GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF3834 - Protein of unknown function (DUF3834)
Pfam: PF12916 (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: CL0177
Length: 201
Sequences: 6595
Seq/Len: 32.81
HH_delta: 0.429 (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
72_A115_V1.450084.530
170_D173_G1.448374.525
166_L170_D1.384314.325
70_R96_E1.248943.902
69_P116_D1.122413.507
70_R98_V1.121013.502
154_D158_S1.04113.253
165_D169_E0.742092.318
155_Y159_A0.71662.239
81_D85_R0.707452.210
100_T109_M0.70242.194
173_G176_E0.697282.178
176_E180_S0.668652.089
106_I118_A0.631961.974
86_A89_D0.587521.836
161_E165_D0.583741.824
133_L136_S0.583081.822
71_I117_S0.567521.773
36_V149_V0.564551.764
67_G94_K0.55811.744
176_E179_A0.556831.740
70_R116_D0.53591.674
166_L173_G0.526461.645
172_E176_E0.517631.617
177_Y181_K0.516251.613
110_L115_V0.508641.589
66_I117_S0.508491.589
71_I95_A0.498021.556
159_A162_E0.469251.466
39_D43_S0.463891.449
158_S162_E0.460671.439
88_L93_I0.457961.431
54_V157_I0.454351.419
36_V153_P0.448851.402
108_K111_N0.445391.392
60_M63_Y0.431381.348
86_A90_L0.429541.342
115_V118_A0.425871.331
149_V153_P0.423361.323
32_G150_N0.420311.313
50_R151_G0.418171.306
171_P175_A0.416241.300
67_G93_I0.411761.286
73_V97_V0.407841.274
88_L95_A0.396361.238
110_L118_A0.394121.231
122_S126_K0.392181.225
36_V156_F0.390431.220
66_I69_P0.383881.199
167_I174_S0.380921.190
53_Y146_G0.380861.190
164_I168_R0.377361.179
173_G177_Y0.374491.170
102_D105_E0.370951.159
55_T157_I0.369571.155
159_A163_G0.363111.134
123_E126_K0.360921.128
157_I161_E0.357261.116
162_E166_L0.353151.103
45_V49_L0.350411.095
61_S65_N0.349861.093
107_V111_N0.345451.079
81_D99_Y0.3341.043
154_D157_I0.328561.026
156_F160_Y0.326171.019
109_M115_V0.320761.002
41_I45_V0.317480.992
172_E175_A0.313560.980
162_E165_D0.312680.977
109_M114_E0.311870.974
165_D168_R0.309630.967
177_Y180_S0.309290.966
76_K99_Y0.309060.966
105_E109_M0.308730.965
72_A110_L0.308030.962
166_L169_E0.305740.955
108_K112_E0.299180.935
100_T106_I0.295510.923
155_Y158_S0.295420.923
161_E164_I0.294920.921
133_L137_L0.290360.907
56_I144_S0.290150.906
72_A98_V0.286820.896
59_L117_S0.286340.895
88_L91_K0.285630.892
160_Y164_I0.283780.887
54_V153_P0.283620.886
52_D151_G0.279530.873
74_W80_A0.279410.873
72_A106_I0.279130.872
106_I110_L0.273410.854
67_G88_L0.271560.848
72_A109_M0.271260.847
87_L91_K0.268210.838
148_Y152_D0.267410.835
69_P117_S0.266760.833
84_T97_V0.265510.830
103_M121_G0.263260.822
73_V81_D0.26280.821
122_S125_S0.261920.818
45_V48_G0.26180.818
105_E108_K0.261230.816
158_S161_E0.261030.816
141_A144_S0.260580.814
153_P157_I0.257120.803
171_P176_E0.256710.802
129_T132_D0.25390.793
175_A179_A0.252130.788
78_S81_D0.25020.782
43_S46_K0.246870.771
55_T161_E0.246770.771
