GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Glyco_hydro_3 - Glycosyl hydrolase family 3 N terminal domain
Pfam: PF00933 (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: CL0058
Length: 299
Sequences: 4804
Seq/Len: 16.07
HH_delta: 0.072 (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
88_Y142_R1.149553.791
153_A195_A1.001123.301
174_S177_E0.986693.254
179_R224_E0.97323.209
111_V137_A0.941683.105
219_D223_N0.857782.829
214_P218_T0.795242.622
214_P219_D0.771352.544
152_T197_A0.766492.528
256_N288_R0.734512.422
134_A188_A0.730712.410
150_A196_D0.719722.373
215_K219_D0.717952.367
288_R291_E0.706542.330
260_D295_R0.70562.327
175_E179_R0.674752.225
88_Y146_G0.67422.223
200_T211_S0.672192.217
84_P135_E0.66772.202
276_V280_E0.666912.199
222_R291_E0.666212.197
87_A136_M0.654692.159
277_E281_S0.639792.110
113_V181_I0.61652.033
233_S259_C0.606462.000
286_E290_D0.605581.997
141_V151_A0.596671.968
92_R146_G0.593361.957
215_K220_L0.586281.933
145_Q151_A0.563631.859
72_F93_I0.56111.850
78_L87_A0.561061.850
95_A147_A0.553591.825
153_A198_V0.544771.796
70_T97_E0.541281.785
217_L231_V0.53841.775
158_G173_V0.529351.746
285_S288_R0.525571.733
91_G140_F0.516641.704
290_D293_V0.509441.680
88_Y92_R0.50781.675
141_V189_A0.504831.665
252_V256_N0.495771.635
105_V197_A0.495661.634
221_L231_V0.489041.613
145_Q196_D0.486081.603
92_R147_A0.48561.601
111_V153_A0.484571.598
135_E188_A0.484391.597
88_Y139_A0.482571.591
88_Y143_G0.482531.591
218_T223_N0.477711.575
190_I198_V0.469541.548
200_T217_L0.466741.539
252_V278_A0.466571.539
144_L151_A0.451051.487
292_A295_R0.449571.482
153_A189_A0.43731.442
78_L90_V0.430161.418
198_V221_L0.423021.395
176_R180_E0.421641.390
275_L284_I0.419781.384
248_E277_E0.41751.377
135_E138_R0.414171.366
210_A213_S0.410461.354
252_V283_R0.409451.350
89_E92_R0.407391.343
187_R225_L0.407251.343
184_P188_A0.402091.326
288_R292_A0.401581.324
201_S210_A0.398191.313
256_N285_S0.397171.310
255_L275_L0.391991.293
138_R142_R0.390751.289
255_L292_A0.384511.268
85_E89_E0.378721.249
92_R96_R0.378391.248
134_A138_R0.377291.244
139_A143_G0.376521.242
111_V189_A0.376051.240
140_F144_L0.375661.239
106_N144_L0.373961.233
91_G144_L0.373191.231
138_R188_A0.371681.226
276_V279_V0.371621.225
188_A192_D0.366411.208
53_I103_I0.366231.208
273_D277_E0.363821.200
254_A259_C0.362551.196
184_P187_R0.359181.184
84_P139_A0.358421.182
39_Q43_E0.358211.181
127_G132_L0.352781.163
44_Q47_L0.350951.157
208_T213_S0.348751.150
113_V133_V0.348671.150
277_E280_E0.34671.143
157_P216_I0.346261.142
96_R147_A0.342181.128
200_T259_C0.341641.127
179_R187_R0.336191.109
139_A142_R0.33591.108
84_P136_M0.335221.105
81_T136_M0.334541.103
164_S169_P0.331121.092
135_E192_D0.329021.085
256_N284_I0.328121.082
222_R295_R0.328041.082
110_V125_S0.327821.081
274_A277_E0.32771.081
293_V297_L0.327311.079
126_F140_F0.327081.079
158_G178_L0.326991.078
108_A144_L0.321381.060
287_E290_D0.320871.058
173_V177_E0.318691.051
54_A105_V0.318371.050
