GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Glyco_hydro_3_C - Glycosyl hydrolase family 3 C-terminal domain
Pfam: PF01915 (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: 227
Sequences: 3400
Seq/Len: 14.98
HH_delta: 0.058 (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
140_S158_A1.062643.853
55_R177_D0.917513.326
93_V124_I0.842623.055
150_E217_Y0.804172.916
1_I173_V0.791632.870
179_N224_S0.774932.810
48_P92_F0.735322.666
150_E156_I0.712322.583
136_V153_V0.709862.574
56_F175_F0.708872.570
165_E168_E0.651882.363
52_L175_F0.646782.345
49_L53_K0.640722.323
173_V178_V0.632992.295
172_D177_D0.609562.210
91_V127_V0.57982.102
162_P166_G0.550981.998
54_Q168_E0.542091.965
47_T50_D0.53251.931
125_K152_N0.50151.818
218_P221_Y0.500231.814
8_G154_D0.489471.775
15_P177_D0.488661.772
115_A145_D0.486291.763
2_V160_Y0.48451.757
91_V124_I0.483881.754
190_K214_P0.475811.725
137_V159_A0.471741.710
159_A162_P0.46471.685
128_A153_V0.461991.675
168_E172_D0.458671.663
46_V51_A0.457491.659
13_L88_V0.454871.649
10_L155_A0.454531.648
81_A84_K0.450531.633
126_A129_A0.440631.598
90_I137_V0.434441.575
28_D49_L0.433381.571
122_E126_A0.432321.567
48_P170_I0.430161.560
46_V168_E0.428221.553
133_K154_D0.427161.549
51_A171_A0.423031.534
138_V158_A0.416691.511
52_L174_L0.412961.497
89_V127_V0.411771.493
61_V64_P0.410761.489
195_I208_Y0.410681.489
159_A170_I0.408011.479
127_V134_V0.401091.454
19_K60_G0.397281.440
22_V49_L0.39361.427
81_A85_E0.390031.414
150_E216_L0.385421.397
7_E154_D0.381611.384
10_L154_D0.380861.381
148_P152_N0.379621.376
138_V146_L0.376111.364
128_A154_D0.376091.364
22_V52_L0.375161.360
75_G78_E0.373091.353
125_K148_P0.372851.352
89_V131_G0.367581.333
20_V88_V0.367081.331
34_G37_S0.362671.315
55_R172_D0.361661.311
23_I89_V0.361191.310
5_K217_Y0.3591.302
118_A122_E0.357251.295
122_E125_K0.355531.289
13_L135_I0.351091.273
191_S194_D0.350471.271
76_I80_V0.348541.264
82_A86_A0.346531.256
64_P78_E0.346481.256
119_N122_E0.346441.256
26_N139_N0.344751.250
1_I159_A0.34421.248
88_V135_I0.343181.244
77_D81_A0.338171.226
93_V136_V0.336681.221
23_I91_V0.333351.209
79_A83_A0.330211.197
215_P218_P0.328471.191
80_V126_A0.327211.186
136_V149_W0.323211.172
93_V138_V0.322861.171
121_Q125_K0.322741.170
157_L180_P0.320161.161
189_P195_I0.31981.159
17_K88_V0.318891.156
21_A86_A0.317681.152
190_K216_L0.317281.150
172_D178_V0.315341.143
157_L174_L0.313191.135
114_L145_D0.312781.134
19_K85_E0.308541.119
146_L149_W0.307181.114
46_V167_G0.30561.108
196_P208_Y0.300031.088
80_V130_A0.300021.088
173_V180_P0.298661.083
50_D53_K0.288631.046
89_V134_V0.287251.041
121_Q149_W0.287111.041
26_N94_G0.285381.035
10_L88_V0.284121.030
21_A82_A0.284041.030
207_T211_D0.283541.028
52_L61_V0.28231.023
179_N226_T0.279811.014
51_A167_G0.279441.013
48_P139_N0.278011.008
179_N183_K0.275861.000
76_I126_A0.273030.990
124_I149_W0.272290.987
28_D50_D0.269150.976
139_N159_A0.26630.965
126_A130_A0.265990.964
62_V86_A0.265790.964
23_I127_V0.265290.962
115_A121_Q0.26410.958
92_F137_V0.263920.957
1_I169_A0.262830.953
46_V165_E0.262590.952
136_V156_I0.262060.950
60_G63_V0.260260.944
160_Y188_I0.260060.943
165_E172_D0.258020.935
190_K215_P0.256340.929
10_L135_I0.255110.925
178_V181_S0.255080.925
145_D192_M0.253580.919
44_Y165_E0.251720.913
80_V84_K0.251620.912
92_F170_I0.251290.911
89_V132_K0.245660.891
47_T51_A0.242930.881
132_K154_D0.242090.878
78_E82_A0.2420.877
184_L188_I0.241470.875
83_A86_A0.240280.871
147_D216_L0.235340.853
50_D54_Q0.234870.852
52_L171_A0.229290.831
146_L216_L0.228260.828
114_L143_P0.227930.826
141_G160_Y0.227810.826
6_N155_A0.226950.823
128_A134_V0.226040.820
91_V123_L0.22560.818
19_K87_D0.224890.815
22_V27_A0.224240.813
73_D77_D0.22280.808
143_P188_I0.222350.806
130_A133_K0.221650.804
22_V90_I0.221610.803
61_V65_E0.221550.803
