GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RabGAP-TBC - Rab-GTPase-TBC domain
Pfam: PF00566 (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: 214
Sequences: 2676
Seq/Len: 12.5
HH_delta: 0.085 (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
148_D210_R0.570043.410
162_P165_Y0.479632.869
51_D74_E0.477862.859
56_R91_Q0.442012.644
75_R107_E0.405822.428
183_V187_W0.364232.179
53_D56_R0.344552.061
57_T94_N0.342722.050
89_Y92_G0.3392.028
4_R8_W0.332341.988
80_Y84_N0.331031.980
100_L117_L0.328251.964
80_Y118_L0.315261.886
83_Y111_F0.313881.878
152_Y156_K0.308241.844
49_Q52_K0.305951.830
73_L97_A0.302361.809
125_F136_I0.301061.801
150_E210_R0.31.795
47_F78_S0.298921.788
53_D89_Y0.292411.749
141_E156_K0.28991.734
35_K38_N0.287271.719
72_S107_E0.281891.686
151_L154_H0.281561.684
168_P177_S0.279731.674
97_A114_F0.276021.651
93_M114_F0.275141.646
148_D207_K0.271391.624
83_Y115_V0.257921.543
142_Q145_K0.249951.495
12_L113_C0.248861.489
151_L213_I0.246821.477
50_I53_D0.246651.476
80_Y114_F0.246511.475
9_K14_I0.245541.469
209_L212_Q0.245341.468
168_P172_T0.243281.455
104_F113_C0.241631.446
53_D91_Q0.236511.415
145_K156_K0.236321.414
137_L166_A0.235111.407
170_F202_A0.234661.404
141_E161_D0.232511.391
169_W202_A0.232331.390
95_D176_R0.231311.384
169_W174_F0.225811.351
106_D109_E0.224781.345
62_F67_E0.22411.341
179_P182_D0.223471.337
145_K152_Y0.220091.317
140_F202_A0.215081.287
178_L183_V0.213131.275
207_K210_R0.212861.273
174_F202_A0.212761.273
199_F203_L0.211981.268
140_F144_L0.211581.266
35_K39_S0.209341.252
91_Q94_N0.207631.242
54_V74_E0.207621.242
84_N123_P0.207081.239
48_E52_K0.20561.230
100_L113_C0.204241.222
148_D151_L0.203491.217
168_P176_R0.200731.201
192_E200_F0.20061.200
96_I99_P0.199521.194
141_E152_Y0.197421.181
151_L206_L0.18991.136
178_L186_L0.187871.124
50_I56_R0.187791.123
143_L147_H0.187231.120
34_S37_S0.185961.113
154_H158_L0.183381.097
9_K109_E0.182541.092
195_K200_F0.182451.092
97_A110_A0.181441.085
7_V11_L0.180871.082
153_N157_Q0.177961.065
101_L110_A0.177831.064
5_G9_K0.17731.061
58_F98_A0.177091.059
114_F118_L0.176921.058
140_F170_F0.176421.055
105_L113_C0.175821.052
143_L203_L0.174751.045
140_F166_A0.174151.042
37_S40_N0.171591.027
77_L81_A0.171541.026
78_S82_K0.17111.024
192_E195_K0.170711.021
91_Q95_D0.168941.011
76_I97_A0.168661.009
4_R11_L0.168661.009
37_S41_K0.1681.005
9_K12_L0.166730.997
95_D167_F0.16590.993
154_H213_I0.165860.992
9_K113_C0.165560.990
149_P153_N0.164840.986
56_R89_Y0.164420.984
172_T177_S0.164280.983
133_L167_F0.163180.976
120_Y123_P0.162790.974
36_S40_N0.162790.974
99_P175_S0.162460.972
38_N41_K0.161790.968
4_R188_D0.161520.966
53_D57_T0.160120.958
189_F195_K0.159890.957
144_L203_L0.159420.954
172_T176_R0.158820.950
36_S39_S0.158470.948
69_N101_L0.158450.948
84_N115_V0.158150.946
50_I77_L0.157610.943
71_K75_R0.156740.938
55_N70_Q0.156730.938
3_L7_V0.15660.937
10_I15_E0.155930.933
67_E70_Q0.154930.927
58_F95_D0.15430.923
146_K153_N0.154110.922
185_R201_I0.153660.919
79_A111_F0.152920.915
53_D73_L0.152870.915
77_L94_N0.152180.910
76_I107_E0.151330.905
175_S183_V0.150850.902
84_N87_V0.150220.899
88_G91_Q0.150080.898
130_F171_L0.150070.898
62_F66_N0.149650.895
14_I116_Q0.149540.895
64_F67_E0.149490.894
130_F133_L0.148130.886
141_E162_P0.147270.881
144_L206_L0.147130.880
48_E134_Q0.145890.873
182_D186_L0.145750.872
6_Q15_E0.145520.871
53_D92_G0.145470.870
58_F175_S0.144930.867
