Summary: Protein of unknown function (DUF933)
This is the Wikipedia entry entitled "YchF-GTPase C terminal protein domain". More...
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YchF-GTPase C terminal protein domain Edit Wikipedia article
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|C terminal domain of YchF-GTPase|
ychf protein (hi0393)
The function of this protein domain remains unknown, however, it is putatively thought to be necessary for ribosome function or for signal transduction from the ribosome to downstream targets. Additionally, GTPases are often described as a molecular switch. 
The crystal structure of Haemophilus influenzae has been determined. This protein consists of three domains, of which the C-terminal domain which is composed of a six-stranded half-barrel curved around an alpha helix.
- Caldon CE, Yoong P, March PE (2001). "Evolution of a molecular switch: universal bacterial GTPases regulate ribosome function.". Mol Microbiol 41 (2): 289–97. doi:10.1046/j.1365-2958.2001.02536.x. PMID 11489118.
- Teplyakov A, Obmolova G, Chu SY, Toedt J, Eisenstein E, Howard AJ, Gilliland GL (July 2003). "Crystal structure of the YchF protein reveals binding sites for GTP and nucleic acid". J. Bacteriol. 185 (14): 4031–7. doi:10.1128/jb.185.14.4031-4037.2003. PMC 164861. PMID 12837776.
Protein of unknown function (DUF933) Provide feedback
This domain is found at the C terminus of the YchF GTP-binding protein (O13998) and is possibly related to the ubiquitin-like and MoaD/ThiS superfamilies.
Internal database links
|Similarity to PfamA using HHSearch:||TGS|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR013029
This domain is found at the C terminus of family of conserved hypothetical proteins found in both prokaryotes and eukaryotes. While the function of these proteins is not known, the crystal structure of SWISSPROT from Haemophilus influenzae has been determined [PUBMED:12837776]. This protein consists of three domains: an N-terminal domain which has a mononucleotide binding fold typical for the P-loop NTPases, a central domain which forms an alpha-helical coiled coil, and this C-terminal domain which is composed of a six-stranded half-barrel curved around an alpha helix. The central domain and this domain are topologically similar to RNA-binding proteins, while the N-terminal region contains the features typical of GTP-dependent molecular switches. The purified protein was capable of binding both double-stranded nucleic acid and GTP. It was suggested, therefore, that this protein might be part of a nucleoprotein complex and could function as a GTP-dependent translation factor.
- 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 family includes proteins that share the ubiquitin fold. It currently unites four SCOP superfamilies.
The clan contains the following 41 members:APG12 Atg8 Blt1 Caps_synth_GfcC CIDE-N Cobl DUF1315 DUF2407 DUF4430 DWNN FERM_N Lambda_tail_I Multi_ubiq NQRA_SLBB PB1 PI3K_rbd Plug Prok_Ub RA Rad60-SLD Rad60-SLD_2 Ras_bdg_2 RBD SLBB Telomere_Sde2 TGS ThiS ThiS-like TmoB TUG-UBL1 Ub-Mut7C Ub-RnfH ubiquitin Ubiquitin_2 Ubiquitin_3 UBX Ufm1 UN_NPL4 Urm1 YchF-GTPase_C YukD
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:
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
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Curation and family details
|Seed source:||Pfam-B_10000 (release 9.0)|
|Author:||Moxon SJ, Studholme DJ|
|Number in seed:||44|
|Number in full:||5012|
|Average length of the domain:||82.60 aa|
|Average identity of full alignment:||63 %|
|Average coverage of the sequence by the domain:||22.65 %|
|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:||8|
|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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There are 2 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 YchF-GTPase_C domain has been found. There are 7 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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