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Table 2 High-scoring partners of Ras and SNARE domains (pw-score ≤ 0.05)

From: Predicting domain-domain interactions using a parsimony approach

Domain A

Domain B

Pfam A

Pfam B

LP-score

pw-score

GS

Diff

DPEA

Ras

Yip1

PF00071

PF04893

1

0.035

  

Yes

Ras

GDI

PF00071

PF00996

1

0.037

Yes

 

Yes

Ras

Hrf1

PF00071

PF03878

0.999

0.005

  

Yes

Ras

Rho_GDI

PF00071

PF02115

0.871

0.002

Yes

 

Yes

Ras

TBC

PF00071

PF00566

0.773

0.022

 

Yes

 

Ras

Peptidase_M18

PF00071

PF02127

0.765

0.014

  

Yes

Ras

Mss4

PF00071

PF04421

0.762

0.019

 

Yes

 

Ras

PBD

PF00071

PF00786

0.711

0.013

 

Yes

 

Ras

Y_phosphatase2

PF00071

PF03162

0.677

0.027

   

Ras

IF4E

PF00071

PF01652

0.675

0.039

  

Yes

Ras

Porin_3

PF00071

PF01459

0.673

0.047

   

Ras

NAC

PF00071

PF01849

0.61

0.019

   

Ras

RasGAP

PF00071

PF00616

0.545

0.002

Yes

Yes

 

Ras

SNARE

PF00071

PF05739

0.545

0.042

 

Yes

 

Ras

PMM

PF00071

PF03332

0.528

0.007

  

Yes

Ras

Hexapep

PF00071

PF00132

0.519

0.046

   

Ras

DHO_dh

PF00071

PF01180

0.516

0.01

  

Yes

Ras

Arginase

PF00071

PF00491

0.516

0.011

  

Yes

Ras

Thi4

PF00071

PF01946

0.514

0.006

  

Yes

Ras

Pept_C1-like

PF00071

PF03051

0.514

0.01

  

Yes

Ras

AA_kinase

PF00071

PF00696

0.513

0.008

 

Yes

 

Ras

Glyco_hydro_47

PF00071

PF01532

0.513

0.025

   

Ras

Pfam-B_5516

PF00071

PB005516

0.512

0.005

   

Ras

UDPGT

PF00071

PF00201

0.512

0.045

  

Yes

Ras

Pfam-B_17923

PF00071

PB017923

0.511

0.009

  

Yes

Ras

Aminotran_3

PF00071

PF00202

0.511

0.041

   

Ras

Pfam-B_90255

PF00071

PB090255

0.51

0.006

  

Yes

Ras

F_actin_cap_B

PF00071

PF01115

0.509

0.026

  

Yes

Ras

dUTPase

PF00071

PF00692

0.508

0.032

  

Yes

Ras

Cpn10

PF00071

PF00166

0.507

0.021

  

Yes

Ras

NIF3

PF00071

PF01784

0.505

0.02

  

Yes

Ras

NDK

PF00071

PF00334

0.505

0.025

  

Yes

Ras

ALAD

PF00071

PF00490

0.503

0.003

  

Yes

Ras

Pfam-B_52661

PF00071

PB052661

0.501

0.01

  

Yes

Ras

Pfam-B_99124

PF00071

PB099124

0.501

0.012

  

Yes

SNARE

Synaptobrevin

PF05739

PF00957

0.982

0.001

Yes

Yes

 

SNARE

V-SNARE

PF05739

PF05008

0.976

0.005

Yes

Yes

 

SNARE

SNARE

PF05739

PF05739

0.943

0

Yes

Yes

 

SNARE

Sec1

PF05739

PF00995

0.941

0.002

Yes

Yes

 

SNARE

Adaptin_N

PF05739

PF01602

0.858

0.003

 

Yes

 

SNARE

MAP1_LC3

PF05739

PF02991

0.596

0.001

 

Yes

 

SNARE

Ras

PF05739

PF00071

0.545

0.042

 

Yes

 

SNARE

Prenyltrans

PF05739

PF00432

0.518

0.005

  

Yes

  1. Prediction of Ras and SNARE interactions with a LP-score ≥ 0.5 and a pw-score ≤ 0.05. Out of 35 putative Ras interactions, six are difficult, three (among them one difficult) are documented by a crystal structure. More than 70% of easy predictions belong to the high-confidence DPEA predictions. The interaction between Ras and Mss4 is known from literature, with the caveat discussed in the text. All but one of our predictions of SNARE interactions are in the difficult category. Of the predictions above a LP-score of 0.6, all but one are documented with crystal structure. 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.
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Genome Biology

ISSN: 1474-760X

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