GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF2855 - Protein of unknown function (DUF2855)
Pfam: PF11017 (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: 314
Sequences: 8281
Seq/Len: 26.37
HH_delta: 0.426 (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
299_A302_A1.536574.757
50_A53_E1.065283.298
296_G299_A1.060063.282
140_V200_P1.04933.248
158_K184_D1.048953.247
305_Q309_A0.993453.075
138_Q164_K0.988343.060
164_K185_E0.949432.939
220_L227_S0.940632.912
172_R188_T0.922222.855
175_A178_E0.908372.812
295_A306_D0.877412.716
302_A306_D0.835012.585
144_A167_G0.834712.584
140_V168_L0.827512.562
302_A305_Q0.771262.388
139_V157_K0.769442.382
154_Y183_Y0.737882.284
220_L262_I0.734492.274
225_V263_K0.720172.229
220_L224_L0.719052.226
295_A303_A0.718292.224
201_V221_G0.703872.179
43_E51_V0.698332.162
188_T191_D0.694132.149
40_T54_R0.680612.107
172_R191_D0.673382.085
129_F161_G0.665292.060
225_V265_W0.660592.045
134_F137_A0.65072.014
49_I53_E0.639431.979
169_T175_A0.612531.896
167_G183_Y0.605571.875
48_G99_A0.602011.864
137_A225_V0.601211.861
257_Q264_E0.579381.794
172_R175_A0.571821.770
127_F230_V0.57141.769
171_A188_T0.570151.765
176_F179_S0.565611.751
164_K184_D0.562471.741
293_E306_D0.561791.739
223_N261_R0.552511.710
166_V200_P0.537761.665
203_I220_L0.535451.658
283_A286_Q0.532771.649
62_A65_L0.532721.649
129_F280_R0.529811.640
170_S189_Y0.516031.597
170_S190_D0.490731.519
138_Q166_V0.486741.507
301_E305_Q0.478941.483
284_D288_W0.47371.466
175_A186_V0.465991.443
178_E186_V0.462151.431
49_I102_A0.453841.405
65_L73_S0.453651.404
205_D208_G0.450521.395
280_R284_D0.449171.390
154_Y167_G0.44231.369
279_K283_A0.437251.354
257_Q266_G0.436321.351
295_A299_A0.433821.343
169_T186_V0.432331.338
138_Q201_V0.431871.337
142_S203_I0.426231.319
214_A218_E0.424551.314
154_Y157_K0.42191.306
257_Q262_I0.418631.296
140_V219_H0.417451.292
133_F137_A0.416881.291
216_L227_S0.413461.280
42_V94_Y0.413211.279
41_V49_I0.41181.275
261_R271_F0.399551.237
166_V185_E0.393581.218
305_Q308_L0.38751.200
227_S264_E0.385791.194
177_V186_V0.380391.178
168_L189_Y0.37631.165
141_L153_A0.375041.161
130_D277_A0.373931.158
37_G90_I0.371131.149
200_P203_I0.366281.134
109_D294_V0.365041.130
177_V183_Y0.364841.129
218_E256_D0.363931.127
280_R283_A0.36391.127
142_S168_L0.356211.103
138_Q200_P0.354371.097
306_D309_A0.353461.094
166_V187_L0.349731.083
144_A169_T0.348281.078
167_G177_V0.347981.077
157_K184_D0.346121.071
42_V51_V0.344921.068
108_E111_Q0.339181.050
54_R107_R0.336131.041
185_E195_L0.336041.040
37_G73_S0.335781.039
116_P120_T0.335281.038
139_V163_P0.333881.034
40_T43_E0.332961.031
207_A212_V0.330441.023
120_T123_L0.329371.020
144_A177_V0.326781.012
130_D263_K0.324261.004
258_I266_G0.32270.999
128_L161_G0.322360.998
137_A201_V0.321890.996
297_P300_V0.320410.992
152_L155_C0.320150.991
129_F277_A0.319820.990
281_F285_A0.319630.989
119_I122_F0.319580.989
62_A73_S0.319320.989
