GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Aldolase - KDPG and KHG aldolase
Pfam: PF01081 (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: CL0036
Length: 196
Sequences: 19881
Seq/Len: 101.43
HH_delta: 0.168 (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
27_E56_E1.716352.858
54_R82_Q1.671992.784
162_L173_V1.60042.665
163_A167_K1.421322.367
21_D24_P1.326462.209
143_R171_V1.315432.190
74_E78_A1.296672.159
28_A32_G1.252762.086
27_E31_E1.249282.080
74_E96_Y1.201332.000
152_M172_A1.18661.976
118_L148_D1.17651.959
164_E167_K1.150041.915
158_N161_N1.145681.908
74_E100_Y1.098721.830
115_M145_P1.094481.822
27_E30_I1.084921.807
48_E51_E1.07731.794
52_A55_K1.071761.785
75_A78_A1.032481.719
47_L75_A1.014691.690
51_E55_K1.009751.681
26_A37_I0.994581.656
150_P171_V0.990161.649
23_V52_A0.989341.647
157_V165_Y0.98661.643
137_S140_K0.986041.642
140_K168_A0.96511.607
23_V27_E0.941961.569
116_Q120_A0.940171.566
96_Y99_E0.932511.553
143_R151_F0.932081.552
140_K144_G0.928681.546
141_A145_P0.907881.512
24_P28_A0.899081.497
118_L149_L0.898641.496
51_E79_A0.895411.491
98_R123_D0.888841.480
30_I58_P0.885411.474
158_N178_W0.875131.457
166_L173_V0.870411.449
49_A52_A0.858561.430
115_M119_E0.857941.429
91_P95_E0.847071.411
23_V56_E0.837681.395
115_M118_L0.828111.379
137_S141_A0.809151.347
24_P27_E0.807271.344
159_P163_A0.805071.341
28_A31_E0.797411.328
116_Q119_E0.792791.320
48_E52_A0.787411.311
95_E99_E0.782571.303
111_P141_A0.764321.273
94_I98_R0.761321.268
75_A79_A0.76071.267
47_L79_A0.760671.267
92_E95_E0.759421.265
71_E75_A0.754291.256
70_A96_Y0.745071.241
71_E74_E0.74181.235
161_N164_E0.740461.233
160_D164_E0.72891.214
72_Q75_A0.7151.191
105_I124_I0.714311.189
25_I28_A0.703591.172
153_P165_Y0.69651.160
30_I60_L0.691691.152
73_A97_A0.687311.144
69_T72_Q0.687251.144
146_F149_L0.686021.142
141_A144_G0.685451.141
113_E116_Q0.677951.129
136_P165_Y0.673781.122
136_P164_E0.669581.115
77_I102_I0.669531.115
138_Y141_A0.665281.108
96_Y100_Y0.662421.103
92_E96_Y0.658531.097
36_A83_F0.65771.095
26_A53_L0.652211.086
139_I143_R0.651221.084
51_E78_A0.636991.061
83_F105_I0.62941.048
45_N48_E0.623551.038
112_T115_M0.622711.037
165_Y170_A0.615151.024
95_E120_A0.614141.023
153_P170_A0.612181.019
124_I150_P0.602081.003
46_A49_A0.599210.998
77_I100_Y0.595490.992
23_V26_A0.592380.986
164_E168_A0.587060.978
159_P178_W0.584420.973
21_D25_I0.582060.969
177_S181_P0.579230.965
47_L51_E0.571180.951
150_P172_A0.569460.948
161_N165_Y0.564230.940
30_I57_F0.563820.939
139_I170_A0.560660.934
52_A56_E0.552450.920
30_I33_G0.552270.920
160_D163_A0.550630.917
91_P121_G0.548590.913
110_T113_E0.548340.913
76_A81_A0.548030.913
39_I53_L0.546050.909
165_Y173_V0.545710.909
175_G178_W0.543540.905
112_T141_A0.542340.903
70_A99_E0.531010.884
97_A104_Y0.520960.867
136_P140_K0.515510.858
117_A120_A0.511870.852
127_L142_L0.507870.846
22_A26_A0.507590.845
40_T176_G0.505090.841
54_R79_A0.504160.840
139_I153_P0.498690.830
