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47  structures 2457  species 2  interactions 10733  sequences 33  architectures

Family: IclR (PF01614)

Summary: Bacterial transcriptional regulator

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

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

Bacterial transcriptional regulator Provide feedback

This family of bacterial transcriptional regulators includes the glycerol operon regulatory protein and acetate operon repressor both of which are members of the iclR family. These proteins have a Helix-Turn-Helix motif at the N-terminus. However this family covers the C-terminal region that may bind to the regulatory substrate (unpublished observation, Bateman A.).

Literature references

  1. Galinier A, Bleicher F, Negre D, Perriere G, Duclos B, Cozzone AJ, Cortay JC; , Gene 1991;97:149-150.: Primary structure of the intergenic region between aceK and iclR in the Escherichia coli chromosome. PUBMED:1995429 EPMC:1995429

  2. Smith CP, Chater KF; , J Mol Biol 1988;204:569-580.: Structure and regulation of controlling sequences for the Streptomyces coelicolor glycerol operon. PUBMED:3225846 EPMC:3225846


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR014757

The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including:

  • gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces.

These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [PUBMED:1840643].

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 GAF (CL0161), which has the following description:

A clan of related transcriptional regulator domains.

The clan contains the following 10 members:

Autoind_bind CodY DUF2930 DUF3369 DUF484 GAF GAF_2 GAF_3 IclR PHY

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...

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.

  Seed
(23)
Full
(10733)
Representative proteomes NCBI
(8004)
Meta
(908)
RP15
(689)
RP35
(1722)
RP55
(2433)
RP75
(2964)
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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
(23)
Full
(10733)
Representative proteomes NCBI
(8004)
Meta
(908)
RP15
(689)
RP35
(1722)
RP55
(2433)
RP75
(2964)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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.

  Seed
(23)
Full
(10733)
Representative proteomes NCBI
(8004)
Meta
(908)
RP15
(689)
RP35
(1722)
RP55
(2433)
RP75
(2964)
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: Pfam-B_755 (release 4.1)
Previous IDs: none
Type: Family
Author: Bashton M, Bateman A
Number in seed: 23
Number in full: 10733
Average length of the domain: 124.00 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 46.91 %

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 20.6 20.6
Trusted cut-off 20.6 20.6
Noise cut-off 20.5 20.5
Model length: 129
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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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...

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Interactions

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

HTH_IclR IclR

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 IclR domain has been found. There are 47 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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