GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RhoGEF - RhoGEF domain
Pfam: PF00621 (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. )
Length: 180
Sequences: 2736
Seq/Len: 15.2
HH_delta: -0.053 (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
10_R61_E0.698523.826
63_R75_D0.649723.558
15_D135_K0.532352.916
17_E54_Q0.420952.305
8_T139_R0.409492.243
5_L150_L0.386722.118
13_V53_H0.371952.037
134_I138_Q0.370982.032
135_K142_R0.3631.988
156_P161_Y0.357991.961
17_E50_I0.346331.897
59_S79_K0.340141.863
128_S131_S0.330881.812
12_Y16_L0.322661.767
149_R152_K0.320531.755
4_E9_E0.313641.718
148_K172_K0.311761.707
4_E8_T0.309871.697
142_R145_L0.306781.680
24_L28_R0.304221.666
141_P144_P0.302061.654
23_F124_S0.295471.618
74_G167_A0.294911.615
114_F118_I0.293111.605
138_Q141_P0.287761.576
9_E12_Y0.286481.569
165_Q169_D0.284271.557
90_Y136_P0.284011.555
144_P172_K0.283011.550
35_S38_E0.282241.546
141_P175_I0.277471.520
4_E138_Q0.273291.497
139_R143_Y0.269911.478
163_S166_K0.269121.474
151_L161_Y0.26891.473
9_E16_L0.266981.462
57_L61_E0.256911.407
155_P158_H0.254891.396
77_F147_L0.254291.393
59_S62_E0.253611.389
140_L178_I0.252821.385
13_V50_I0.2511.375
144_P148_K0.248671.362
111_F115_L0.245971.347
63_R76_I0.239871.314
138_Q146_L0.235341.289
104_L111_F0.234611.285
74_G160_D0.233731.280
147_L164_L0.233131.277
12_Y87_Y0.229751.258
21_E25_K0.225261.234
87_Y90_Y0.222551.219
94_Y98_L0.220611.208
19_L46_I0.219451.202
161_Y165_Q0.218111.195
9_E143_Y0.217751.193
38_E104_L0.217671.192
53_H57_L0.217571.192
131_S134_I0.216831.188
151_L164_L0.216251.184
91_C137_I0.215811.182
45_N48_E0.211681.159
6_I60_L0.209221.146
129_L136_P0.208351.141
138_Q145_L0.206921.133
4_E145_L0.205181.124
134_I137_I0.204711.121
28_R47_E0.203431.114
24_L47_E0.201931.106
7_E11_S0.201161.102
28_R39_I0.200971.101
44_G93_N0.200631.099
104_L108_N0.21.095
11_S15_D0.199861.095
94_Y137_I0.199571.093
139_R145_L0.199541.093
53_H87_Y0.198741.088
72_S163_S0.19831.086
81_E84_L0.197461.081
50_I54_Q0.196021.074
171_I174_L0.195271.069
20_V50_I0.192181.053
168_L172_K0.190991.046
149_R153_N0.19011.041
93_N97_A0.189051.035
87_Y136_P0.187651.028
116_E120_N0.186511.021
13_V57_L0.186381.021
91_C141_P0.182040.997
129_L133_L0.181360.993
137_I141_P0.181330.993
25_K29_K0.181160.992
44_G90_Y0.180710.990
141_P145_L0.179440.983
154_T158_H0.175960.964
162_K165_Q0.175960.964
49_L53_H0.175740.962
15_D125_K0.175520.961
3_N7_E0.174470.956
22_V118_I0.17420.954
43_F46_I0.173530.950
85_K177_H0.173480.950
23_F119_E0.171990.942
151_L165_Q0.171430.939
133_L136_P0.170420.933
42_L101_L0.169740.930
162_K166_K0.1690.926
8_T138_Q0.168630.924
17_E21_E0.168110.921
165_Q168_L0.16790.920
91_C144_P0.167830.919
124_S127_L0.16730.916
62_E66_E0.166940.914
4_E16_L0.166830.914
143_Y146_L0.165780.908
43_F129_L0.164870.903
152_K179_N0.161460.884
115_L119_E0.161290.883
93_N96_D0.159760.875
101_L111_F0.159720.875
145_L179_N0.159420.873
12_Y53_H0.159410.873
139_R146_L0.15910.871
170_Q173_E0.158970.871
140_L144_P0.158930.870
151_L168_L0.158370.867
150_L154_T0.158350.867
147_L171_I0.157990.865
109_S112_K0.157940.865
88_I177_H0.157670.864
103_E107_K0.15710.860
127_L131_S0.15660.858
