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365  structures 6749  species 0  interactions 146371  sequences 121  architectures

Family: LysR_substrate (PF03466)

Summary: LysR substrate binding domain

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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.

LysR substrate binding domain Provide feedback

The structure of this domain is known and is similar to the periplasmic binding proteins [1]. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).

Literature references

  1. Tyrrell R, Verschueren KH, Dodson EJ, Murshudov GN, Addy C, Wilkinson AJ; , Structure 1997;5:1017-1032.: The structure of the cofactor-binding fragment of the LysR family member, CysB: a familiar fold with a surprising subunit arrangement. PUBMED:9309218 EPMC:9309218


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005119

The structure of this domain is known and is similar to the periplasmic binding proteins [ PUBMED:9309218 ]. This domain is found in members of the LysR family of prokaryotic transcriptional regulatory proteins INTERPRO which share sequence similarities over approximately 280 residues including a putative helix-turn-helix DNA-binding motif at their N terminus.

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 PBP (CL0177), which has the following description:

Periplasmic binding proteins (PBPs) consist of two large lobes that close around the bound ligand. This architecture is reiterated in transcriptional regulators, such as the lac repressors. In the process of evolution, genes encoding the PBPs have fused with genes for integral membrane proteins. Thus, diverse mammalian receptors contain extracellular ligand binding domains that are homologous to the PBPs; these include glutamate/glycine-gated ion channels such as the NMDA receptor, G protein-coupled receptors, including metabotropic glutamate, GABA-B, calcium sensing, and pheromone receptors, and atrial natriuretic peptide-guanylate cyclase receptors [2].

The clan contains the following 27 members:

CypI DctP DUF3834 HisG Lig_chan-Glu_bd Lipoprotein_8 Lipoprotein_9 LysR_substrate NMT1 NMT1_2 NMT1_3 OpuAC PBP_like PBP_like_2 PDT Phosphonate-bd Porphobil_deam SBP_bac_1 SBP_bac_11 SBP_bac_3 SBP_bac_5 SBP_bac_6 SBP_bac_8 TctC Transferrin VitK2_biosynth YhfZ_C

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...

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
(294)
Full
(146371)
Representative proteomes UniProt
(877632)
RP15
(10834)
RP35
(57135)
RP55
(152471)
RP75
(328256)
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HTML View             
PP/heatmap 1            

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

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

Format an alignment

  Seed
(294)
Full
(146371)
Representative proteomes UniProt
(877632)
RP15
(10834)
RP35
(57135)
RP55
(152471)
RP75
(328256)
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
(294)
Full
(146371)
Representative proteomes UniProt
(877632)
RP15
(10834)
RP35
(57135)
RP55
(152471)
RP75
(328256)
Raw Stockholm Download     Download   Download        
Gzipped 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: Bateman A
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 294
Number in full: 146371
Average length of the domain: 203.20 aa
Average identity of full alignment: 16 %
Average coverage of the sequence by the domain: 67.70 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 28.0 28.0
Trusted cut-off 28.0 28.0
Noise cut-off 27.9 27.9
Model length: 209
Family (HMM) version: 23
Download: download the raw HMM for this family

Species distribution

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

Selections

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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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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 LysR_substrate domain has been found. There are 365 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0T0G2 View 3D Structure Click here
A0T0V5 View 3D Structure Click here
A6TDS6 View 3D Structure Click here
A8ACM1 View 3D Structure Click here
A8APC5 View 3D Structure Click here
A9MRG1 View 3D Structure Click here
B2VF18 View 3D Structure Click here
B4F0Q1 View 3D Structure Click here
L7N677 View 3D Structure Click here
O07906 View 3D Structure Click here
O32186 View 3D Structure Click here
O32255 View 3D Structure Click here
O34685 View 3D Structure Click here
O34701 View 3D Structure Click here
O34827 View 3D Structure Click here
O35038 View 3D Structure Click here
O52399 View 3D Structure Click here
O68014 View 3D Structure Click here
P03030 View 3D Structure Click here
P03031 View 3D Structure Click here
P05827 View 3D Structure Click here
P06614 View 3D Structure Click here
P07774 View 3D Structure Click here
P08719 View 3D Structure Click here
P0A2Q0 View 3D Structure Click here
P0A2Q2 View 3D Structure Click here
P0A2Q4 View 3D Structure Click here
P0A4T6 View 3D Structure Click here
P0A8R9 View 3D Structure Click here
P0A8S0 View 3D Structure Click here
P0A8S1 View 3D Structure Click here
P0A8S3 View 3D Structure Click here
P0A8S4 View 3D Structure Click here
P0A9F3 View 3D Structure Click here
P0A9F5 View 3D Structure Click here
P0A9F6 View 3D Structure Click here
P0A9F8 View 3D Structure Click here
P0A9F9 View 3D Structure Click here
P0A9G0 View 3D Structure Click here
P0A9G1 View 3D Structure Click here