GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ras - Ras family
Pfam: PF00071 (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: CL0023
Length: 162
Sequences: 34509
Seq/Len: 213.02
HH_delta: 0.002 (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
18_R146_G2.128243.026
139_F155_E1.920772.731
81_V111_G1.654952.353
110_V141_V1.540272.190
137_P155_E1.503082.137
7_D89_N1.493032.123
76_I110_V1.481972.107
114_S140_E1.449772.062
15_L78_V1.390021.977
110_V152_I1.380221.963
78_V112_N1.370021.948
3_V72_S1.363621.939
124_V128_Q1.298161.846
114_S147_E1.236781.759
4_V16_I1.225031.742
111_G140_E1.198341.704
148_N151_E1.196061.701
141_V152_I1.190541.693
14_S143_A1.187251.688
28_Y31_T1.17731.674
108_I139_F1.146311.630
112_N143_A1.131031.608
127_A131_A1.129961.607
128_Q132_K1.044961.486
108_I155_E1.003991.428
94_L107_I0.997181.418
81_V114_S0.994261.414
4_V76_I0.992991.412
58_Q61_F0.979661.393
79_F138_Y0.958861.363
79_F109_V0.949091.350
15_L152_I0.943031.341
82_T116_L0.942111.340
95_E99_K0.938821.335
50_L157_I0.933081.327
76_I156_L0.93261.326
74_A156_L0.928261.320
120_R123_S0.923121.313
15_L149_V0.918191.306
130_F134_L0.899681.279
80_D83_D0.890341.266
125_E129_E0.890051.266
18_R149_V0.886831.261
85_E88_E0.8731.241
94_L98_Q0.860211.223
83_D86_S0.855661.217
128_Q131_A0.843331.199
151_E154_Q0.836981.190
150_K154_Q0.832421.184
89_N92_K0.827281.176
96_E99_K0.824381.172
129_E133_E0.816851.162
34_I37_Y0.814031.158
62_D65_R0.810291.152
115_D142_S0.783951.115
84_E126_E0.783921.115
74_A108_I0.780721.110
15_L143_A0.778951.108
124_V140_E0.777481.106
29_I32_I0.770331.095
96_E100_Y0.762671.085
61_F64_L0.762631.084
113_K116_L0.761881.083
123_S126_E0.758561.079
54_D57_G0.753491.071
27_N32_I0.750921.068
79_F111_G0.74831.064
92_K95_E0.747831.063
17_N21_N0.746721.062
149_V153_F0.740211.053
87_F91_K0.739981.052
151_E155_E0.737651.049
26_E30_P0.737071.048
2_I74_A0.736441.047
7_D10_V0.735181.045
92_K96_E0.734371.044
28_Y32_I0.72951.037
36_S39_K0.729351.037
127_A130_F0.727211.034
153_F156_L0.717251.020
27_N30_P0.716971.020
69_Y72_S0.713541.015
152_I156_L0.713151.014
42_S47_P0.707961.007
95_E98_Q0.704111.001
35_D38_S0.699830.995
143_A146_G0.698280.993
80_D113_K0.697450.992
120_R124_V0.696650.991
88_E91_K0.68960.981
64_L68_F0.688760.979
26_E29_I0.688660.979
111_G138_Y0.666880.948
126_E129_E0.665270.946
15_L141_V0.657760.935
76_I108_I0.654370.931
129_E132_K0.642220.913
60_R64_L0.642140.913
120_R140_E0.642120.913
64_L67_I0.636040.904
122_V126_E0.635680.904
27_N31_T0.635140.903
35_D41_V0.635110.903
32_I35_D0.634390.902
39_K43_I0.632140.899
145_N148_N0.631870.899
87_F90_L0.630310.896
109_V138_Y0.629250.895
121_E125_E0.628630.894
26_E31_T0.626990.892
154_Q157_I0.625180.889
6_G11_G0.625010.889
98_Q102_P0.621740.884
99_K102_P0.618820.880
