Table 2

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

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