GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF2871 - Protein of unknown function (DUF2871)
Pfam: PF11070 (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: 132
Sequences: 4625
Seq/Len: 35.04
HH_delta: 0.183 (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
62_F131_A1.536834.516
88_M110_A1.043463.066
83_L113_G1.034153.039
76_V120_G1.007522.961
80_G116_L0.926442.723
59_E70_F0.764092.245
104_A108_G0.741592.179
44_L82_V0.723462.126
69_K126_V0.71392.098
68_K72_K0.683932.010
69_K123_L0.650951.913
59_E73_F0.644561.894
72_K123_L0.614041.805
55_L124_L0.592161.740
67_N71_K0.586341.723
73_F77_Y0.56351.656
76_V123_L0.553721.627
126_V130_K0.533291.567
105_A108_G0.518231.523
86_G90_V0.500551.471
115_I119_V0.473871.393
31_F70_F0.463541.362
55_L59_E0.443681.304
123_L127_A0.442881.302
112_L116_L0.442481.300
70_F127_A0.430341.265
48_G81_L0.426011.252
80_G120_G0.418541.230
96_V107_S0.40991.205
76_V119_V0.400641.177
105_A109_I0.380981.120
73_F120_G0.379631.116
77_Y117_L0.374651.101
58_L62_F0.374261.100
55_L73_F0.372671.095
44_L86_G0.371871.093
40_V89_L0.367621.080
34_K38_S0.366461.077
67_N70_F0.365221.073
122_I126_V0.364471.071
29_N33_G0.359421.056
60_K75_I0.353531.039
80_G113_G0.35221.035
53_L56_L0.345881.016
118_G122_I0.337520.992
82_V86_G0.335680.986
32_T38_S0.334750.984
110_A113_G0.334610.983
94_L105_A0.330950.973
84_T114_H0.327750.963
69_K72_K0.327090.961
75_I129_K0.323450.951
73_F124_L0.322320.947
99_S103_N0.321720.945
72_K76_V0.320170.941
95_Q98_G0.320080.941
52_F74_F0.319640.939
124_L128_L0.316570.930
48_G84_T0.315190.926
55_L121_L0.314680.925
127_A131_A0.312160.917
126_V129_K0.311330.915
84_T117_L0.309590.910
94_L119_V0.308060.905
88_M91_R0.299760.881
69_K127_A0.297090.873
115_I118_G0.296020.870
57_L61_N0.291230.856
62_F65_S0.290220.853
83_L116_L0.288580.848
73_F127_A0.284990.838
111_G115_I0.284080.835
107_S111_G0.281630.828
72_K75_I0.281220.826
108_G112_L0.281070.826
50_I54_I0.280320.824
29_N99_S0.277270.815
108_G115_I0.277250.815
60_K65_S0.274820.808
100_E103_N0.273790.805
125_F129_K0.273780.805
105_A115_I0.273150.803
123_L126_V0.271780.799
58_L128_L0.271430.798
40_V87_M0.266420.783
103_N107_S0.266340.783
70_F105_A0.263770.775
58_L65_S0.263590.775
76_V116_L0.26070.766
38_S42_T0.258920.761
69_K122_I0.255920.752
94_L104_A0.255320.750
75_I79_I0.254710.749
77_Y121_L0.253570.745
51_F117_L0.252090.741
68_K115_I0.251830.740
67_N75_I0.25010.735
76_V79_I0.249960.735
44_L85_V0.248920.732
92_G98_G0.247480.727
101_L106_I0.246840.725
73_F121_L0.245280.721
87_M106_I0.244990.720
60_K67_N0.242030.711
29_N35_T0.240860.708
60_K70_F0.24030.706
100_E106_I0.238750.702
68_K126_V0.23760.698
90_V106_I0.235240.691
89_L93_I0.233470.686
105_A121_L0.23290.684
119_V123_L0.232530.683
112_L115_I0.231550.680
63_D69_K0.231050.679
29_N38_S0.230530.677
81_L117_L0.230480.677
57_L67_N0.22950.674
32_T37_L0.229090.673
83_L109_I0.228890.673
69_K75_I0.228110.670
40_V88_M0.226780.666
31_F112_L0.224810.661
46_V49_M0.223790.658
57_L70_F0.223650.657
65_S99_S0.221810.652
36_Q96_V0.220160.647
42_T98_G0.220120.647
59_E105_A0.219080.644
44_L89_L0.218560.642
58_L124_L0.216750.637
104_A115_I0.216110.635
76_V80_G0.215990.635
94_L115_I0.215610.634
54_I124_L0.215350.633
72_K119_V0.215180.632
89_L97_L0.214860.631
34_K50_I0.212830.625
45_L49_M0.21280.625
58_L94_L0.212580.625
31_F115_I0.212430.624
104_A112_L0.212410.624
51_F90_V0.211420.621
120_G123_L0.211390.621
78_N82_V0.207520.610
100_E104_A0.206690.607
77_Y80_G0.20420.600
68_K71_K0.20350.598
65_S131_A0.203160.597
47_L84_T0.202080.594
99_S102_S0.202060.594
56_L60_K0.202020.594
45_L86_G0.20180.593
79_I83_L0.200830.590
45_L50_I0.199760.587
108_G126_V0.199370.586
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
1fftA0.992499.90.183
2yevA0.992499.90.184
1v54A0.992499.90.212
3mk7A0.992499.90.213
2gsmA0.992499.90.215
3s8fA0.992499.90.217
3o0rB0.992499.90.222
3ayfA0.992499.90.23
3ayfA0.954597.90.729
3mk7A0.939497.90.731

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