GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AA_kinase - Amino acid kinase family
Pfam: PF00696 (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: 242
Sequences: 7598
Seq/Len: 31.4
HH_delta: 0.223 (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
2_T35_K1.286654.117
183_G197_L1.001243.203
146_D150_E0.92322.954
27_A31_Q0.863612.763
174_K239_H0.858462.747
187_A194_D0.754972.416
186_T196_R0.738572.363
167_A175_L0.738282.362
207_E232_E0.708892.268
182_D242_N0.701962.246
37_V170_L0.659712.111
139_V166_L0.628972.012
129_E133_Q0.58951.886
128_R132_E0.589111.885
182_D185_Y0.587381.879
4_V172_A0.586131.875
176_I241_I0.584231.869
202_S205_E0.579731.855
205_E208_E0.573331.834
231_A238_V0.563291.802
207_E228_L0.559351.790
185_Y197_L0.556961.782
203_Y228_L0.552731.768
24_D110_G0.51051.633
35_K132_E0.508421.627
198_I201_L0.498541.595
164_A231_A0.496221.588
3_I34_I0.487451.560
130_L135_I0.485631.554
124_K128_R0.483111.546
179_T240_I0.478031.529
183_G199_P0.474221.517
30_S35_K0.473991.517
30_S136_I0.473941.516
9_G45_F0.473011.513
204_D232_E0.465421.489
21_E25_D0.465371.489
21_E24_D0.461961.478
35_K134_G0.456121.459
113_S135_I0.452581.448
205_E218_G0.446941.430
201_L206_A0.445741.426
28_L32_L0.444811.423
45_F48_E0.444091.421
178_L241_I0.443811.420
26_I136_I0.437721.400
174_K237_P0.432871.385
168_A236_I0.426131.363
5_I26_I0.425341.361
129_E132_E0.423691.356
24_D27_A0.421971.350
24_D98_L0.418551.339
127_I139_V0.411221.316
186_T198_I0.410531.313
30_S134_G0.410251.313
112_I136_I0.409631.311
20_R24_D0.407071.302
184_V201_L0.406681.301
29_L34_I0.40411.293
206_A228_L0.402351.287
30_S36_V0.394891.263
204_D208_E0.384211.229
187_A193_P0.378661.212
28_L31_Q0.377521.208
180_D190_R0.373191.194
27_A100_A0.372751.193
198_I218_G0.372021.190
124_K171_G0.365391.169
14_D18_E0.363181.162
10_S13_T0.360361.153
168_A233_E0.355551.138
117_R130_L0.35151.125
229_E232_E0.349331.118
186_T195_A0.349141.117
2_T128_R0.348131.114
126_A129_E0.348021.113
115_A135_I0.345541.106
207_E225_P0.343661.100
173_D236_I0.338781.084
163_A175_L0.337691.080
125_E129_E0.336971.078
95_G100_A0.334121.069
176_I239_H0.334031.069
23_A94_A0.331241.060
189_P195_A0.331191.060
166_L170_L0.330361.057
27_A136_I0.329931.056
39_V100_A0.329921.056
197_L242_N0.328821.052
143_A157_V0.3271.046
100_A136_I0.325971.043
20_R110_G0.324261.037
161_Y225_P0.319771.023
225_P229_E0.319621.023
49_L53_Y0.31871.020
165_L168_A0.316771.014
171_G234_G0.316551.013
164_A168_A0.314411.006
37_V131_L0.314061.005
95_G102_A0.309060.989
126_A130_L0.30890.988
139_V170_L0.308650.988
9_G41_G0.308440.987
187_A195_A0.306520.981
39_V163_A0.305780.978
26_I36_V0.303610.971
10_S43_G0.301560.965
227_A238_V0.301460.965
93_S97_R0.301320.964
164_A175_L0.299910.960
185_Y195_A0.298050.954
94_A97_R0.296680.949
92_V96_E0.296290.948
106_S110_G0.296210.948
122_V125_E0.293950.940
29_L32_L0.293650.940
27_A110_G0.291360.932
51_E54_G0.289070.925
99_G107_L0.288990.925
7_L12_L0.288850.924
107_L112_I0.288020.922
6_K219_G0.286790.918
2_T131_L0.286070.915
127_I137_P0.284980.912
30_S100_A0.283880.908
100_A140_S0.282790.905
182_D197_L0.280320.897
30_S33_G0.280270.897
48_E52_K0.277660.888
7_L38_V0.276630.885
227_A231_A0.276420.884
91_I101_H0.275620.882
161_Y229_E0.273940.876
8_G160_D0.273750.876
15_K18_E0.273150.874
140_S162_I0.273150.874
100_A116_K0.271410.868
93_S96_E0.270030.864
93_S151_V0.26910.861
130_L137_P0.269020.861
186_T194_D0.267540.856
24_D28_L0.265120.848
92_V102_A0.263390.843
20_R97_R0.263050.842
220_M223_K0.262890.841