126_F136_M0.314631.038
114_N122_G0.314411.037
72_F97_E0.313941.035
107_F232_I0.313561.034
205_I210_A0.312451.030
137_A189_A0.309841.022
98_L106_N0.308491.017
175_E224_E0.308091.016
256_N283_R0.307971.016
131_D135_E0.307621.014
39_Q42_S0.30711.013
72_F90_V0.306691.011
141_V195_A0.3061.009
279_V285_S0.305841.009
156_F183_L0.303040.999
230_V261_M0.301050.993
54_A107_F0.300380.991
190_I225_L0.299460.987
142_R193_A0.29940.987
187_R192_D0.296140.977
218_T257_A0.295220.974
99_R149_V0.293960.969
291_E295_R0.290840.959
197_A230_V0.29020.957
293_V296_I0.288680.952
150_A230_V0.287490.948
217_L259_C0.286780.946
95_A143_G0.284610.939
235_D263_L0.282430.931
138_R193_A0.281890.930
95_A144_L0.281670.929
282_G285_S0.279750.922
49_I297_L0.275290.908
278_A283_R0.273780.903
261_M296_I0.271740.896
210_A216_I0.27090.893
85_E88_Y0.270780.893
74_S123_E0.270010.890
151_A196_D0.269070.887
236_L262_L0.268310.885
107_F263_L0.267140.881
255_L289_L0.26680.880
253_R256_N0.266640.879
249_E283_R0.2660.877
76_M127_G0.264730.873
152_T232_I0.263880.870
190_I195_A0.262120.864
279_V289_L0.261850.863
228_D298_R0.259850.857
189_A195_A0.259620.856
194_G227_F0.257930.851
279_V282_G0.257520.849
130_P134_A0.257520.849
205_I216_I0.256110.845
86_L89_E0.254790.840
279_V284_I0.253770.837
183_L220_L0.25370.837
90_V93_I0.250420.826
157_P183_L0.250150.825
205_I215_K0.249790.824
284_I289_L0.248880.821
214_P256_N0.24820.818
127_G133_V0.247860.817
83_D86_L0.247090.815
175_E215_K0.246510.813
157_P210_A0.245240.809
141_V145_Q0.245210.809
279_V286_E0.242830.801
212_L253_R0.242420.799
248_E281_S0.240290.792
291_E294_R0.239970.791
156_F221_L0.239910.791
105_V232_I0.239280.789
200_T237_E0.239190.789
61_I98_L0.238660.787
249_E253_R0.238430.786
220_L224_E0.237170.782
260_D292_A0.236410.780
198_V227_F0.235770.777
177_E181_I0.235190.776
131_D184_P0.234180.772
294_R298_R0.233570.770
82_W132_L0.232980.768
105_V150_A0.231620.764
232_I261_M0.230150.759
76_M80_A0.228970.755
77_A80_A0.228780.754
280_E286_E0.228250.753
99_R147_A0.228180.752
114_N120_G0.226970.748
85_E139_A0.226770.748
52_L104_N0.226750.748
212_L250_A0.226580.747
194_G228_D0.225950.745
131_D188_A0.224160.739
79_A132_L0.223260.736
93_I96_R0.223230.736
223_N226_G0.221940.732
179_R183_L0.22150.730
98_L103_I0.221460.730
114_N125_S0.221270.730
76_M114_N0.221160.729
253_R257_A0.220850.728
222_R298_R0.219650.724
114_N127_G0.21810.719
211_S259_C0.216760.715
106_N149_V0.216220.713
165_H168_L0.215930.712
179_R220_L0.215870.712
138_R141_V0.215290.710
129_D132_L0.215260.710
86_L143_G0.21350.704
119_W160_G0.210660.695
59_G74_S0.209550.691
131_D134_A0.207850.685
248_E278_A0.207660.685
79_A127_G0.207510.684
87_A91_G0.207320.684
133_V185_P0.207250.683
132_L135_E0.205760.679
260_D288_R0.203380.671
251_A274_A0.203120.670
107_F261_M0.203070.670
87_A140_F0.202560.668
295_R298_R0.202050.666
75_P126_F0.201990.666
97_E100_A0.201940.666
94_I144_L0.201360.664
204_A209_P0.201280.664
75_P140_F0.200720.662
116_N119_W0.199510.658
