Table 1

High-scoring pairs with a pw-score ≤ 0.01

Domain A

Domain B

Pfam A

Pfam B

LP-score

pw-score

GS

Diff

DPEA


IL8

7tm_1

PF00048

PF00001

1

0.0000

Yes

LSM

LSM

PF01423

PF01423

1

0.0000

Yes

Yes

Pkinase

Pkinase

PF00069

PF00069

1

0.0000

Yes

Proteasome

Proteasome

PF00227

PF00227

1

0.0000

Yes

Yes

RRM_1

RRM_1

PF00076

PF00076

1

0.0000

Yes

Yes

zf-C2H2

zf-C2H2

PF00096

PF00096

1

0.0000

Yes

Yes

WD40

Cpn60_TCP1

PF00400

PF00118

1

0.0002

Yes

Pkinase

Cyclin_N

PF00069

PF00134

1

0.0004

Yes

Yes

zf-C3HC4

UQ_con

PF00097

PF00179

1

0.0004

Yes

Yes

RRM_1

LSM

PF00076

PF01423

1

0.0019

Yes

Chitin_bind_4

Chitin_bind_4

PF00379

PF00379

1

0.0039

Yes

TNFR_c6

TNF

PF00020

PF00229

1

0.0010

Yes

Yes

PCI

PCI

PF01399

PF01399

0.999

0.0010

Yes

Ras

Hrf1

PF00071

PF03878

0.999

0.0050

Yes

HATPase_c

HATPase_c

PF02518

PF02518

0.998

0.0050

Yes

Yes

GTP_CDC

GTP_CDC

PF00735

PF00735

0.998

0.0010

Yes

Pfam-B_1

Nnf1

PB000001

PF03980

0.997

0.0070

Yes

Prefoldin

KE2

PF02996

PF01920

0.997

0.0100

Yes

Yes

C1-set

C1-set

PF07654

PF07654

0.996

0.0020

Yes

Yes

Ferritin

Ferritin

PF00210

PF00210

0.996

0.0039

Yes

Yes

SH3_1

Pfam-B_18104

PF00018

PB018104

0.995

0.0010

Yes

Adap_comp_sub

Adaptin_N

PF00928

PF01602

0.994

0.0010

Yes

Yes

Globin

Globin

PF00042

PF00042

0.991

0.0040

Yes

Yes

BTB

BTB

PF00651

PF00651

0.99

0.0090

Yes

Yes

WD40

Nrap

PF00400

PF03813

0.987

0.0090

Yes

EMP24_GP25L

EMP24_GP25L

PF01105

PF01105

0.986

0.0030

Yes

Yes

Pribosyltran

Pribosyltran

PF00156

PF00156

0.984

0.0030

Yes

Yes

Prenyltrans

PPTA

PF00432

PF01239

0.984

0.0020

Yes

Yes

Synaptobrevin

SNARE

PF00957

PF05739

0.982

0.0010

Yes

Yes

V-SNARE

SNARE

PF05008

PF05739

0.976

0.0050

Yes

Yes

bZIP

bZIP

PF00170

PF00170

0.976

0.0070

Yes

Clat_adaptor_s

Adaptin_N

PF01217

PF01602

0.974

0.0030

Yes

Yes

Hexapep

Hexapep

PF00132

PF00132

0.973

0.0060

Yes

Yes

Autotransporter

Autotransporter

PF03797

PF03797

0.97

0.0000

Yes

CK_II_beta

CK_II_beta

PF01214

PF01214

0.968

0.0020

Yes

Yes

MCM

MCM

PF00493

PF00493

0.953

0.0000

Yes

zf-U1

LSM

PF06220

PF01423

0.948

0.0080

Yes

Ribonuc_red_sm

Ribonuc_red_sm

PF00268

PF00268

0.944

0.0010

Yes

Yes

SNARE

SNARE

PF05739

PF05739

0.943

0.0000

Yes

Yes

CBFD_NFYB_HMF

CBFD_NFYB_HMF

PF00808

PF00808

0.942

0.0040

Yes

Yes

SNARE

Sec1

PF05739

PF00995

0.941

0.0020

Yes

Yes

ubiquitin

UBA

PF00240

PF00627

0.94

0.0090

Yes

IF-2B

IF-2B

PF01008

PF01008

0.94

0.0060

Yes

Yes

KH_1

KH_1

PF00013

PF00013

0.94

0.0090

Yes

Yes

Chorion_3

CBM_14

PF05387

PF01607

0.939

0.0050

Yes

SH3_1

Pfam-B_62907

PF00018

PB062907

0.936

0.0010

Yes

Clat_adaptor_s

Adap_comp_sub

PF01217

PF00928

0.935

0.0030

Yes

Yes

Bac_DNA_binding

Bac_DNA_binding

PF00216

PF00216

0.933

0.0010

Yes

Yes

Cyclin_N

CKS

PF00134

PF01111

0.933

0.0090

Yes


Columns GS, Diff, and DPEa indicate, respectively, if the pair is in the gold standard set, if it is difficult (does not have a witness), and if it was predicted among the high-confidence pairs by the DPEA method. Among these 50 predictions, only 17 are not in the gold standard set. Out of the 14 pairs that are in the difficult category, nine are confirmed by crystal structures, three have been inferred to interact in literature [28-30], and one is between a PFAM-A and a PFAM-B domain (thus no literature evidence is expected). The last one, involving cyclin and cyclin-dependent kinase regulatory subunit (CKS), has been investigated by Aloy and Russell [31], and may represent a wrong prediction introduced by an error in the high-throughput data.

Guimarães et al. Genome Biology 2006 7:R104   doi:10.1186/gb-2006-7-11-r104

Open Data