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0  structures 3216  species 1  interaction 14356  sequences 16  architectures

Family: DeoRC (PF00455)

Summary: DeoR C terminal sensor domain

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DeoR C terminal sensor domain Provide feedback

The sensor domains of the DeoR are catalytically inactive versions of the ISOCOT fold, but retain the substrate binding site [1]. DeorC senses diverse sugar derivatives such as deoxyribose nucleoside (DeoR), tagatose phosphate (LacR), galactosamine (AgaR), myo-inositol (Bacillus IolR) and L-ascorbate (UlaR) [1] [2] [3].

Literature references

  1. Anantharaman V, Aravind L;, J Mol Biol. 2006;356:823-842.: Diversification of catalytic activities and ligand interactions in the protein fold shared by the sugar isomerases, eIF2B, DeoR transcription factors, acyl-CoA transferases and methenyltetrahydrofolate synthetase. PUBMED:16376935 EPMC:16376935

  2. Garces F, Fernandez FJ, Gomez AM, Perez-Luque R, Campos E, Prohens R, Aguilar J, Baldoma L, Coll M, Badia J, Vega MC;, Biochemistry. 2008;47:11424-11433.: Quaternary structural transitions in the DeoR-type repressor UlaR control transcriptional readout from the L-ascorbate utilization regulon in Escherichia coli. PUBMED:18844374 EPMC:18844374

  3. Müller FH, Bandeiras TM, Urich T, Teixeira M, Gomes CM, Kletzin A , Mol Microbiol 2004;0:0-0.: Coupling of the Pathway of Sulfur Oxidation to Dioxygen Reduction: Characterization of a Novel Membrane-Bound Thiosulfate:Quinone Oxidoreductase 2 PUBMED:0 EPMC:0


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR014036

DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for DeoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway.

The C-terminal sensor domain of DeoR-like transcription repressors represents a catalytically inactive version of the ISOCOT fold, but retains the substrate binding site [PUBMED:16376935]. This sensor domain binds the inducer and often acts as an oligomerisation domain. It senses diverse sugar derivatives such as deoxyribose nucleoside (in the case of DeoR), tagatose phosphate (LacR), galactosamine (AgaR), myo-inositol (Bacillus IolR) and L-ascorbate (UlaR) [PUBMED:18844374].

Domain organisation

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Pfam Clan

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
(91)
Full
(14356)
Representative proteomes NCBI
(7048)
Meta
(402)
RP15
(508)
RP35
(1030)
RP55
(1467)
RP75
(1875)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(91)
Full
(14356)
Representative proteomes NCBI
(7048)
Meta
(402)
RP15
(508)
RP35
(1030)
RP55
(1467)
RP75
(1875)
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
(91)
Full
(14356)
Representative proteomes NCBI
(7048)
Meta
(402)
RP15
(508)
RP35
(1030)
RP55
(1467)
RP75
(1875)
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

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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.

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Curation and family details

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Curation View help on the curation process

Seed source: Anantharaman V
Previous IDs: deoR; DeoR;
Type: Domain
Author: Finn RD, Anantharaman V
Number in seed: 91
Number in full: 14356
Average length of the domain: 159.00 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 63.33 %

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 31.8 31.8
Trusted cut-off 31.8 31.9
Noise cut-off 31.7 31.4
Model length: 162
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

Rib_5-P_isom_A