70_Q74_E0.143660.859
92_G95_D0.143370.858
73_L89_Y0.143340.858
200_F203_L0.142830.855
154_H157_Q0.141780.848
34_S38_N0.141340.846
108_E112_W0.141050.844
72_S101_L0.140940.843
43_D82_K0.140290.839
112_W116_Q0.140190.839
57_T73_L0.138650.829
133_L137_L0.138490.829
35_K40_N0.138120.826
144_L148_D0.137430.822
68_Q72_S0.136730.818
57_T91_Q0.13660.817
89_Y94_N0.136130.814
186_L201_I0.136020.814
3_L9_K0.135740.812
56_R92_G0.134190.803
3_L6_Q0.13410.802
80_Y83_Y0.133090.796
122_L173_L0.132790.794
136_I139_I0.132790.794
147_H150_E0.132340.792
126_F133_L0.132090.790
192_E196_F0.131880.789
125_F130_F0.131840.789
6_Q9_K0.131640.788
73_L101_L0.131390.786
140_F203_L0.130780.782
167_F176_R0.130560.781
204_A208_Y0.130450.780
100_L104_F0.130280.779
57_T95_D0.130270.779
136_I199_F0.128640.770
116_Q120_Y0.127670.764
124_D132_G0.1270.760
111_F115_V0.126120.755
38_N42_L0.125830.753
191_L196_F0.125230.749
10_I13_G0.125080.748
90_C130_F0.125030.748
193_G200_F0.124870.747
50_I89_Y0.12420.743
175_S187_W0.123830.741
127_Q131_K0.123720.740
107_E111_F0.123510.739
199_F207_K0.122030.730
137_L165_Y0.121780.729
50_I58_F0.121180.725
40_N43_D0.120750.722
74_E78_S0.120560.721
150_E153_N0.120440.721
54_V59_P0.12040.720
81_A88_G0.119670.716
179_P186_L0.119610.716
205_I209_L0.119190.713
172_T175_S0.118630.710
83_Y86_D0.118590.709
9_K13_G0.11790.705
193_G203_L0.117480.703
77_L89_Y0.117350.702
145_K211_D0.117160.701
138_K141_E0.117050.700
51_D55_N0.116780.699
160_V163_E0.116720.698
118_L123_P0.116690.698
166_A169_W0.116690.698
7_V10_I0.116270.696
84_N111_F0.116080.694
80_Y111_F0.116020.694
76_I101_L0.115850.693
60_N64_F0.115460.691
155_L160_V0.115370.690
47_F82_K0.115250.690
11_L143_L0.114960.688
59_P98_A0.114610.686
76_I81_A0.114510.685
43_D46_I0.114430.685
185_R188_D0.114170.683
114_F126_F0.114130.683
67_E71_K0.113770.681
124_D127_Q0.11330.678
183_V186_L0.113270.678
57_T98_A0.113130.677
36_S41_K0.113090.677
146_K150_E0.11290.675
41_K45_K0.112660.674
90_C95_D0.112140.671
91_Q172_T0.111990.670
48_E55_N0.111970.670
8_W11_L0.111650.668
92_G96_I0.111520.667
88_G213_I0.11120.665
81_A90_C0.11110.665
190_L193_G0.110790.663
206_L210_R0.110420.661
62_F65_K0.110250.660
39_S42_L0.109860.657
133_L209_L0.109550.655
122_L125_F0.109490.655
86_D89_Y0.109480.655
165_Y169_W0.109350.654
5_G14_I0.109320.654
5_G105_L0.109020.652
148_D206_L0.108810.651
77_L90_C0.108620.650
155_L206_L0.108590.650
171_L177_S0.108390.648
178_L182_D0.108180.647
90_C93_M0.108060.646
166_A170_F0.108010.646
43_D78_S0.10760.644
91_Q171_L0.107560.643
50_I81_A0.107460.643
35_K41_K0.107440.643
50_I54_V0.107410.643
147_H207_K0.107330.642
142_Q146_K0.107220.641
198_L205_I0.107130.641
90_C122_L0.106550.637
196_F210_R0.106290.636
95_D171_L0.106160.635
145_K157_Q0.106160.635
68_Q71_K0.106090.635
35_K107_E0.105380.630
80_Y115_V0.10530.630
148_D155_L0.105260.630
52_K176_R0.10510.629
3_L14_I0.10490.628
44_N47_F0.104760.627
91_Q164_I0.104610.626
140_F169_W0.10450.625
53_D94_N0.104460.625
166_A172_T0.104130.623
76_I82_K0.103770.621
123_P132_G0.103760.621
52_K56_R0.103550.620
54_V73_L0.103280.618
117_L152_Y0.102990.616
83_Y88_G0.102940.616
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
1fkmA0.99071000.085
2qfzA0.99071000.092
3qyeA0.97661000.101
4hl4A0.92991000.103
3hzjA0.93931000.103
2qq8A0.99531000.104
3qwlA0.929999.90.312
1h2vC0.710336.80.924
4ellA0.827132.80.926
3tduA0.6215170.935

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