97_V102_A0.319170.988
132_D228_C0.318280.985
203_I216_L0.316480.980
63_S221_G0.313960.972
54_R111_Q0.312810.968
193_D196_D0.312590.968
276_A280_R0.309770.959
168_L187_L0.308610.955
232_A258_I0.307260.951
65_L68_E0.306190.948
91_Y304_Y0.302060.935
119_I123_L0.301460.933
160_R284_D0.301070.932
105_P111_Q0.298450.924
38_F57_G0.297510.921
178_E185_E0.29680.919
153_A157_K0.295740.916
137_A202_V0.294230.911
207_A231_G0.288080.892
277_A280_R0.288010.892
61_M64_H0.287540.890
152_L156_L0.287170.889
160_R288_W0.285610.884
304_Y308_L0.285590.884
132_D202_V0.284550.881
141_L165_V0.284390.880
222_D260_K0.28310.876
278_W282_A0.282040.873
135_G162_P0.281860.873
253_F256_D0.281490.871
118_F121_S0.280680.869
276_A279_K0.280390.868
165_V184_D0.278280.861
256_D259_D0.273480.847
225_V228_C0.272140.842
170_S175_A0.271520.841
203_I227_S0.270680.838
129_F156_L0.270650.838
142_S215_A0.270190.836
91_Y300_V0.270050.836
121_S148_T0.269560.834
229_L264_E0.266910.826
38_F95_L0.266660.826
141_L167_G0.265930.823
105_P108_E0.265870.823
228_C265_W0.264990.820
284_D287_P0.263890.817
131_N202_V0.263790.817
67_L72_V0.263520.816
168_L219_H0.262170.812
205_D227_S0.261770.810
157_K163_P0.260820.807
36_W73_S0.260230.806
59_F62_A0.259680.804
157_K165_V0.259590.804
59_F101_P0.258820.801
69_P72_V0.257490.797
47_P99_A0.257440.797
109_D114_L0.256620.794
169_T188_T0.256420.794
39_A43_E0.255770.792
278_W281_F0.254470.788
115_R120_T0.253780.786
115_R119_I0.253530.785
256_D260_K0.25330.784
232_A255_P0.25250.782
153_A204_V0.249970.774
155_C180_L0.249010.771
69_P223_N0.246310.763
175_A188_T0.24620.762
122_F281_F0.246190.762
115_R121_S0.245710.761
156_L288_W0.244920.758
169_T174_V0.244710.758
116_P119_I0.244660.757
117_L121_S0.243550.754
54_R106_E0.24280.752
144_A154_Y0.242750.751
40_T51_V0.242240.750
41_V53_E0.239420.741
114_L285_A0.239240.741
138_Q199_Q0.23910.740
115_R118_F0.23840.738
46_H53_E0.23730.735
37_G62_A0.236390.732
142_S216_L0.236320.732
171_A174_V0.235930.730
38_F111_Q0.235890.730
143_S206_F0.235790.730
202_V228_C0.235770.730
176_F180_L0.234110.725
120_T148_T0.233590.723
46_H99_A0.233150.722
63_S74_P0.232720.720
98_S101_P0.232680.720
279_K282_A0.232220.719
202_V225_V0.230640.714
48_G51_V0.230280.713
139_V202_V0.230060.712
191_D194_S0.229520.711
141_L149_A0.227320.704
37_G175_A0.225620.698
55_L102_A0.224870.696
92_N96_R0.224830.696
156_L161_G0.224420.695
134_F202_V0.224380.695
301_E304_Y0.223820.693
47_P53_E0.223690.692
142_S212_V0.223350.691
133_F163_P0.221380.685
200_P219_H0.221210.685
282_A285_A0.221120.685
111_Q115_R0.220530.683
166_V195_L0.22010.681
103_Y282_A0.219790.680
134_F163_P0.219560.680
287_P290_K0.219210.679
170_S188_T0.219130.678
236_D251_F0.218890.678
37_G40_T0.217980.675
169_T189_Y0.217970.675
304_Y307_L0.217020.672
222_D261_R0.216040.669
103_Y279_K0.215570.667
142_S219_H0.215550.667
213_L216_L0.214960.665
51_V54_R0.213780.662
292_E306_D0.21290.659
203_I219_H0.212460.658
