GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SusD - SusD family
Pfam: PF07980 (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: 266
Sequences: 2852
Seq/Len: 10.72
HH_delta: 0.105 (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
132_L136_Y1.209545.580
251_Q255_D0.993264.582
134_E138_I0.959914.428
145_R181_L0.831143.834
139_Y155_Y0.793953.663
3_V6_A0.686273.166
44_P48_D0.668783.085
185_L207_G0.662853.058
185_L205_W0.658793.039
148_N151_E0.65133.005
144_A181_L0.590142.723
144_A184_I0.581232.681
188_R201_D0.543892.509
139_Y143_L0.50252.318
49_L189_R0.49792.297
161_K167_P0.491732.269
188_R192_L0.4842.233
49_L186_D0.469282.165
143_L151_E0.461132.127
132_L158_Q0.45412.095
180_L184_I0.453292.091
136_Y158_Q0.442232.040
6_A126_D0.43372.001
134_E188_R0.405981.873
186_D190_R0.40571.872
3_V128_P0.402831.858
67_T193_A0.401711.853
151_E154_E0.400511.848
199_W203_K0.392051.809
154_E158_Q0.388661.793
46_L193_A0.383331.768
192_L197_Q0.376331.736
47_V64_F0.373851.725
4_I130_M0.372141.717
144_A177_Q0.369881.706
198_R202_L0.364121.680
45_E189_R0.360191.662
150_A154_E0.359451.658
143_L148_N0.350991.619
253_E256_A0.346911.600
137_L188_R0.340321.570
207_G210_D0.340011.569
181_L185_L0.338251.560
49_L190_R0.326271.505
130_M135_V0.320511.479
47_V68_F0.310721.433
257_N260_L0.308421.423
133_A159_V0.307611.419
107_I194_G0.30211.394
137_L192_L0.299621.382
143_L146_L0.29851.377
144_A149_T0.292711.350
157_N161_K0.292171.348
153_L157_N0.283311.307
59_N64_F0.280561.294
144_A180_L0.278951.287
131_R195_E0.277341.279
135_V138_I0.276591.276
140_A156_L0.276581.276
158_Q161_K0.27611.274
46_L49_L0.271261.251
155_Y158_Q0.271111.251
202_L207_G0.26961.244
145_R177_Q0.266331.229
177_Q181_L0.26331.215
110_F128_P0.259811.199
136_Y155_Y0.257021.186
253_E260_L0.252661.166
44_P105_Y0.251581.161
250_P253_E0.251341.160
262_Q266_Y0.249681.152
179_A182_D0.245841.134
46_L189_R0.244991.130
183_A190_R0.242371.118
182_D186_D0.24171.115
64_F68_F0.238991.103
6_A128_P0.238731.101
153_L180_L0.238311.099
169_T172_E0.238211.099
207_G211_R0.236531.091
159_V192_L0.235851.088
145_R185_L0.235491.086
47_V105_Y0.232291.072
58_D190_R0.232281.072
182_D207_G0.232221.071
249_I254_I0.231921.070
159_V163_A0.228051.052
182_D185_L0.225621.041
151_E155_Y0.223461.031
168_L183_A0.223371.031
183_A186_D0.219461.012
144_A156_L0.217331.003
7_I129_I0.215820.996
133_A192_L0.214910.991
178_D182_D0.211450.976
134_E197_Q0.211240.975
254_I257_N0.209550.967
138_I197_Q0.208210.961
185_L202_L0.205020.946
46_L50_F0.204020.941
2_E133_A0.203380.938
156_L168_L0.202730.935
130_M197_Q0.20220.933
157_N167_P0.202040.932
188_R197_Q0.201510.930
249_I263_N0.201110.928
143_L155_Y0.199160.919
254_I260_L0.199010.918
262_Q265_G0.197170.910
254_I258_P0.196180.905
139_Y158_Q0.193230.891
165_L168_L0.193180.891
65_D70_T0.192040.886
180_L183_A0.191610.884
155_Y159_V0.189510.874
44_P47_V0.189350.874
160_R187_E0.184770.852
109_K195_E0.182160.840
186_D189_R0.182140.840
263_N266_Y0.181990.840
101_N106_Y0.181450.837
60_R65_D0.180570.833
251_Q254_I0.179650.829
159_V162_R0.178360.823
136_Y159_V0.177810.820
145_R205_W0.177360.818
208_I211_R0.177090.817
197_Q200_F0.176840.816
246_L264_P0.176520.814
70_T73_D0.173640.801
60_R64_F0.172950.798
206_N209_D0.171790.793
45_E217_N0.171690.792
252_S255_D0.171530.791
4_I132_L0.171470.791
246_L263_N0.171150.790
172_E179_A0.170970.789
46_L67_T0.170850.788
42_P68_F0.17060.787
208_I212_I0.169180.781
125_I128_P0.168910.779
