GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF249 - Multigene family 530 protein
Pfam: PF03158 (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: 192
Sequences: 9588
Seq/Len: 49.94
HH_delta: 0.217 (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_L91_I1.33692.626
92_V119_L1.259722.475
159_V185_I1.12132.203
57_N88_K1.110662.182
96_G99_L1.061712.086
154_G182_H1.007331.979
120_Y158_F0.930111.827
59_L90_D0.914611.797
148_E173_V0.913031.794
64_K68_D0.907881.784
63_Q94_W0.903311.775
105_E140_T0.902031.772
175_S178_V0.883651.736
87_Q116_D0.881431.732
125_K129_N0.853261.676
58_M61_I0.847041.664
81_E107_I0.83551.641
115_K155_L0.817941.607
80_F92_V0.808421.588
59_L94_W0.806181.584
161_E165_Y0.761851.497
160_L188_Y0.757191.488
51_Y79_L0.756351.486
156_L188_Y0.751611.477
108_F120_Y0.7381.450
53_A62_L0.723971.422
66_K94_W0.712431.400
59_L63_Q0.710591.396
89_Y118_S0.705561.386
54_V91_I0.700661.377
167_G170_D0.694451.364
109_D146_H0.687851.351
50_L62_L0.681071.338
38_H41_N0.680561.337
93_K125_K0.678221.332
125_K128_F0.676341.329
121_S161_E0.666521.309
116_D119_L0.655321.287
155_L158_F0.652811.282
89_Y119_L0.650961.279
77_Q101_I0.645361.268
147_L159_V0.641061.259
174_L186_L0.6411.259
163_L188_Y0.639491.256
144_T152_A0.63651.250
89_Y125_K0.632631.243
51_Y82_L0.630481.239
88_K91_I0.630411.238
178_V181_N0.62931.236
182_H185_I0.628971.236
158_F162_T0.627611.233
168_N171_I0.625821.229
111_A120_Y0.625071.228
48_C51_Y0.622981.224
156_L184_K0.615031.208
36_K39_E0.605381.189
148_E176_Q0.59831.175
54_V57_N0.595951.171
151_A154_G0.590721.161
131_M134_E0.579431.138
77_Q85_E0.578681.137
63_Q67_E0.578581.137
81_E109_D0.57711.134
159_V162_T0.569211.118
117_L121_S0.564991.110
183_R187_D0.559251.099
121_S128_F0.558531.097
105_E113_A0.558151.097
109_D148_E0.555131.091
151_A185_I0.554171.089
84_C119_L0.553771.088
37_C40_L0.550311.081
178_V186_L0.550291.081
69_L72_E0.538591.058
54_V79_L0.536241.053
84_C87_Q0.535431.052
89_Y93_K0.532691.047
156_L185_I0.529311.040
112_F115_K0.528211.038
140_T144_T0.525861.033
150_A159_V0.524841.031
177_A186_L0.524161.030
163_L169_V0.523791.029
83_A92_V0.522981.027
148_E175_S0.52031.022
174_L190_I0.519581.021
81_E110_I0.518941.019
172_I175_S0.516761.015
117_L157_P0.514041.010
117_L161_E0.510221.002
94_W98_N0.503490.989
178_V190_I0.501660.986
185_I188_Y0.501530.985
96_G100_H0.501490.985
105_E110_I0.501430.985
54_V62_L0.500240.983
156_L160_L0.493790.970
175_S190_I0.493310.969
36_K40_L0.491560.966
166_G169_V0.490170.963
106_D109_D0.484030.951
84_C107_I0.48320.949
147_L163_L0.480930.945
81_E148_E0.47860.940
59_L91_I0.472740.929
139_P143_L0.469840.923
64_K67_E0.468190.920
139_P171_I0.4670.917
160_L164_K0.465310.914
151_A182_H0.46530.914
77_Q82_L0.465180.914
140_T149_K0.46160.907
66_K72_E0.461530.907
