Table 2.
Cooperative domains detected by our method from MIPS protein interaction data, where GO annotations are denoted in italic
| Cooperative domains (Interactor I) | Descriptions | Interactor II | Descriptions |
| PF00069, PF00786 | (1) Protein kinase domain, ATP binding, protein kinase activity, protein amino acid phosphorylation (2) P21-Rho-binding domain |
PF00018 | SH3 domain, in a variety of proteins with enzymatic activity |
| PF00400, PF00646 | (1) WD domain, G-beta repeat, coordinating multi-protein complex assemblies (2) F-box domain, mediating protein-protein interactions in a variety of contexts |
PF01466 | Skp1 family, dimerisation domain |
| PF00439, PF00176 | (1) Bromodomain, interacting specifically with acetylated lysine (2) SNF2 family N-terminal domain, DNA binding, ATP binding |
PF04433 | SWIRM domain, mediating protein-protein interactions |
| PF00169, PF00787 | (1) PH domain (2) PX domain, protein-protein interaction domain, protein binding, phosphoinositide binding, intracellular signaling cascade |
PF08632 | Sporulation protein Zds1 C terminal region, suppress the calcium sensitivity of Zds1 deletions |
| PF00069, PF00169 | (1) Protein kinase domain, ATP binding, protein kinase activity, protein amino acid phosphorylation (2) PH domain |
PF00018 | SH3 domain, in a variety of proteins with enzymatic activity |
| PF00018, PF00063 | (1) SH3 domain, in a variety of proteins with enzymatic activity (2) Myosin head (motor domain), myosin, ATP binding, motor activity |
PF02205 | WH2 motif, actin-binding motif |
| PF00806, PF00076 | (1)Pumilio-family RNA binding repeat, DNA binding (2) RNA recognition motif |
PF00501 | AMP-binding enzyme, catalytic activity, metabolism |
| PF02985, PF03810 | (1) HEAT repeat, involved in intracellular transport processes (2) Importin-beta N-terminal domain, nuclear pore, nucleus, cytoplasm, protein transporter activity, protein import into nucleus, docking |
PF04096 | Nucleoporin autopeptidase, nuclear pore, transport |
| PF02178, PF00271 | (1) AT hook motif, DNA binding motifs (2) Helicase conserved C-terminal domain, ATP binding, helicase activity, nucleic acid binding |
PF00249 | Myb-like DNA-binding domain, nucleus, DNA binding |