GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF1749 - Protein of unknown function (DUF1749)
Pfam: PF08538 (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: CL0028
Length: 303
Sequences: 19466
Seq/Len: 64.24
HH_delta: 0.172 (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
111_V140_G2.685275.289
241_G276_P1.776893.500
273_G297_R1.569483.091
236_L301_F1.562653.078
109_K139_D1.511332.977
126_L141_A1.447152.850
112_L122_V1.380362.719
275_I297_R1.295732.552
111_V139_D1.180522.325
55_L295_V1.16732.299
111_V302_L1.104332.175
144_Q294_L1.086222.139
91_A125_Y1.079482.126
286_S293_W1.073292.114
119_C146_P1.058582.085
241_G274_I1.037562.043
145_A243_D1.022722.014
35_A65_S1.018932.007
122_V141_A1.007771.985
143_L146_P1.000311.970
35_A67_F0.9971.964
95_E137_P0.989961.950
125_Y129_P0.984711.939
124_H128_S0.981771.934
142_I298_V0.977081.924
296_E300_K0.974881.920
77_G81_S0.971041.912
111_V142_I0.923321.818
63_G299_V0.898551.770
297_R300_K0.897721.768
88_E128_S0.876361.726
141_A235_L0.872941.719
58_A295_V0.86021.694
123_L143_L0.854361.683
130_N136_P0.850351.675
91_A129_P0.819891.615
129_P137_P0.817661.610
91_A95_E0.813421.602
227_T230_K0.812371.600
271_L297_R0.809461.594
39_I122_V0.804141.584
142_I236_L0.798481.573
278_A286_S0.788151.552
33_P65_S0.783361.543
275_I278_A0.775111.527
263_T270_P0.748581.474
69_V90_I0.747081.471
94_V110_I0.743021.463
64_W111_V0.742611.463
248_P274_I0.739611.457
39_I71_L0.735631.449
129_P136_P0.726091.430
124_H127_S0.722961.424
294_L298_V0.717091.412
140_G234_P0.712211.403
38_F113_M0.708781.396
260_K270_P0.708031.394
71_L121_D0.703221.385
46_L70_Q0.699951.379
58_A299_V0.698651.376
41_G116_S0.698341.375
113_M144_Q0.69291.365
40_G71_L0.687371.354
236_L273_G0.685611.350
38_F66_L0.684611.348
114_G122_V0.683541.346
56_A68_Q0.683231.346
34_N111_V0.676611.333
229_G262_A0.673871.327
36_L64_W0.660261.300
258_R262_A0.655421.291
140_G301_F0.653331.287
39_I90_I0.652581.285
257_E261_A0.649831.280
44_D48_T0.642541.265
87_V124_H0.641421.263
64_W302_L0.641361.263
40_G78_W0.638931.258
107_R110_I0.638841.258
142_I302_L0.63811.257
90_I125_Y0.637341.255
114_G119_C0.635791.252
239_Y272_S0.634781.250
293_W296_E0.630431.242
293_W297_R0.626331.234
116_S280_H0.618741.219
235_L263_T0.612771.207
35_A107_R0.611811.205
36_L113_M0.610881.203
58_A61_E0.608741.199
39_I69_V0.599411.181
239_Y248_P0.592691.167
238_L294_L0.591221.164
67_F97_L0.588471.159
91_A128_S0.586211.155
241_G277_G0.584841.152
78_W81_S0.577851.138
60_E66_L0.568431.120
34_N109_K0.565831.114
236_L271_L0.563371.110
34_N139_D0.563291.109
36_L59_L0.563071.109
42_L117_T0.562191.107
113_M142_I0.561971.107
115_H281_N0.560451.104
34_N64_W0.560371.104
43_T116_S0.558141.099
39_I112_L0.55761.098
114_G118_G0.557251.097
67_F93_L0.555311.094
40_G69_V0.554971.093
