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5  structures 1600  species 2  interactions 1810  sequences 3  architectures

Family: FlgM (PF04316)

Summary: Anti-sigma-28 factor, FlgM

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Anti-sigma-28 factor, FlgM Provide feedback

FlgM binds and inhibits the activity of the transcription factor sigma 28. Inhibition of sigma 28 prevents the expression of genes from flagellar transcriptional class 3, which include genes for the filament and chemotaxis. Correctly assembled basal body-hook structures export FlgM, relieving inhibition of sigma 28 and allowing expression of class 3 genes. NMR studies show that free FlgM is mostly unfolded, which may facilitate its export. The C terminal half of FlgM adopts a tertiary structure when it binds to sigma 28. All mutations in FlgM that prevent sigma 28 inhibition affect the C-terminal domain and is the region thought to constitute the binding domain. A minimal binding domain has been identified between Glu 64 and Arg 88 in Salmonella typhimurium (P26477). The N-terminal portion remains unstructured and may be necessary for recognition by the export machinery [1].

Literature references

  1. Daughdrill GW, Chadsey MS, Karlinsey JE, Hughes KT, Dahlquist FW; , Nat Struct Biol 1997;4:285-291.: The C-terminal half of the anti-sigma factor, FlgM, becomes structured when bound to its target, sigma 28. PUBMED:9095196 EPMC:9095196

  2. Sorenson MK, Ray SS, Darst SA; , Mol Cell 2004;14:127-138.: Crystal structure of the flagellar sigma/anti-sigma complex sigma(28)/FlgM reveals an intact sigma factor in an inactive conformation. PUBMED:15068809 EPMC:15068809


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007412

FlgM binds and inhibits the activity of the transcription factor sigma 28. Inhibition of sigma 28 prevents the expression of genes from flagellar transcriptional class 3, which include genes for the filament and chemotaxis. Correctly assembled basal body-hook structures export FlgM, relieving inhibition of sigma 28 and allowing expression of class 3 genes. NMR studies show that free FlgM is mostly unfolded, which may facilitate its export. The C-terminal half of FlgM adopts a tertiary structure when it binds to sigma 28. All mutations in FlgM that prevent sigma 28 inhibition affect the C-terminal domain and is the region thought to constitute the binding domain. A minimal binding domain has been identified between Glu 64 and Arg 88 in Salmonella typhimurium (SWISSPROT).The N-terminal portion remains unstructured and may be necessary for recognition by the export machinery [PUBMED:9095196].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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

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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
(135)
Full
(1810)
Representative proteomes NCBI
(1076)
Meta
(250)
RP15
(135)
RP35
(267)
RP55
(349)
RP75
(419)
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Format an alignment

  Seed
(135)
Full
(1810)
Representative proteomes NCBI
(1076)
Meta
(250)
RP15
(135)
RP35
(267)
RP55
(349)
RP75
(419)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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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
(135)
Full
(1810)
Representative proteomes NCBI
(1076)
Meta
(250)
RP15
(135)
RP35
(267)
RP55
(349)
RP75
(419)
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.

Pfam alignments:

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: COG2747
Previous IDs: none
Type: Family
Author: Kerrison ND, Finn RD
Number in seed: 135
Number in full: 1810
Average length of the domain: 64.00 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 67.14 %

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 20.7 20.7
Trusted cut-off 20.7 20.8
Noise cut-off 20.6 20.6
Model length: 57
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

Sigma70_r4 Sigma70_r2

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 FlgM domain has been found. There are 5 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 seqence.

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