93_V96_Y0.492750.821
94_I120_A0.491590.819
70_A74_E0.49060.817
115_M146_F0.486570.810
50_I62_V0.484420.807
95_E121_G0.482260.803
74_E77_I0.481650.802
121_G149_L0.480610.800
88_G107_G0.476790.794
175_G179_L0.474550.790
80_G104_Y0.473460.788
85_V107_G0.471330.785
29_L34_I0.470640.784
124_I152_M0.468110.779
139_I151_F0.465590.775
140_K167_K0.465140.775
95_E98_R0.464870.774
73_A84_I0.461170.768
91_P116_Q0.457420.762
27_E57_F0.456310.760
94_I104_Y0.449830.749
91_P120_A0.448490.747
154_T174_G0.447990.746
122_A125_V0.44710.744
108_V114_I0.446270.743
138_Y142_L0.443710.739
90_D96_Y0.443280.738
127_L138_Y0.441320.735
136_P168_A0.436830.727
85_V105_I0.42950.715
125_V149_L0.429460.715
58_P62_V0.427720.712
117_A125_V0.424550.707
151_F170_A0.420710.701
152_M174_G0.419750.699
128_F132_A0.419450.698
124_I172_A0.418950.698
157_V162_L0.418560.697
26_A30_I0.412610.687
41_L44_P0.411940.686
146_F151_F0.410230.683
117_A122_A0.410080.683
64_A81_A0.409860.682
25_I29_L0.409430.682
142_L146_F0.403990.673
86_S104_Y0.403860.672
140_K164_E0.402780.671
30_I59_D0.401470.669
65_G81_A0.401040.668
70_A92_E0.400330.667
57_F60_L0.399010.664
123_D150_P0.39840.663
108_V131_G0.397580.662
151_F171_V0.397160.661
114_I146_F0.397130.661
50_I54_R0.395690.659
128_F131_G0.391210.651
98_R120_A0.389990.649
143_R168_A0.389190.648
103_P106_P0.388090.646
166_L170_A0.387520.645
54_R62_V0.387110.645
86_S106_P0.386760.644
97_A100_Y0.386490.644
107_G126_K0.382960.638
127_L139_I0.381090.635
104_Y123_D0.380790.634
133_L138_Y0.380060.633
136_P139_I0.379110.631
30_I85_V0.37420.623
62_V82_Q0.374010.623
23_V53_L0.372050.620
50_I78_A0.371050.618
25_I180_F0.369970.616
47_L78_A0.365370.608
134_G137_S0.365210.608
36_A172_A0.364160.606
50_I79_A0.363990.606
84_I102_I0.362030.603
76_A80_G0.360810.601
29_L37_I0.360020.599
73_A96_Y0.358320.597
111_P138_Y0.357670.596
83_F124_I0.356960.594
139_I142_L0.356220.593
90_D106_P0.355090.591
36_A152_M0.355050.591
29_L33_G0.354590.590
114_I142_L0.35410.590
158_N181_P0.353170.588
85_V126_K0.353020.588
101_G104_Y0.349410.582
179_L182_K0.349390.582
61_L64_A0.347230.578
159_P162_L0.345620.576
107_G128_F0.344450.574
29_L180_F0.344330.573
38_E154_T0.344020.573
176_G180_F0.343950.573
39_I62_V0.342950.571
109_M113_E0.342590.570
60_L64_A0.342210.570
111_P145_P0.341550.569
118_L146_F0.341470.569
78_A100_Y0.340440.567
126_K154_T0.339070.565
38_E174_G0.338610.564
29_L179_L0.337790.562
61_L83_F0.337520.562
91_P119_E0.336170.560
26_A57_F0.335240.558
94_I121_G0.33420.556
35_R172_A0.333410.555
126_K174_G0.33060.551
51_E75_A0.329440.549
86_S90_D0.32570.542
53_L57_F0.324260.540
142_L145_P0.323730.539
54_R81_A0.323440.539
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
4e38A11000.168
1wbhA0.99491000.191
1mxsA0.99491000.192
1vhcA0.994999.90.196
3labA199.90.211
2yw3A0.984799.90.232
2v82A0.979699.90.318
1wa3A0.984799.90.324
3f4wA0.954199.80.408
3o63A0.989899.80.417

Page generated in 0.0388 seconds.