GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4384 - Domain of unknown function (DUF4384)
Pfam: PF14326 (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: 390
Seq/Len: 4.7
HH_delta: 0.82 (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
23_L76_A0.357713.395
15_S19_G0.229792.181
13_V52_Y0.201131.909
18_D47_K0.199581.894
24_F34_L0.194641.847
5_V69_F0.186871.773
19_G78_A0.175251.663
3_Y7_E0.172481.637
24_F55_P0.17241.636
18_D45_F0.166151.577
5_V67_P0.162841.545
17_R80_T0.161011.528
18_D48_A0.158311.502
47_K50_Q0.154471.466
21_L76_A0.153531.457
34_L55_P0.150011.424
24_F75_V0.14971.421
23_L82_P0.13131.246
65_V68_P0.129541.229
20_Y44_N0.126691.202
5_V68_P0.126261.198
18_D49_G0.120711.146
65_V70_G0.119991.139
20_Y48_A0.119321.132
4_R29_D0.11731.113
59_D62_S0.116851.109
33_T81_E0.11481.089
63_F74_I0.114461.086
28_A64_T0.114241.084
22_Y77_I0.112931.072
3_Y53_T0.11261.069
21_L36_F0.112271.065
54_I67_P0.111431.057
25_Y34_L0.111.044
42_P53_T0.108671.031
13_V21_L0.108441.029
4_R26_I0.107451.020
37_P75_V0.105210.998
11_F74_I0.105070.997
46_V49_G0.104780.994
9_V78_A0.104730.994
25_Y72_E0.104470.991
7_E15_S0.104190.989
23_L54_I0.102460.972
4_R7_E0.101040.959
12_R46_V0.100530.954
14_T60_R0.100160.951
25_Y33_T0.099280.942
20_Y79_S0.099040.940
13_V54_I0.098550.935
12_R21_L0.095630.908
19_G54_I0.095160.903
32_V80_T0.094560.897
13_V24_F0.09440.896
20_Y77_I0.094310.895
25_Y73_R0.094080.893
35_L61_F0.093480.887
14_T80_T0.092890.882
75_V79_S0.092280.876
12_R53_T0.092250.875
42_P46_V0.092030.873
47_K54_I0.091810.871
31_K66_D0.08970.851
10_R28_A0.089370.848
5_V26_I0.088830.843
15_S46_V0.088670.841
22_Y34_L0.087460.830
32_V78_A0.087460.830
40_Y61_F0.087270.828
35_L46_V0.086730.823
8_R58_G0.085820.814
4_R73_R0.085390.810
19_G72_E0.084910.806
7_E73_R0.084760.804
3_Y76_A0.084440.801
65_V76_A0.084440.801
4_R17_R0.084390.801
49_G53_T0.083920.796
45_F76_A0.083740.795
14_T58_G0.083650.794
64_T81_E0.083240.790
9_V22_Y0.082910.787
2_V24_F0.082320.781
50_Q74_I0.082270.781
21_L43_D0.082110.779
22_Y72_E0.081950.778
36_F75_V0.081890.777
35_L71_K0.08180.776
30_G65_V0.081670.775
15_S18_D0.081120.770
19_G77_I0.080720.766
36_F43_D0.080570.765
23_L45_F0.080410.763
24_F73_R0.08030.762
2_V69_F0.080270.762
6_G32_V0.079630.756
37_P72_E0.079480.754
32_V41_Q0.079170.751
30_G44_N0.079110.751
51_T81_E0.078470.745
27_D34_L0.078220.742
27_D33_T0.07770.737
5_V11_F0.077510.736
46_V77_I0.077490.735
54_I61_F0.076580.727
50_Q73_R0.076180.723
9_V66_D0.076110.722
15_S73_R0.075540.717
7_E44_N0.075440.716
13_V25_Y0.075360.715
8_R82_P0.075270.714
9_V36_F0.075050.712
28_A70_G0.075040.712
51_T64_T0.074990.712
50_Q53_T0.074370.706
15_S34_L0.074030.703
12_R30_G0.073810.700
9_V33_T0.073550.698
37_P44_N0.073230.695
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
4acqA0.927762.60.82
1lm8V0.867541.90.84
2pn5A0.927734.80.846
2p9rA0.8675330.848
4eweA0.879531.50.849
2hr0A0.879531.50.849
3hrzA0.879531.20.85
2wgnB0.903629.50.851
3uc1A0.975929.40.852
3l6vA0.975924.10.857
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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