GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF3391 - Domain of unknown function (DUF3391)
Pfam: PF11871 (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: 128
Sequences: 620
Seq/Len: 4.84
HH_delta: 0.515 (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
15_Y55_D0.246822.556
28_F33_F0.208142.156
23_W28_F0.205262.126
12_P41_I0.201192.084
55_D58_K0.176471.828
8_D45_R0.171741.779
23_W33_F0.167931.739
26_H33_F0.162281.681
23_W27_P0.159171.648
38_Q42_E0.157141.627
23_W26_H0.154131.596
20_D44_L0.152191.576
3_K14_M0.143491.486
74_K77_A0.141521.466
15_Y58_K0.137651.426
54_I59_S0.132711.374
55_D97_A0.127571.321
20_D51_E0.12641.309
41_I52_V0.126081.306
71_A77_A0.125861.303
7_V10_L0.125321.298
31_Q49_I0.124831.293
22_S49_I0.122511.269
21_R49_I0.120621.249
10_L13_G0.119791.241
7_V25_E0.118291.225
20_D49_I0.118231.224
68_P71_A0.115841.200
22_S26_H0.114921.190
76_A79_P0.112941.170
12_P35_I0.111891.159
24_L108_V0.109451.134
54_I112_F0.108081.119
19_L44_L0.10621.100
112_F115_V0.10541.092
119_K122_D0.105011.088
122_D125_P0.105011.088
75_Q89_S0.104781.085
68_P76_A0.104521.082
79_P86_K0.104161.079
52_V125_P0.104141.079
44_L52_V0.103681.074
75_Q79_P0.103531.072
42_E46_R0.103281.070
93_E97_A0.101361.050
21_R30_F0.10021.038
51_E93_E0.09991.035
24_L27_P0.099681.032
73_A86_K0.09941.029
73_A77_A0.099131.027
15_Y34_L0.098621.021
21_R26_H0.098411.019
53_Y104_A0.098181.017
19_L53_Y0.097891.014
89_S122_D0.097591.011
31_Q40_D0.09721.007
69_P73_A0.096951.004
70_E74_K0.095740.992
19_L34_L0.095620.990
92_E95_R0.095450.989
48_G123_V0.094910.983
28_F119_K0.094850.982
46_R57_D0.094370.977
16_V19_L0.094070.974
20_D26_H0.093550.969
97_A100_L0.09320.965
69_P79_P0.093050.964
68_P77_A0.092620.959
42_E92_E0.092330.956
4_K51_E0.092040.953
111_L126_A0.092010.953
27_P33_F0.09150.948
67_P70_E0.091230.945
21_R112_F0.091110.944
36_K104_A0.091010.943
98_E105_K0.090910.942
21_R27_P0.090840.941
23_W116_R0.090750.940
62_V68_P0.089630.928
23_W40_D0.089590.928
15_Y97_A0.089020.922
100_L108_V0.088590.917
93_E96_R0.088350.915
26_H47_L0.088320.915
21_R33_F0.088260.914
19_L97_A0.088030.912
32_G49_I0.0880.911
67_P76_A0.087840.910
110_S114_D0.087530.907
25_E33_F0.087450.906
5_I37_S0.087350.905
6_P12_P0.087280.904
5_I13_G0.087230.903
20_D53_Y0.086830.899
17_S56_P0.086210.893
75_Q78_P0.086120.892
73_A76_A0.086080.892
55_D93_E0.085390.884
21_R35_I0.084660.877
123_V126_A0.084540.876
100_L118_G0.08450.875
11_K42_E0.084160.872
7_V48_G0.084150.872
19_L23_W0.084150.872
67_P71_A0.08380.868
26_H31_Q0.083380.864
14_M97_A0.083240.862
26_H32_G0.082590.855
86_K95_R0.082180.851
93_E121_I0.081960.849
34_L125_P0.08160.845
7_V35_I0.081340.842
24_L94_L0.080730.836
33_F49_I0.080710.836
47_L112_F0.080460.833
36_K78_P0.080370.832
71_A76_A0.080340.832
118_G121_I0.080090.829
28_F40_D0.079810.827
16_V41_I0.07960.824
16_V36_K0.079540.824
67_P86_K0.079510.823
17_S58_K0.079450.823
26_H49_I0.079360.822
69_P75_Q0.078890.817
24_L103_E0.078680.815
8_D102_Q0.078470.813
12_P38_Q0.078410.812
23_W45_R0.078380.812
54_I93_E0.078310.811
58_K61_D0.078230.810
53_Y105_K0.078210.810
49_I100_L0.077780.806
10_L41_I0.077660.804
107_V111_L0.07750.803
100_L122_D0.077420.802
66_K70_E0.077380.801
20_D101_Y0.07730.801
19_L105_K0.077240.800
70_E77_A0.077230.800
6_P9_Q0.076690.794
71_A75_Q0.076630.794
97_A121_I0.076340.791
114_D117_A0.076250.790
37_S106_Q0.075890.786
110_S123_V0.075270.780
24_L28_F0.075130.778
8_D111_L0.075080.778
33_F40_D0.0750.777
20_D47_L0.074950.776
5_I11_K0.074920.776
100_L105_K0.074890.776
15_Y37_S0.074490.771
47_L59_S0.074360.770
90_L94_L0.073990.766
41_I106_Q0.073980.766
60_R107_V0.073810.764
3_K61_D0.073770.764
51_E56_P0.073670.763
70_E73_A0.073340.760
24_L102_Q0.073280.759
43_K47_L0.073150.758
21_R28_F0.073060.757
47_L119_K0.073060.757
34_L58_K0.073050.757
67_P125_P0.072990.756
15_Y33_F0.072970.756
68_P75_Q0.072880.755
19_L22_S0.072740.753
74_K79_P0.072670.753
39_A71_A0.072660.753
15_Y20_D0.072590.752
69_P102_Q0.072450.750
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
3tm8A0.882898.90.515
3ltiA0.789175.10.841
4kn7C0.789146.60.867
3lu0C0.789146.60.867
3lu0D0.671923.20.885
4kn7D0.671923.20.885
2p5dA0.359421.30.887
3qe9Y0.867216.80.892
2f1mA0.33599.70.902
1t8sA0.3759.30.903
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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