Summary: Fungal ubiquitin-associated domain
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Fungal ubiquitin-associated domain Provide feedback
Members of this family of ubiquitin binding domains adopt a structure consisting of a three alpha-helix bundle. They are predominantly found in fungal ubiquitin-protein ligases .
Merkley N, Shaw GS; , J Biol Chem. 2004;279:47139-47147.: Solution structure of the flexible class II ubiquitin-conjugating enzyme Ubc1 provides insights for polyubiquitin chain assembly. PUBMED:15328341 EPMC:15328341
Internal database links
|SCOOP:||UBA UCH UCH_1|
|Similarity to PfamA using HHSearch:||UBA|
External database links
- 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 includes domains related to the UBA domain. These domains are often involved in ubiquitin binding.
The clan contains the following 15 members:CUE DMA DUF1296 DUF1421 E3_UbLigase_EDD HOIP-UBA RuvA_C TAP_C UBA UBA_2 UBA_3 UBA_4 UBA_5 Ubiq-assoc WIYLD
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 UniProtKB sequence database using the family HMM
- 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:
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:||6|
|Number in full:||351|
|Average length of the domain:||49.70 aa|
|Average identity of full alignment:||34 %|
|Average coverage of the sequence by the domain:||18.49 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||9|
|Download:||download the raw HMM for this family|
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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 UBA_3 domain has been found. There are 1 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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