GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Guanylate_kin - Guanylate kinase
Pfam: PF00625 (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: 183
Sequences: 12724
Seq/Len: 69.53
HH_delta: 0.02 (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
25_E177_K1.876333.657
127_V130_R1.794623.498
21_R173_V1.682673.280
168_D171_E1.296582.527
121_K163_V1.254312.445
21_R24_Q1.221872.382
140_E144_E1.200532.340
58_E61_R1.103512.151
25_E173_V1.084262.113
129_K133_R1.072732.091
18_L173_V1.069052.084
7_L19_A0.957981.867
129_K144_E0.940991.834
167_D175_E0.935271.823
26_F177_K0.9171.787
85_A88_K0.916771.787
18_L176_L0.898851.752
169_L173_V0.896361.747
148_E152_K0.882461.720
164_I172_A0.869481.695
162_Y179_I0.866461.689
144_E148_E0.848641.654
133_R140_E0.821271.601
61_R65_A0.812771.584
171_E175_E0.791031.542
21_R170_E0.790671.541
121_K165_V0.789881.540
60_E64_K0.789491.539
21_R25_E0.788691.537
25_E174_K0.784841.530
62_M67_E0.774811.510
139_S142_E0.75671.475
36_H82_S0.756621.475
142_E145_E0.755041.472
174_K178_E0.752871.467
175_E178_E0.751221.464
145_E149_R0.750481.463
83_K87_D0.74851.459
125_P151_E0.74171.446
23_I27_P0.741231.445
84_S88_K0.728091.419
173_V177_K0.727461.418
171_E174_K0.71191.388
130_R134_R0.705881.376
17_T169_L0.695781.356
116_I162_Y0.695181.355
122_P128_L0.692311.349
125_P144_E0.682921.331
141_E145_E0.676141.318
174_K177_K0.661921.290
20_K24_Q0.642561.252
107_Q110_K0.642261.252
73_E78_Y0.640631.249
20_K23_I0.636771.241
119_F163_V0.631821.231
120_I166_N0.61661.202
145_E148_E0.615841.200
126_E130_R0.61371.196
128_L132_L0.601081.172
123_P167_D0.596321.162
9_G13_S0.591041.152
19_A23_I0.587791.146
149_R153_E0.585011.140
106_K110_K0.580551.132
60_E78_Y0.579551.130
87_D91_E0.578991.128
123_P127_V0.576071.123
151_E155_E0.573771.118
13_S122_P0.571351.114
167_D171_E0.569261.110
122_P127_V0.568991.109
41_P78_Y0.568151.107
18_L120_I0.561011.093
85_A89_V0.555481.083
88_K92_E0.540361.053
18_L172_A0.535951.045
7_L22_L0.530221.033
175_E179_I0.529371.032
60_E63_I0.524131.022
118_I176_L0.513251.000
106_K109_K0.507040.988
109_K161_D0.505230.985
22_L176_L0.502420.979
116_I179_I0.500410.975
126_E129_K0.497420.970
66_G70_E0.494850.964
9_G14_G0.494030.963
118_I162_Y0.492130.959
38_T42_R0.487970.951
120_I176_L0.484570.944
141_E144_E0.481630.939
74_Y101_D0.481560.939
8_V117_V0.479360.934
16_S99_D0.477620.931
6_V117_V0.472670.921
10_P128_L0.468870.914
62_M70_E0.46630.909
132_L143_I0.465320.907
5_I116_I0.459230.895
125_P129_K0.454750.886
82_S85_A0.453060.883
35_S38_T0.452430.882
12_G132_L0.441210.860
21_R169_L0.441130.860
122_P166_N0.43570.849
58_E62_M0.431460.841
89_V92_E0.429170.836
127_V131_R0.428770.836
123_P126_E0.42710.832
18_L169_L0.426660.832
155_E158_N0.425750.830
138_E142_E0.425570.829
89_V94_K0.424720.828
19_A99_D0.423420.825
18_L21_R0.422870.824
61_R64_K0.422860.824
