GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Pkinase - Protein kinase domain
Pfam: PF00069 (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: CL0016
Length: 260
Sequences: 56673
Seq/Len: 217.97
HH_delta: -0.207 (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
242_S247_Q3.022143.645
104_A189_L2.698193.254
130_L140_I2.525673.046
17_K26_K2.314752.792
5_K17_K2.296522.770
6_K14_T2.192662.645
112_A116_S2.058982.483
20_N23_N2.010962.426
18_A29_V1.950762.353
112_A252_E1.945272.346
182_I240_M1.915562.310
239_K249_P1.904752.297
56_R62_Q1.868012.253
18_A27_V1.867152.252
6_K9_S1.8122.186
86_Q127_E1.742572.102
108_L185_L1.716032.070
111_L185_L1.671492.016
106_Q136_E1.647521.987
78_E138_K1.635841.973
107_I129_I1.623941.959
57_H113_Y1.622621.957
132_D136_E1.609841.942
81_P133_E1.605791.937
17_K79_Y1.59141.919
244_D247_Q1.589151.917
96_S99_E1.549311.869
64_L78_E1.545351.864
19_K26_K1.488641.796
125_K161_T1.469131.772
106_Q137_V1.450211.749
186_G240_M1.424651.718
84_S87_D1.414311.706
166_A180_S1.377451.661
124_I188_I1.371191.654
108_L254_L1.367721.650
62_Q78_E1.360151.641
132_D138_K1.349861.628
193_L233_L1.318551.590
6_K16_Y1.308141.578
29_V76_V1.307091.577
112_A255_L1.285171.550
182_I251_A1.281571.546
160_G165_M1.274131.537
110_A139_L1.273811.536
129_I137_V1.25111.509
240_M254_L1.249811.507
100_I193_L1.244621.501
119_I145_S1.241921.498
104_A192_L1.236461.491
249_P254_L1.216211.467
104_A185_L1.213531.464
80_C132_D1.211191.461
59_N109_E1.210261.460
111_L124_I1.19491.441
105_Y109_E1.193371.439
250_S253_E1.191721.437
116_S252_E1.191541.437
164_Y191_E1.167091.408
189_L236_L1.137681.372
59_N110_A1.123731.355
27_V76_V1.11771.348
129_I188_I1.111051.340
102_K106_Q1.104131.332
111_L251_A1.103171.331
31_I72_Y1.097411.324
100_I192_L1.092861.318
179_K250_S1.084081.308
25_Q64_L1.076171.298
9_S14_T1.076041.298
118_G178_R1.068091.288
86_Q90_Q1.067021.287
126_P188_I1.062091.281
126_P164_Y1.050921.268
80_C138_K1.042541.257
235_D239_K1.039961.254
113_Y117_K1.038521.253
237_I241_L1.03691.251
15_V28_A1.026861.239
251_A254_L1.024751.236
236_L240_M1.0241.235
123_D128_N1.01731.227
234_R238_K1.015931.225
210_I214_I0.994151.199
103_I137_V0.967161.167
19_K24_G0.964431.163
214_I217_R0.957651.155
239_K242_S0.950081.146
67_F76_V0.945421.140
31_I74_Y0.941191.135
166_A169_V0.937581.131
61_V77_M0.934721.127
61_V80_C0.930441.122
115_H251_A0.928061.119
16_Y31_I0.926591.118
108_L255_L0.924191.115
86_Q191_E0.924111.115
20_N25_Q0.916311.105
26_K79_Y0.913991.102
54_R117_K0.900551.086
236_L254_L0.899591.085
63_I66_V0.895841.081
122_R176_Y0.895491.080
121_H124_I0.893821.078
61_V140_I0.889311.073
108_L251_A0.885761.068
171_Q174_K0.88561.068
185_L240_M0.883991.066
187_I241_L0.878481.060
107_I188_I0.871451.051
109_E112_A0.869841.049
27_V64_L0.865071.043
10_G13_G0.864111.042
89_L191_E0.862471.040
122_R159_V0.862131.040
109_E255_L0.853261.029
29_V74_Y0.851891.027
191_E197_L0.851671.027