125_Y138_V0.553281.090
92_Q95_E0.549281.082
110_I138_V0.54681.077
36_L66_L0.542831.069
241_G248_P0.541641.067
127_S227_T0.541051.066
112_L138_V0.53911.062
238_L275_I0.538821.061
88_E91_A0.538191.060
239_Y274_I0.537031.058
278_A282_V0.530951.046
57_E61_E0.521631.027
93_L96_Y0.51991.024
37_L110_I0.517521.019
69_V93_L0.516321.017
95_E129_P0.516041.016
238_L297_R0.51521.015
242_K277_G0.514761.014
56_A60_E0.513451.011
71_L117_T0.512371.009
91_A137_P0.510281.005
35_A110_I0.502270.989
125_Y137_P0.500940.987
43_T117_T0.500790.986
145_A240_S0.493240.971
130_N137_P0.490560.966
70_Q79_G0.489430.964
295_V299_V0.48940.964
113_M298_V0.482910.951
273_G300_K0.471250.928
143_L237_V0.466980.920
240_S282_V0.46570.917
54_D57_E0.462350.911
37_L112_L0.460980.908
112_L125_Y0.460180.906
56_A66_L0.454370.895
106_G109_K0.454060.894
64_W299_V0.449390.885
94_V125_Y0.449330.885
115_H283_S0.445830.878
93_L97_L0.445150.877
53_P57_E0.44220.871
278_A285_P0.441090.869
52_L55_L0.438530.864
124_H227_T0.438180.863
87_V121_D0.437150.861
37_L94_V0.435890.858
38_F68_Q0.435790.858
237_V270_P0.434420.856
140_G302_L0.43280.852
256_L260_K0.430860.849
127_S230_K0.429540.846
257_E260_K0.427040.841
296_E299_V0.425870.839
258_R261_A0.42550.838
40_G68_Q0.425190.837
256_L270_P0.423170.833
238_L273_G0.422740.833
110_I137_P0.420130.827
38_F59_L0.420.827
46_L68_Q0.419360.826
65_S107_R0.418260.824
144_Q283_S0.415080.817
41_G115_H0.412660.813
67_F107_R0.411830.811
35_A64_W0.411020.809
32_A65_S0.410690.809
142_I301_F0.408080.804
38_F52_L0.407240.802
92_Q96_Y0.403940.796
126_L138_V0.400460.789
288_A293_W0.399970.788
276_P293_W0.39970.787
271_L300_K0.398980.786
279_S285_P0.396160.780
122_V126_L0.39560.779
226_K229_G0.395560.779
243_D246_V0.395170.778
239_Y246_V0.392410.773
119_C143_L0.388610.765
44_D281_N0.385850.760
37_L90_I0.385440.759
89_E92_Q0.384970.758
116_S281_N0.38460.757
115_H145_A0.383360.755
94_V138_V0.383110.755
168_A172_E0.381330.751
118_G122_V0.381030.750
141_A233_K0.379790.748
46_L69_V0.379660.748
138_V233_K0.379660.748
256_L272_S0.378030.745
108_E137_P0.377950.744
123_L146_P0.377220.743
60_E63_G0.376350.741
142_I238_L0.375370.739
88_E92_Q0.374160.737
143_L235_L0.374150.737
97_L107_R0.372280.733
140_G236_L0.372220.733
84_D128_S0.371670.732
197_I201_R0.369720.728
44_D115_H0.367310.723
275_I293_W0.364330.718
53_P68_Q0.361530.712
70_Q81_S0.359740.708
281_N284_G0.35890.707
54_D295_V0.358860.707
35_A97_L0.35750.704
273_G293_W0.357250.704
36_L111_V0.356450.702
275_I286_S0.356130.701
110_I139_D0.355810.701
287_Q295_V0.355070.699
126_L231_V0.35410.697
58_A288_A0.350890.691
260_K263_T0.350080.689
237_V272_S0.34960.689
199_A202_F0.349580.688
127_S231_V0.344620.679
139_D142_I0.344580.679
231_V263_T0.342730.675
126_L233_K0.342560.675
46_L80_T0.340290.670
39_I121_D0.340250.670
