GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF2723 - Protein of unknown function (DUF2723)
Pfam: PF11028 (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. )
Clan: CL0111
Length: 178
Sequences: 2034
Seq/Len: 11.43
HH_delta: 0.638 (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_I85_G0.544412.848
57_F117_L0.514162.690
53_L113_L0.484892.537
108_Y152_H0.471632.467
62_I88_G0.435482.278
55_V89_A0.433292.267
64_R127_R0.426632.232
61_S123_L0.409872.144
92_F98_F0.404242.115
59_F89_A0.397822.081
50_S113_L0.375391.964
58_L92_F0.356531.865
114_F151_V0.34691.815
54_T116_A0.34631.812
117_L144_L0.331751.736
121_L144_L0.318241.665
63_T85_G0.307011.606
57_F113_L0.306161.602
67_R84_A0.298591.562
121_L137_W0.295041.544
60_W120_W0.292491.530
39_I42_R0.282271.477
54_T113_L0.279311.461
114_F147_L0.278591.458
120_W124_K0.272741.427
64_R124_K0.266671.395
121_L140_L0.266081.392
85_G89_A0.260771.364
142_A146_G0.260131.361
60_W63_T0.258321.351
59_F85_G0.250671.311
54_T98_F0.247931.297
51_S102_A0.245921.287
62_I66_L0.244171.277
148_S155_N0.243961.276
50_S110_L0.243841.276
49_L53_L0.23931.252
125_W138_L0.239091.251
160_P163_A0.238971.250
22_L25_L0.23791.245
54_T112_S0.235771.233
55_V92_F0.23111.209
114_F144_L0.231011.209
20_Y25_L0.22981.202
58_L88_G0.229691.202
19_G152_H0.229061.198
146_G150_G0.226351.184
56_L60_W0.223811.171
34_P42_R0.220061.151
148_S156_L0.218691.144
85_G88_G0.21841.143
15_P24_T0.215281.126
63_T68_K0.214691.123
111_S152_H0.21181.108
111_S155_N0.210371.101
139_L142_A0.209561.096
23_F46_L0.20941.096
47_S105_A0.206161.079
43_V105_A0.205941.077
157_L160_P0.204411.069
59_F63_T0.204361.069
16_H107_V0.204051.068
24_T106_E0.203841.066
34_P39_I0.203421.064
55_V93_A0.202691.060
124_K128_E0.199061.041
61_S120_W0.197951.036
135_D139_L0.19661.029
66_L84_A0.194921.020
124_K127_R0.193831.014
15_P153_L0.193721.013
41_W45_L0.192921.009
19_G153_L0.192351.006
51_S55_V0.191881.004
42_R45_L0.191341.001
60_W64_R0.189680.992
30_F38_N0.189360.991
118_L145_C0.187650.982
67_R127_R0.186170.974
61_S116_A0.185770.972
23_F110_L0.181070.947
29_L32_L0.178260.933
58_L62_I0.177880.931
134_S137_W0.177130.927
68_K83_G0.175010.916
40_A44_N0.173080.906
62_I65_L0.171720.898
57_F116_A0.171460.897
105_A108_Y0.16930.886
161_A164_L0.168870.883
28_R31_S0.16880.883
110_L114_F0.168260.880
83_G87_V0.167280.875
40_A43_V0.166860.873
16_H152_H0.166210.870
144_L147_L0.166180.869
51_S98_F0.162360.849
47_S50_S0.161170.843
47_S110_L0.160950.842
19_G24_T0.160.837
19_G25_L0.158820.831
150_G153_L0.158390.829
26_L50_S0.15680.820
156_L160_P0.156590.819
102_A109_A0.156150.817
57_F60_W0.155940.816
67_R85_G0.155390.813
18_P107_V0.154060.806
33_L45_L0.153680.804
113_L117_L0.150250.786
20_Y24_T0.150160.786
19_G107_V0.149590.783
46_L50_S0.149280.781
17_P24_T0.148870.779
64_R68_K0.148580.777
38_N41_W0.148250.776
108_Y153_L0.147790.773
153_L156_L0.147530.772
21_P25_L0.146770.768
128_E134_S0.146330.766
16_H19_G0.145910.763
88_G92_F0.14560.762
27_G46_L0.145260.760
20_Y153_L0.145060.759
65_L127_R0.144250.755
57_F120_W0.144240.755
107_V152_H0.143370.750
108_Y155_N0.142960.748
111_S153_L0.14240.745
17_P20_Y0.141830.742
118_L144_L0.14160.741
110_L151_V0.140910.737
16_H153_L0.140860.737
54_T57_F0.140750.736
18_P108_Y0.140360.734
57_F121_L0.140240.734
118_L148_S0.139660.731
148_S152_H0.138990.727
65_L123_L0.138650.725
58_L89_A0.138420.724
16_H27_G0.138370.724
127_R134_S0.137930.722
28_R32_L0.137780.721
122_L141_I0.13770.720
117_L121_L0.137450.719
111_S148_S0.13740.719
54_T92_F0.137320.718
136_R147_L0.136720.715
108_Y150_G0.136630.715
54_T58_L0.136440.714
150_G154_L0.135820.711
48_A89_A0.135240.708
23_F47_S0.134590.704
136_R139_L0.134230.702
97_S101_Q0.132720.694
128_E143_F0.132360.692
95_S98_F0.132210.692
16_H108_Y0.131840.690
63_T67_R0.131760.689
101_Q106_E0.131490.688
47_S109_A0.131380.687
124_K137_W0.131280.687
101_Q154_L0.130970.685
53_L57_F0.130530.683
111_S154_L0.130330.682
19_G23_F0.130280.682
25_L152_H0.129860.679
18_P24_T0.129510.678
20_Y152_H0.128510.672
146_G152_H0.128230.671
18_P153_L0.127560.667
90_L94_F0.127510.667
128_E136_R0.127150.665
116_A119_L0.126970.664
87_V123_L0.126910.664
118_L162_I0.12680.663
19_G108_Y0.126710.663
67_R139_L0.126310.661
53_L158_A0.126110.660
153_L163_A0.125580.657
147_L151_V0.125420.656
13_G24_T0.124740.653
60_W86_L0.124290.650
23_F107_V0.124020.649
38_N43_V0.123620.647
44_N108_Y0.123440.646
42_R46_L0.12320.645
31_S83_G0.123050.644
15_P152_H0.122880.643
26_L110_L0.12280.642
30_F43_V0.122610.641
24_T58_L0.122530.641
124_K166_Y0.122420.640
97_S105_A0.122070.639
38_N45_L0.121450.635
67_R144_L0.120430.630
23_F105_A0.119380.625
56_L64_R0.118930.622
137_W159_L0.118890.622
45_L165_L0.118860.622
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
3rceA0.8876990.638
2l2tA0.24726.50.935
2ks1B0.24725.50.937
3giaA0.865250.938
1wazA0.24724.70.939
2jwaA0.24724.10.94
3hheA0.32023.40.942
3uw1A0.33713.20.943
2f8mA0.34272.60.945
4dveA0.63482.40.946
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