48_E51_I0.84561.020
176_Y180_S0.843121.017
63_I75_I0.840611.014
111_L115_H0.837571.010
51_I145_S0.837031.010
88_Y95_L0.834521.007
236_L249_P0.817580.986
60_I114_L0.817230.986
206_D209_E0.816730.985
209_E213_K0.813080.981
124_I139_L0.81250.980
242_S249_P0.809370.976
112_A251_A0.80870.975
80_C130_L0.807030.973
128_N141_D0.806010.972
169_V180_S0.805860.972
183_W187_I0.805510.972
213_K217_R0.799250.964
126_P191_E0.797070.961
239_K253_E0.793510.957
185_L189_L0.793210.957
144_S159_V0.7910.954
82_G135_G0.789220.952
54_R147_K0.777420.938
102_K136_E0.776390.936
210_I213_K0.773830.933
125_K128_N0.768730.927
95_L103_I0.766970.925
28_A79_Y0.766550.925
114_L119_I0.764270.922
34_K68_Q0.759040.916
207_Q210_I0.758770.915
88_Y131_L0.758420.915
105_Y255_L0.758210.915
107_I124_I0.758160.914
99_E102_K0.757670.914
97_E100_I0.755540.911
114_L142_F0.754010.909
216_K219_L0.752010.907
7_L79_Y0.748950.903
187_I197_L0.744770.898
107_I137_V0.742910.896
42_R45_N0.741240.894
190_Y194_T0.740330.893
211_I214_I0.74020.893
26_K81_P0.737460.889
187_I191_E0.730270.881
207_Q214_I0.730010.880
183_W241_L0.728560.879
55_L119_I0.725040.875
63_I77_M0.721920.871
107_I110_A0.713650.861
113_Y116_S0.712910.860
119_I147_K0.71210.859
219_L222_S0.711990.859
67_F74_Y0.711470.858
212_E216_K0.704390.850
97_E101_L0.703730.849
52_L63_I0.700040.844
101_L233_L0.698880.843
48_E52_L0.697440.841
56_R113_Y0.697060.841
179_K246_E0.696870.841
231_E234_R0.693880.837
182_I254_L0.693550.837
231_E235_D0.691760.834
206_D214_I0.685880.827
120_V176_Y0.684780.826
59_N106_Q0.681210.822
186_G241_L0.680540.821
210_I217_R0.680180.820
219_L223_S0.679390.819
210_I216_K0.678470.818
20_N27_V0.676830.816
196_K200_E0.674490.814
80_C140_I0.672880.812
84_S127_E0.672080.811
49_I66_V0.670870.809
8_G15_V0.668530.806
207_Q211_I0.66640.804
206_D210_I0.665030.802
18_A76_V0.664770.802
80_C131_L0.662650.799
41_E44_E0.660870.797
107_I185_L0.660550.797
81_P132_D0.659760.796
57_H60_I0.656130.791
168_E180_S0.65530.790
103_I131_L0.654920.790
185_L251_A0.654510.789
88_Y99_E0.653960.789
251_A255_L0.652970.788
99_E135_G0.651640.786
86_Q126_P0.65130.786
83_G140_I0.648370.782
62_Q138_K0.647710.781
38_E41_E0.644710.778
89_L192_L0.638360.770
249_P253_E0.637370.769
186_G237_I0.634910.766
158_F165_M0.633640.764
187_I190_Y0.632170.762
95_L100_I0.630790.761
49_I53_R0.626460.756
142_F145_S0.625530.754
220_P223_S0.624810.754
125_K141_D0.624580.753
100_I189_L0.621860.750
240_M249_P0.620460.748
217_R243_K0.618960.747
115_H181_D0.618420.746
55_L113_Y0.615010.742
83_G87_D0.611950.738
58_P109_E0.609420.735
222_S225_Q0.607940.733
163_E197_L0.607860.733
57_H109_E0.607760.733
212_E215_L0.603570.728
215_L218_P0.603160.727
190_Y241_L0.599260.723
214_I221_S0.594350.717
55_L114_L0.592980.715
216_K223_S0.592290.714
208_L211_I0.591150.713
209_E212_E0.58890.710
27_V30_K0.587260.708
182_I249_P0.585380.706
20_N24_G0.584190.705
223_S226_S0.584020.704
