Table 2 |
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|
High-scoring partners of Ras and SNARE domains (pw-score ≤ 0.05) |
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|
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. |
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|
Guimarães et al. Genome Biology 2006 7:R104 doi:10.1186/gb-2006-7-11-r104 |
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