GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ATP_bind_3 - PP-loop family
Pfam: PF01171 (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: CL0039
Length: 182
Sequences: 12720
Seq/Len: 69.89
HH_delta: 0.084 (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
31_I62_Y1.822193.044
3_L97_C1.505792.516
17_H21_E1.331592.225
34_H61_L1.273572.128
17_H159_N1.245242.080
14_A156_A1.237212.067
148_S151_E1.230562.056
51_E55_E1.203012.010
91_I94_E1.196321.999
52_E56_Q1.151371.924
154_A158_E1.097821.834
10_K156_A1.067691.784
21_E159_N1.038271.735
31_I97_C1.011171.689
16_L32_A1.002721.675
13_M53_I1.000721.672
91_I95_E0.990881.655
31_I95_E0.981921.641
10_K149_K0.977211.633
99_K141_I0.965561.613
19_L101_A0.9631.609
48_E52_E0.962871.609
4_V16_L0.96141.606
151_E154_A0.951781.590
52_E55_E0.930991.555
47_A51_E0.926871.549
6_V13_M0.922641.541
155_Y158_E0.911771.523
32_A59_I0.906661.515
31_I60_P0.902281.507
77_E80_A0.900291.504
17_H20_K0.894651.495
3_L33_V0.893181.492
2_I101_A0.877571.466
51_E61_L0.844861.412
62_Y95_E0.813411.359
154_A157_K0.803021.342
48_E51_E0.798931.335
47_A63_I0.790251.320
36_D65_R0.783691.309
87_F90_E0.778721.301
6_V32_A0.775451.296
17_H155_Y0.772131.290
18_L144_L0.761251.272
38_G65_R0.749451.252
34_H47_A0.748211.250
53_I57_L0.747521.249
156_A163_Y0.736551.231
45_E48_E0.733041.225
14_A155_Y0.722911.208
155_Y159_N0.716291.197
51_E63_I0.716181.197
54_C61_L0.709691.186
10_K153_R0.707871.183
17_H57_L0.706691.181
36_D47_A0.703341.175
62_Y91_I0.695151.161
64_V87_F0.694331.160
78_E82_E0.69171.156
92_A100_I0.691651.156
32_A54_C0.69091.154
3_L31_I0.690841.154
33_V91_I0.680751.137
15_L144_L0.675511.129
126_L130_P0.667221.115
45_E49_F0.666371.113
86_Q90_E0.665391.112
14_A152_I0.653731.092
150_D154_A0.651861.089
18_L155_Y0.647061.081
5_A88_L0.642221.073
17_H161_I0.639481.068
101_A141_I0.638881.067
62_Y94_E0.636211.063
149_K153_R0.631861.056
147_V155_Y0.630541.053
93_K137_G0.627471.048
49_F52_E0.62591.046
36_D63_I0.62321.041
64_V90_E0.617281.031
127_A130_P0.608581.017
107_D146_Y0.595560.995
66_I87_F0.595430.995
92_A138_I0.585260.978
4_V15_L0.580960.971
75_N78_E0.579680.968
42_E45_E0.573720.959
15_L101_A0.571920.956
104_H142_R0.570320.953
71_K74_S0.567480.948
56_Q162_P0.561890.939
46_E164_V0.558070.932
10_K152_I0.557460.931
60_P95_E0.550840.920
20_K57_L0.550660.920
6_V50_V0.550290.919
126_L131_P0.549020.917
126_L129_M0.545070.911
128_G131_P0.541010.904
102_L142_R0.540550.903
109_Q145_L0.537850.899
52_E162_P0.530810.887
99_K139_K0.529460.885
18_L22_L0.526570.880
9_G12_S0.523140.874
6_V53_I0.521640.872
10_K163_Y0.519480.868
106_L148_S0.519190.867
6_V16_L0.517920.865
50_V61_L0.517180.864
7_S12_S0.507390.848
53_I56_Q0.506050.845
153_R157_K0.506010.845
89_R93_K0.505240.844
34_H50_V0.501350.838
32_A61_L0.489520.818
39_L76_I0.488630.816
29_K60_P0.488470.816
89_R136_K0.485270.811
33_V87_F0.483410.808
46_E50_V0.48270.806
16_L57_L0.482110.805
40_R46_E0.481750.805
90_E94_E0.480140.802
105_H152_I0.47850.799
2_I99_K0.474550.793
88_L100_I0.471040.787
19_L30_L0.470260.786
35_V66_I0.467970.782
2_I28_I0.467920.782
83_L86_Q0.464070.775
64_V91_I0.462640.773
76_I80_A0.458580.766
16_L59_I0.457470.764
93_K130_P0.445620.745
4_V19_L0.442520.739
107_D149_K0.435440.728
107_D145_L0.435270.727
88_L126_L0.432910.723
4_V30_L0.431910.722
92_A97_C0.431530.721
100_I140_L0.427910.715
54_C59_I0.424910.710
78_E81_R0.424140.709
13_M163_Y0.422310.706
16_L54_C0.421890.705
87_F91_I0.421430.704
147_V152_I0.42130.704
3_L100_I0.419170.700
13_M161_I0.418230.699
22_L28_I0.418060.698
3_L91_I0.416060.695
127_A131_P0.414780.693
144_L147_V0.40440.676
71_K76_I0.401180.670
89_R92_A0.399190.667
16_L30_L0.398580.666
38_G67_D0.397440.664
34_H40_R0.39640.662
34_H63_I0.393560.658
64_V94_E0.387790.648
42_E48_E0.387150.647
150_D153_R0.385820.645
18_L21_E0.38480.643
72_K76_I0.38430.642
74_S77_E0.381320.637
90_E93_K0.380930.636
107_D148_S0.379460.634
50_V54_C0.378970.633
54_C57_L0.376310.629
46_E49_F0.376260.629
14_A144_L0.375820.628
5_A100_I0.374910.626
102_L140_L0.373410.624
33_V95_E0.373250.624
14_A17_H0.372820.623
69_D72_K0.369950.618
18_L147_V0.3670.613
35_V64_V0.366230.612
37_H66_I0.366030.612
10_K14_A0.365850.611
35_V87_F0.364760.609
8_G11_D0.364690.609
33_V88_L0.364340.609
81_R84_R0.364310.609
82_E86_Q0.364160.608
13_M49_F0.363990.608
157_K163_Y0.361980.605
73_G76_I0.361460.604
93_K136_K0.360860.603
47_A50_V0.358460.599
47_A65_R0.355440.594
51_E54_C0.353840.591
105_H108_D0.352740.589
108_D111_E0.352620.589
147_V151_E0.352460.589
70_R73_G0.351950.588
56_Q160_G0.350280.585
156_A161_I0.347110.580
79_C82_E0.344780.576
4_V101_A0.34450.576
40_R47_A0.340070.568
74_S78_E0.337420.564
7_S11_D0.336010.561
7_S103_G0.335810.561
81_R85_Y0.332660.556
142_R145_L0.331440.554
75_N79_C0.326020.545
84_R88_L0.322880.539
11_D108_D0.322670.539
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
3a2kA11000.084
1ni5A0.98351000.107
1wy5A0.9781000.13
3vrhA0.9781000.192
1zunA0.97899.90.317
2derA0.961599.90.347
3k32A0.879199.90.349
2o8vA0.890199.90.352
2oq2A0.917699.90.353
2hmaA0.961599.90.353

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