GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RA - Ras association (RalGDSAF-6) domain
Pfam: PF00788 (v27) Consensus Sequence
Download Alignment
(Note: includes all positions in family; we filtered this alignment to remove sites that had > 75% gaps before running GREMLIN. )
Clan: CL0072
Length: 93
Sequences: 1236
Seq/Len: 13.29
HH_delta: 0.079 (20Jul13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
62_R68_E0.45673.028
19_K40_F0.278241.845
6_R19_K0.270731.795
30_R66_D0.268651.781
52_V63_P0.229791.524
64_L70_P0.223691.483
65_D68_E0.218261.447
29_A70_P0.213611.416
32_V51_L0.21131.401
27_T31_E0.211171.400
21_I35_M0.209331.388
46_P66_D0.2061.366
37_L40_F0.202991.346
64_L73_I0.200061.327
74_Q77_W0.197181.307
18_Y39_K0.195361.295
77_W84_S0.193471.283
5_L32_V0.191191.268
8_Y85_R0.18571.231
11_D32_V0.180891.199
4_V19_K0.180181.195
24_S27_T0.180171.195
26_S69_C0.177981.180
19_K22_K0.176241.169
23_V71_L0.171431.137
86_F90_R0.170341.129
78_P84_S0.169951.127
48_D90_R0.169891.127
33_I49_Y0.169751.126
61_E89_R0.169691.125
38_E64_L0.163531.084
38_E83_N0.161081.068
28_T72_Q0.159961.061
19_K36_A0.157891.047
10_G21_I0.157831.047
20_T23_V0.157491.044
23_V32_V0.15561.032
6_R10_G0.152791.013
41_G90_R0.152491.011
7_V27_T0.151331.003
30_R72_Q0.150470.998
20_T39_K0.150140.996
49_Y67_D0.149330.990
50_C63_P0.149120.989
30_R34_E0.148880.987
21_I32_V0.147460.978
34_E45_D0.143590.952
83_N87_V0.14340.951
26_S47_S0.142380.944
58_G61_E0.139840.927
26_S72_Q0.138260.917
62_R77_W0.136970.908
61_E74_Q0.136960.908
42_L58_G0.136880.908
33_I37_L0.136340.904
42_L83_N0.136230.903
9_D37_L0.13620.903
84_S87_V0.135140.896
85_R89_R0.134640.893
9_D12_G0.13350.885
73_I76_Q0.133080.882
9_D19_K0.132790.881
34_E47_S0.132790.881
26_S31_E0.132060.876
51_L70_P0.131270.870
13_S57_S0.130610.866
9_D52_V0.130110.863
68_E71_L0.129990.862
36_A88_L0.129950.862
34_E66_D0.129850.861
50_C66_D0.129470.858
60_E76_Q0.12890.855
32_V39_K0.128570.853
8_Y51_L0.126950.842
10_G50_C0.126850.841
28_T65_D0.126670.840
31_E86_F0.126620.840
24_S38_E0.126360.838
23_V27_T0.126350.838
5_L70_P0.125910.835
52_V56_E0.125520.832
22_K37_L0.124790.827
83_N89_R0.124610.826
66_D69_C0.124570.826
44_E48_D0.124460.825
6_R40_F0.124330.824
12_G50_C0.124210.824
4_V18_Y0.123960.822
69_C73_I0.123860.821
56_E67_D0.123810.821
86_F89_R0.121950.809
83_N90_R0.121370.805
70_P75_L0.120470.799
50_C86_F0.120470.799
75_L86_F0.12020.797
69_C76_Q0.117760.781
5_L46_P0.117450.779
28_T34_E0.117240.777
50_C79_K0.116990.776
76_Q79_K0.116930.775
44_E83_N0.116880.775
72_Q88_L0.116540.773
26_S34_E0.116080.770
54_V84_S0.115620.767
36_A40_F0.115410.765
49_Y75_L0.115330.765
55_E59_G0.115250.764
9_D13_S0.11520.764
29_A64_L0.114990.762
25_S51_L0.114710.761
7_V36_A0.114620.760
36_A47_S0.114040.756
12_G46_P0.113930.755
4_V12_G0.113360.752
31_E45_D0.112820.748
27_T41_G0.112230.744
34_E67_D0.112140.744
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
1wxaA199.60.079
2m4nA199.60.121
2c5lC0.946299.30.243
3ec8A199.30.251
1wgrA0.935599.20.288
3ddcB0.935599.20.294
3tcaA0.935599.20.299
4gmvA0.935599.20.306
3hk0A0.91499.10.32
2byeA0.978599.10.342

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