GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Choline_kinase - Cholineethanolamine kinase
Pfam: PF01633 (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: 211
Sequences: 6850
Seq/Len: 32.46
HH_delta: 0.205 (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
38_K50_E1.02694.075
146_C175_N0.978033.881
40_I50_E0.913293.624
31_S38_K0.67622.683
156_L167_I0.663432.633
7_V48_V0.639242.537
74_L166_L0.588582.336
149_D168_D0.581642.308
144_V177_R0.564422.240
150_L166_L0.561262.227
70_R73_K0.556292.208
24_N39_I0.544672.161
75_L150_L0.537872.135
52_I165_K0.494411.962
43_F46_G0.492591.955
71_I155_I0.489791.944
149_D154_N0.473591.879
131_E135_L0.434751.725
130_E134_K0.431611.713
69_K72_A0.426851.694
27_L39_I0.421051.671
70_R163_E0.416771.654
39_I42_F0.415261.648
160_K163_E0.410971.631
71_I150_L0.401881.595
70_R74_L0.386221.533
24_N42_F0.368071.461
21_E25_E0.359141.425
73_K76_A0.358691.423
154_N168_D0.356631.415
23_E27_L0.353751.404
26_A172_A0.347781.380
74_L77_K0.347171.378
37_P40_I0.344021.365
122_L126_Q0.342761.360
69_K73_K0.340811.352
146_C173_G0.338721.344
76_A80_S0.338281.342
97_D133_E0.337021.337
148_N175_N0.335921.333
34_G77_K0.334611.328
148_N183_N0.32421.287
8_R23_E0.316811.257
95_R98_K0.315631.253
72_A76_A0.31491.250
175_N180_D0.311681.237
126_Q130_E0.310371.232
28_K32_E0.309671.229
95_R99_Y0.304961.210
27_L169_F0.30431.208
131_E134_K0.301021.195
75_L79_H0.298841.186
124_D127_E0.298591.185
109_K113_K0.297391.180
79_H180_D0.295231.172
130_E133_E0.294091.167
125_L129_L0.293281.164
27_L37_P0.292881.162
20_R171_Y0.290241.152
78_L166_L0.289851.150
110_R114_K0.286241.136
79_H146_C0.285521.133
145_F174_Y0.28441.129
83_I145_F0.281661.118
73_K77_K0.276231.096
127_E130_E0.27381.087
31_S39_I0.272091.080
24_N28_K0.271771.079
20_R170_E0.270311.073
25_E29_L0.269921.071
28_K31_S0.268911.067
173_G179_F0.267931.063
183_N187_E0.267151.060
66_E69_K0.265161.052
71_I184_F0.26481.051
72_A181_I0.26451.050
142_P177_R0.263641.046
54_G156_L0.262571.042
26_A145_F0.260831.035
150_L155_I0.260231.033
29_L32_E0.257571.022
78_L169_F0.257151.020
170_E175_N0.255971.016
147_H180_D0.252391.002
184_F187_E0.247770.983
118_D121_D0.247040.980
155_I166_L0.242160.961
182_A186_C0.242090.961
82_P144_V0.241250.957
72_A79_H0.240330.954
11_G20_R0.239690.951
147_H150_L0.238370.946
21_E42_F0.233730.928
56_T156_L0.233310.926
148_N179_F0.232270.922
25_E28_K0.231790.920
28_K39_I0.231220.918
36_G39_I0.230810.916
22_N26_A0.230660.915
148_N171_Y0.230620.915
143_L174_Y0.229940.913
166_L169_F0.22980.912
74_L164_V0.228610.907
70_R162_G0.227780.904
67_I70_R0.226120.897
30_L78_L0.225340.894
67_I157_I0.224390.890
31_S36_G0.224220.890
55_R160_K0.223260.886
26_A169_F0.222490.883
33_A81_I0.221750.880
29_L33_A0.221590.879
72_A184_F0.221550.879
151_N171_Y0.219730.872
58_S153_G0.21640.859
147_H166_L0.215990.857
184_F188_W0.215820.856
23_E170_E0.215810.856
129_L132_L0.215440.855
145_F172_A0.211670.840
82_P174_Y0.211050.838
151_N187_E0.21080.837
129_L133_E0.210740.836
