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Table 2 Cooperative domains detected by our method from MIPS protein interaction data, where GO annotations are denoted in italic

From: Analysis on multi-domain cooperation for predicting protein-protein interactions

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