GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4062 - Domain of unknown function (DUF4062)
Pfam: PF13271 (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: 83
Sequences: 485
Seq/Len: 5.84
HH_delta: 0.734 (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
7_T10_D0.301222.425
10_D63_R0.294912.374
16_D20_E0.275662.219
61_G64_Y0.211241.700
10_D46_C0.210881.698
6_S15_R0.210531.695
30_V34_F0.208441.678
3_F35_F0.20451.646
2_V29_P0.200121.611
73_I78_L0.19871.600
11_L61_G0.186161.499
43_L47_L0.177241.427
11_L63_R0.171891.384
7_T63_R0.165531.332
8_F63_R0.164231.322
41_S44_E0.162931.312
9_R63_R0.160941.296
41_S52_E0.160681.293
7_T46_C0.158221.274
15_R33_E0.154111.241
18_L22_I0.151591.220
20_E24_R0.14541.170
4_I59_I0.144691.165
31_G34_F0.14441.162
27_C31_G0.144261.161
46_C63_R0.143741.157
17_A21_A0.142561.148
73_I77_E0.139641.124
6_S46_C0.138641.116
18_L52_E0.137841.110
68_P78_L0.137481.107
3_F49_E0.135221.089
18_L26_G0.134431.082
27_C34_F0.134181.080
23_R29_P0.133791.077
64_Y77_E0.130821.053
14_E60_L0.129931.046
23_R27_C0.129181.040
2_V54_D0.126941.022
52_E71_S0.126811.021
29_P58_L0.126771.020
22_I55_I0.126031.015
32_M43_L0.125831.013
40_Q48_K0.124651.003
48_K52_E0.122120.983
1_R49_E0.121360.977
26_G34_F0.120010.966
23_R31_G0.117830.949
5_S46_C0.116810.940
21_A51_D0.115730.932
3_F37_A0.115460.929
6_S76_T0.115440.929
43_L46_C0.114470.921
29_P48_K0.11410.918
58_L62_N0.112080.902
1_R5_S0.112030.902
5_S8_F0.110940.893
1_R35_F0.108780.876
13_E71_S0.108740.875
16_D67_V0.107870.868
14_E45_I0.107810.868
7_T60_L0.10740.865
20_E63_R0.104290.840
32_M35_F0.104180.839
42_P63_R0.104120.838
20_E72_G0.103880.836
39_D51_D0.102920.828
19_I31_G0.102330.824
13_E62_N0.102150.822
2_V62_N0.101780.819
50_V54_D0.101110.814
48_K55_I0.100130.806
49_E61_G0.099950.805
43_L78_L0.099720.803
26_G29_P0.099570.802
25_L30_V0.09930.799
3_F64_Y0.098040.789
7_T75_Y0.097850.788
29_P35_F0.097770.787
4_I22_I0.097430.784
24_R43_L0.097430.784
75_Y78_L0.097380.784
37_A58_L0.097180.782
72_G77_E0.09670.778
28_E31_G0.096490.777
25_L57_I0.09590.772
54_D58_L0.094770.763
2_V11_L0.094660.762
9_R16_D0.094660.762
23_R52_E0.092710.746
6_S33_E0.092230.742
29_P33_E0.092220.742
37_A45_I0.092190.742
56_F62_N0.092180.742
12_K67_V0.092140.742
38_S43_L0.091950.740
4_I70_D0.091680.738
52_E70_D0.091350.735
38_S57_I0.091340.735
47_L73_I0.091240.734
17_A26_G0.091130.734
49_E52_E0.091110.733
20_E70_D0.090880.732
11_L15_R0.090830.731
46_C75_Y0.090190.726
9_R28_E0.089990.724
8_F32_M0.08990.724
39_D59_I0.089750.722
27_C56_F0.089670.722
48_K70_D0.089610.721
19_I23_R0.089330.719
30_V53_C0.089230.718
44_E52_E0.088770.715
39_D73_I0.088760.715
43_L75_Y0.088360.711
28_E40_Q0.087830.707
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
4fykA0.867596.80.734
2khzA0.879596.80.737
3h16A0.927796.20.754
1s2dA0.915794.80.78
1f8yA0.915794.70.78
2j67A0.927794.50.783
3ehdA0.915794.50.783
3jrnA0.927794.50.784
1fyxA0.927794.30.785
1eiwA0.698894.20.786
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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