GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF58 - Protein of unknown function DUF58
Pfam: PF01882 (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: CL0128
Length: 86
Sequences: 2279
Seq/Len: 26.5
HH_delta: 0.547 (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
20_H33_K0.907133.469
44_W85_G0.738162.823
8_R14_D0.719182.750
5_S36_E0.625382.392
45_I70_A0.585482.239
9_P29_E0.568012.172
78_L84_V0.557022.130
43_V77_A0.521561.995
19_I30_L0.508261.944
47_L66_A0.473031.809
3_D36_E0.456991.748
20_H23_A0.444261.699
53_M66_A0.442341.692
24_S30_L0.430071.645
42_P83_P0.419531.604
8_R34_E0.416461.593
47_L70_A0.415841.590
16_L19_I0.404471.547
45_I74_A0.35761.368
23_A31_M0.350061.339
65_R68_S0.338941.296
4_F7_L0.336371.286
48_D53_M0.336091.285
6_G34_E0.333351.275
27_T31_M0.328481.256
18_R35_F0.309781.185
4_F33_K0.305511.168
10_Y14_D0.300411.149
7_L33_K0.298411.141
9_P31_M0.296451.134
7_L23_A0.295241.129
7_L31_M0.293691.123
19_I24_S0.290611.111
42_P85_G0.290451.111
77_A82_D0.291.109
74_A84_V0.28551.092
10_Y13_G0.277211.060
47_L63_F0.27681.059
49_L63_F0.275951.055
7_L20_H0.275151.052
64_E67_L0.268011.025
61_S64_E0.266381.019
10_Y21_W0.262211.003
63_F67_L0.257510.985
53_M62_K0.255310.976
62_K65_R0.249650.955
24_S31_M0.249460.954
52_S55_F0.249410.954
21_W25_A0.248050.949
5_S34_E0.242090.926
72_S76_Q0.239090.914
4_F35_F0.238010.910
36_E72_S0.235470.901
20_H26_R0.2350.899
24_S27_T0.234120.895
77_A84_V0.232990.891
2_E83_P0.229230.877
23_A26_R0.226420.866
76_Q80_Q0.216050.826
18_R44_W0.214960.822
11_Q15_P0.213290.816
74_A78_L0.213250.816
10_Y16_L0.21260.813
21_W33_K0.211010.807
69_A73_L0.208840.799
45_I84_V0.208550.798
14_D32_V0.208170.796
73_L84_V0.207390.793
14_D21_W0.199920.765
64_E71_A0.192750.737
49_L67_L0.191070.731
55_F62_K0.189070.723
9_P69_A0.187680.718
8_R26_R0.186770.714
28_G54_Y0.185220.708
23_A85_G0.185120.708
67_L71_A0.184780.707
7_L24_S0.183650.702
49_L54_Y0.183520.702
2_E35_F0.180840.692
80_Q83_P0.180460.690
12_P29_E0.179550.687
5_S18_R0.176750.676
50_S66_A0.17560.672
15_P18_R0.175510.671
39_R80_Q0.172890.661
45_I73_L0.172560.660
76_Q79_R0.171090.654
37_E76_Q0.170480.652
39_R83_P0.168560.645
61_S65_R0.167970.642
25_A64_E0.167440.640
22_K34_E0.167220.640
3_D38_E0.166960.639
30_L56_G0.165950.635
2_E79_R0.165180.632
37_E48_D0.164650.630
40_S83_P0.164290.628
41_Q71_A0.161910.619
20_H48_D0.161220.617
71_A75_N0.16120.616
10_Y15_P0.159270.609
20_H82_D0.157230.601
6_G23_A0.156280.598
23_A35_F0.15610.597
20_H35_F0.155690.595
49_L78_L0.155660.595
40_S86_L0.155360.594
51_P54_Y0.15480.592
52_S62_K0.15460.591
56_G68_S0.151740.580
54_Y63_F0.151460.579
70_A73_L0.150790.577
27_T30_L0.150770.577
22_K55_F0.149350.571
46_V66_A0.149030.570
52_S75_N0.147480.564
54_Y61_S0.146850.562
22_K68_S0.146710.561
47_L86_L0.146240.559
26_R77_A0.145990.558
15_P53_M0.144130.551
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
2nvoA0.988498.60.547
1yvrA0.976798.30.596
2x31A0.534988.60.806
1jeyB0.616385.80.814
3tvyA0.651283.90.819
2odpA0.581483.40.82
4jduA0.604783.30.82
2x5nA0.558181.40.823
1mjnA0.577.50.83
3ibsA0.639576.80.831
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