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118  structures 6982  species 0  interactions 73262  sequences 2110  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 common to chemoreceptors and histidine kinases that is present in several multidomain sensor proteins that participate in a variety of signal transduction processes. 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 3 members:



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...

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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.

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

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

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Representative proteomes UniProt

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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.

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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...


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: 73262
Average length of the domain: 53.60 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 9.47 %

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 25.0 15.0
Trusted cut-off 25.0 31.6
Noise cut-off 24.9 -1000000.0
Model length: 53
Family (HMM) version: 28
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


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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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The tree shows the occurrence of this domain across different species. More...


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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 118 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
A0QTK3 View 3D Structure Click here
A0R3I7 View 3D Structure Click here
A1TEL6 View 3D Structure Click here
A1UL69 View 3D Structure Click here
C0SP89 View 3D Structure Click here
G3XD24 View 3D Structure Click here
G3XDA3 View 3D Structure Click here
I6X7Z3 View 3D Structure Click here
O07777 View 3D Structure Click here
O31516 View 3D Structure Click here
O32193 View 3D Structure Click here
O32239 View 3D Structure Click here
O34638 View 3D Structure Click here
O69729 View 3D Structure Click here
P02941 View 3D Structure Click here
P02942 View 3D Structure Click here
P05704 View 3D Structure Click here
P07017 View 3D Structure Click here
P07018 View 3D Structure Click here
P0A4I7 View 3D Structure Click here
P0AE82 View 3D Structure Click here
P0AE84 View 3D Structure Click here
P0AFA2 View 3D Structure Click here
P0AFA3 View 3D Structure Click here
P0AFA4 View 3D Structure Click here
P0DMI3 View 3D Structure Click here
P0DMK6 View 3D Structure Click here
P20169 View 3D Structure Click here
P27896 View 3D Structure Click here
P30847 View 3D Structure Click here
P35164 View 3D Structure Click here
P37979 View 3D Structure Click here
P39214 View 3D Structure Click here
P39215 View 3D Structure Click here
P39216 View 3D Structure Click here
P39217 View 3D Structure Click here
P54576 View 3D Structure Click here
P55652 View 3D Structure Click here
P71815 View 3D Structure Click here
P71914 View 3D Structure Click here