GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SusD-like_3 - Starch-binding associating with outer membrane
Pfam: PF14322 (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: CL0020
Length: 190
Sequences: 4613
Seq/Len: 24.28
HH_delta: 0.141 (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_Y158_E1.446033.793
83_G117_Y1.295023.397
157_D185_L1.230943.229
112_F175_I1.176273.086
132_T151_F1.012092.655
160_I182_Y0.968162.540
143_S147_E0.959992.518
127_D142_R0.941322.469
158_E162_L0.940242.466
150_D154_A0.874212.293
147_E150_D0.870892.284
114_R155_D0.86832.278
127_D144_T0.852272.236
144_T147_E0.840542.205
104_N162_L0.82752.171
108_A162_L0.809832.124
92_E134_P0.806832.116
154_A158_E0.806562.116
107_L111_Y0.800862.101
130_Y151_F0.799542.097
95_D107_L0.79522.086
158_E161_N0.792662.079
105_R109_E0.791282.076
92_E133_E0.761721.998
146_E150_D0.758331.989
100_E104_N0.745061.954
151_F155_D0.737851.935
153_I157_D0.731061.918
109_E174_R0.709281.861
153_I185_L0.692221.816
111_Y155_D0.681011.786
91_I107_L0.677231.776
152_I188_V0.67611.774
130_Y143_S0.657711.725
160_I181_A0.657571.725
151_F154_A0.652971.713
185_L189_Y0.649481.704
127_D145_R0.64811.700
130_Y148_V0.633541.662
119_F188_V0.627051.645
153_I189_Y0.624151.637
177_K182_Y0.616121.616
24_A87_A0.611781.605
90_V106_Y0.604491.586
122_V149_Y0.571471.499
90_V110_A0.568851.492
94_I107_L0.566961.487
153_I188_V0.562911.477
121_L128_V0.559111.467
156_L184_L0.54941.441
111_Y162_L0.547181.435
163_L181_A0.546981.435
88_N114_R0.544791.429
116_Y120_Q0.529441.389
120_Q123_R0.529291.388
127_D143_S0.519871.364
127_D148_V0.519521.363
87_A110_A0.519071.362
122_V145_R0.506351.328
119_F123_R0.506241.328
100_E103_K0.503691.321
21_L110_A0.50241.318
176_T179_A0.498161.307
99_S102_E0.489051.283
165_D177_K0.48871.282
143_S148_V0.482181.265
84_I118_Y0.481581.263
157_D160_I0.478961.256
112_F181_A0.478221.254
122_V148_V0.467661.227
113_L117_Y0.464541.219
121_L125_Y0.462961.214
118_Y131_I0.461191.210
84_I87_A0.45711.199
45_D50_N0.455421.195
149_Y188_V0.451921.185
91_I110_A0.449941.180
5_V8_D0.446231.171
90_V94_I0.444131.165
157_D161_N0.442241.160
179_A182_Y0.440631.156
128_V148_V0.435441.142
108_A111_Y0.424321.113
155_D159_A0.4231.110
21_L90_V0.422131.107
107_L158_E0.422111.107
118_Y128_V0.41881.099
156_L188_V0.415691.090
145_R149_Y0.411151.079
116_Y184_L0.409981.075
112_F180_A0.408341.071
113_L175_I0.407021.068
108_A163_L0.406981.068
132_T154_A0.387761.017
24_A113_L0.382991.005
131_I140_L0.380020.997
115_A152_I0.376260.987
122_V152_I0.372880.978
118_Y148_V0.372290.977
126_G142_R0.372290.977
17_T25_Y0.369550.969
175_I180_A0.368510.967
187_R190_L0.359240.942
144_T148_V0.354020.929
24_A90_V0.353540.927
80_Y117_Y0.351060.921
25_Y109_E0.346190.908
142_R145_R0.340860.894
145_R148_V0.337960.887
17_T94_I0.336590.883
73_I125_Y0.335710.881
18_E22_N0.335510.880
21_L106_Y0.335390.880
18_E102_E0.335360.880
41_E46_I0.333720.875
165_D179_A0.332650.873
157_D189_Y0.332520.872
108_A158_E0.332240.872
108_A159_A0.326810.857
119_F187_R0.324810.852
115_A156_L0.322840.847
80_Y120_Q0.319290.838
126_G145_R0.316340.830
140_L143_S0.314840.826
154_A157_D0.314510.825
150_D153_I0.311760.818
143_S151_F0.311620.817
83_G87_A0.311550.817
123_R187_R0.310910.816
160_I185_L0.310220.814
18_E106_Y0.310080.813
129_P148_V0.309630.812
102_E106_Y0.309510.812
111_Y151_F0.309220.811
93_N134_P0.308110.808
44_D49_D0.30480.800
102_E105_R0.304260.798
142_R148_V0.304020.797