172_A175_E0.421950.822
118_I179_I0.417720.814
5_I180_I0.415160.809
65_A68_F0.415150.809
142_E146_R0.413610.806
170_E174_K0.412340.804
63_I71_Y0.410780.801
24_Q173_V0.408960.797
9_G16_S0.408060.795
14_G17_T0.407440.794
81_T84_S0.403620.787
164_I179_I0.402810.785
125_P147_L0.40190.783
8_V160_F0.400810.781
10_P150_A0.400360.780
170_E173_V0.39790.776
57_E60_E0.395480.771
9_G15_K0.392370.765
4_P98_L0.391750.764
22_L177_K0.391550.763
164_I176_L0.386250.753
80_G83_K0.385880.752
77_N81_T0.384660.750
22_L173_V0.381110.743
106_K159_E0.380990.743
156_H159_E0.375850.733
109_K159_E0.374420.730
38_T41_P0.37410.729
59_F62_M0.372750.727
17_T21_R0.371970.725
82_S86_I0.370060.721
68_F72_G0.368880.719
101_D104_G0.365330.712
147_L151_E0.365280.712
11_S135_R0.35870.699
62_M65_A0.358030.698
35_S39_R0.357050.696
169_L172_A0.356990.696
59_F63_I0.356820.695
88_K91_E0.356380.695
74_Y77_N0.355280.692
13_S121_K0.3510.684
72_G103_E0.350550.683
16_S20_K0.349140.680
173_V176_L0.34880.680
36_H94_K0.345560.674
35_S40_P0.344610.672
57_E61_R0.344120.671
150_A154_F0.342020.667
70_E73_E0.340610.664
149_R152_K0.340290.663
37_T40_P0.339490.662
138_E143_I0.338140.659
26_F173_V0.3370.657
69_I74_Y0.336920.657
107_Q111_A0.335740.654
6_V115_P0.334820.653
86_I96_C0.333530.650
153_E156_H0.333130.649
16_S19_A0.332580.648
4_P115_P0.329090.641
87_D112_G0.328130.640
6_V98_L0.327470.638
102_P105_V0.327440.638
136_G139_S0.327340.638
105_V150_A0.326730.637
127_V167_D0.326270.636
22_L26_F0.325610.635
102_P106_K0.322870.629
116_I180_I0.322370.628
79_Y82_S0.321020.626
65_A69_I0.319650.623
79_Y110_K0.319470.623
7_L176_L0.319040.622
132_L147_L0.318040.620
77_N80_G0.31780.619
89_V96_C0.316880.618
63_I66_G0.316270.616
96_C99_D0.315360.615
13_S16_S0.314990.614
70_E74_Y0.314980.614
11_S128_L0.312230.609
148_E151_E0.309420.603
22_L180_I0.307950.600
10_P13_S0.305690.596
11_S146_R0.301350.587
123_P166_N0.301210.587
166_N172_A0.299620.584
5_I22_L0.298120.581
62_M68_F0.29720.579
25_E170_E0.29540.576
89_V93_G0.2950.575
84_S87_D0.294860.575
39_R42_R0.294440.574
132_L135_R0.293650.572
19_A37_T0.291340.568
10_P122_P0.290360.566
79_Y101_D0.289870.565
24_Q27_P0.289620.564
125_P148_E0.289460.564
18_L22_L0.288730.563
154_F157_Y0.288060.561
66_G69_I0.287920.561
119_F161_D0.286630.559
5_I95_H0.286130.558
165_V175_E0.284850.555
37_T42_R0.284620.555
21_R177_K0.282920.551
129_K132_L0.282440.550
143_I147_L0.282330.550
13_S120_I0.280930.548
12_G143_I0.280230.546
158_N163_V0.28010.546
120_I172_A0.279670.545
150_A153_E0.279190.544
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
1ex7A0.99451000.02
3tvtA0.972799.90.133
3tauA199.90.148
2qorA0.994599.90.167
3a00A0.994599.90.172
1kjwA0.967299.90.189
3neyA0.945499.90.195
2xkxA0.967299.90.203
1kgdA0.950899.80.253
3tr0A0.994599.80.256

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