GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4118 - Domain of unknown function (DUF4118)
Pfam: PF13493 (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. )
Length: 105
Sequences: 1087
Seq/Len: 10.35
HH_delta: 0.165 (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
13_T33_Y0.625334.102
12_A36_A0.42872.812
20_R69_F0.41372.714
6_I51_F0.338172.218
38_L95_T0.304952.000
3_I7_V0.293331.924
81_D85_F0.269561.768
14_A18_L0.25021.641
53_A92_A0.246181.615
38_L91_V0.241271.583
8_L36_A0.22471.474
40_I44_Y0.220331.445
31_M34_L0.214071.404
31_M88_F0.20881.370
76_V82_W0.207441.361
62_F74_F0.203251.333
84_T88_F0.201111.319
57_S88_F0.193931.272
78_D81_D0.193621.270
5_T48_P0.192131.260
12_A16_S0.191441.256
4_E44_Y0.190271.248
45_G48_P0.18921.241
44_Y54_L0.186111.221
58_L62_F0.185111.214
31_M96_G0.181571.191
4_E7_V0.18031.183
58_L74_F0.175671.152
37_V92_A0.174581.145
61_N68_P0.171021.122
7_V11_L0.171011.122
81_D88_F0.169981.115
90_V94_V0.167761.100
54_L90_V0.167641.100
61_N81_D0.16741.098
9_F55_L0.159781.048
47_R93_L0.159711.048
37_V96_G0.158781.041
9_F96_G0.158491.040
45_G49_G0.15841.039
4_E43_R0.158141.037
17_L86_A0.158021.037
8_L39_L0.156221.025
15_L21_P0.156041.024
70_Y74_F0.155841.022
93_L102_Y0.1551.017
53_A96_G0.152541.001
52_A79_P0.151240.992
68_P74_F0.150530.987
30_P38_L0.149930.983
32_I87_V0.145620.955
64_F69_F0.145080.952
57_S85_F0.144510.948
28_N34_L0.143490.941
3_I15_L0.142020.932
30_P88_F0.142020.932
56_S69_F0.141120.926
25_F43_R0.140290.920
81_D84_T0.140220.920
10_L14_A0.14020.920
20_R86_A0.140070.919
57_S82_W0.13970.916
62_F70_Y0.138160.906
63_F73_T0.137450.902
16_S32_I0.1370.899
91_V99_A0.136450.895
11_L21_P0.136220.894
57_S84_T0.135710.890
53_A89_L0.134770.884
64_F73_T0.134760.884
8_L44_Y0.134720.884
41_A49_G0.134620.883
50_L73_T0.134020.879
35_L88_F0.133430.875
30_P60_L0.132970.872
87_V102_Y0.132450.869
15_L90_V0.132340.868
96_G102_Y0.132340.868
37_V99_A0.131010.859
43_R79_P0.13090.859
60_L100_D0.130540.856
73_T76_V0.12960.850
3_I6_I0.129080.847
23_D89_L0.128790.845
8_L22_F0.127920.839
52_A85_F0.12730.835
38_L49_G0.125990.826
61_N73_T0.125010.820
45_G75_L0.123990.813
46_L50_L0.12190.800
28_N87_V0.121380.796
64_F68_P0.120690.792
44_Y100_D0.120360.789
85_F88_F0.119780.786
49_G96_G0.119710.785
8_L102_Y0.11950.784
57_S81_D0.118680.778
33_Y56_S0.118380.776
37_V98_L0.118110.775
18_L28_N0.118080.775
73_T98_L0.117710.772
33_Y55_L0.117640.772
31_M57_S0.117440.770
39_L94_V0.116980.767
31_M91_V0.116220.762
49_G102_Y0.115410.757
54_L75_L0.115350.757
11_L18_L0.115130.755
3_I22_F0.114840.753
36_A40_I0.114070.748
17_L104_R0.114030.748
26_A83_I0.113950.747
91_V104_R0.112980.741
6_I104_R0.112870.740
60_L98_L0.112670.739
38_L101_R0.111380.731
49_G97_Y0.111310.730
20_R90_V0.111060.728
31_M87_V0.110590.725
70_Y103_R0.110510.725
61_N74_F0.110480.725
42_L103_R0.110470.725
62_F73_T0.110450.724
41_A97_Y0.110410.724
17_L77_Y0.109930.721
20_R70_Y0.109640.719
26_A30_P0.109190.716
13_T63_F0.109170.716
47_R51_F0.109010.715
6_I21_P0.108910.714
20_R26_A0.108890.714
61_N69_F0.10880.714
45_G50_L0.108750.713
17_L91_V0.108740.713
57_S89_L0.108590.712
8_L52_A0.108480.712
11_L47_R0.108330.711
3_I10_L0.107730.707
47_R90_V0.10720.703
3_I34_L0.106830.701
27_S77_Y0.10650.699
36_A49_G0.106420.698
50_L90_V0.105870.694
95_T99_A0.105510.692
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
2ksfA0.942999.40.165
4hzuS0.895280.40.772
3rlbA0.914372.10.787
4dveA0.9619690.791
3p5nA0.895244.40.82
4gc0A0.733326.80.839
4huqS0.857121.40.845
2xq2A0.34294.70.883
2gfpA0.6194.10.887
4eneA0.93333.90.887

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