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 |
||||||||