91_G141_V0.198290.654
278_A281_S0.198070.653
57_Q98_L0.197820.652
286_E293_V0.197760.652
129_D134_A0.196980.650
278_A284_I0.196720.649
190_I227_F0.196670.649
138_R192_D0.196610.648
81_T86_L0.195510.645
115_R128_E0.194740.642
56_D235_D0.194590.642
216_I220_L0.194450.641
89_E93_I0.192080.633
292_A296_I0.191470.631
75_P90_V0.190820.629
134_A185_P0.190670.629
233_S248_E0.189590.625
170_S204_A0.18940.625
59_G71_A0.189120.624
211_S237_E0.188760.622
75_P110_V0.187640.619
57_Q94_I0.187530.618
88_Y147_A0.187450.618
70_T93_I0.186930.616
178_L183_L0.186610.615
54_A261_M0.186530.615
151_A195_A0.185160.611
134_A184_P0.184640.609
54_A263_L0.183370.605
57_Q106_N0.182630.602
274_A278_A0.182550.602
143_G146_G0.182450.602
235_D264_V0.181440.598
285_S291_E0.180890.596
177_E180_E0.18070.596
248_E274_A0.179760.593
79_A133_V0.179750.593
218_T291_E0.179520.592
93_I97_E0.179390.592
56_D263_L0.179170.591
161_A185_P0.178920.590
74_S77_A0.178510.589
230_V296_I0.17850.589
220_L225_L0.178390.588
208_T253_R0.178390.588
170_S207_G0.178050.587
132_L136_M0.177620.586
235_D265_C0.176720.583
143_G147_A0.176340.581
52_L105_V0.176080.581
217_L257_A0.175970.580
94_I106_N0.175750.580
287_E291_E0.175490.579
121_R125_S0.175130.578
230_V292_A0.174980.577
153_A190_I0.174250.575
86_L90_V0.173680.573
43_E51_L0.173240.571
107_F235_D0.1730.570
251_A262_L0.172170.568
108_A140_F0.172030.567
91_G143_G0.171810.567
59_G75_P0.171510.566
90_V140_F0.170830.563
264_V267_D0.170610.563
275_L279_V0.170270.561
81_T84_P0.170220.561
173_V178_L0.170180.561
216_I221_L0.16980.560
61_I123_E0.169550.559
197_A232_I0.169370.559
290_D294_R0.168670.556
178_L216_I0.168110.554
142_R194_G0.167980.554
157_P220_L0.167650.553
73_P78_L0.167640.553
157_P178_L0.167360.552
219_D224_E0.167060.551
120_G166_R0.166980.551
137_A153_A0.166840.550
221_L227_F0.166630.549
160_G163_D0.166380.549
222_R260_D0.166210.548
117_P121_R0.16610.548
91_G95_A0.165930.547
40_A53_I0.165820.547
276_V286_E0.165640.546
280_E283_R0.164540.543
185_P188_A0.164080.541
280_E287_E0.163730.540
151_A197_A0.163650.540
56_D62_V0.163620.540
157_P225_L0.163260.538
138_R194_G0.162150.535
162_Q169_P0.162130.535
158_G205_I0.162050.534
275_L278_A0.161680.533
171_V206_D0.161430.532
294_R297_L0.161340.532
237_E264_V0.161140.531
55_I103_I0.160670.530
115_R181_I0.160540.529
105_V152_T0.159730.527
115_R120_G0.159640.526
52_L230_V0.15930.525
56_D155_H0.159170.525
183_L225_L0.159030.524
247_I251_A0.158940.524
181_I184_P0.158880.524
70_T100_A0.158180.522
78_L81_T0.157940.521
248_E283_R0.157750.520
175_E220_L0.15760.520
284_I288_R0.157340.519
212_L254_A0.157190.518
208_T215_K0.1570.518
230_V295_R0.155990.514
251_A265_C0.155920.514
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
3bmxA0.97991000.072
3rrxA0.98331000.078
1x38A0.98661000.081
3u48A0.95991000.085
3sqlA0.97321000.085
3tevA0.96321000.128
3abzA0.88291000.16
2x41A0.93311000.161
3zyzA0.8931000.182
4i3gA0.92641000.186

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