53_H139_R0.156260.856
132_L136_P0.15510.849
26_P114_F0.154820.848
56_L60_L0.15470.847
167_A171_I0.154360.845
8_T12_Y0.153830.842
94_Y134_I0.153580.841
136_P139_R0.153430.840
46_I50_I0.151790.831
75_D79_K0.151590.830
40_K89_S0.151270.828
5_L77_F0.150990.827
34_L38_E0.150940.827
147_L168_L0.150320.823
6_I10_R0.149950.821
127_L134_I0.14960.819
138_Q142_R0.149390.818
4_E142_R0.148860.815
154_T164_L0.148720.814
5_L9_E0.148330.812
78_L166_K0.14820.812
140_L175_I0.145790.798
53_H56_L0.145740.798
18_I132_L0.145050.794
137_I145_L0.144680.792
105_R112_K0.142260.779
4_E146_L0.142020.778
48_E85_K0.141890.777
46_I49_L0.141420.775
100_L104_L0.141310.774
169_D173_E0.141190.773
74_G154_T0.140580.770
124_S132_L0.140320.768
41_S100_L0.140240.768
116_E119_E0.139510.764
114_F117_E0.13940.763
155_P173_E0.139040.761
18_I23_F0.138770.760
52_I56_L0.138660.759
2_I70_I0.13820.757
144_P171_I0.137980.756
2_I73_I0.13780.755
37_D82_P0.137610.754
72_S75_D0.137090.751
20_V46_I0.136660.748
108_N111_F0.136630.748
141_P178_I0.136630.748
157_D166_K0.136490.748
60_L73_I0.136280.746
8_T11_S0.136070.745
103_E106_K0.135910.744
166_K169_D0.135840.744
151_L154_T0.135270.741
105_R130_S0.134980.739
137_I149_R0.134510.737
49_L86_V0.134510.737
173_E176_Q0.134240.735
5_L146_L0.134040.734
19_L49_L0.13370.732
10_R57_L0.132570.726
148_K152_K0.131210.719
23_F27_L0.131120.718
138_Q179_N0.130840.717
87_Y111_F0.130510.715
80_F83_F0.130440.714
156_P165_Q0.130250.713
43_F74_G0.130150.713
89_S92_S0.12970.710
26_P118_I0.128840.706
44_G133_L0.128710.705
63_R66_E0.128550.704
38_E100_L0.127070.696
112_K116_E0.126430.692
64_M67_W0.125430.687
131_S138_Q0.125430.687
147_L167_A0.125280.686
22_V125_K0.124820.684
171_I175_I0.124810.684
74_G164_L0.124730.683
45_N89_S0.124570.682
12_Y136_P0.124460.682
19_L129_L0.124230.680
88_I92_S0.124030.679
100_L103_E0.123980.679
173_E177_H0.123840.678
45_N97_A0.123830.678
120_N124_S0.12290.673
2_I67_W0.122230.669
136_P140_L0.122090.669
14_E166_K0.1220.668
4_E12_Y0.121980.668
3_N150_L0.121670.666
119_E137_I0.120740.661
36_E40_K0.120490.660
2_I9_E0.119740.656
126_R131_S0.11950.654
169_D172_K0.118630.650
44_G179_N0.118560.649
9_E13_V0.118320.648
52_I86_V0.118130.647
2_I6_I0.11750.644
94_Y141_P0.117440.643
42_L100_L0.117390.643
67_W73_I0.117370.643
62_E65_K0.117340.643
127_L135_K0.117330.643
53_H72_S0.117180.642
101_L105_R0.116520.638
111_F119_E0.116510.638
36_E112_K0.116380.637
16_L50_I0.116230.637
98_L102_E0.11620.636
145_L152_K0.116180.636
23_F118_I0.11550.633
67_W71_Q0.115430.632
33_L38_E0.115410.632
128_S132_L0.115290.631
139_R142_R0.115090.630
74_G158_H0.115080.630
72_S160_D0.115070.630
26_P29_K0.114990.630
142_R175_I0.11490.629
78_L167_A0.114230.626
35_S104_L0.114070.625
77_F171_I0.113890.624
24_L39_I0.113780.623
94_Y144_P0.113520.622
130_S150_L0.11350.622
19_L95_P0.113470.621
8_T146_L0.113430.621
59_S80_F0.112940.619
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
2z0qA0.9889100-0.053
1xcgA0.9944100-0.041
3mpxA1100-0.036
2dfkA0.9944100-0.032
3t06A0.9944100-0.03
1by1A0.9722100-0.027
2pz1A0.9944100-0.027
3jzyA0.9944100-0.027
2vrwB0.9722100-0.025
3jv3A0.9944100-0.025

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