GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF970 - Protein of unknown function (DUF970)
Pfam: PF06153 (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: CL0089
Length: 109
Sequences: 1923
Seq/Len: 17.64
HH_delta: 0.011 (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
47_G103_V1.250374.111
48_V56_V0.883232.904
52_K55_E0.871492.865
6_A60_I0.722652.376
5_I101_L0.698492.297
16_L64_C0.656042.157
23_N59_I0.614932.022
54_D58_E0.584681.922
49_E52_K0.582491.915
61_K65_K0.575391.892
29_K33_T0.571681.880
12_D15_D0.552871.818
57_L100_V0.536461.764
59_I63_N0.508031.670
13_A30_L0.494081.624
3_L47_G0.473731.558
4_I56_V0.471441.550
58_E62_E0.460371.514
57_L98_V0.447511.471
2_K50_D0.443611.459
55_E59_I0.423541.393
54_D105_Q0.413651.360
25_F56_V0.400661.317
58_E61_K0.391351.287
20_L56_V0.384691.265
55_E58_E0.384321.264
11_E15_D0.376731.239
8_V44_L0.372031.223
21_N36_F0.364211.197
2_K104_E0.360021.184
31_S43_T0.359131.181
19_A62_E0.358041.177
1_M50_D0.355491.169
47_G99_F0.352511.159
3_L101_L0.34121.122
31_S45_L0.334271.099
23_N55_E0.333831.098
52_K56_V0.329361.083
53_V57_L0.325661.071
7_I99_F0.325081.069
26_R56_V0.318221.046
5_I47_G0.316281.040
19_A59_I0.315551.037
53_V100_V0.313231.030
66_K95_G0.291740.959
8_V16_L0.289360.951
9_Q92_E0.287370.945
2_K102_D0.282830.930
39_E93_V0.265820.874
20_L25_F0.263990.868
2_K53_V0.262130.862
19_A22_E0.261760.861
55_E62_E0.261220.859
37_L97_T0.257990.848
2_K100_V0.257880.848
37_L94_G0.255720.841
100_V105_Q0.254520.837
97_T106_F0.253850.835
7_I29_K0.251730.828
19_A63_N0.24960.821
46_I56_V0.248310.816
17_S105_Q0.248040.816
5_I45_L0.246440.810
21_N26_R0.245920.809
48_V53_V0.245640.808
67_R95_G0.242850.798
3_L103_V0.233750.769
5_I43_T0.232130.763
18_D22_E0.231050.760
4_I48_V0.230560.758
26_R49_E0.228720.752
61_K107_E0.228230.750
1_M4_I0.227190.747
17_S44_L0.226860.746
21_N33_T0.226440.744
59_I62_E0.226320.744
11_E36_F0.224970.740
54_D61_K0.224680.739
48_V52_K0.224070.737
6_A46_I0.218390.718
62_E65_K0.217930.717
33_T43_T0.21740.715
27_V108_K0.21570.709
16_L63_N0.211950.697
11_E92_E0.209120.688
98_V107_E0.207530.682
10_D42_T0.207120.681
36_F67_R0.206620.679
8_V60_I0.203620.669
39_E97_T0.201670.663
57_L105_Q0.201120.661
6_A64_C0.200120.658
41_N67_R0.198960.654
53_V102_D0.198690.653
9_Q95_G0.1970.648
101_L104_E0.19360.637
18_D42_T0.193010.635
21_N40_G0.191650.630
49_E59_I0.189720.624
17_S92_E0.188980.621
40_G67_R0.18890.621
37_L96_A0.187770.617
32_S40_G0.187090.615
15_D63_N0.18670.614
22_E55_E0.186640.614
27_V32_S0.185790.611
93_V108_K0.183290.603
11_E32_S0.182680.601
55_E105_Q0.181930.598
7_I106_F0.181840.598
25_F46_I0.181760.598
13_A39_E0.181080.595
17_S21_N0.180910.595
10_D39_E0.179540.590
30_L41_N0.179160.589
25_F92_E0.177880.585
50_D62_E0.177730.584
9_Q33_T0.175510.577
61_K102_D0.175380.577
12_D95_G0.175040.576
56_V105_Q0.174110.572
22_E62_E0.173960.572
50_D53_V0.173810.571
23_N56_V0.17380.571
51_E60_I0.173690.571
34_G92_E0.172620.568
37_L95_G0.172520.567
25_F34_G0.172070.566
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
3m05A11000.011
3t9zA0.779899.90.234
3ncqA0.779899.90.239
4affA0.779899.80.242
3mhyA0.779899.80.272
3l7pA0.779899.80.272
2ns1B0.779899.80.275
2o66A0.779899.80.279
1hwuA0.779899.80.284
2eg2A0.779899.80.289

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