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117  structures 7619  species 4  interactions 97023  sequences 2075  architectures

Family: HAMP (PF00672)

Summary: HAMP domain

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HAMP domain Provide feedback

No Pfam abstract.

Literature references

  1. Aravind L, Ponting CP; , FEMS Microbiol Lett 1999;176:111-116.: The cytoplasmic helical linker domain of receptor histidine kinase and methyl-accepting proteins is common to many prokaryotic signalling proteins. PUBMED:10418137 EPMC:10418137


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003660

The HAMP domain (present in Histidine kinases, Adenyl cyclases, Methyl-accepting proteins and Phosphatases) is an approximately 50-amino acid alpha-helical region. It is found in bacterial sensor and chemotaxis proteins and in eukaryotic histidine kinases. The bacterial proteins are usually integral membrane proteins and part of a two-component signal transduction pathway. One or several copies of the HAMP domain can be found in association with other domains, such as the histidine kinase domain, the bacterial chemotaxis sensory transducer domain, the PAS repeat, the EAL domain, the GGDEF domain, the protein phosphatase 2C-like domain, the guanylate cyclase domain, or the response regulatory domain. It has been suggested that the HAMP domain possesses a role of regulating the phosphorylation or methylation of homodimeric receptors by transmitting the conformational changes in periplasmic ligand-binding domains to cytoplasmic signalling kinase and methyl-acceptor domains [PUBMED:10418137].

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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Pfam Clan

This family is a member of clan HAMP (CL0681), which has the following description:

The ability of single-celled organisms to sense, respond to, and adapt to their changing environment requires receptor proteins to convert extracellular signals into cellular responses. Central to many of these signal transduction systems are HAMP (histidine kinases, adenylyl cyclases, methylaccepting proteins, and other prokaryotic signaling proteins) domains, which act to couple sensory and output domains in different receptor proteins. In transmembrane receptors, HAMP domains connect to transmembrane helices entering the cytoplasm and translate chemical, photo, and thermo stimuli to the output of cytoplasmic catalytic domains (mainly histidine kinases, adenylyl cyclases, methyl-accepting chemotaxis proteins [MCPs], and phosphatases). Deletion of HAMP domains disrupts the link between input and output units, generating receptors incapable of switching activity states upon stimulation. HAMP domains are small modules, approximately 50 amino acids, that dimerize to form an entirely parallel four-helix bundle with two helices (AS1 and AS2) supplied from each subunit. The AS1 and AS2 helices form a seven-residue pattern characteristic of coiled coils, termed a heptad repeat [1].

The clan contains the following 2 members:

HAMP HAMP_N3

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, the UniProtKB sequence database, 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
(212)
Full
(97023)
Representative proteomes UniProt
(284647)
NCBI
(482044)
Meta
(3581)
RP15
(19823)
RP35
(59558)
RP55
(97032)
RP75
(148884)
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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
(212)
Full
(97023)
Representative proteomes UniProt
(284647)
NCBI
(482044)
Meta
(3581)
RP15
(19823)
RP35
(59558)
RP55
(97032)
RP75
(148884)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(212)
Full
(97023)
Representative proteomes UniProt
(284647)
NCBI
(482044)
Meta
(3581)
RP15
(19823)
RP35
(59558)
RP55
(97032)
RP75
(148884)
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.

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_113 (release 2.1)
Previous IDs: DUF5;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 212
Number in full: 97023
Average length of the domain: 53.40 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 9.95 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 15.0
Trusted cut-off 25.0 15.0
Noise cut-off 24.9 14.9
Model length: 53
Family (HMM) version: 25
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

Selections

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Interactions

There are 4 interactions for this family. More...

HisKA Bac_rhodopsin HAMP MCPsignal

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 HAMP domain has been found. There are 117 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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