200_Y204_S0.337850.665
288_A296_E0.336320.662
37_L69_V0.335180.660
213_D217_S0.333660.657
178_K181_E0.333050.656
298_V302_L0.332830.656
88_E94_V0.332310.654
52_L113_M0.329890.650
57_E60_E0.329610.649
91_A94_V0.325490.641
209_G213_D0.325120.640
180_D184_P0.324910.640
55_L59_L0.320360.631
223_R226_K0.317150.625
282_V285_P0.316920.624
237_V256_L0.316550.623
243_D247_P0.316480.623
243_D280_H0.316120.623
116_S146_P0.315880.622
59_L298_V0.315390.621
232_S264_N0.314490.619
168_A171_K0.313580.618
109_K137_P0.312540.616
52_L115_H0.310390.611
203_L207_S0.309770.610
114_G143_L0.309380.609
117_T121_D0.309170.609
200_Y203_L0.309170.609
77_G80_T0.308050.607
144_Q238_L0.306030.603
264_N270_P0.305440.602
297_R301_F0.304890.600
283_S294_L0.303510.598
238_L282_V0.303260.597
63_G66_L0.302820.596
87_V91_A0.302470.596
182_I185_R0.301610.594
119_C145_A0.300190.591
45_G78_W0.299660.590
259_W263_T0.298960.589
242_K278_A0.298680.588
185_R188_T0.295490.582
41_G117_T0.295280.582
89_E93_L0.294740.580
129_P138_V0.293360.578
223_R227_T0.291980.575
36_L302_L0.291010.573
235_L270_P0.290630.572
235_L259_W0.290370.572
240_S277_G0.289970.571
123_L148_S0.286950.565
203_L206_A0.285310.562
58_A296_E0.285080.561
202_F205_L0.28490.561
169_L173_L0.284730.561
145_A281_N0.284560.560
112_L141_A0.284010.559
279_S282_V0.28340.558
146_P243_D0.283190.558
41_G44_D0.283050.557
164_E168_A0.282730.557
37_L67_F0.281070.554
210_G213_D0.280030.552
35_A111_V0.279620.551
145_A239_Y0.279590.551
120_Q147_V0.278560.549
261_A264_N0.278360.548
61_E299_V0.278340.548
231_V235_L0.278060.548
114_G126_L0.276790.545
34_N140_G0.275660.543
277_G286_S0.275550.543
41_G280_H0.274640.541
195_T198_T0.274480.541
40_G52_L0.273460.539
86_D117_T0.273370.538
59_L66_L0.273330.538
120_Q123_L0.271930.536
271_L301_F0.271790.535
179_G183_L0.270940.534
182_I186_E0.26940.531
184_P187_F0.268850.529
111_V301_F0.26830.528
43_T281_N0.268220.528
78_W117_T0.267930.528
116_S145_A0.267570.527
224_L227_T0.267520.527
187_F190_L0.26550.523
212_D216_S0.265250.522
119_C123_L0.265050.522
122_V138_V0.264640.521
40_G45_G0.264210.520
115_H144_Q0.264150.520
128_S227_T0.263820.520
175_A179_G0.263490.519
44_D116_S0.263360.519
47_L53_P0.262860.518
136_P232_S0.262610.517
165_E168_A0.262430.517
52_L56_A0.261890.516
205_L208_P0.261890.516
170_A174_I0.261710.515
114_G121_D0.261330.515
118_G121_D0.260660.513
245_Y279_S0.260640.513
117_T120_Q0.260510.513
179_G182_I0.254760.502
207_S211_D0.254260.501
138_V141_A0.253850.500
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
3om8A0.84161000.172
2yysA0.84491000.19
3v48A0.81521000.191
3afiE0.87461000.196
3fobA0.85811000.201
1b6gA0.85811000.202
2xuaA0.82841000.204
3w06A0.82511000.21
2wueA0.88121000.21
1zoiA0.85481000.212

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