210_A221_K0.261350.836
179_T238_V0.260580.834
48_E51_E0.26010.832
90_E94_A0.259610.831
130_L133_Q0.258050.826
19_L90_E0.257790.825
7_L11_S0.256410.820
35_K131_L0.255460.817
103_V107_L0.254820.815
23_A95_G0.251560.805
10_S45_F0.251310.804
40_H103_V0.249370.798
50_L92_V0.249060.797
7_L22_L0.247250.791
27_A112_I0.246770.790
104_G114_A0.245090.784
8_G219_G0.245080.784
165_L169_A0.244350.782
2_T173_D0.244280.782
46_T50_L0.243350.779
96_E102_A0.242690.776
10_S180_D0.242570.776
11_S178_L0.242560.776
123_D126_A0.242520.776
34_I173_D0.241460.773
51_E55_I0.240690.770
229_E233_E0.240680.770
115_A121_E0.240240.769
204_D207_E0.239560.766
46_T49_L0.238430.763
221_K225_P0.238210.762
23_A38_V0.237670.760
128_R171_G0.237510.760
184_V198_I0.235640.754
181_V185_Y0.234140.749
51_E56_E0.233470.747
134_G137_P0.233460.747
184_V224_H0.233410.747
124_K169_A0.231550.741
171_G236_I0.229710.735
10_S44_S0.228680.732
94_A98_L0.228030.730
120_R145_I0.227520.728
187_A190_R0.227130.727
164_A226_A0.227030.726
44_S47_D0.226280.724
3_I29_L0.225460.721
207_E210_A0.22510.720
44_S48_E0.225060.720
9_G43_G0.224580.719
143_A162_I0.224440.718
3_I174_K0.224240.717
184_V240_I0.222420.712
115_A120_R0.222210.711
52_K55_I0.22020.705
104_G108_S0.219980.704
15_K19_L0.219040.701
8_G40_H0.217940.697
95_G99_G0.217860.697
46_T156_N0.21760.696
106_S109_D0.217540.696
45_F49_L0.217510.696
5_I176_I0.217360.695
185_Y189_P0.216250.692
8_G220_M0.216080.691
103_V106_S0.213970.685
39_V103_V0.213740.684
105_L108_S0.213740.684
20_R94_A0.21360.683
19_L94_A0.213490.683
24_D31_Q0.213460.683
108_S113_S0.213060.682
203_Y207_E0.212580.680
8_G223_K0.212440.680
117_R137_P0.212150.679
20_R109_D0.212130.679
54_G57_P0.209880.672
190_R194_D0.208610.667
230_A238_V0.208010.666
167_A172_A0.207780.665
5_I29_L0.207730.665
188_D195_A0.207260.663
90_E93_S0.207050.662
218_G223_K0.206930.662
127_I166_L0.206890.662
50_L53_Y0.20680.662
121_E147_D0.206390.660
107_L110_G0.205850.659
25_D28_L0.205830.659
186_T189_P0.20510.656
111_G117_R0.204620.655
95_G107_L0.203910.652
27_A98_L0.203530.651
27_A30_S0.203450.651
35_K173_D0.203250.650
157_V162_I0.203080.650
18_E208_E0.202660.648
105_L109_D0.202060.646
13_T46_T0.201470.645
210_A225_P0.201470.645
37_V139_V0.201190.644
182_D194_D0.201190.644
29_L174_K0.2010.643
142_F158_S0.20040.641
203_Y232_E0.199480.638
168_A229_E0.198950.637
29_L36_V0.198780.636
177_F227_A0.197980.633
228_L232_E0.197320.631
34_I174_K0.197120.631
161_Y226_A0.19710.631
41_G157_V0.19680.630
47_D156_N0.196560.629
22_L26_I0.19640.628
96_E101_H0.194430.622
49_L52_K0.194370.622
203_Y231_A0.194310.622
5_I178_L0.194120.621
2_T34_I0.193190.618
98_L101_H0.19310.618
15_K20_R0.192840.617
203_Y227_A0.192690.617
99_G102_A0.192640.616
40_H157_V0.192270.615
131_L137_P0.192230.615
18_E21_E0.19150.613
223_K238_V0.190340.609
40_H159_S0.19030.609
47_D51_E0.189840.607
108_S130_L0.189690.607
126_A135_I0.189330.606
103_V130_L0.189160.605
44_S221_K0.187980.601
123_D129_E0.187250.599
117_R127_I0.187070.599
207_E229_E0.187050.598
95_G98_L0.186550.597
219_G232_E0.186260.596
8_G180_D0.186260.596
177_F180_D0.185670.594
7_L25_D0.184910.592
196_R199_P0.18480.591
177_F223_K0.184190.589
5_I36_V0.183460.587
158_S220_M0.183350.587
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
3l86A0.91741000.223
3ll9A0.91321000.231
2rd5A0.94211000.233
2ap9A0.93391000.239
3l76A0.92561000.239
2v5hA0.94211000.241
3ab4A0.92561000.246
3tviA0.96281000.249
1gs5A0.92561000.253
4ab7A0.9051000.257

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