Summary: EF-hand domain pair
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This is the Wikipedia entry entitled "EF hand". More...
EF hand Edit Wikipedia article
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EF-hand domain pair Provide feedback
No Pfam abstract.
Internal database links
SCOOP: | Dockerin_1 DUF1103 DUF5580 EF-hand_1 EF-hand_10 EF-hand_11 EF-hand_4 EF-hand_5 EF-hand_6 EF-hand_7 EF-hand_9 EFhand_Ca_insen Exo_endo_phos Pro_dh S_100 SPARC_Ca_bdg |
Similarity to PfamA using HHSearch: | EF-hand_1 EF-hand_4 EF-hand_5 EF-hand_6 EF-hand_7 EF-hand_7 EF-hand_9 |
This tab holds annotation information from the InterPro database.
No InterPro data for this Pfam family.
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 EF_hand (CL0220), which has the following description:
The EF hand is a calcium binding domain found in a wide variety of proteins [1].
The clan contains the following 30 members:
Ca_chan_IQ Caleosin Cbl_N2 Cullin_binding DAG_kinase_N Dockerin_1 EF-hand_1 EF-hand_10 EF-hand_11 EF-hand_12 EF-hand_13 EF-hand_14 EF-hand_2 EF-hand_3 EF-hand_4 EF-hand_5 EF-hand_6 EF-hand_7 EF-hand_8 EF-hand_9 EF-hand_like EF_assoc_2 EFhand_Ca_insen Internalin_N IQ IQCJ-SCHIP1 NADPH_Ox p25-alpha S_100 SPARC_Ca_bdgAlignments
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...
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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.
Seed (34) |
Full (18887) |
Representative proteomes | UniProt (37381) |
NCBI (201507) |
Meta (1225) |
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RP15 (2873) |
RP35 (7685) |
RP55 (13678) |
RP75 (19692) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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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.
Seed (34) |
Full (18887) |
Representative proteomes | UniProt (37381) |
NCBI (201507) |
Meta (1225) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (2873) |
RP35 (7685) |
RP55 (13678) |
RP75 (19692) |
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Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | Jackhmmer:B4DPI1 |
Previous IDs: | EF_hand_6; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Coggill P |
Number in seed: | 34 |
Number in full: | 18887 |
Average length of the domain: | 49.60 aa |
Average identity of full alignment: | 23 % |
Average coverage of the sequence by the domain: | 15.32 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 54 | ||||||||||||
Family (HMM) version: | 7 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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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Interactions
There are 25 interactions for this family. More...
CaMBD Calpain_inhib EF-hand_6 Troponin EF-hand_8 EF-hand_5 EF-hand_1 EF-hand_11 Shal-type BTB_2 Death Shal-type Pkinase EF-hand_11 CaMBD Myosin_head Peptidase_C2 MARCKS Calpain_III Troponin EF-hand_7 Ca_chan_IQ EF-hand_7 BTB_2 EF-hand_1Structures
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 EF-hand_8 domain has been found. There are 282 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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