183_A187_R0.303920.797
104_N107_L0.303810.797
21_L24_A0.302260.793
98_G103_K0.300080.787
182_Y185_L0.299210.785
88_N91_I0.29810.782
41_E44_D0.296780.778
94_I103_K0.296190.777
101_E104_N0.295640.776
149_Y152_I0.29510.774
118_Y130_Y0.293760.771
103_K107_L0.293680.770
161_N177_K0.293560.770
84_I88_N0.292450.767
19_A22_N0.291430.764
147_E151_F0.290050.761
84_I117_Y0.289640.760
186_A190_L0.28740.754
13_E93_N0.28450.746
92_E95_D0.281220.738
114_R151_F0.280840.737
23_G26_N0.280370.735
81_Y129_P0.280030.735
28_L113_L0.279920.734
25_Y29_Y0.27830.730
118_Y122_V0.277070.727
104_N158_E0.276920.726
89_N93_N0.276640.726
105_R164_P0.276430.725
108_A155_D0.274960.721
112_F156_L0.273060.716
155_D158_E0.273040.716
82_K86_R0.271510.712
84_I121_L0.27110.711
81_Y121_L0.269610.707
111_Y154_A0.269510.707
17_T20_L0.269170.706
115_A184_L0.267830.703
111_Y159_A0.267580.702
2_F5_V0.26730.701
20_L23_G0.26540.696
112_F184_L0.261230.685
27_G86_R0.259730.681
160_I177_K0.259430.681
1_D4_D0.257820.676
111_Y115_A0.255810.671
24_A110_A0.255010.669
15_F25_Y0.252080.661
181_A185_L0.248630.652
176_T180_A0.248410.652
148_V152_I0.247270.649
80_Y121_L0.245310.643
122_V128_V0.241170.633
17_T90_V0.239680.629
156_L185_L0.239330.628
22_N26_N0.238450.625
87_A117_Y0.237950.624
15_F18_E0.237870.624
128_V152_I0.236760.621
171_N174_R0.234780.616
74_T78_N0.234560.615
118_Y151_F0.233030.611
89_N92_E0.232310.609
107_L162_L0.229690.603
17_T106_Y0.229570.602
46_I49_D0.226660.595
81_Y84_I0.226530.594
168_S171_N0.224810.590
48_S52_N0.22420.588
22_N25_Y0.22360.587
78_N82_K0.223020.585
81_Y128_V0.222360.583
91_I111_Y0.222110.583
81_Y118_Y0.221880.582
27_G83_G0.221820.582
15_F19_A0.220740.579
25_Y113_L0.22040.578
17_T29_Y0.218710.574
20_L25_Y0.218110.572
88_N155_D0.216710.568
122_V127_D0.216120.567
76_M124_L0.214410.562
20_L90_V0.210980.553
76_M125_Y0.210360.552
20_L24_A0.210330.552
7_P10_S0.209630.550
48_S51_F0.207830.545
105_R171_N0.207380.544
22_N174_R0.207250.544
85_R134_P0.207140.543
180_A184_L0.205420.539
44_D47_A0.204380.536
163_L175_I0.203660.534
23_G86_R0.202120.530
99_S103_K0.201380.528
115_A155_D0.201250.528
164_P177_K0.201170.528
41_E45_D0.200810.527
122_V126_G0.200390.526
123_R149_Y0.1990.522
26_N29_Y0.198940.522
80_Y125_Y0.197270.517
6_E9_S0.197250.517
41_E49_D0.197150.517
112_F159_A0.197080.517
127_D146_E0.194730.511
111_Y114_R0.194360.510
95_D103_K0.193410.507
23_G27_G0.193180.507
91_I94_I0.192810.506
43_F48_S0.192780.506
160_I163_L0.19260.505
77_W129_P0.19180.503
98_G102_E0.189510.497
26_N86_R0.1890.496
44_D50_N0.188830.495
70_N73_I0.188740.495
17_T77_W0.185750.487
131_I135_D0.185610.487
120_Q187_R0.185170.486
167_Y176_T0.183950.483
98_G101_E0.183010.480
153_I160_I0.182970.480
39_T43_F0.182920.480
21_L25_Y0.181570.476
91_I114_R0.181540.476
45_D48_S0.18150.476
156_L160_I0.181340.476
42_L49_D0.180910.475
25_Y175_I0.180610.474
85_R131_I0.180020.472
38_G41_E0.176820.464
183_A186_A0.176550.463
17_T93_N0.176460.463
126_G148_V0.175010.459
186_A189_Y0.174720.458
112_F116_Y0.173430.455
15_F29_Y0.173380.455
15_F20_L0.173280.455
40_G43_F0.172650.453
85_R89_N0.171390.450
182_Y189_Y0.171230.449
159_A181_A0.169510.445
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
3ckcA0.97371000.141
3nqpA0.98421000.142
3i4gA0.98951000.153
3mcxA0.96841000.169
3kezA0.96321000.174
3ihvA0.97891000.183
3qnkA0.94211000.187
3jq0A0.95791000.187
3lewA0.98951000.191
3jysA0.95261000.196

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