Table 3.
Strongly 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 |
| PF00618, PF00018 | (1) Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif, intracellular, regulation of small GTPase mediated signal transduction (2) SH3 domain, in a variety of proteins with enzymatic activity |
PF00012 | Hsp70 protein, involved in different cellular compartments (nuclear, cytosolic, mitochondrial, endoplasmic reticulum, etc |
| PF01466, PF03931 | (1) Skp1 family, dimerisation domain (2) Skp1 family, tetramerisation domain |
PF00646 | F-box domain, mediating protein-protein interactions |
| PF04998, PF00623 | (1) RNA polymerase Rpb1, domain 5, DNA-directed RNA polymerase activity, DNA binding, transcription (2) RNA polymerase Rpb1, domain 2, nucleus, DNA-directed RNA polymerase activity, DNA binding, transcription |
PF01191 | RNA polymerase Rpb5, C-terminal domain, DNA-directed RNA polymerase activity, DNA binding, transcription |
| PF00806, PF00076 | (1) Pumilio-family RNA binding repeat, RNA binding (2) RNA recognition motif, nucleic acid binding |
PF00660 | Seripauperin and TIP1 family, response to stress |
| PF00036, PF08226 | (1) EF hand, calcium ion binding (2) Domain of unknown function (DUF1720), in different combinations with cortical patch components EF hand, SH3 and ENTH |
PF07651 | ANTH domain, phospholipid binding |
| PF00443, PF00581 | (1) Ubiquitin carboxyl-terminal hydro-lase, cysteine-type endopeptidase activity, ubiquitin thiolesterase activity, ubiquitin-dependent protein catabolism (2) Rhodanese-like domain |
PF00611 | Fes/CIP4 homology domain, regulatory processes |
| PF00620, PF00787 | (1) RhoGAP domain, intracellular, signal transduction (2) PX domain, protein binding, phos-phoinositide binding, intracellular signaling cascade |
PF08632 | Sporulation protein Zds1 C terminal region, sporulation, suppress the calcium sensitivity of Zds1 deletions |
| PF01426, PF00439 | (1) BAH domain, DNA binding, involved in protein-protein interaction (2) bromodomain, involved in protein-protein interactions |
PF00076 | RNA recognition motif, nucleic acid binding |