123_D161_T0.582280.702
183_W214_I0.581440.701
43_E46_I0.581270.701
169_V176_Y0.580520.700
180_S184_S0.579590.699
132_D135_G0.579110.698
42_R46_I0.578570.698
120_V177_T0.577270.696
48_E55_L0.575080.694
217_R220_P0.572070.690
60_I113_Y0.571470.689
92_N99_E0.571230.689
131_L137_V0.569780.687
49_I63_I0.569740.687
168_E245_P0.566380.683
96_S100_I0.565830.682
153_E156_N0.565110.682
211_I215_L0.564630.681
85_L188_I0.560810.676
65_D76_V0.557790.673
234_R237_I0.556160.671
189_L233_L0.555350.670
115_H178_R0.554090.668
222_S226_S0.552320.666
165_M169_V0.551350.665
121_H128_N0.5510.665
213_K216_K0.55090.664
245_P248_R0.55010.663
50_K53_R0.54990.663
8_G28_A0.549290.663
214_I218_P0.548630.662
238_K242_S0.54670.659
171_Q215_L0.542750.655
79_Y83_G0.542730.655
52_L77_M0.542050.654
46_I50_K0.541950.654
97_E226_S0.541080.653
14_T31_I0.540570.652
59_N136_E0.536430.647
244_D248_R0.535040.645
88_Y103_I0.532550.642
193_L237_I0.528180.637
218_P223_S0.526690.635
85_L192_L0.525840.634
14_T33_D0.525590.634
223_S234_R0.520940.628
210_I215_L0.518960.626
189_L237_I0.518170.625
50_K54_R0.516930.623
51_I119_I0.513420.619
108_L182_I0.512450.618
98_E101_L0.510950.616
97_E233_L0.510280.615
57_H110_A0.508840.614
168_E248_R0.508640.613
152_N156_N0.506760.611
83_G130_L0.504980.609
176_Y179_K0.504040.608
190_Y199_F0.503060.607
10_G28_A0.502440.606
220_P224_Q0.500930.604
9_S33_D0.500790.604
104_A108_L0.499160.602
213_K219_L0.498630.601
187_I198_P0.497620.600
168_E183_W0.497580.600
208_L212_E0.4970.599
190_Y237_I0.495540.598
68_Q73_L0.493230.595
103_I107_I0.493040.595
58_P136_E0.492880.594
89_L126_P0.491030.592
82_G132_D0.490870.592
97_E193_L0.489180.590
165_M170_L0.488450.589
214_I220_P0.487820.588
166_A170_L0.487570.588
114_L139_L0.484650.585
8_G13_G0.483620.583
209_E214_I0.483480.583
7_L15_V0.48280.582
111_L139_L0.482740.582
221_S234_R0.48270.582
103_I106_Q0.481920.581
83_G91_K0.480690.580
185_L254_L0.480070.579
217_R221_S0.479940.579
232_E235_D0.479360.578
166_A245_P0.478860.578
182_I186_G0.47850.577
167_P183_W0.477590.576
146_V155_F0.477250.576
207_Q213_K0.477170.576
83_G88_Y0.476980.575
106_Q110_A0.474350.572
161_T164_Y0.473960.572
69_D72_Y0.472920.570
163_E183_W0.47190.569
120_V178_R0.47180.569
80_C83_G0.470560.568
122_R146_V0.469440.566
40_E43_E0.467060.563
19_K23_N0.465880.562
199_F202_S0.461760.557
95_L99_E0.461480.557
60_I110_A0.461230.556
206_D217_R0.460880.556
171_Q243_K0.460360.555
237_I240_M0.459220.554
7_L17_K0.458820.553
190_Y198_P0.458560.553
13_G30_K0.45760.552
88_Y92_N0.457280.552
101_L105_Y0.457250.552
215_L219_L0.45720.551
36_E41_E0.456540.551
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
4fieA0.9692100-0.207
4fihA0.9692100-0.204
3ubdA0.9692100-0.189
3zduA0.9962100-0.179
4fg7A0.9769100-0.178
3hyhA0.9654100-0.174
3fpqA0.9692100-0.174
3v5wA0.9769100-0.171
4g3fA0.9538100-0.162
4ic7A0.9962100-0.161

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