169_T172_R0.211470.655
270_F278_W0.210650.652
92_N95_L0.209040.647
238_V252_F0.20860.646
130_D261_R0.208550.646
210_G214_A0.207670.643
131_N265_W0.207610.643
47_P50_A0.206490.639
278_W285_A0.205610.637
128_L139_V0.205390.636
49_I55_L0.203780.631
39_A42_V0.203290.629
136_A163_P0.203290.629
211_E215_A0.20320.629
141_L157_K0.203050.629
255_P259_D0.202950.628
232_A268_A0.202610.627
113_L290_K0.202560.627
216_L220_L0.202340.626
215_A218_E0.202280.626
63_S67_L0.202130.626
117_L152_L0.201960.625
212_V215_A0.201410.624
32_I88_P0.201030.622
64_H67_L0.200560.621
132_D225_V0.198780.615
141_L163_P0.19780.612
282_A290_K0.197680.612
64_H222_D0.197550.612
66_V69_P0.197310.611
132_D265_W0.197150.610
146_S149_A0.196250.608
133_F202_V0.196020.607
217_H227_S0.195880.606
198_P201_V0.195830.606
118_F122_F0.19560.606
161_G284_D0.195540.605
209_N212_V0.194760.603
110_W113_L0.194460.602
99_A102_A0.194340.602
36_W143_S0.193310.598
103_Y278_W0.193040.598
229_L266_G0.192950.597
117_L122_F0.192390.596
130_D265_W0.191590.593
208_G231_G0.191570.593
235_W238_V0.1910.591
281_F284_D0.190550.590
178_E183_Y0.190490.590
105_P114_L0.190320.589
156_L281_F0.190210.589
267_A270_F0.19020.589
127_F267_A0.189680.587
287_P291_V0.189350.586
128_L133_F0.188880.585
232_A259_D0.188520.584
120_T152_L0.186890.579
155_C158_K0.186860.578
130_D223_N0.186060.576
119_I281_F0.185340.574
256_D262_I0.184620.572
112_M115_R0.183630.568
56_Y59_F0.183330.568
115_R123_L0.182070.564
38_F90_I0.181860.563
117_L120_T0.181730.563
89_P290_K0.181570.562
45_R99_A0.181210.561
172_R178_E0.1810.560
123_L277_A0.180160.558
154_Y158_K0.180120.558
117_L123_L0.179580.556
307_L310_G0.179510.556
204_V230_V0.179280.555
131_N134_F0.178770.553
107_R110_W0.178550.553
128_L141_L0.178530.553
128_L131_N0.17830.552
37_G56_Y0.178270.552
238_V251_F0.17770.550
68_E276_A0.176970.548
61_M66_V0.176890.548
143_S146_S0.176780.547
168_L171_A0.176430.546
162_P165_V0.176120.545
122_F270_F0.175610.544
300_V304_Y0.175380.543
35_V297_P0.175290.543
116_P122_F0.175080.542
283_A287_P0.174920.542
303_A306_D0.174860.541
36_W56_Y0.173610.537
54_R89_P0.173120.536
267_A271_F0.173060.536
123_L261_R0.172890.535
179_S290_K0.172270.533
206_F233_T0.172230.533
122_F129_F0.172170.533
119_I269_E0.172010.532
205_D213_L0.171740.532
90_I95_L0.171660.531
115_R148_T0.171580.531
114_L282_A0.170490.528
38_F61_M0.170260.527
206_F230_V0.169530.525
154_Y177_V0.168870.523
172_R190_D0.168790.523
106_E109_D0.168250.521
259_D268_A0.1680.520
64_H69_P0.167550.519
105_P109_D0.166950.517
114_L119_I0.166940.517
196_D199_Q0.166670.516
214_A253_F0.166370.515
144_A149_A0.165930.514
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
1uufA0.92041000.426
2h6eA0.91081000.433
3twoA0.91721000.435
3ukoA0.93951000.437
1rjwA0.9141000.438
4ej6A0.91081000.438
1f8fA0.93631000.438
1e3iA0.93311000.441
2dphA0.9651000.442
4jbgA0.90761000.442

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