GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AAA_6 - Hydrolytic ATP binding site of dynein motor region D1
Pfam: PF12774 (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: 231
Sequences: 15534
Seq/Len: 67.25
HH_delta: 0.013 (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
121_S130_K1.596233.419
122_F133_P1.440713.086
25_L48_T1.4223.046
123_T130_K1.414263.029
89_C140_T1.370452.935
121_S132_N1.171622.509
40_P170_S1.113682.385
66_S102_S1.031042.208
127_Q131_L1.010712.165
176_L200_K1.00882.161
38_S163_A0.962392.061
22_F25_L0.960132.056
211_F219_V0.95882.054
196_F199_C0.942822.019
33_L221_R0.9321.996
95_R143_P0.924671.980
199_C203_L0.906181.941
50_K62_V0.889841.906
109_Q217_K0.879591.884
179_S220_L0.854841.831
23_L26_T0.849031.818
46_T106_Q0.833931.786
48_T166_V0.827191.772
38_S165_M0.819341.755
85_G134_N0.805841.726
207_D211_F0.779811.670
172_I175_I0.77111.652
122_F132_N0.752981.613
176_L207_D0.748711.604
28_A162_V0.743651.593
22_F48_T0.741941.589
94_N141_M0.733251.570
146_A149_S0.731161.566
96_L100_V0.716361.534
176_L179_S0.713551.528
172_I176_L0.712881.527
66_S95_R0.68261.462
195_L220_L0.682211.461
154_N158_L0.662961.420
75_S82_A0.662691.419
217_K221_R0.657891.409
168_D171_L0.653251.399
124_L127_Q0.639411.370
174_E200_K0.631891.353
124_L131_L0.626081.341
139_I159_F0.624431.337
84_S133_P0.616821.321
209_Y215_A0.615641.319
107_Q122_F0.610821.308
201_E208_H0.589651.263
179_S195_L0.587811.259
33_L188_L0.584561.252
180_Q200_K0.580611.244
154_N157_A0.578261.239
195_L199_C0.577741.237
171_L174_E0.576181.234
197_Q201_E0.576011.234
195_L200_K0.574051.230
172_I210_D0.565971.212
70_D99_E0.565581.211
34_G120_K0.56431.209
173_A178_L0.560181.200
71_Y74_L0.555581.190
36_A139_I0.549631.177
53_A171_L0.541841.161
94_N142_N0.5381.152
108_I137_I0.536461.149
40_P43_T0.535921.148
197_Q200_K0.535491.147
84_S134_N0.53121.138
219_V223_A0.530681.137
43_T166_V0.528361.132
62_V106_Q0.522281.119
37_L49_I0.519491.113
175_I179_S0.51611.105
46_T62_V0.509581.091
203_L219_V0.5051.082
200_K207_D0.50351.078
75_S83_Q0.499371.070
173_A207_D0.497011.065
220_L223_A0.495461.061
60_V86_A0.4941.058
120_K132_N0.492971.056
65_C90_F0.490131.050
76_R81_L0.485911.041
151_L156_K0.483551.036
22_F26_T0.48241.033
152_P156_K0.480891.030
33_L161_P0.480091.028
78_L81_L0.478191.024
152_P155_L0.47811.024
72_Q75_S0.475331.018
32_N187_S0.474061.015
46_T91_D0.471761.010
190_K193_V0.471151.009
199_C202_Q0.464080.994
69_M74_L0.463790.993
208_H211_F0.461910.989
70_D75_S0.460370.986
37_L48_T0.457440.980
22_F51_D0.447570.959
122_F131_L0.446950.957
201_E207_D0.445520.954
92_E142_N0.445270.954
174_E178_L0.444050.951
58_R85_G0.443670.950
87_W138_F0.441710.946
69_M125_E0.437760.938
176_L180_Q0.437140.936
151_L155_L0.435680.933
123_T128_E0.435280.932
88_L137_I0.433570.929
156_K160_R0.433540.929
160_R163_A0.43310.928
179_S223_A0.430830.923
186_K190_K0.43030.922
110_S121_S0.429370.920
187_S221_R0.42810.917
189_A192_L0.427590.916
171_L175_I0.424720.910
94_N143_P0.4230.906
24_T27_Q0.419180.898
64_N95_R0.417680.895
172_I177_L0.417650.895
106_Q110_S0.412120.883
100_V103_V0.408640.875
106_Q109_Q0.40670.871
198_L201_E0.406340.870
198_L202_Q0.404070.865
105_S109_Q0.402260.862
23_L27_Q0.402150.861
110_S120_K0.400420.858
172_I179_S0.400080.857
173_A176_L0.39650.849
77_I81_L0.392010.840
70_D97_S0.390140.836
53_A60_V0.389860.835
75_S79_K0.389850.835
