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Table 1 High-confidence inferred domain interactions

From: Inferring protein domain interactions from databases of interacting proteins

Domain I     Domain j     Inferred interaction
Pfam ID i Pfam accession i n i m i Pfam ID j Pfam accession j n j m j S ij θ ij E ij Domains interact in PDB Organisms providing evidence
LSM PF01423 33 1.0 LSM PF01423 33 1.0 0.18 0.174 387 x Ce, Dm, Ec, Sc
IL8 PF00048 34 1.6 7tm_1 PF00001 44 1.7 0.12 0.070 139   Hs, Mm
Proteasome PF00227 37 1.2 Proteasome PF00227 37 1.2 0.076 0.060 103 x Dm, Ec, Sc
Ferritin PF00210 9 1.0 Ferritin PF00210 9 1.0 0.35 0.360 47 x Ce, Dm, Ec, Hp
Globin PF00042 9 1.2 Globin PF00042 9 1.2 0.37 0.381 42 x Ai, Hs
EMP24_GP25L PF01105 6 1.0 EMP24_GP25L PF01105 6 1.0 0.33 0.350 35   Sc
CK_II_beta PF01214 6 1.0 CK_II_beta PF01214 6 1.0 0.63 0.600 32 x Hs, Oc, Sc
Zf-C3HC4 PF00097 108 3.9 UQ_con PF00179 39 1.1 0.017 0.011 29 x Ce, Dm, Hs, Sc
WD40 PF00400 207 3.1 Cpn60_TCP1 PF00118 24 1.5 0.041 0.010 28   Dm, Sc
Cofilin_ADF PF00241 9 1.9 Actin PF00022 28 1.4 0.11 0.092 27   Dm, Sc
Ras PF00071 69 1.8 Hrf1 PF03878 1 1.0 0.44 0.279 23   Sc
Lsm_interact PF05391 1 2.0 LSM PF01423 33 1.0 0.38 0.386 23   Sc
Pkinase PF00069 399 3.7 Cyclin_N PF00134 42 2.4 0.013 0.006 23 x Ce, Dm, Hs, Mm, Sc, Sp
Bac_DNA_binding PF00216 4 1.0 Bac_DNA_binding PF00216 4 1.0 0.25 0.278 23 x Ec
IF-2B PF01008 7 1.0 IF-2B PF01008 7 1.0 0.24 0.263 22   Sc
Clat_adaptor_s PF01217 6 1.2 Adap_comp_sub PF00928 8 2.2 0.20 0.227 22 x Sc
Y_phosphatase2 PF03162 5 1.0 Y_phosphatase2 PF03162 5 1.0 0.16 0.185 21   Sc
LSM PF01423 33 1.0 DIM1 PF02966 2 1.0 0.138 0.161 20   Sc
Zf-U1 PF06220 2 1.0 LSM PF01423 33 1.0 0.138 0.161 20   Sc
Chorion_3 PF05387 2 1.0 CBM_14 PF01607 20 1.7 0.133 0.156 20   Dm
P5CR PF01089 3 1.0 P5CR PF01089 3 1.0 1.000 0.800 20   Dm, Hp, Sc
Tektin PF03148 3 1.0 gamma-BBH PF03322 3 1.0 1.000 0.800 20   Dm
P-II PF00543 2 1.0 P-II PF00543 2 1.0 0.750 0.667 20 x Ec
HSP20 PF00011 18 1.2 HSP20 PF00011 18 1.2 0.041 0.048 19   Ce, Dm, Sc
Pfam-B_9658 PB009658 1 2.0 Histone PF00125 19 1.8 0.571 0.555 19   Sc
TRAPP_Bet3 PF04051 4 1.0 Sybindin PF04099 3 1.0 0.600 0.571 19   Ce, Sc
IF-2B PF01008 7 1.0 DUF292 PF03398 2 1.0 0.600 0.571 19   Sc
Prenyltrans PF00432 7 1.6 PPTA PF01239 6 2.2 0.583 0.441 19 x Dm, Rn, Sc
