GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF721 - Protein of unknown function (DUF721)
Pfam: PF05258 (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: CL0424
Length: 89
Sequences: 1138
Seq/Len: 12.79
HH_delta: 0.817 (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
40_H56_D0.46932.562
29_W41_T0.43432.371
29_W33_V0.362651.980
49_G85_K0.360081.966
50_T86_D0.346491.892
40_H60_W0.338651.849
46_I84_I0.337121.841
68_K86_D0.329491.799
33_V71_I0.314371.716
42_R54_E0.314291.716
31_Q78_F0.311431.700
63_E67_M0.306861.675
73_K77_E0.288921.577
64_L89_F0.283811.550
44_V54_E0.27631.509
37_L60_W0.271711.483
68_K72_L0.264931.446
65_R68_K0.260421.422
11_K16_K0.256771.402
55_V58_S0.254621.390
3_G7_E0.254461.389
72_L87_I0.251971.376
72_L76_N0.238931.305
9_L13_S0.236251.290
74_K77_E0.236141.289
34_G38_A0.233341.274
41_T64_L0.229561.253
30_K35_P0.224111.224
5_L9_L0.22351.220
29_W53_I0.219721.200
67_M70_Q0.216171.180
29_W34_G0.208391.138
43_P51_L0.205991.125
28_N31_Q0.205611.123
8_E12_K0.205141.120
28_N75_L0.204971.119
29_W32_I0.203241.110
62_Q65_R0.202971.108
70_Q73_K0.201331.099
30_K39_Q0.199071.087
79_L83_A0.197431.078
33_V38_A0.195341.067
80_G83_A0.195041.065
35_P39_Q0.19321.055
59_A63_E0.192861.053
62_Q66_Y0.189321.034
68_K87_I0.18921.033
33_V41_T0.188741.030
4_D10_L0.183111.000
28_N42_R0.179520.980
69_P72_L0.176770.965
50_T88_R0.173440.947
60_W63_E0.173390.947
46_I78_F0.173140.945
68_K89_F0.172390.941
76_N83_A0.170970.933
66_Y84_I0.169070.923
8_E11_K0.167070.912
22_L45_S0.165090.901
71_I76_N0.164240.897
16_K66_Y0.162560.888
25_L50_T0.162450.887
7_E11_K0.161890.884
15_L40_H0.159370.870
65_R69_P0.15690.857
76_N79_L0.154980.846
25_L78_F0.150130.820
57_S61_A0.149370.816
55_V89_F0.148650.812
43_P62_Q0.147910.808
51_L77_E0.147910.808
47_K52_V0.147010.803
55_V61_A0.145850.796
47_K88_R0.145240.793
75_L79_L0.143630.784
4_D12_K0.143130.781
11_K14_G0.141970.775
4_D7_E0.141310.772
16_K86_D0.140440.767
37_L41_T0.140110.765
34_G46_I0.13920.760
37_L87_I0.138640.757
6_L19_A0.138630.757
24_R87_I0.138580.757
70_Q74_K0.138080.754
12_K88_R0.136180.744
72_L84_I0.135260.738
11_K87_I0.135210.738
72_L82_P0.134020.732
43_P53_I0.133870.731
3_G8_E0.132510.723
15_L60_W0.131490.718
26_Q43_P0.131090.716
5_L24_R0.1310.715
33_V70_Q0.130840.714
5_L14_G0.130760.714
14_G58_S0.130620.713
5_L13_S0.130480.712
61_A65_R0.129930.709
19_A44_V0.129110.705
49_G52_V0.129070.705
24_R41_T0.128140.700
82_P85_K0.127840.698
32_I75_L0.127480.696
29_W43_P0.126520.691
35_P38_A0.125450.685
74_K87_I0.124110.678
53_I71_I0.122910.671
10_L52_V0.122270.668
22_L46_I0.121080.661
28_N78_F0.120410.657
18_R31_Q0.120010.655
10_L26_Q0.119770.654
22_L87_I0.119680.653
66_Y79_L0.119570.653
59_A62_Q0.119370.652
24_R28_N0.11930.651
44_V56_D0.11930.651
65_R73_K0.119140.650
40_H53_I0.118750.648
22_L27_Q0.11870.648
23_A45_S0.118010.644
70_Q78_F0.116890.638
53_I75_L0.116810.638
7_E59_A0.116450.636
43_P61_A0.116390.635
25_L38_A0.116210.634
43_P54_E0.115620.631
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
2e0gA0.786562.60.817
2z4sA0.752846.20.833
2wp0C0.831532.20.846
2d28C0.898928.50.85
2vqeC0.57313.20.87
3qxzA0.629211.90.873
1cq4A0.505610.80.875
4iqjM0.86529.50.878
1th5A0.7649.40.878
2ayaA0.95517.60.883
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