52_D149_V0.24670.771
168_R172_E0.245780.768
120_V124_F0.244440.764
60_M65_N0.243320.760
80_A83_L0.239970.750
82_V86_A0.239870.749
120_V125_S0.239690.749
65_N68_K0.239430.748
36_V160_Y0.237280.741
65_N69_P0.236470.739
164_I167_I0.234770.733
74_W121_G0.233290.729
174_S177_Y0.231830.724
38_L164_I0.230710.721
79_A82_V0.230230.719
43_S47_R0.229910.718
77_G81_D0.229240.716
38_L147_A0.229010.715
156_F159_A0.227960.712
44_L47_R0.227950.712
74_W102_D0.226490.708
132_D135_G0.225620.705
36_V54_V0.225390.704
139_L142_P0.224890.703
150_N154_D0.220780.690
130_F133_L0.219660.686
41_I44_L0.219490.686
80_A121_G0.218270.682
60_M125_S0.217390.679
81_D97_V0.216810.677
91_K95_A0.215630.674
122_S142_P0.213890.668
104_S124_F0.212850.665
104_S108_K0.21280.665
121_G124_F0.212660.664
42_V48_G0.211780.662
68_K94_K0.211220.660
89_D92_G0.211030.659
39_D53_Y0.21060.658
81_D121_G0.210050.656
80_A119_V0.208660.652
72_A100_T0.208020.650
84_T119_V0.207760.649
106_I109_M0.206460.645
153_P156_F0.205320.641
113_G116_D0.205160.641
70_R115_V0.202170.632
166_L174_S0.201710.630
132_D136_S0.200440.626
82_V85_R0.200370.626
72_A116_D0.200140.625
72_A118_A0.199940.625
73_V76_K0.199770.624
103_M106_I0.197670.618
45_V50_R0.196540.614
40_S44_L0.193940.606
157_I160_Y0.193340.604
73_V78_S0.192480.601
125_S145_C0.191930.600
80_A84_T0.191580.599
46_K94_K0.190260.594
33_K114_E0.189660.593
39_D44_L0.189120.591
59_L63_Y0.188840.590
32_G152_D0.188610.589
57_K122_S0.188290.588
170_D174_S0.18820.588
107_V110_L0.188140.588
77_G80_A0.187820.587
41_I46_K0.187710.586
168_R171_P0.187330.585
178_I181_K0.186980.584
134_L137_L0.186820.584
171_P174_S0.186040.581
121_G145_C0.186010.581
74_W84_T0.184850.578
162_E169_E0.183770.574
88_L97_V0.183630.574
36_V148_Y0.181990.569
39_D42_V0.180250.563
39_D56_I0.179390.560
79_A84_T0.178060.556
38_L41_I0.177010.553
98_V114_E0.176990.553
169_E172_E0.176450.551
68_K95_A0.176340.551
67_G95_A0.176050.550
54_V149_V0.175910.550
128_E132_D0.175630.549
93_I117_S0.174940.547
69_P95_A0.174890.546
110_L119_V0.174550.545
163_G166_L0.174350.545
52_D161_E0.174320.545
66_I93_I0.174320.545
55_T147_A0.174040.544
90_L137_L0.173870.543
49_L52_D0.173290.541
58_K145_C0.171630.536
55_T164_I0.171440.536
84_T87_L0.171010.534
38_L139_L0.170580.533
163_G167_I0.170150.532
127_G130_F0.169970.531
78_S121_G0.169710.530
45_V60_M0.169390.529
131_E134_L0.169150.528
79_A106_I0.169110.528
91_K164_I0.169040.528
129_T134_L0.167990.525
85_R97_V0.167620.524
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
3hn0A0.985199.70.429
3un6A0.970199.70.429
3mstA0.955299.70.463
2i49A0.980199.60.476
3ksxA0.960299.60.48
2g29A0.980199.60.484
4gvoA0.915499.60.484
4eswA0.970199.60.488
1zbmA0.965299.60.498
3vv5A0.895599.60.51

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