101_I104_P0.456920.898
52_H56_Y0.456160.896
109_D175_S0.452560.889
93_K97_Q0.452360.889
33_T37_C0.448380.881
144_T149_K0.446640.877
61_I64_K0.445990.876
51_Y109_D0.442360.869
78_E81_E0.440310.865
144_T176_Q0.438170.861
97_Q100_H0.436790.858
84_C92_V0.435130.855
55_K86_E0.434050.853
51_Y81_E0.428050.841
97_Q129_N0.427930.841
50_L66_K0.424180.833
186_L190_I0.422910.831
109_D149_K0.421670.828
55_K82_L0.421010.827
33_T36_K0.420020.825
105_E144_T0.419170.823
67_E98_N0.418910.823
128_F165_Y0.416360.818
37_C41_N0.415930.817
161_E164_K0.411990.809
65_Y70_E0.409280.804
126_L131_M0.407060.800
82_L149_K0.405260.796
151_A180_Y0.402920.792
113_A152_A0.40270.791
127_L133_S0.402680.791
113_A149_K0.400650.787
110_I149_K0.399420.785
158_F161_E0.394440.775
159_V163_L0.392770.772
149_K152_A0.390640.767
127_L165_Y0.387510.761
174_L178_V0.387170.761
82_L110_I0.38560.758
127_L161_E0.384640.756
32_E35_E0.384450.755
84_C151_A0.383920.754
54_V88_K0.382590.752
162_T166_G0.380870.748
32_E37_C0.379710.746
96_G125_K0.378920.744
112_F120_Y0.376390.739
32_E36_K0.376180.739
130_R133_S0.375780.738
126_L130_R0.371940.731
166_G170_D0.370860.729
35_E38_H0.365990.719
146_H150_A0.36490.717
152_A176_Q0.362710.713
176_Q180_Y0.360880.709
152_A180_Y0.359250.706
95_I100_H0.358940.705
167_G171_I0.358840.705
84_C114_K0.358710.705
30_D33_T0.358230.704
77_Q144_T0.356990.701
151_A159_V0.356040.699
54_V86_E0.352680.693
119_L185_I0.351750.691
113_A153_K0.351060.690
112_F158_F0.350320.688
77_Q110_I0.35010.688
110_I176_Q0.349360.686
90_D93_K0.349010.686
110_I113_A0.347660.683
144_T148_E0.346220.680
70_E73_R0.345230.678
51_Y175_S0.343470.675
101_I105_E0.343230.674
173_V177_A0.343110.674
112_F146_H0.341010.670
91_I95_I0.340170.668
148_E172_I0.339080.666
157_P160_L0.338990.666
107_I126_L0.33420.657
145_Q148_E0.333260.655
82_L86_E0.332470.653
175_S179_K0.332180.653
52_H82_L0.331150.651
85_E113_A0.331040.650
66_K98_N0.331040.650
140_T143_L0.330720.650
81_E175_S0.330.648
84_C116_D0.329470.647
108_F127_L0.328450.645
87_Q119_L0.325710.640
51_Y54_V0.324710.638
176_Q179_K0.323570.636
120_Y161_E0.323120.635
151_A173_V0.322660.634
56_Y61_I0.322420.633
148_E151_A0.321640.632
77_Q81_E0.320380.629
139_P145_Q0.319540.628
108_F126_L0.318730.626
130_R134_E0.316450.622
85_E152_A0.316380.622
110_I114_K0.315620.620
79_L95_I0.315340.620
62_L94_W0.314420.618
61_I65_Y0.31410.617
38_H42_N0.312860.615
182_H186_L0.310390.610
91_I94_W0.310010.609
101_I110_I0.309370.608
162_T167_G0.307670.604
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
2etbA0.911599.90.217
3ljnA0.968899.90.219
2ajaA0.953199.90.219
3jxiA0.916799.90.225
2pnnA0.916799.90.231
2rfaA0.880299.90.234
1oy3D0.890699.90.235
3ljnA0.895899.90.239
3utmA0.968899.90.246
1iknD0.895899.90.247

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