Machinery gene
Locus tag   LCA_RS02545 Genome accession   NC_007576
Coordinates   509945..511282 (+) Length   445 a.a.
NCBI ID   WP_011374200.1    Uniprot ID   Q38YD5
Organism   Latilactobacillus sakei subsp. sakei 23K     
Function   ssDNA transport into the cell   
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: 504945..516282
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  LCA_RS02530 (LCA_0489) rny 506382..507947 (+) 1566 WP_011374197.1 ribonuclease Y -
  LCA_RS02535 (LCA_0490) - 508103..509191 (+) 1089 WP_041821010.1 glycosyltransferase family 4 protein -
  LCA_RS02540 (LCA_0491) - 509218..509883 (-) 666 WP_011374199.1 YigZ family protein -
  LCA_RS02545 (LCA_0492) comFA 509945..511282 (+) 1338 WP_011374200.1 DEAD/DEAH box helicase Machinery gene
  LCA_RS09740 comFC 511525..511953 (+) 429 WP_148664867.1 ComF family protein Machinery gene
  LCA_RS02555 (LCA_0494) hpf 512080..512625 (+) 546 WP_011374202.1 ribosome hibernation-promoting factor, HPF/YfiA family -
  LCA_RS02560 (LCA_0495) secA 512874..515237 (+) 2364 WP_011374203.1 preprotein translocase subunit SecA -

Regulatory network

Positive effect      
Negative effect
Regulator Target Regulation
  sigH comFA 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 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: 445 a.a.        Molecular weight: 50436.85 Da        Isoelectric Point: 9.9066

>NTDB_id=615 LCA_RS02545 WP_011374200.1 509945..511282(+) (comFA) [Latilactobacillus sakei subsp. sakei 23K]
MGQQVIACGRQFTAAQLADTQNNNYSLPQIKRRPAFLRVKHRLVCQRCQQVVPPQTCLPDGRHYCAQCLLFGRLVEGDWL
YTVPECHLFENNIPKLTWEGQLTPHQEKAAQAVVEVVQTQKRHVLTAVTGAGKTEMLFQGILVALQKGQRVCLAAPRVAV
CLELYPRLQAAFATTSIMLMHGEQTEPYRYTQLVICTTHQLLKFYHAFDTVIVDEVDAFPFVDNPVLATAVEQACKPQCA
LLYLTATPTPAIKRAIAAKQMTVSELPLRFHGHLLPEPQRHVAFNWRAQLKKGRLPKRLERDCQTYLKTQQILLFVPQVR
LLQPVANRLSTLLPAVRIETLHANDPDQIKKITAFRAQQIQLMVTTTILERGVTFKNVAVLVLGAEHMVFNEAVLVQIAG
RAGRHKDYAQNPVHFYYQDYTRAIKGACRQIKTQNQRGRRLQSTV

Nucleotide


Download         Length: 1338 bp        

>NTDB_id=615 LCA_RS02545 WP_011374200.1 509945..511282(+) (comFA) [Latilactobacillus sakei subsp. sakei 23K]
ATGGGACAACAAGTAATTGCCTGTGGTCGCCAGTTTACGGCGGCCCAGTTAGCCGATACGCAAAATAATAACTATAGTTT
ACCACAGATTAAGCGGCGACCTGCGTTTTTACGGGTCAAGCACCGCTTAGTCTGCCAACGTTGTCAGCAAGTGGTGCCGC
CGCAAACCTGCTTACCAGATGGGCGCCATTATTGCGCGCAATGTTTGTTATTTGGTCGTTTGGTAGAGGGCGATTGGTTA
TACACGGTACCGGAGTGTCATTTATTCGAAAATAACATACCAAAATTGACGTGGGAGGGGCAATTAACACCGCATCAGGA
AAAAGCTGCCCAAGCGGTGGTTGAGGTGGTTCAAACACAAAAACGGCACGTATTAACGGCCGTGACCGGTGCAGGGAAGA
CTGAGATGCTTTTTCAAGGAATTTTAGTTGCGCTTCAAAAGGGTCAGCGGGTATGTCTGGCAGCGCCTAGAGTCGCCGTT
TGCTTGGAACTTTATCCGCGCCTGCAAGCCGCCTTTGCAACGACTAGTATCATGTTGATGCACGGTGAGCAAACTGAGCC
CTATCGCTATACGCAGTTAGTGATTTGCACGACGCATCAGTTGCTAAAGTTTTATCACGCTTTTGACACGGTAATCGTTG
ATGAAGTCGATGCTTTTCCTTTTGTTGATAATCCCGTTTTAGCCACGGCAGTTGAACAAGCCTGCAAGCCCCAATGTGCT
TTATTATATTTAACGGCGACTCCGACCCCCGCTATTAAACGGGCAATTGCTGCTAAACAAATGACGGTTAGCGAATTACC
GCTCCGCTTTCATGGTCATCTATTACCAGAACCACAGCGGCACGTCGCTTTTAATTGGCGGGCCCAATTAAAAAAAGGTC
GGTTACCTAAACGACTTGAACGGGATTGCCAGACTTACTTAAAAACGCAACAGATTTTGTTATTCGTGCCGCAAGTGCGG
TTATTGCAACCAGTTGCCAATCGGTTATCAACCTTATTGCCGGCGGTCAGAATTGAAACATTGCATGCTAACGATCCGGA
TCAGATCAAAAAGATTACGGCGTTTAGAGCACAACAAATTCAGCTAATGGTGACGACCACCATTTTAGAACGGGGCGTTA
CGTTTAAAAACGTTGCAGTTTTGGTCTTAGGCGCGGAACATATGGTGTTTAACGAAGCCGTTTTGGTCCAGATTGCCGGG
CGAGCGGGACGGCATAAAGATTACGCCCAAAATCCGGTTCATTTTTATTATCAAGACTATACGCGGGCGATCAAAGGCGC
TTGTCGGCAAATTAAGACCCAAAATCAGAGGGGACGGCGATTACAATCAACTGTTTAA

Domains

Predicted by InterProScan.

Type III restriction enzyme, res subunit (ResIII)

(101-248)

Helicase conserved C-terminal domain (Helicase_C)

(306-405)


Secondary structure

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



3D structure

Source ID Structure
  AlphaFold DB Q38YD5

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
  comFA/cflA Streptococcus pneumoniae TIGR4

39.211

99.769

0.391
  comFA/cflA Streptococcus mitis SK321

38.621

100

0.389
  comFA/cflA Streptococcus pneumoniae D39

38.979

99.769

0.389
  comFA/cflA Streptococcus pneumoniae R6

38.979

99.769

0.389
  comFA/cflA Streptococcus pneumoniae Rx1

38.979

99.769

0.389
  comFA/cflA Streptococcus mitis NCTC 12261

38.515

99.769

0.384
  comFA Bacillus subtilis subsp. subtilis str. 168

39.268

92.135

0.362

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]