Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
0  structures 317  species 0  interactions 710  sequences 1  architecture

Family: SR1P (PF13790)

Summary: SR1 protein

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "SR1 RNA". More...

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.[1] 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.[2][3] 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.[4][5][6]

In addition to acting as a sRNA, SR1 also encodes a small peptide, SR1P. SR1P binds to glyceraldehyde-3-phosphate dehydrogenase (GapA) and stabilises the gapA operon mRNAs.[7]

SR1 expression is regulated by CcpA and CcpN.[8][9]

See also


  1. ^ 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. 
  2. ^ 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. 
  3. ^ 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. 
  4. ^ 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. 
  5. ^ "Purification and initial characterization of AhrC: the regulator of arginine metabolism genes in Bacillus subtilis" 6 (2). January 1992. pp. 267–75. doi:10.1111/j.1365-2958.1992.tb02008.x. PMID 1312212. 
  6. ^ 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. 
  7. ^ 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. 
  8. ^ 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. 
  9. ^ "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. 

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

SR1 protein Provide feedback

This family of proteins is encoded by the dual function SR1 RNA. SR1 is a sRNA which regulates arginine metabolism [1] it also encodes a short protein that binds to glyceraldehyde-3-phosphate dehydrogenase (GapA) and stabilises the gapA operon mRNAs [2].

Literature references

  1. Heidrich N, Chinali A, Gerth U, Brantl S;, Mol Microbiol. 2006;62:520-536.: The small untranslated RNA SR1 from the Bacillus subtilis genome is involved in the regulation of arginine catabolism. PUBMED:17020585 EPMC:17020585

  2. Gimpel M, Heidrich N, Mader U, Krugel H, Brantl S;, Mol Microbiol. 2010;76:990-1009.: A dual-function sRNA from B. subtilis: SR1 acts as a peptide encoding mRNA on the gapA operon. PUBMED:20444087 EPMC:20444087

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR025236

This protein of unknown function contains a number of highly conserved cysteine residues, which may form disulphide bonds.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...


We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

Representative proteomes NCBI
Jalview View  View  View  View  View  View  View   
HTML View  View  View  View  View  View     
PP/heatmap 1 View  View  View  View  View     
Pfam viewer View  View             

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

Representative proteomes NCBI

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

Representative proteomes NCBI
Raw Stockholm Download   Download   Download   Download   Download   Download   Download    
Gzipped Download   Download   Download   Download   Download   Download   Download    

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...


This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Jackhmmer:D3EDS0
Previous IDs: DUF4182;
Type: Family
Author: Eberhardt R
Number in seed: 12
Number in full: 710
Average length of the domain: 37.50 aa
Average identity of full alignment: 75 %
Average coverage of the sequence by the domain: 88.01 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.0 26.0
Trusted cut-off 26.5 27.3
Noise cut-off 25.0 21.9
Model length: 37
Family (HMM) version: 2
Download: download the raw HMM for this family

Species distribution

Sunburst controls


Weight segments by...

Change the size of the sunburst


Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls


The tree shows the occurrence of this domain across different species. More...


Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.