Skip to main content

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.
Back to article page

Genome Biology

ISSN: 1474-760X

Contact us