GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF3280 - Protein of unknown function (DUF2380)
Pfam: PF11684 (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: 140
Sequences: 687
Seq/Len: 4.91
HH_delta: 0.51 (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
9_F87_G0.281772.937
85_L103_V0.244772.551
4_I103_V0.190981.991
96_I118_D0.190891.990
73_A76_A0.175531.830
105_D108_T0.172041.793
68_C71_C0.16711.742
92_V97_L0.165281.723
33_L99_M0.159381.661
90_Q100_N0.155391.620
47_Y107_E0.152951.594
7_F84_V0.148761.551
76_A106_V0.144171.503
98_N118_D0.143221.493
6_V41_L0.139271.452
5_A79_L0.136191.420
105_D110_K0.136091.418
52_L55_V0.133771.394
91_K95_L0.131851.374
38_R52_L0.131141.367
3_K81_A0.121211.263
8_D113_R0.118791.238
57_A111_V0.117281.222
9_F60_A0.112441.172
43_E49_V0.112191.169
85_L101_V0.108281.129
65_L70_G0.107341.119
83_Y112_V0.106851.114
73_A106_V0.106021.105
57_A81_A0.105481.099
63_Q114_G0.103721.081
68_C84_V0.103621.080
71_C76_A0.102791.071
3_K48_R0.102721.071
52_L61_A0.102291.066
9_F99_M0.101091.054
25_A33_L0.100311.046
39_E116_S0.100271.045
44_S48_R0.100171.044
68_C72_E0.099761.040
58_E61_A0.099211.034
34_T75_I0.099041.032
57_A61_A0.098981.032
65_L68_C0.098691.029
7_F101_V0.097821.020
6_V92_V0.097351.015
44_S85_L0.095850.999
84_V106_V0.095480.995
64_N78_E0.094760.988
4_I42_A0.094660.987
42_A111_V0.094560.986
70_G109_G0.094550.986
31_A63_Q0.09380.978
35_D38_R0.093570.975
71_C110_K0.093230.972
25_A77_R0.092870.968
40_A84_V0.092830.968
75_I78_E0.092090.960
99_M107_E0.091790.957
59_I82_D0.090780.946
50_V81_A0.090770.946
82_D94_N0.089920.937
99_M118_D0.089830.936
31_A56_A0.089640.934
48_R83_Y0.089360.931
81_A84_V0.08930.931
78_E109_G0.088580.923
15_S61_A0.088490.922
6_V49_V0.087680.914
3_K82_D0.087630.913
42_A110_K0.087090.908
94_N98_N0.086340.900
84_V107_E0.086310.900
42_A51_D0.085750.894
16_A104_R0.085270.889
45_G92_V0.085070.887
4_I85_L0.0850.886
50_V108_T0.084890.885
73_A109_G0.084840.884
32_A97_L0.084710.883
17_E31_A0.08470.883
70_G77_R0.084130.877
31_A111_V0.083970.875
52_L56_A0.083960.875
75_I112_V0.083490.870
33_L114_G0.083430.870
56_A118_D0.083330.869
5_A81_A0.082970.865
92_V104_R0.082820.863
42_A49_V0.082670.862
32_A88_E0.082630.861
60_A116_S0.082170.856
40_A43_E0.082010.855
86_V112_V0.081950.854
35_D57_A0.081570.850
3_K43_E0.080820.842
13_D18_P0.080820.842
8_D86_V0.080790.842
83_Y103_V0.080710.841
6_V97_L0.080570.840
80_G107_E0.080340.837
103_V112_V0.080030.834
38_R42_A0.079060.824
35_D114_G0.078850.822
51_D108_T0.078780.821
71_C91_K0.078770.821
52_L80_G0.078630.820
32_A101_V0.078150.815
79_L103_V0.078150.815
76_A108_T0.077990.813
14_T25_A0.077740.810
82_D107_E0.07760.809
35_D88_E0.077570.809
64_N103_V0.077570.809
103_V113_R0.077260.805
39_E88_E0.076940.802
80_G110_K0.076880.801
31_A114_G0.076370.796
40_A82_D0.076320.795
58_E99_M0.076180.794
37_L40_A0.076140.794
102_Y114_G0.075910.791
88_E100_N0.075750.790
88_E114_G0.075730.789
89_V112_V0.075730.789
95_L115_R0.075690.789
58_E95_L0.075230.784
61_A78_E0.07520.784
45_G101_V0.074980.782
100_N114_G0.074820.780
90_Q116_S0.074680.778
58_E78_E0.074230.774
39_E69_N0.074150.773
94_N116_S0.074130.773
100_N116_S0.074110.772
33_L85_L0.07410.772
84_V116_S0.074010.771
10_E69_N0.073840.770
10_E68_C0.073650.768
87_G114_G0.073650.768
61_A116_S0.073630.767
35_D52_L0.073620.767
3_K41_L0.073370.765
107_E110_K0.073320.764
14_T88_E0.072790.759
18_P24_P0.072380.754
91_K118_D0.072220.753
36_Q39_E0.072180.752
17_E25_A0.071740.748
32_A98_N0.071740.748
34_T43_E0.07170.747
48_R74_R0.071690.747
8_D90_Q0.071540.746
61_A104_R0.07150.745
53_A86_V0.071310.743
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
4hrvA0.999.30.51
3w1eA0.921499.30.51
3ly7A0.842998.70.629
2hqsA0.8598.10.703
2iqiA0.807177.90.866
3ne8A0.864328.40.902
4jv8B0.4071220.907
3t5gB0.4071220.907
3vtfA0.735718.70.909
3gnnA0.6429170.911
If you are interested in a protein containing this domain,
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