GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF1273 - Protein of unknown function (DUF1273)
Pfam: PF06908 (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: CL0349
Length: 177
Sequences: 2241
Seq/Len: 12.66
HH_delta: 0.066 (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
127_V155_Y1.158294.139
56_L91_N0.999033.570
52_L90_A0.894893.197
84_G111_R0.748532.674
50_G95_Y0.747522.671
138_D143_G0.663492.371
3_R47_I0.642972.297
76_L98_I0.641942.294
5_C133_L0.579062.069
57_W61_V0.554371.981
60_E97_S0.548311.959
74_L98_I0.534691.910
89_E92_Q0.52831.888
9_Y12_Y0.527661.885
86_N95_Y0.496231.773
31_L35_I0.494511.767
97_S101_Q0.492191.759
32_K64_E0.486011.737
5_C130_S0.475951.701
30_A166_I0.467761.671
12_Y54_V0.460691.646
93_E97_S0.457371.634
6_F58_A0.448451.602
61_V65_L0.44451.588
50_G76_L0.444211.587
92_Q96_Q0.443291.584
46_F58_A0.435991.558
132_G164_D0.433741.550
108_V121_K0.430581.538
130_S133_L0.425851.522
20_K137_Y0.423821.514
120_Q147_Y0.420411.502
6_F35_I0.415881.486
5_C126_M0.411.465
128_D155_Y0.407011.454
133_L152_A0.397411.420
59_A74_L0.394511.410
54_V136_V0.390341.395
56_L94_R0.388291.387
4_C134_I0.385871.379
93_E96_Q0.381141.362
45_W75_A0.374461.338
78_L95_Y0.369521.320
39_I72_I0.369511.320
31_L136_V0.368551.317
35_I61_V0.366541.310
35_I39_I0.364811.303
150_R154_K0.363421.298
115_S118_Q0.352681.260
4_C46_F0.351631.256
46_F62_V0.346811.239
12_Y57_W0.341361.220
45_W73_K0.337451.206
31_L61_V0.327471.170
152_A163_I0.323571.156
136_V166_I0.318261.137
99_L103_D0.31641.130
97_S100_E0.311271.112
39_I65_L0.304011.086
77_V125_F0.303941.086
127_V148_T0.300071.072
109_S112_P0.297721.064
28_K57_W0.295491.056
36_I64_E0.288971.032
32_K61_V0.287241.026
36_I40_E0.286171.022
79_P118_Q0.285831.021
134_I166_I0.283551.013
95_Y104_F0.282121.008
7_T149_V0.282071.008
75_A103_D0.281961.007
135_A149_V0.281811.007
81_E114_Y0.278350.995
108_V112_P0.278090.994
34_Q166_I0.277840.993
85_N113_Y0.275940.986
147_Y151_A0.275730.985
82_N106_V0.275710.985
50_G78_L0.274140.979
28_K60_E0.271950.972
77_V129_H0.271750.971
139_G145_T0.270350.966
107_V124_R0.268890.961
64_E97_S0.267140.954
80_F86_N0.266790.953
32_K60_E0.264430.945
48_T59_A0.261570.935
108_V118_Q0.259020.925
149_V163_I0.258310.923
49_G122_R0.257190.919
33_K37_E0.256810.918
153_K156_Q0.255550.913
3_R130_S0.254760.910
87_W119_L0.252460.902
22_P30_A0.251170.897
88_N91_N0.251080.897
51_A55_D0.247090.883
36_I65_L0.246760.882
126_M148_T0.243590.870
151_A154_K0.243220.869
12_Y28_K0.240680.860
39_I62_V0.238240.851
85_N111_R0.237930.850
9_Y145_T0.237250.848
39_I61_V0.236590.845
138_D146_K0.2330.833
98_I102_A0.226320.809
9_Y139_G0.225950.807
10_R49_G0.225390.805
37_E40_E0.225120.804
118_Q121_K0.223950.800
56_L60_E0.22190.793
35_I65_L0.219510.784
79_P120_Q0.217970.779
123_N148_T0.21790.779
4_C132_G0.216840.775
80_F85_N0.215190.769
106_V110_E0.21460.767
21_D28_K0.211460.756
79_P108_V0.210170.751
6_F134_I0.207650.742
4_C38_L0.207480.741
117_G121_K0.206670.738
51_A144_G0.205880.736
133_L163_I0.204780.732
119_L123_N0.204610.731
28_K32_K0.204610.731
21_D29_K0.204470.731
145_T149_V0.203790.728
78_L104_F0.203350.727
96_Q100_E0.203130.726
47_I126_M0.202450.723
55_D144_G0.201290.719
62_V72_I0.201150.719
125_F128_D0.200530.716
11_P139_G0.198740.710
35_I46_F0.197670.706
55_D122_R0.197290.705
3_R45_W0.194450.695
122_R148_T0.194410.695
135_A165_L0.193650.692
2_K43_V0.192330.687
94_R98_I0.192140.687
78_L82_N0.191720.685
122_R144_G0.191180.683
112_P118_Q0.191150.683
60_E64_E0.189990.679
34_Q134_I0.18990.679
119_L143_G0.186330.666
123_N144_G0.185740.664
80_F108_V0.18540.662
49_G55_D0.185190.662
61_V64_E0.184770.660
62_V74_L0.184740.660
109_S121_K0.184140.658
107_V110_E0.181710.649
52_L89_E0.181710.649
48_T144_G0.179790.642
146_K149_V0.179680.642
59_A63_L0.17960.642
11_P117_G0.177570.634
2_K131_D0.177130.633
48_T74_L0.176380.630
28_K31_L0.175980.629
127_V151_A0.175970.629
82_N85_N0.173510.620
80_F114_Y0.171620.613
32_K65_L0.17160.613
11_P52_L0.170730.610
48_T55_D0.170550.609
86_N104_F0.170190.608
10_R122_R0.169620.606
127_V153_K0.168210.601
133_L136_V0.167690.599
85_N112_P0.167460.598
147_Y150_R0.167340.598
55_D123_N0.166580.595
131_D161_Y0.164110.586
28_K61_V0.163810.585
43_V131_D0.163340.584
21_D64_E0.162790.582
20_K30_A0.161150.576
31_L57_W0.161120.576
12_Y58_A0.160620.574
96_Q99_L0.160120.572
120_Q162_P0.15990.571
9_Y137_Y0.159540.570
132_G162_P0.158280.566
7_T123_N0.158180.565
96_Q101_Q0.157070.561
104_F107_V0.156660.560
49_G144_G0.156520.559
7_T148_T0.15650.559
50_G104_F0.15620.558
32_K40_E0.155740.556
59_A76_L0.155530.556
107_V111_R0.155420.555
9_Y138_D0.154940.554
63_L94_R0.153440.548
79_P106_V0.152990.547
37_E41_E0.152690.546
85_N89_E0.152540.545
120_Q138_D0.152070.543
34_Q37_E0.150780.539
36_I61_V0.150480.538
121_K151_A0.150010.536
116_P151_A0.148820.532
29_K32_K0.14880.532
75_A106_V0.147780.528
40_E65_L0.147510.527
88_N119_L0.146390.523
42_G65_L0.145720.521
49_G143_G0.145630.520
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
2nx2A11000.066
3uqzA0.86441000.32
3majA0.85881000.323
2iz6A0.762799.60.627
1rcuA0.77499.50.633
2a33A0.785399.40.667
1wehA0.79199.30.68
1t35A0.79199.30.68
1wekA0.79199.30.681
1ydhA0.7853990.729

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