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101  structures 7153  species 0  interactions 83948  sequences 2403  architectures

Clan: HAMP (CL0681)


HAMP domains Add an annotation

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].

This clan contains 3 families and the total number of domains in the clan is 83948. The clan was built by S El-Gebali.

Literature references

  1. Airola MV, Sukomon N, Samanta D, Borbat PP, Freed JH, Watts KJ, Crane BR;, PLoS Biol. 2013;11:e1001479.: HAMP domain conformers that propagate opposite signals in bacterial chemoreceptors. PUBMED:23424282 EPMC:23424282


This clan contains the following 3 member families:


Domain organisation

Below is a listing of the unique domain organisations or architectures from this clan. More...

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The table below shows the number of occurrences of each domain throughout the sequence database. More...

Pfam family Num. domains Alignment
HAMP (PF00672) 73262 (87.3%) View
HAMP_2 (PF18947) 10265 (12.2%) View
HAMP_N3 (PF18575) 421 (0.5%) View
Total: 3 Total: 83948 Clan alignment

Please note: Clan alignments can be very large and can cause problems for some browsers. Read the note above before viewing.

Family relationships

This diagram shows the relationships between members of this clan. More...

Species distribution

Tree controls


This tree shows the occurrence of the domains in this clan across different species. More...



For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the MSD group, to allow us to map Pfam domains onto UniProt three-dimensional structures. The table below shows the mapping between the Pfam families in this clan, the corresponding UniProt entries, and the region of the three-dimensional structures that are available for that sequence.

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