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16  structures 1170  species 0  interactions 1310  sequences 9  architectures

Family: MucB_RseB (PF03888)

Summary: MucB/RseB N-terminal domain

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MucB/RseB N-terminal domain Provide feedback

Members of this family are regulators of the anti-sigma E protein RseD.

Literature references

  1. Martin DW, Schurr MJ, Mudd MH, Deretic V; , Mol Microbiol 1993;9:497-506.: Differentiation of Pseudomonas aeruginosa into the alginate-producing form: inactivation of mucB causes conversion to mucoidy. PUBMED:8412698 EPMC:8412698

  2. Martinez-Salazar JM, Moreno S, Najera R, Boucher JC, Espin G, Soberon-Chavez G, Deretic V; , J Bacteriol 1996;178:1800-1808.: Characterization of the genes coding for the putative sigma factor AlgU and its regulators MucA, MucB, MucC, and MucD in Azotobacter vinelandii and evaluation of their roles in alginate biosynthesis. PUBMED:8606151 EPMC:8606151

  3. Kim DY, Jin KS, Kwon E, Ree M, Kim KK;, Proc Natl Acad Sci U S A. 2007;104:8779-8784.: Crystal structure of RseB and a model of its binding mode to RseA. PUBMED:17496148 EPMC:17496148


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR033434

This entry represents the N-terminal domain of sigma-E factor regulatory protein RseB and sigma factor AlgU regulatory protein MucB. RseB negatively modulates the activity of sigma-E (RpoE) by stabilizing RseA under non-stress conditions [ PUBMED:9159523 , PUBMED:21245315 ]. MucB is a negative regulator of the sigma factor AlgU. It plays a role in the differentiation of P.aeruginosa into the alginate-producing form [ PUBMED:8412698 ].

Domain organisation

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

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Pfam Clan

This family is a member of clan LolA_LolB (CL0048), which has the following description:

Gram-negative bacteria lipoproteins are anchored to the periplasmic surface of the inner or outer membrane depending on the sorting signal, which is the residue at position 2 of the polypeptide. Five Lol proteins are involved in the sorting and membrane localisation of lipoprotein. An ATP-binding cassette (ABC) transporter, LolCDE, releases outer membrane-specific lipoproteins from the inner membrane, causing the formation of a complex between the released lipoproteins and the periplasmic molecular chaperone LolA. When this complex interacts with outer membrane receptor LolB, the lipoproteins are transferred from LolA to LolB and then localised to the outer membrane. The structures of LolA and LolB are remarkably similar to each other. Both have a hydrophobic cavity consisting of an unclosed beta-barrel and an alpha-helical lid [1,2].

The clan contains the following 17 members:

DUF1329 DUF1571 DUF2092 DUF3108 DUF3261 DUF4292 DUF4412 DUF576 LolA LolA_2 LolA_3 LolA_like LolB LppX_LprAFG MucB_RseB Porph_ging VioE

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(96)
Full
(1310)
Representative proteomes UniProt
(8151)
RP15
(165)
RP35
(606)
RP55
(1347)
RP75
(2685)
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PP/heatmap 1 View           

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

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

Format an alignment

  Seed
(96)
Full
(1310)
Representative proteomes UniProt
(8151)
RP15
(165)
RP35
(606)
RP55
(1347)
RP75
(2685)
Alignment:
Format:
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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
(96)
Full
(1310)
Representative proteomes UniProt
(8151)
RP15
(165)
RP35
(606)
RP55
(1347)
RP75
(2685)
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.

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: COG3026
Previous IDs: MucB_ResB;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Finn RD
Number in seed: 96
Number in full: 1310
Average length of the domain: 171.10 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 50.68 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.3 22.3
Trusted cut-off 22.3 22.3
Noise cut-off 22.2 22.2
Model length: 178
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the MucB_RseB domain has been found. There are 16 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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