91_D94_D0.210540.836
123_E126_Q0.210410.835
119_K122_L0.210140.834
86_N89_K0.209260.830
143_L176_D0.208510.827
148_N173_G0.208130.826
66_E70_R0.207980.825
76_A79_H0.207650.824
169_F173_G0.206550.820
64_N67_I0.205470.815
147_H154_N0.20540.815
148_N180_D0.204310.811
112_K126_Q0.203610.808
147_H155_I0.203550.808
127_E131_E0.201840.801
108_F111_K0.200750.797
35_L77_K0.198810.789
68_L188_W0.197020.782
72_A185_F0.19570.777
169_F172_A0.195110.774
155_I167_I0.194620.772
181_I185_F0.193060.766
41_Y48_V0.192710.765
77_K80_S0.190540.756
146_C179_F0.19040.756
94_D98_K0.190290.755
93_W97_D0.18970.753
78_L145_F0.188170.747
89_K92_L0.187930.746
31_S53_E0.186030.738
85_P88_K0.183880.730
42_F45_N0.181860.722
147_H169_F0.181850.722
55_R59_P0.181670.721
114_K126_Q0.181380.720
171_Y183_N0.180620.717
55_R161_D0.180520.716
123_E130_E0.180020.714
114_K160_K0.178380.708
70_R164_V0.17830.708
52_I156_L0.176930.702
133_E136_L0.176840.702
93_W98_K0.176730.701
179_F184_F0.176560.701
79_H181_I0.176110.699
37_P49_E0.175770.698
28_K42_F0.175430.696
118_D122_L0.173620.689
43_F47_R0.173390.688
151_N185_F0.173320.688
83_I174_Y0.173190.687
170_E173_G0.172920.686
162_G165_K0.172290.684
120_E124_D0.171670.681
54_G167_I0.171370.680
167_I170_E0.171090.679
179_F183_N0.170860.678
29_L86_N0.170330.676
24_N44_E0.169220.672
115_K118_D0.168990.671
30_L34_G0.16860.669
67_I156_L0.168190.667
75_L184_F0.168030.667
114_K117_I0.167940.666
22_N25_E0.167330.664
68_L153_G0.166950.663
68_L152_P0.166740.662
41_Y46_G0.166680.661
147_H167_I0.165610.657
124_D128_E0.164990.655
46_G123_E0.164710.654
121_D124_D0.164490.653
37_P50_E0.163870.650
50_E165_K0.163230.648
146_C180_D0.162260.644
20_R167_I0.162160.644
134_K137_E0.160420.637
65_P69_K0.160170.636
88_K91_D0.159260.632
150_L187_E0.159210.632
28_K38_K0.158980.631
29_L85_P0.158770.630
149_D167_I0.158540.629
154_N167_I0.158170.628
174_Y177_R0.1580.627
94_D110_R0.157870.627
120_E123_E0.157840.626
8_R171_Y0.157670.626
8_R169_F0.157640.626
8_R170_E0.157370.625
26_A30_L0.156720.622
72_A177_R0.154890.615
98_K108_F0.15480.614
23_E26_A0.154020.611
110_R138_K0.153960.611
46_G91_D0.15270.606
78_L182_A0.15250.605
139_S176_D0.152190.604
98_K110_R0.152040.603
65_P127_E0.152010.603
151_N166_L0.151730.602
68_L72_A0.151690.602
27_L36_G0.151390.601
55_R61_D0.151320.601
148_N170_E0.150320.597
57_L67_I0.150280.596
141_S177_R0.150030.595
113_K120_E0.149550.593
112_K141_S0.14890.591
150_L183_N0.148760.590
121_D126_Q0.148710.590
23_E49_E0.148080.588
35_L129_L0.147330.585
67_I72_A0.146690.582
157_I164_V0.146620.582
79_H177_R0.14620.580
89_K143_L0.146130.580
146_C171_Y0.146030.580
111_K121_D0.145860.579
134_K138_K0.145290.577
26_A146_C0.145140.576
80_S83_I0.1450.575
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
3fegA0.9811000.205
2qg7A199.90.219
3f2sA0.995399.90.224
3mesA0.976399.90.23
4da5A0.995399.90.232
3g15A199.90.237
3dxqA0.947999.90.242
3c5iA0.962199.90.247
1nw1A0.990599.90.247
3d1uA0.938499.90.351

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