Summary: Domain of unknown function (DUF4182)
This is the Wikipedia entry entitled "SR1 RNA". More...
The Wikipedia text that you see displayed here is a download from Wikipedia. This means that the information we display is a copy of the information from the Wikipedia database. The button next to the article title ("Edit Wikipedia article") takes you to the edit page for the article directly within Wikipedia. You should be aware you are not editing our local copy of this information. Any changes that you make to the Wikipedia article will not be displayed here until we next download the article from Wikipedia. We currently download new content on a nightly basis.
Does Pfam agree with the content of the Wikipedia entry ?
Pfam has chosen to link families to Wikipedia articles. In some case we have created or edited these articles but in many other cases we have not made any direct contribution to the content of the article. The Wikipedia community does monitor edits to try to ensure that (a) the quality of article annotation increases, and (b) vandalism is very quickly dealt with. However, we would like to emphasise that Pfam does not curate the Wikipedia entries and we cannot guarantee the accuracy of the information on the Wikipedia page.
Editing Wikipedia articles
Before you edit for the first time
Wikipedia is a free, online encyclopedia. Although anyone can edit or contribute to an article, Wikipedia has some strong editing guidelines and policies, which promote the Wikipedia standard of style and etiquette. Your edits and contributions are more likely to be accepted (and remain) if they are in accordance with this policy.
You should take a few minutes to view the following pages:
How your contribution will be recorded
Anyone can edit a Wikipedia entry. You can do this either as a new user or you can register with Wikipedia and log on. When you click on the "Edit Wikipedia article" button, your browser will direct you to the edit page for this entry in Wikipedia. If you are a registered user and currently logged in, your changes will be recorded under your Wikipedia user name. However, if you are not a registered user or are not logged on, your changes will be logged under your computer's IP address. This has two main implications. Firstly, as a registered Wikipedia user your edits are more likely seen as valuable contribution (although all edits are open to community scrutiny regardless). Secondly, if you edit under an IP address you may be sharing this IP address with other users. If your IP address has previously been blocked (due to being flagged as a source of 'vandalism') your edits will also be blocked. You can find more information on this and creating a user account at Wikipedia.
If you have problems editing a particular page, contact us at firstname.lastname@example.org and we will try to help.
The community annotation is a new facility of the Pfam web site. If you have problems editing or experience problems with these pages please contact us.
SR1 RNA Edit Wikipedia article
In molecular biology, the SR1 RNA is a small RNA (sRNA) produced by species of Bacillus and closely related bacteria. It is a dual-function RNA which acts both as a protein-coding RNA and as a regulatory sRNA.
SR1 RNA is involved in the regulation of arginine catabolism. SR1 RNA binds to complementary stretches of ahrC mRNA (also known as argR and inhibits translation. AhrC endodes an arginine repressor protein which represses synthesis of arginine biosynthetic enzymes and activates arginine catabolic enzymes via regulation of the rocABC and rocDEF operons.
- Gimpel, M; Preis, H; Barth, E; Gramzow, L; Brantl, S (Oct 13, 2012). "SR1--a small RNA with two remarkably conserved functions.". Nucleic Acids Research 40 (22): 11659–72. doi:10.1093/nar/gks895. PMC 3526287. PMID 23034808.
- Heidrich, N; Moll, I; Brantl, S (2007). "In vitro analysis of the interaction between the small RNA SR1 and its primary target ahrC mRNA.". Nucleic Acids Research 35 (13): 4331–46. doi:10.1093/nar/gkm439. PMC 1935000. PMID 17576690.
- Heidrich, N; Chinali, A; Gerth, U; Brantl, S (Oct 2006). "The small untranslated RNA SR1 from the Bacillus subtilis genome is involved in the regulation of arginine catabolism.". Molecular microbiology 62 (2): 520–36. doi:10.1111/j.1365-2958.2006.05384.x. PMID 17020585.
- North, AK; Smith, MC; Baumberg, S (Aug 1, 1989). "Nucleotide sequence of a Bacillus subtilis arginine regulatory gene and homology of its product to the Escherichia coli arginine repressor.". Gene 80 (1): 29–38. doi:10.1016/0378-1119(89)90247-3. PMID 2507400.
- Purification and initial characterization of AhrC: the regulator of arginine metabolism genes in Bacillus subtilis 6 (2). January 1992. pp. 267–75. PMID 1312212.
- Dennis C, CA; Glykos, NM; Parsons, MR; Phillips, SE (Mar 2002). "The structure of AhrC, the arginine repressor/activator protein from Bacillus subtilis.". Acta crystallographica. Section D, Biological crystallography 58 (Pt 3): 421–30. doi:10.1107/s0907444901021692. PMID 11856827.
- Gimpel, M; Heidrich, N; Mäder, U; Krügel, H; Brantl, S (May 2010). "A dual-function sRNA from B. subtilis: SR1 acts as a peptide encoding mRNA on the gapA operon.". Molecular microbiology 76 (4): 990–1009. doi:10.1111/j.1365-2958.2010.07158.x. PMID 20444087.
- Licht, A; Preis, S; Brantl, S (Oct 2005). "Implication of CcpN in the regulation of a novel untranslated RNA (SR1) in Bacillus subtilis.". Molecular microbiology 58 (1): 189–206. doi:10.1111/j.1365-2958.2005.04810.x. PMID 16164558.
- The transcriptional repressor CcpN from Bacillus subtilis uses different repression mechanisms at different promoters 284 (44). October 2009. pp. 30032–8. doi:10.1074/jbc.M109.033076. PMC 2781557. PMID 19726675.
"DUF" families are annotated with the Domain of unknown function Wikipedia article. This is a general article, with no specific information about individual Pfam DUFs. If you have information about this particular DUF, please let us know using the "Add annotation" button below.
Domain of unknown function (DUF4182) Provide feedback
This protein of unknown function contains a number of highly conserved cysteine residues, which may form disulphide bonds.
Internal database links
|SCOOP:||DUF4451 PyrI_C zf-dskA_traR DUF2082|
External database links
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Loading domain graphics...
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
If you find these logos useful in your own work, please consider citing the following article:
Note: You can also download the data file for the tree.
Curation and family details
|Number in seed:||13|
|Number in full:||277|
|Average length of the domain:||38.50 aa|
|Average identity of full alignment:||73 %|
|Average coverage of the sequence by the domain:||89.38 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||1|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
How the sunburst is generated
Colouring and labels
Anomalies in the taxonomy tree
Missing taxonomic levels
Unmapped species names
Too many species/sequences
The tree shows the occurrence of this domain across different species. More...
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree