Table 1 Superdomains detected by our method from MIPS protein interaction data, where GO annotations are denoted in italic

PF00488, PF05192

(1) MutS domain V, ATP binding, damaged DNA binding, mismatch repair

(2) MutS domain III, DNA metabolism

2-1-2-5-11-27-1-8-10

2-1-2-5-11-27-1

Similarity: 7

PF02775, PF00205

(1) Thiamine pyrophosphate enzyme, C-terminal TPP binding domain, catalytic activity, thiamin pyrophosphate binding

(2) Thiamine pyrophosphate enzyme, central domain, magnesium ion binding, thiamin pyrophosphate binding

1-1-2-12-1-8

1-1-2-12-1-8

Similarity: 6

PF08033, PF04810

(1) Sec23/Sec24 beta-sandwich domain

(2) Sec23/Sec24 zinc finger, COPII vesicle coat, protein binding, intracellular protein transport, ER to Golgi vesicle-mediated transport

PF03953, PF00091

(1) Tubulin/FtsZ family, C-terminal domain, protein complex, GTP binding, GTPase activity, protein polymerization

(2) Tubulin/FtsZ family, GTPase domain

PF07687, PF01546

(1) Peptidase dimerisation domain, hydrolase activity, protein dimerization activity

(2) Peptidase family M20/M25/M40, metallopeptidase activity, proteolysis

1-1-3-16

1-1-3-16-18-6

Similarity: 4

PF05000, PF00623

(1) RNA polymerase Rpb1, domain 4, DNA-directed RNA polymerase activity, DNA binding, transcription

(2) RNA polymerase Rpb1, domain 2, nucleus, DNA-directed RNA polymerase activity, DNA binding, transcription

1-1-3-39-16-3-16

1-1-3-39-16-3-16

Similarity: 7

PF08544, PF00288

(1) GHMP kinases C terminal

(2) GHMP kinases N terminal domain, ATP binding, kinase activity, phosphorylation

PF01798, PF08060

(1) Putative snoRNA binding domain

(2) NOSIC (NUC001) domain

PF02800, PF00044

(1) Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain, NAD binding, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) activity, glycolysis

(2) Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain, NAD binding, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) activity, glycolysis

2-1-2-5-11-1-4-9-1-5-1

2-1-2-5-11-1-4-9-1-5-1

Similarity: 11

PF08030, PF08022

(1) Ferric reductase NAD binding domain

(2) FAD-binding domain