GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4212 - Domain of unknown function (DUF4212)
Pfam: PF13937 (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: 81
Sequences: 375
Seq/Len: 4.63
HH_delta: 0.888 (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
28_V32_F0.485892.869
9_K76_K0.440652.602
9_K77_Y0.398052.350
13_L69_R0.3652.155
16_I20_I0.342122.020
32_F35_E0.32531.921
20_I65_V0.295261.743
25_S59_F0.294041.736
35_E38_Q0.288371.703
69_R72_R0.287621.698
61_I65_V0.282421.668
33_A37_N0.262631.551
44_F67_A0.262181.548
17_L65_V0.253141.495
65_V69_R0.236381.396
37_N47_G0.231971.370
46_L50_F0.229441.355
75_R80_D0.219031.293
68_W72_R0.214351.266
7_W10_N0.210911.245
23_V28_V0.210051.240
5_A75_R0.209041.234
23_V27_G0.20641.219
24_V58_V0.206271.218
15_A19_A0.204861.210
27_G50_F0.204441.207
60_V64_F0.199991.181
66_Y70_M0.196121.158
12_R16_I0.186351.100
25_S50_F0.185271.094
10_N14_I0.184521.090
61_I68_W0.180511.066
3_A9_K0.175971.039
49_W52_A0.174831.032
48_F51_A0.173931.027
52_A56_I0.173151.022
37_N57_I0.170561.007
3_A77_Y0.167340.988
48_F52_A0.167220.987
33_A52_A0.16470.972
5_A58_V0.164320.970
7_W63_I0.164220.970
11_L15_A0.163490.965
74_D81_E0.161230.952
3_A26_F0.160550.948
65_V68_W0.159680.943
22_F26_F0.157070.927
34_D38_Q0.155270.917
9_K67_A0.154980.915
30_I48_F0.154010.909
71_N81_E0.151710.896
41_F46_L0.150590.889
23_V35_E0.14960.883
10_N17_L0.149410.882
12_R15_A0.148780.878
23_V80_D0.147250.869
40_T45_P0.144960.856
47_G55_S0.143570.848
6_Y48_F0.14140.835
20_I62_L0.14110.833
10_N66_Y0.140980.832
17_L69_R0.140290.828
41_F44_F0.139430.823
12_R19_A0.13880.820
6_Y63_I0.138650.819
38_Q72_R0.138070.815
26_F60_V0.137690.813
44_F47_G0.137690.813
27_G32_F0.137090.809
6_Y66_Y0.136460.806
25_S54_G0.133360.787
18_L71_N0.133070.786
4_R61_I0.132530.783
71_N80_D0.132330.781
24_V53_Q0.131740.778
37_N45_P0.130840.773
30_I56_I0.130710.772
60_V79_V0.130570.771
39_I57_I0.129730.766
67_A71_N0.129250.763
33_A45_P0.12790.755
63_I70_M0.12720.751
78_G81_E0.12720.751
30_I51_A0.12580.743
37_N44_F0.125770.743
21_W49_W0.125680.742
19_A23_V0.125450.741
8_R12_R0.12540.740
40_T44_F0.123320.728
28_V50_F0.12290.726
3_A78_G0.121750.719
38_Q68_W0.121590.718
8_R74_D0.121420.717
16_I19_A0.121180.716
33_A44_F0.119410.705
17_L70_M0.119140.703
35_E75_R0.117180.692
18_L47_G0.117070.691
74_D78_G0.117070.691
44_F71_N0.116610.689
14_I44_F0.116520.688
16_I68_W0.116480.688
48_F56_I0.116420.687
23_V38_Q0.116360.687
4_R26_F0.116140.686
5_A9_K0.115330.681
33_A38_Q0.114510.676
39_I68_W0.114380.675
3_A19_A0.113670.671
42_G49_W0.113290.669
7_W66_Y0.113070.668
27_G60_V0.112860.666
5_A78_G0.112260.663
61_I80_D0.112190.662
3_A80_D0.111730.660
57_I60_V0.111240.657
42_G64_F0.110690.654
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
4ev6A0.827259.90.888
2iubA0.876547.30.896
4i0uA0.876544.60.897
4il3A0.975323.50.911
2jlnA0.839520.50.913
4aw6A0.9506190.914
2lonA0.96314.80.918
3nd0A0.987714.20.918
3hd7A0.419813.10.92
3dh4A0.888911.80.921
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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