99_E103_V0.389430.834
152_P157_A0.389330.834
207_D210_D0.388280.832
55_A134_N0.386440.828
70_D103_V0.385790.826
151_L154_N0.385030.825
149_S153_E0.383770.822
140_T147_G0.383290.821
64_N67_E0.382490.819
68_Q73_S0.379010.812
36_A141_M0.37630.806
76_R79_K0.375130.803
170_S174_E0.373810.801
95_R142_N0.373630.800
62_V123_T0.372350.798
169_L175_I0.371780.796
75_S78_L0.371470.796
49_I140_T0.370670.794
53_A56_L0.37040.793
187_S217_K0.369880.792
24_T162_V0.369520.791
40_P168_D0.368480.789
104_I107_Q0.367850.788
188_L192_L0.367350.787
164_M167_P0.365840.784
60_V89_C0.363780.779
84_S135_C0.36310.778
186_K189_A0.356550.764
168_D172_I0.354910.760
94_N145_Y0.350940.752
36_A167_P0.350850.751
145_Y169_L0.350740.751
88_L107_Q0.348720.747
64_N96_L0.348170.746
153_E157_A0.347330.744
199_C223_A0.346450.742
213_L216_L0.346320.742
161_P218_S0.345890.741
49_I89_C0.345020.739
127_Q130_K0.343760.736
180_Q194_S0.343310.735
75_S84_S0.342770.734
92_E158_L0.342760.734
179_S200_K0.33960.727
175_I178_L0.339530.727
122_F130_K0.336990.722
47_E51_D0.336290.720
123_T127_Q0.3360.720
149_S156_K0.334470.716
64_N92_E0.33360.715
202_Q219_V0.333580.714
25_L51_D0.333410.714
38_S94_N0.332920.713
92_E214_R0.332080.711
145_Y151_L0.331660.710
42_G214_R0.328180.703
34_G139_I0.327540.702
168_D178_L0.326620.700
191_K194_S0.324320.695
153_E156_K0.319990.685
138_F154_N0.318920.683
160_R222_M0.31860.682
77_I125_E0.317910.681
170_S173_A0.316740.678
169_L178_L0.31470.674
120_K135_C0.314240.673
196_F200_K0.313610.672
43_T47_E0.311960.668
70_D73_S0.310920.666
41_A94_N0.310570.665
93_F139_I0.309690.663
177_L180_Q0.309610.663
154_N159_F0.309060.662
41_A95_R0.308940.662
49_I60_V0.308140.660
151_L157_A0.308120.660
171_L178_L0.30770.659
69_M72_Q0.307480.659
67_E70_D0.305230.654
192_L195_L0.304970.653
93_F101_L0.303310.650
49_I138_F0.301380.646
35_G52_L0.301220.645
74_L77_I0.300820.644
51_D54_R0.299590.642
131_L167_P0.2990.640
47_E50_K0.298570.639
149_S154_N0.298310.639
169_L176_L0.297450.637
39_G42_G0.297370.637
155_L158_L0.296810.636
62_V65_C0.29670.635
169_L173_A0.295650.633
39_G45_K0.294410.631
162_V222_M0.291570.624
22_F166_V0.291190.624
135_C158_L0.290630.622
202_Q207_D0.290060.621
176_L216_L0.290040.621
168_D179_S0.289510.620
61_V86_A0.287820.616
59_F86_A0.286850.614
137_I159_F0.284590.610
50_K110_S0.284430.609
91_D140_T0.283970.608
32_N55_A0.283830.608
33_L162_V0.283330.607
156_K161_P0.282950.606
202_Q208_H0.282090.604
64_N90_F0.281670.603
212_G215_A0.28140.603
165_M171_L0.278620.597
163_A222_M0.278360.596
25_L30_S0.278190.596
66_S69_M0.278130.596
168_D173_A0.277980.595
172_I207_D0.277170.594
94_N140_T0.275180.589
36_A93_F0.274810.589
148_R152_P0.274160.587
101_L108_I0.272720.584
188_L191_K0.272110.583
170_S201_E0.271980.583
170_S175_I0.271050.581
62_V121_S0.270680.580
211_F215_A0.269430.577
75_S81_L0.267760.573
95_R104_I0.267660.573
25_L52_L0.266730.571
25_L164_M0.266610.571
79_K83_Q0.266480.571
46_T110_S0.265630.569
44_G91_D0.265280.568
38_S142_N0.264560.567
80_G83_Q0.264230.566
37_L164_M0.264120.566
172_I213_L0.263840.565
91_D214_R0.26320.564
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
3vkgA11000.013
4akgA11000.036
1ojlA0.917799.90.389
2bjvA0.939499.80.411
4akgA0.991399.80.431
3pxiA0.956799.80.444
3vkgA0.991399.80.445
3dzdA0.956799.80.449
1ny5A0.952499.80.449
3pfiA0.922199.80.45

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