58_Q65_R0.614040.873
139_F148_N0.613380.872
122_V125_E0.612910.872
3_V55_T0.610820.869
15_L19_L0.609470.867
86_S89_N0.606630.863
61_F65_R0.605050.860
2_I156_L0.602990.857
85_E89_N0.602570.857
38_S51_E0.600170.853
123_S127_A0.599070.852
121_E124_V0.59620.848
127_A138_Y0.594030.845
8_S58_Q0.593370.844
59_E62_D0.593190.844
19_L153_F0.59140.841
48_V157_I0.590620.840
18_R143_A0.590540.840
110_V139_F0.584750.832
32_I36_S0.584720.831
93_W96_E0.582980.829
109_V136_V0.582850.829
75_I105_I0.58240.828
67_I70_R0.582080.828
142_S145_N0.581610.827
16_I52_I0.578610.823
25_P28_Y0.572440.814
91_K95_E0.56520.804
46_K157_I0.560790.797
77_I90_L0.560440.797
74_A152_I0.557310.792
76_I152_I0.554380.788
6_G12_K0.553920.788
77_I93_W0.553690.787
79_F127_A0.549360.781
130_F133_E0.543960.774
142_S148_N0.543930.773
24_F27_N0.543670.773
65_R68_F0.538010.765
40_E49_N0.533860.759
74_A106_P0.53360.759
153_F157_I0.530070.754
17_N23_E0.528480.751
59_E65_R0.527940.751
131_A134_L0.527090.750
97_I101_K0.526910.749
112_N115_D0.525760.748
126_E130_F0.524920.746
81_V117_S0.524720.746
2_I52_I0.523290.744
2_I50_L0.522550.743
125_E128_Q0.520630.740
84_E88_E0.517720.736
91_K133_E0.517610.736
60_R65_R0.516780.735
40_E43_I0.515240.733
124_V127_A0.509760.725
62_D66_D0.507760.722
98_Q101_K0.50730.721
146_G149_V0.506740.721
13_T17_N0.504230.717
42_S49_N0.503690.716
97_I100_Y0.502580.715
32_I37_Y0.50220.714
90_L93_W0.50210.714
91_K94_L0.500340.711
7_D83_D0.498860.709
89_N93_W0.495290.704
25_P29_I0.494180.703
15_L110_V0.493440.702
137_P140_E0.491930.700
80_D112_N0.491070.698
59_E64_L0.490630.698
31_T35_D0.490320.697
139_F151_E0.487020.693
65_R69_Y0.485810.691
40_E51_E0.484490.689
144_K147_E0.481410.685
72_S75_I0.481310.684
127_A140_E0.480190.683
11_G14_S0.478150.680
90_L94_L0.477610.679
78_V141_V0.47710.678
25_P30_P0.474760.675
93_W98_Q0.474160.674
19_L52_I0.473510.673
42_S45_G0.472540.672
43_I46_K0.472130.671
34_I39_K0.471170.670
131_A138_Y0.469470.668
17_N20_I0.462270.657
147_E151_E0.460750.655
63_S66_D0.459020.653
24_F28_Y0.458960.653
31_T34_I0.454930.647
36_S53_W0.453370.645
40_E47_P0.453220.644
2_I6_G0.452670.644
35_D39_K0.450720.641
31_T36_S0.449110.639
107_I136_V0.44770.637
111_G114_S0.4470.636
29_I34_I0.446520.635
10_V13_T0.446170.634
14_S17_N0.445780.634
76_I80_D0.444350.632
28_Y35_D0.444170.632
30_P37_Y0.442520.629
147_E150_K0.440830.627
150_K153_F0.440380.626
58_Q62_D0.440190.626
45_G157_I0.436720.621
108_I152_I0.435290.619
53_W56_S0.434240.617
34_I41_V0.433390.616
44_D157_I0.431810.614
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
2ew1A199.90.002
2hupA199.90.004
2fu5C199.90.007
3l0iB199.90.008
3dz8A199.90.009
3cpjB199.90.012
4dkxA199.90.016
2a5jA199.90.016
3tklA199.90.017
2bcgY199.90.017

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