Summary: Zinc knuckle
Zinc knuckle Provide feedback
The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.
Internal database links
|SCOOP:||zf-CCHC_4 zf-CCHC_5 zf-CCHC_6 CLIP1_ZNF|
|Similarity to PfamA using HHSearch:||zf-CCHC|
External database links
This tab holds annotation information from the InterPro database.
No InterPro data for this Pfam family.
- 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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This superfamily has zinc-finger domains from GAG proteins, HIV nucleocapsids, nucleocapsid proteins from mason-pfizer monkey virus, and from other nucleic-acid binding proteins. Sometimes the domains appears in duplicate.
The clan contains the following 6 members:zf-CCHC zf-CCHC_2 zf-CCHC_3 zf-CCHC_4 zf-CCHC_5 zf-CCHC_6
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
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
|Number in seed:||21|
|Number in full:||717|
|Average length of the domain:||39.50 aa|
|Average identity of full alignment:||31 %|
|Average coverage of the sequence by the domain:||16.35 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||2|
|Download:||download the raw HMM for this family|
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