Glycogen_syn PF05693 4 1.0 Glycogen_syn PF05693 4 1.0 0.500 0.500 19   Sc
CBFD_NFYB_HMF PF00808 13 1.4 CBFD_NFYB_HMF PF00808 13 1.4 0.109 0.097 19 x Dm, Rn, Sc
Ras PF00071 69 1.8 GDI PF00996 5 1.2 0.165 0.077 18   Mm, Sc
Cpn60_TCP1 PF00118 24 1.5 Cpn60_TCP1 PF00118 24 1.5 0.035 0.035 18 x Dm, Ec, Sc, Ta
Porin_1 PF00267 3 1.0 Porin_1 PF00267 3 1.0 0.333 0.364 18 x Ec
PNP_UDP_1 PF01048 3 1.0 PNP_UDP_1 PF01048 3 1.0 0.333 0.364 18 x Ec
Prefoldin PF02996 10 1.6 KE2 PF01920 10 1.3 0.323 0.237 18 x Ce, Dm, Sc
Yip1 PF04893 4 1.0 Ras PF00071 69 1.8 0.143 0.069 17   Sc
Autotransporter PF03797 5 3.2 Autotransporter PF03797 5 3.2 0.412 0.278 17   Ec, Hp
Chitin_bind_4 PF00379 35 1.3 Chitin_bind_4 PF00379 35 1.3 0.007 0.008 17   Dm
ATP_bind_1 PF03029 5 1.0 ATP_bind_1 PF03029 5 1.0 0.231 0.267 17   Ce, Sc
UQ_con PF00179 39 1.1 Ubiquitin PF00240 42 2.3 0.013 0.015 16   Hs, Sc
Pkinase PF00069 399 3.7 CK_II_beta PF01214 6 1.0 0.015 0.015 16 x Dm, Hs, Sc
Ribosomal_S28e PF01200 1 1.0 LSM PF01423 33 1.0 0.188 0.222 16   Sc
Proteasome PF00227 37 1.2 Pfam-B_57010 PB057010 2 3.0 0.464 0.434 16   Sc
RRM_1 PF00076 179 2.5 Pfam-B_4884 PB004884 3 1.3 0.049 0.038 16   Dm, Sc
Profilin PF00235 3 1.0 Actin PF00022 28 1.4 0.150 0.182 16   Bt, Dm, Sc
Adap_comp_sub PF00928 8 2.2 Adaptin_N PF01602 17 2.6 0.182 0.122 15 x Sc
vATP-synt_AC39 PF01992 2 1.0 adh_short PF00106 30 1.3 0.125 0.154 15   Sc
Rho_GDI PF02115 1 1.0 Ras PF00071 69 1.8 0.120 0.148 15 x Sc
Pfam-B_4092 PB004092 1 2.0 LIM PF00412 37 2.4 0.238 0.257 15   Dm
ADH_zinc_N PF00107 29 1.6 ADH_zinc_N PF00107 29 1.6 0.016 0.019 15 x Ec, Sc
  1. Domain pairs are ranked by their E score. For domain i, n i is the number of DIP proteins that contain domain i; m i is the average number of domains in a protein that contains domain i. Domain pairs known to interact in PDB complexes are marked with an 'x'. Organisms whose protein interaction data provided evidence for each domain interaction are given. Ai, Anser indicus (Bar-headed goose); Bt, Bos taurus; Ce, Caenorhabditis elegans; Dm, Drosophila melanogaster, Ec, Escherichia coli; Hp, Helicobacter pylori 26695; Hs, Homo sapiens; Mm, Mus musculus; Oc, Oryctolagus cuniculus; Rn, Rattus norvegicus; Sc, Saccharomyces cerevisiae; Sp, Schizosaccharomyces pombe; Ta, Thermoplasma acidophilum.