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Table 3 Strongly 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
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