GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF1904 - Domain of unknown function (DUF1904)
Pfam: PF08921 (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: CL0082
Length: 108
Sequences: 1455
Seq/Len: 13.47
HH_delta: 0.18 (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
66_G69_V0.405382.319
6_F21_L0.39422.255
74_A94_F0.372752.132
27_E76_A0.372052.128
39_E44_T0.347071.985
78_T90_V0.327881.875
79_E83_K0.321511.839
4_L21_L0.313721.794
7_R41_I0.311021.779
67_Q100_S0.310951.779
20_E84_A0.305531.748
23_D27_E0.269461.541
23_D33_R0.268691.537
25_L36_F0.266361.523
75_Q79_E0.264411.512
5_R59_E0.263151.505
14_V44_T0.256461.467
67_Q71_D0.254651.457
10_E13_Q0.25181.440
82_K87_Y0.251061.436
72_K76_A0.24391.395
20_E80_H0.24071.377
16_E84_A0.235051.344
20_E83_K0.229671.314
61_L95_T0.228951.310
23_D80_H0.225531.290
22_I26_A0.225041.287
29_C62_W0.224841.286
70_Q101_N0.222091.270
72_K75_Q0.219471.255
76_A79_E0.218261.248
70_Q96_D0.217841.246
52_S89_D0.21671.239
73_V77_I0.210931.206
24_E80_H0.201331.152
31_C91_A0.200811.149
97_L101_N0.198291.134
8_G39_E0.196041.121
97_L102_Y0.195531.118
32_P35_N0.192811.103
4_L25_L0.192111.099
9_I54_G0.188651.079
19_K23_D0.18791.075
15_Q46_I0.186351.066
24_E76_A0.186221.065
37_T91_A0.184581.056
22_I33_R0.182661.045
59_E95_T0.181551.038
18_S21_L0.180641.033
66_G70_Q0.178181.019
64_D96_D0.177131.013
55_Y91_A0.175041.001
10_E19_K0.173710.994
57_F93_I0.172430.986
68_E72_K0.170770.977
19_K79_E0.170020.972
68_E71_D0.167160.956
18_S36_F0.166960.955
27_E80_H0.166710.954
18_S46_I0.166160.950
63_F99_P0.165920.949
10_E20_E0.165510.947
23_D72_K0.164240.939
76_A80_H0.163210.934
59_E93_I0.162310.928
16_E20_E0.161770.925
28_I76_A0.16080.920
61_L93_I0.160030.915
5_R61_L0.159960.915
22_I38_L0.159570.913
37_T57_F0.15910.910
4_L58_V0.156640.896
70_Q74_A0.156430.895
67_Q96_D0.154380.883
4_L60_V0.154310.883
94_F102_Y0.152480.872
18_S37_T0.151690.868
26_A33_R0.151430.866
9_I13_Q0.150320.860
74_A78_T0.149190.853
18_S35_N0.147840.846
95_T101_N0.14620.836
62_W70_Q0.146110.836
20_E82_K0.145920.835
30_G69_V0.145690.833
24_E73_V0.145310.831
13_Q54_G0.145170.830
50_E68_E0.14490.829
51_I89_D0.144650.827
3_H102_Y0.144570.827
13_Q84_A0.144360.826
71_D75_Q0.143940.823
78_T92_V0.143130.819
65_R73_V0.141610.810
16_E52_S0.141390.809
33_R50_E0.139850.800
93_I102_Y0.139840.800
63_F97_L0.139020.795
22_I25_L0.138890.794
17_L84_A0.138840.794
45_F90_V0.137870.789
36_F61_L0.137850.788
31_C64_D0.135290.774
18_S28_I0.135010.772
74_A92_V0.134860.771
72_K83_K0.134010.766
31_C62_W0.133520.764
65_R70_Q0.13250.758
18_S93_I0.132250.756
91_A97_L0.13220.756
25_L66_G0.132090.756
60_V96_D0.131940.755
43_S47_F0.131440.752
63_F93_I0.1310.749
80_H84_A0.130870.749
30_G72_K0.130440.746
59_E63_F0.130210.745
70_Q94_F0.129840.743
58_V73_V0.129780.742
35_N91_A0.12920.739
46_I49_G0.129090.738
6_F26_A0.128340.734
16_E19_K0.128340.734
61_L97_L0.127370.729
13_Q79_E0.126930.726
10_E16_E0.126730.725
79_E87_Y0.126160.722
53_E88_Q0.126080.721
45_F55_Y0.126070.721
93_I97_L0.125910.720
22_I36_F0.125840.720
63_F74_A0.12560.718
21_L25_L0.124470.712
6_F81_V0.123070.704
23_D84_A0.123060.704
35_N48_D0.122750.702
54_G89_D0.122110.698
3_H55_Y0.121870.697
8_G14_V0.121660.696
51_I54_G0.121360.694
37_T102_Y0.120660.690
8_G44_T0.12030.688
96_D101_N0.120270.688
3_H14_V0.119160.682
18_S62_W0.118860.680
9_I15_Q0.118850.680
15_Q43_S0.118540.678
56_P60_V0.118230.676
17_L38_L0.118070.675
13_Q16_E0.117730.673
12_E23_D0.117540.672
5_R18_S0.11670.667
7_R20_E0.116590.667
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
1u9dA0.972299.80.18
3t5sA0.990799.70.2
1uizA0.990799.70.213
2os5A0.990799.70.214
2xczA0.990799.70.215
3fwtA0.981599.70.228
2aalA199.70.237
4dh4A0.990799.70.24
3fwuA0.981599.70.243
2wkbA0.990799.70.249

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