Detailed information    

experimental Experimentally validated

Overview

Name   comFC   Type   Machinery gene
Locus tag   LCA_RS09740 Genome accession   NC_007576
Coordinates   511525..511953 (+) Length   142 a.a.
NCBI ID   WP_148664867.1    Uniprot ID   -
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.


Related MGE

Note: This gene co-localizes with putative mobile genetic elements (MGEs) in the genome predicted by VRprofile2, as detailed below.

Gene-MGE association summary

MGE type MGE coordinates Gene coordinates Relative position Distance (bp)
ICE 491416..532113 511525..511953 within 0


Gene organization within MGE regions


Location: 491416..532113
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  LCA_RS02465 (LCA_0475) - 492343..492780 (-) 438 WP_011374184.1 GNAT family N-acetyltransferase -
  LCA_RS02470 (LCA_0476) - 492944..493921 (-) 978 WP_011374185.1 GMP reductase -
  LCA_RS02475 (LCA_0477) - 494068..495021 (-) 954 WP_011374186.1 magnesium transporter CorA family protein -
  LCA_RS02480 (LCA_0478) - 495110..495946 (+) 837 WP_011374187.1 methyltransferase domain-containing protein -
  LCA_RS02485 (LCA_0479) trmL 496199..496708 (+) 510 WP_011374188.1 tRNA (uridine(34)/cytosine(34)/5- carboxymethylaminomethyluridine(34)-2'-O)- methyltransferase TrmL -
  LCA_RS02490 (LCA_0480) - 496720..497127 (+) 408 WP_011374189.1 DUF1149 family protein -
  LCA_RS02495 (LCA_0481) - 497267..499636 (+) 2370 WP_011374190.1 DNA translocase FtsK -
  LCA_RS02500 (LCA_0482) yfmF 499834..501105 (+) 1272 WP_011374191.1 EF-P 5-aminopentanol modification-associated protein YfmF -
  LCA_RS02505 (LCA_0483) yfmH 501095..502399 (+) 1305 WP_011374192.1 EF-P 5-aminopentanol modification-associated protein YfmH -
  LCA_RS02510 (LCA_0484) ymfI 502399..503130 (+) 732 WP_011374193.1 elongation factor P 5-aminopentanone reductase -
  LCA_RS02515 (LCA_0485) - 503212..504135 (+) 924 WP_011374194.1 helix-turn-helix domain-containing protein -
  LCA_RS02520 (LCA_0486) pgsA 504161..504745 (+) 585 WP_011374195.1 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase -
  LCA_RS02525 (LCA_0487) recA 504928..505995 (+) 1068 WP_011374196.1 recombinase RecA Machinery gene
  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 -
  LCA_RS02565 (LCA_0496) prfB 515307..516423 (+) 1117 WP_099049013.1 peptide chain release factor 2 -
  LCA_RS02570 (LCA_0497) ftsE 516554..517240 (+) 687 WP_011374205.1 cell division ATP-binding protein FtsE -
  LCA_RS02575 (LCA_0498) ftsX 517230..518117 (+) 888 WP_041821015.1 permease-like cell division protein FtsX -
  LCA_RS02580 (LCA_0499) - 518311..519444 (+) 1134 WP_011374207.1 PDZ domain-containing protein -
  LCA_RS02585 (LCA_0500) - 519464..520177 (+) 714 WP_011374208.1 response regulator transcription factor -
  LCA_RS02590 (LCA_0501) pnpS 520164..521825 (+) 1662 WP_011374209.1 two-component system histidine kinase PnpS -
  LCA_RS02595 (LCA_0502) - 521918..522778 (+) 861 WP_011374210.1 phosphate ABC transporter substrate-binding protein PstS family protein -
  LCA_RS02600 (LCA_0503) pstC 522788..523711 (+) 924 WP_011374211.1 phosphate ABC transporter permease subunit PstC -
  LCA_RS02605 (LCA_0504) pstA 523711..524595 (+) 885 WP_011374212.1 phosphate ABC transporter permease PstA -
  LCA_RS02610 (LCA_0505) pstB 524605..525414 (+) 810 WP_011374213.1 phosphate ABC transporter ATP-binding protein PstB -
  LCA_RS02615 (LCA_0506) pstB 525435..526193 (+) 759 WP_011374214.1 phosphate ABC transporter ATP-binding protein PstB -
  LCA_RS02620 (LCA_0507) phoU 526210..526887 (+) 678 WP_011374215.1 phosphate signaling complex protein PhoU -
  LCA_RS02625 (LCA_0508) - 527101..527571 (+) 471 WP_011374216.1 nucleoside 2-deoxyribosyltransferase -
  LCA_RS02630 (LCA_0509) - 527761..528948 (+) 1188 WP_011374217.1 glycine C-acetyltransferase -
  LCA_RS02635 (LCA_0511) - 528968..529915 (+) 948 Protein_490 L-threonine 3-dehydrogenase -
  LCA_RS02640 (LCA_0512) liaX 530102..531577 (+) 1476 WP_011374220.1 daptomycin-sensing surface protein LiaX -
  LCA_RS02645 (LCA_0513) - 531605..531841 (+) 237 WP_011374221.1 PspC domain-containing protein -
  LCA_RS02650 (LCA_0514) - 531841..532113 (+) 273 WP_011374222.1 hypothetical protein -

Regulatory network

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

Sequence

Protein


Download         Length: 142 a.a.        Molecular weight: 16670.11 Da        Isoelectric Point: 9.8198

>NTDB_id=616 LCA_RS09740 WP_148664867.1 511525..511953(+) (comFC) [Latilactobacillus sakei subsp. sakei 23K]
MQLYFQRYKGQGDYQLRLLFERDIRTRFPVKPNVTYVPIPSDEQHQQERGFNPVQGLFETCFPLTSLLKKRPTEKGQAQK
NRAERLASPQFFELIPQELPYKPQSIIILDDIYTTGRTVWHAQQCLRANYPQATINAITLAR

Nucleotide


Download         Length: 429 bp        

>NTDB_id=616 LCA_RS09740 WP_148664867.1 511525..511953(+) (comFC) [Latilactobacillus sakei subsp. sakei 23K]
ATGCAGTTATATTTTCAACGTTATAAGGGCCAAGGAGACTATCAATTACGGCTGTTATTCGAACGCGACATTCGAACTCG
GTTTCCAGTAAAACCCAATGTAACTTACGTGCCTATTCCATCTGATGAGCAACATCAACAAGAACGGGGCTTTAATCCAG
TCCAAGGCTTATTCGAAACTTGTTTTCCGTTAACATCGCTATTGAAAAAGCGGCCAACAGAGAAGGGCCAAGCACAAAAA
AATCGTGCAGAACGTCTTGCAAGTCCACAATTTTTTGAATTAATACCGCAAGAATTACCGTATAAGCCGCAATCGATAAT
AATCTTGGATGATATTTATACGACGGGCCGAACGGTGTGGCATGCACAACAATGTCTGCGTGCTAATTATCCCCAAGCTA
CAATTAATGCGATTACTTTAGCCAGATAG

Domains


No domain identified.



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
  comFC Lactococcus lactis subsp. cremoris KW2

37.241

100

0.403

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]