GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF659 - Protein of unknown function (DUF 659)
Pfam: PF04937 (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: 153
Sequences: 1769
Seq/Len: 11.56
HH_delta: 0.266 (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
38_S82_L0.366332.424
101_N123_P0.360462.385
127_H131_L0.348032.303
40_G50_I0.321272.125
74_T77_Y0.291421.928
83_D115_K0.275631.824
75_A104_N0.260411.723
85_V89_V0.257661.705
19_K88_E0.247541.638
37_M55_Y0.241821.600
34_C94_V0.238091.575
42_T48_S0.237391.571
102_A105_M0.236741.566
123_P128_C0.233511.545
48_S73_K0.230951.528
78_L108_A0.228811.514
72_I77_Y0.224211.483
57_P61_V0.223591.479
34_C54_V0.22091.461
79_F111_L0.212631.407
17_E21_Q0.208351.378
14_E17_E0.208181.377
20_E24_E0.20771.374
41_W49_L0.20691.369
37_M53_M0.2061.363
101_N128_C0.20581.362
56_C66_V0.204121.350
80_E84_E0.19711.304
86_I91_E0.196831.302
63_L67_D0.193951.283
42_T46_G0.192081.271
20_E23_K0.186511.234
52_F85_V0.186181.232
73_K104_N0.184561.221
40_G73_K0.18431.219
100_D127_H0.182731.209
54_V63_L0.179351.187
99_T121_W0.178771.183
35_S95_V0.178591.182
36_I97_V0.177591.175
74_T104_N0.177481.174
130_N134_E0.175241.159
75_A79_F0.174981.158
126_A129_I0.174931.157
16_K88_E0.174331.153
64_K67_D0.173991.151
63_L66_V0.173471.148
15_Y18_V0.173341.147
79_F83_D0.173211.146
37_M98_V0.173181.146
40_G49_L0.172321.140
39_D131_L0.171631.135
43_D47_R0.168921.118
40_G48_S0.168791.117
45_K49_L0.166771.103
62_F68_A0.166511.102
22_V26_K0.166261.100
21_Q24_E0.166211.100
99_T106_K0.162951.078
76_E80_E0.162751.077
40_G78_L0.161451.068
14_E18_V0.158721.050
11_L15_Y0.158181.047
111_L114_E0.1581.045
97_V119_I0.157261.040
13_K16_K0.155781.031
39_D127_H0.154891.025
101_N131_L0.154831.024
31_R90_G0.15451.022
101_N105_M0.152791.011
66_V85_V0.151631.003
25_H56_C0.15141.002
73_K102_A0.150470.995
58_E62_F0.150020.993
79_F115_K0.148980.986
113_M120_F0.146690.970
84_E92_E0.145740.964
64_K69_S0.145570.963
78_L105_M0.144160.954
28_S59_G0.143430.949
11_L23_K0.142360.942
49_L55_Y0.141830.938
37_M41_W0.140470.929
32_T93_N0.139720.924
72_I82_L0.136150.901
17_E20_E0.136090.900
101_N127_H0.133920.886
75_A107_K0.133460.883
73_K78_L0.132530.877
62_F67_D0.132310.875
15_Y20_E0.13230.875
16_K20_E0.131930.873
99_T105_M0.131830.872
126_A135_D0.131740.872
73_K79_F0.131680.871
51_N67_D0.131610.871
74_T78_L0.13110.867
56_C61_V0.130750.865
102_A127_H0.129030.854
102_A131_L0.128660.851
34_C91_E0.128490.850
103_S106_K0.128380.849
23_K27_K0.128210.848
40_G55_Y0.12750.844
33_G93_N0.127120.841
41_W51_N0.127050.841
65_S69_S0.126580.837
96_Q120_F0.126490.837
123_P131_L0.1260.834
23_K56_C0.125530.830
35_S55_Y0.125120.828
94_V103_S0.125030.827
93_N134_E0.124660.825
36_I95_V0.124410.823
103_S127_H0.123080.814
42_T50_I0.122620.811
41_W73_K0.121350.803
21_Q25_H0.120990.800
40_G105_M0.120860.800
34_C92_E0.120510.797
97_V109_G0.120350.796
107_K111_L0.120320.796
51_N91_E0.120190.795
36_I86_I0.119920.793
59_G62_F0.119620.791
80_E88_E0.119590.791
40_G54_V0.119570.791
106_K121_W0.11930.789
122_T132_M0.118870.786
15_Y19_K0.118630.785
35_S96_Q0.118340.783
14_E19_K0.117850.780
57_P60_T0.11710.775
52_F116_Y0.117090.775
19_K23_K0.116750.772
17_E28_S0.11640.770
81_L84_E0.116240.769
16_K32_T0.116020.768
24_E27_K0.115750.766
124_C129_I0.115550.764
39_D42_T0.115450.764
34_C96_Q0.1150.761
68_A76_E0.114280.756
64_K129_I0.114150.755
65_S68_A0.113540.751
95_V98_V0.113110.748
73_K77_Y0.112960.747
62_F65_S0.112040.741
61_V66_V0.111980.741
15_Y41_W0.1110.734
123_P133_L0.110810.733
125_A132_M0.110630.732
125_A129_I0.110530.731
43_D49_L0.110440.731
44_R49_L0.109970.728
97_V113_M0.109950.727
67_D112_L0.109890.727
93_N119_I0.109880.727
91_E112_L0.109650.725
64_K85_V0.109230.723
125_A128_C0.108780.720
19_K129_I0.108260.716
20_E32_T0.108020.715
132_M135_D0.107670.712
28_S58_E0.107630.712
79_F86_I0.107630.712
49_L53_M0.107580.712
52_F112_L0.107120.709
50_I78_L0.106990.708
84_E88_E0.106850.707
73_K100_D0.106420.704
62_F69_S0.10630.703
26_K89_V0.106210.703
20_E58_E0.106080.702
47_R94_V0.105980.701
71_I78_L0.105660.699
26_K86_I0.105530.698
76_E111_L0.105210.696
51_N128_C0.10440.691
110_K114_E0.103920.688
16_K23_K0.103640.686
41_W55_Y0.103560.685
61_V112_L0.103190.683
95_V130_N0.103150.682
31_R93_N0.103130.682
15_Y24_E0.103120.682
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
2bw3A0.941299.90.266
3adoA0.921629.90.907
4ap5A0.908527.50.908
2hpiA0.90211.80.922
3k6jA0.90211.60.922
4fcyA0.934610.30.924
3kksA0.719100.924
2dpoA0.83669.90.925
2e9xB0.50339.80.925
3f9kA0.9028.10.927

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