Summary: NUMOD3 motif (2 copies)
NUMOD3 motif (2 copies) Provide feedback
NUMOD3 is a DNA-binding motif found in homing endonucleases and related proteins. It occurs on its own or in tandem repeats in GIY-YIG (PF01541) and HTH proteins. It constitutes a beta-turn-loop-helix subregion of the the DNA-binding domain of I-TevI homing endonuclease (P13299) .
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR003611This is a short helical motif of unknown function found in intron-associated nuclease 2, which is involved in intron homing.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||endonuclease activity (GO:0004519)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
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We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
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- alignment generated by searching the NCBI sequence database using the family HMM
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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Curation and family details
|Seed source:||Pietrokovski S|
|Number in seed:||25|
|Number in full:||485|
|Average length of the domain:||32.80 aa|
|Average identity of full alignment:||29 %|
|Average coverage of the sequence by the domain:||23.99 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||6|
|Download:||download the raw HMM for this family|
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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 NUMOD3 domain has been found. There are 2 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 seqence.
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