5_K221_Y0.219990.798
52_L90_I0.219660.796
25_P120_Q0.219040.794
76_I119_N0.218060.791
110_D164_Q0.215710.782
55_R175_F0.213710.775
76_I79_A0.213590.774
29_N32_A0.212360.770
1_I157_L0.211620.767
179_N225_Y0.211350.766
125_K129_A0.209750.760
34_G38_G0.208210.755
3_L157_L0.2080.754
131_G154_D0.207940.754
57_G60_G0.206770.750
19_K62_V0.206110.747
205_G209_D0.205960.747
91_V134_V0.204730.742
129_A152_N0.20460.742
146_L156_I0.203640.738
20_V56_F0.203330.737
35_G141_G0.202340.734
19_K86_A0.20120.729
137_V170_I0.200920.728
187_T208_Y0.20070.728
141_G161_Y0.200580.727
49_L63_V0.200340.726
51_A168_E0.199730.724
89_V130_A0.199480.723
23_I79_A0.196830.714
44_Y168_E0.196420.712
5_K156_I0.195950.710
37_S164_Q0.19440.705
64_P82_A0.193490.702
117_P120_Q0.193450.701
191_S211_D0.193040.700
21_A89_V0.192960.700
131_G134_V0.192050.696
26_N32_A0.191610.695
28_D47_T0.190230.690
62_V82_A0.189820.688
153_V156_I0.189650.688
78_E81_A0.189470.687
90_I174_L0.189430.687
194_D213_G0.188630.684
121_Q148_P0.18780.681
32_A42_P0.187310.679
197_A201_Y0.187270.679
73_D122_E0.187230.679
5_K150_E0.186130.675
56_F61_V0.186010.674
194_D215_P0.185320.672
35_G38_G0.184670.670
143_P189_P0.184170.668
14_K17_K0.183180.664
145_D148_P0.1830.663
15_P55_R0.182880.663
48_P167_G0.182050.660
51_A54_Q0.181770.659
92_F139_N0.181120.657
207_T210_Y0.180480.654
171_A175_F0.179330.650
37_S40_V0.178810.648
198_Y208_Y0.178720.648
23_I83_A0.177870.645
49_L61_V0.177080.642
5_K223_L0.176770.641
192_M198_Y0.176710.641
30_P166_G0.176290.639
31_V161_Y0.175250.635
124_I128_A0.174540.633
160_Y186_V0.174510.633
93_V116_L0.174270.632
62_V85_E0.173990.631
4_L158_A0.17390.630
82_A85_E0.173760.630
27_A92_F0.173170.628
94_G117_P0.173070.627
157_L173_V0.17290.627
60_G64_P0.17270.626
6_N225_Y0.172570.626
3_L226_T0.17250.625
21_A83_A0.172480.625
33_Q39_N0.172170.624
173_V181_S0.1720.624
160_Y185_P0.171920.623
197_A210_Y0.170660.619
73_D76_I0.170510.618
217_Y221_Y0.170360.618
140_S188_I0.170020.616
52_L56_F0.168920.612
6_N11_L0.168480.611
137_V157_L0.168030.609
36_G109_S0.168020.609
46_V50_D0.167430.607
189_P208_Y0.166920.605
203_M206_R0.166870.605
37_S110_D0.166650.604
207_T213_G0.166260.603
173_V179_N0.165760.601
146_L188_I0.165360.600
193_E199_Y0.165280.599
51_A55_R0.165170.599
72_D76_I0.164260.596
151_D190_K0.164110.595
35_G96_P0.163320.592
1_I180_P0.163030.591
52_L59_A0.162460.589
24_G27_A0.162380.589
11_L135_I0.162290.588
25_P94_G0.161940.587
156_I217_Y0.161320.585
34_G45_G0.160960.584
20_V175_F0.160350.581
30_P47_T0.160010.580
194_D197_A0.159960.580
115_A192_M0.159730.579
192_M195_I0.159530.578
87_D132_K0.159220.577
140_S144_Y0.158390.574
135_I174_L0.157860.572
80_V127_V0.156520.567
198_Y201_Y0.156430.567
26_N161_Y0.15640.567
159_A173_V0.156340.567
203_M207_T0.156170.566
28_D53_K0.155940.565
33_Q166_G0.155760.565
79_A123_L0.155750.565
3_L6_N0.155650.564
37_S142_N0.155590.564
20_V61_V0.154830.561
36_G39_N0.154590.560
13_L175_F0.154530.560
204_Y209_D0.154390.560
37_S95_R0.154310.559
21_A79_A0.154230.559
128_A152_N0.153810.558
23_I82_A0.152830.554
36_G110_D0.152720.554
7_E10_L0.152190.552
139_N162_P0.15190.551
59_A62_V0.151390.549
34_G40_V0.151160.548
176_G180_P0.151160.548
156_I221_Y0.150390.545
147_D190_K0.150350.545
116_L124_I0.149470.542
113_D192_M0.149210.541
88_V133_K0.149090.541
118_A121_Q0.149050.540
65_E75_G0.148860.540
34_G205_G0.147450.535
89_V92_F0.146990.533
65_E71_D0.146470.531
187_T215_P0.146260.530
47_T94_G0.145930.529
121_Q124_I0.145780.529
31_V34_G0.144870.525
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
3abzA0.96041000.058
4iibA0.9781000.065
3zyzA0.97361000.075
4i3gA0.96041000.095
3u48A0.96921000.098
2x41A0.95151000.11
3rrxA0.87671000.17
1x38A0.88551000.215
3bmxA0.80181000.335
3sqlA0.656497.60.875

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