Table 2.
Motif namesa
| Motif name | Pfam annotation or other comment |
|---|---|
| AAA | ATPase family associated with various cellular activities |
| BBOX | B-Box-type zinc finger |
| BS1 box | BS1 (binding site 1) is a p97-interacting domain |
| C2 | Ca2+-dependent membrane-targeting module |
| CUE | CUE domains may be involved in binding ubiquitin-conjugating enzymes (UBCs) or ubiquitin. |
| Cullin | Cullins are a family of hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3). |
| DER1 | Der1-like family |
| DnaJ | DnaJ domain |
| FBA | F-box associated region |
| F-box | The F-box domain has a role in mediating protein–protein interactions. |
| Fn2 | Fibronectin type 2 domain |
| Glyco_hydro_47 | Glycosyl hydrolase family 47 |
| HECT | The name HECT-domain (ubiquitin-transferase) comes from Homologous to the E6-AP Carboxyl Terminus. |
| IBR | The IBR (in between ring fingers) domain is often found to occur between pairs of ring finger. |
| Josephin | The name Josephin comes from Machado–Joseph Disease protein MJD. |
| MRH | Mannose 6-phosphate receptor homology domain |
| MYND finger | The MYND (myeloid, Nervy, and DEAF-1) zinc finger domain might be involved in protein–protein interactions. |
| NBD | Nucleotide binding domain. |
| OTU | The ovarian tumor (OTU) -like cysteine protease |
| Peptidase_A22B | Signal peptide peptidase domain |
| PFU | PFU is the ubiquitin binding domain of Doa1 |
| PH | PH (pleckstrin homology) is involved in intracellular signaling or as constituents of the cytoskeleton. |
| Pro_isomerase | Cyclophilin type peptidyl-prolyl cis-trans isomerase |
| PUB | The PUB (also known as PUG) domain is found in peptide N-glycanase where it functions as a AAA ATPase binding domain. |
| PUL | The PUL (PLAP, Ufd3p and Lub1p) domain is a novel α-helical Ub-associated domain; it directly binds to Cdc48. |
| RING | RING finger is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions and plays a key role in the ubiquitination pathway. |
| SBD | Substrate binding domain |
| SEL1 | This short repeat is found in the Sel1 protein; it is related to TPR repeats. |
| Skp1 | SKP1 (together with SKP2) was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. |
| STI1 | Heat shock chaperonin-binding motif is found in the stress-inducible phosphoprotein STI1. |
| TPR | The tetratrico peptide repeat (TPR) mediates protein–protein interactions and the assembly of multiprotein complexes. |
| Trx | Thioredoxin domain |
| UAS | UAS is a domain of unknown function found in FAF1 proteins (FAS-associated factor 1) and in other proteins. |
| UBA | Ubiquitin associated domain |
| UBC | Ubiquitin-conjugating enzyme (E2) catalytic domain |
| UBL | Ubiquitin-like (UBL) domain |
| U-box | U-box has a similar structure to the RING-finger domain and bears ligase activity. |
| UBX | UBX domain is present in ubiquitin-regulatory proteins and is a general Cdc48-interacting module. |
| UCH | Ubiquitin carboxy-terminal hydrolase |
| UIM | Ubiquitin interacting motif (UIM) containing domains all interact with ubiquitin. |
| VIM | p97/VCP-interacting motif |
| VWA | The von Willebrand factor is a large multimeric glycoprotein found in blood plasma. |
| WD40 | Repeated WD40 motifs act as a site for protein–protein interaction. |
| WW | The WW domain is a protein module with two highly conserved tryptophans that binds proline-rich peptide motifs in vitro. |
The majority of the annotations are taken from the Pfam and SMART databases.
aEven if the human gene lacks a yeast homolog, another functionally relevant gene might exit.