GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF1687 - Protein of unknown function (DUF1687)
Pfam: PF07955 (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: CL0172
Length: 133
Sequences: 2525
Seq/Len: 18.98
HH_delta: 0.241 (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
56_T59_Q0.922042.878
33_K39_A0.837632.614
57_L61_K0.799262.495
62_Y66_Y0.767212.394
57_L98_S0.757912.365
96_F99_P0.739032.307
49_E52_E0.703682.196
18_H47_E0.599161.870
16_L114_V0.597271.864
51_T107_G0.582391.818
116_D119_N0.56711.770
64_L75_V0.563841.760
30_N34_Q0.56131.752
128_S131_E0.555121.733
64_L97_G0.543391.696
16_L29_L0.540931.688
95_E103_C0.533941.666
66_Y120_G0.509471.590
22_S111_R0.50051.562
31_L35_A0.500471.562
67_C75_V0.481411.503
55_P109_F0.473681.478
59_Q115_V0.453931.417
39_A47_E0.445191.389
114_V129_L0.443981.386
67_C113_L0.442441.381
61_K97_G0.438531.369
59_Q62_Y0.438361.368
57_L102_K0.434591.356
87_L90_F0.433561.353
75_V113_L0.416841.301
70_N74_S0.406141.268
58_D61_K0.403671.260
63_I115_V0.394371.231
121_K132_I0.388221.212
63_I113_L0.387191.208
18_H25_S0.385431.203
29_L47_E0.382931.195
126_E130_K0.379641.185
31_L130_K0.379351.184
60_L101_K0.37911.183
33_K38_N0.377941.180
92_E95_E0.375871.173
17_F63_I0.371971.161
81_P85_D0.371741.160
82_E85_D0.369821.154
18_H29_L0.366871.145
69_K75_V0.366591.144
29_L33_K0.362391.131
127_K130_K0.351081.096
24_A27_R0.346281.081
64_L68_G0.345011.077
19_N25_S0.341411.066
129_L133_L0.339631.060
57_L101_K0.338981.058
16_L25_S0.335021.046
80_F107_G0.331691.035
116_D132_I0.327751.023
91_S95_E0.32611.018
87_L92_E0.323091.008
99_P103_C0.319010.996
64_L69_K0.317770.992
48_L59_Q0.313930.980
78_G84_E0.312860.976
125_D128_S0.308930.964
31_L124_N0.306240.956
20_P29_L0.304530.950
76_L100_L0.29860.932
61_K65_D0.296560.926
17_F115_V0.29320.915
15_T46_F0.289440.903
83_Y108_I0.288470.900
63_I120_G0.284410.888
121_K133_L0.282970.883
48_L54_P0.281440.878
27_R126_E0.280510.875
54_P109_F0.280220.875
28_L129_L0.280220.875
39_A50_V0.276530.863
82_E107_G0.273480.854
77_K110_Q0.267780.836
83_Y87_L0.267020.833
64_L109_F0.266760.833
20_P52_E0.258210.806
67_C120_G0.255440.797
82_E103_C0.253590.791
31_L129_L0.249870.780
62_Y65_D0.248890.777
77_K80_F0.248530.776
48_L55_P0.247990.774
96_F103_C0.244850.764
60_L109_F0.24370.761
66_Y118_E0.24360.760
25_S50_V0.242960.758
66_Y115_V0.241920.755
87_L91_S0.2410.752
57_L97_G0.240710.751
47_E50_V0.239290.747
27_R30_N0.239020.746
121_K128_S0.238950.746
83_Y86_A0.233970.730
113_L122_I0.230.718
30_N33_K0.229680.717
80_F85_D0.228240.712
20_P49_E0.228060.712
81_P84_E0.227840.711
82_E86_A0.227540.710
39_A48_L0.227340.710
96_F100_L0.226850.708
19_N51_T0.226690.708
100_L108_I0.226110.706
90_F102_K0.225490.704
25_S108_I0.224330.700
29_L39_A0.223590.698
74_S122_I0.22260.695
35_A130_K0.221520.691
15_T49_E0.220680.689
127_K131_E0.21920.684
28_L124_N0.218420.682
59_Q63_I0.218160.681
50_V109_F0.217480.679
75_V101_K0.21730.678
21_S26_N0.214590.670
115_V120_G0.213920.668
98_S102_K0.213180.665
46_F53_K0.212160.662
39_A46_F0.207960.649
83_Y95_E0.207650.648
19_N107_G0.204640.639
17_F48_L0.204220.637
84_E123_A0.203950.637
80_F106_S0.202580.632
48_L53_K0.201530.629
24_A110_Q0.201370.628
14_I37_S0.201280.628
83_Y100_L0.200260.625
114_V121_K0.199930.624
64_L74_S0.198930.621
22_S25_S0.198860.621
16_L28_L0.197490.616
26_N54_P0.19650.613
31_L126_E0.195320.610
93_D97_G0.193960.605
25_S29_L0.193360.603
62_Y120_G0.192460.601
76_L82_E0.190930.596
26_N30_N0.189330.591
15_T115_V0.18830.588
76_L83_Y0.188090.587
98_S101_K0.187640.586
119_N132_I0.187620.586
110_Q123_A0.186930.583
121_K131_E0.186010.581
109_F122_I0.185760.580
27_R79_A0.185520.579
92_E96_F0.184880.577
14_I116_D0.184620.576
84_E91_S0.184180.575
33_K47_E0.183980.574
38_N46_F0.182980.571
74_S79_A0.182460.569
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
2m46A0.932399.90.241
3fz4A0.864799.90.276
3f0iA0.879799.90.279
3l78A0.842199.90.3
3rdwA0.887299.90.303
3gkxA0.872299.90.303
1s3cA0.857199.90.319
1rw1A0.827199.90.35
2kokA0.864799.90.356
1z3eA0.849699.80.366

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