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0  structures 1191  species 0  interactions 1246  sequences 2  architectures

Family: RseC_MucC (PF04246)

Summary: Positive regulator of sigma(E), RseC/MucC

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Positive regulator of sigma(E), RseC/MucC Provide feedback

This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions) [1]. In Pseudomonas aeruginosa, de-repression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonisation in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium [2]. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains an ApbE domain PF02424 which is itself involved in thiamine biosynthesis.

Literature references

  1. Missiakas D, Mayer MP, Lemaire M, Georgopoulos C, Raina S; , Mol Microbiol 1997;24:355-371.: Modulation of the Escherichia coli sigmaE (RpoE) heat-shock transcription-factor activity by the RseA, RseB and RseC proteins. PUBMED:9159522 EPMC:9159522

  2. Beck BJ, Connolly LE, De Las Penas A, Downs DM; , J Bacteriol 1997;179:6504-6508.: Evidence that rseC, a gene in the rpoE cluster, has a role in thiamine synthesis in Salmonella typhimurium. PUBMED:9335303 EPMC:9335303

  3. Schmehl M, Jahn A, Meyer zu Vilsendorf A, Hennecke S, Masepohl B, Schuppler M, Marxer M, Oelze J, Klipp W; , Mol Gen Genet 1993;241:602-615.: Identification of a new class of nitrogen fixation genes in Rhodobacter capsulatus: a putative membrane complex involved in electron transport to nitrogenase. PUBMED:8264535 EPMC:8264535


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007359

This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions) [PUBMED:9159522]. In Pseudomonas aeruginosa, derepression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonization in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium [PUBMED:9335303]. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains a domain found in ApbE protein INTERPRO, which is itself involved in thiamine biosynthesis.

Domain organisation

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Alignments

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...

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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.

  Seed
(118)
Full
(1246)
Representative proteomes NCBI
(726)
Meta
(78)
RP15
(81)
RP35
(160)
RP55
(208)
RP75
(247)
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Format an alignment

  Seed
(118)
Full
(1246)
Representative proteomes NCBI
(726)
Meta
(78)
RP15
(81)
RP35
(160)
RP55
(208)
RP75
(247)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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.

  Seed
(118)
Full
(1246)
Representative proteomes NCBI
(726)
Meta
(78)
RP15
(81)
RP35
(160)
RP55
(208)
RP75
(247)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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...

Trees

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: COG3086
Previous IDs: none
Type: Family
Author: Mifsud W
Number in seed: 118
Number in full: 1246
Average length of the domain: 133.00 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 87.61 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.2 23.2
Trusted cut-off 23.2 23.4
Noise cut-off 23.1 23.1
Model length: 135
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

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