45_E214_E0.168530.778
154_E161_K0.168430.777
45_E211_R0.168080.775
252_S256_A0.166970.770
133_A136_Y0.166930.770
203_K246_L0.165620.764
132_L135_V0.165430.763
42_P47_V0.163050.752
46_L190_R0.162430.749
67_T194_G0.161790.746
8_Q126_D0.161160.744
62_P164_G0.161030.743
181_L205_W0.160920.742
42_P193_A0.160860.742
50_F190_R0.160780.742
50_F66_A0.160580.741
73_D76_D0.159980.738
157_N169_T0.159510.736
144_A179_A0.159460.736
203_K208_I0.158910.733
254_I261_T0.158840.733
141_E204_R0.15650.722
185_L192_L0.156190.721
152_A180_L0.155550.718
220_E223_N0.155170.716
215_Y218_N0.15480.714
64_F70_T0.154140.711
62_P163_A0.153870.710
189_R198_R0.152410.703
130_M134_E0.151940.701
138_I192_L0.150730.695
202_L212_I0.149550.690
134_E201_D0.148930.687
58_D61_D0.146630.676
199_W208_I0.144070.665
61_D70_T0.143870.664
181_L184_I0.143380.661
104_G109_K0.142630.658
5_F8_Q0.142590.658
105_Y109_K0.141640.653
38_G41_Y0.141540.653
197_Q201_D0.140480.648
133_A195_E0.140190.647
40_F127_Y0.139650.644
144_A153_L0.139020.641
50_F193_A0.138910.641
72_G75_Y0.138910.641
134_E159_V0.138770.640
137_L191_E0.138490.639
187_E248_P0.138110.637
248_P262_Q0.137880.636
177_Q180_L0.137780.636
208_I213_N0.137090.632
150_A153_L0.136970.632
143_L152_A0.136920.632
69_Y108_R0.136220.628
183_A187_E0.136040.628
112_D123_S0.135940.627
159_V190_R0.135860.627
140_A159_V0.135830.627
149_T177_Q0.135670.626
196_G247_W0.135170.624
156_L183_A0.134070.619
3_V8_Q0.133280.615
143_L147_G0.132860.613
68_F105_Y0.131320.606
246_L266_Y0.130880.604
153_L177_Q0.130760.603
148_N171_A0.130530.602
142_A155_Y0.130430.602
157_N160_R0.130010.600
222_N227_D0.129640.598
149_T180_L0.129590.598
1_K132_L0.129460.597
258_P261_T0.128830.594
144_A148_N0.128760.594
157_N170_A0.128630.593
149_T153_L0.128180.591
254_I262_Q0.127610.589
209_D213_N0.126640.584
160_R198_R0.126580.584
1_K158_Q0.126210.582
138_I188_R0.126010.581
6_A9_Y0.125520.579
191_E195_E0.125180.578
61_D165_L0.124860.576
142_A148_N0.124820.576
201_D205_W0.124740.575
73_D108_R0.124510.574
146_L151_E0.123280.569
61_D64_F0.121690.561
209_D212_I0.121680.561
48_D105_Y0.121070.559
211_R214_E0.120810.557
134_E200_F0.120790.557
125_I266_Y0.120660.557
165_L190_R0.120410.556
142_A146_L0.119570.552
75_Y99_G0.119510.551
133_A137_L0.119120.550
152_A156_L0.118460.547
218_N221_D0.118450.546
153_L179_A0.118190.545
130_M138_I0.117760.543
148_N155_Y0.117720.543
250_P254_I0.11760.543
139_Y142_A0.117270.541
221_D224_I0.117170.541
171_A179_A0.116810.539
131_R191_E0.116620.538
192_L195_E0.116190.536
249_I262_Q0.116130.536
37_W266_Y0.115850.534
148_N154_E0.11530.532
106_Y109_K0.11510.531
46_L198_R0.1150.531
146_L149_T0.114690.529
42_P107_I0.114220.527
121_N154_E0.11390.525
202_L211_R0.11290.521
133_A162_R0.112140.517
254_I259_N0.112130.517
45_E48_D0.111920.516
256_A260_L0.111530.515
60_R190_R0.111360.514
162_R191_E0.111020.512
147_G177_Q0.109940.507
5_F129_I0.109750.506
161_K165_L0.108930.503
139_Y146_L0.108780.502
3_V126_D0.108420.500
42_P108_R0.108280.500
100_N129_I0.107960.498
172_E183_A0.107780.497
42_P105_Y0.107770.497
166_P170_A0.107490.496
222_N226_A0.107170.494
166_P169_T0.107130.494
184_I192_L0.106660.492
45_E104_G0.106550.492
73_D110_F0.106050.489
214_E217_N0.105980.489
160_R165_L0.105740.488
115_K118_N0.105470.487
246_L262_Q0.105080.485
115_K120_N0.104720.483
62_P165_L0.104610.483
147_G150_A0.1040.480
96_S99_G0.10360.478
10_S124_G0.103530.478
60_R75_Y0.103390.477
128_P194_G0.103280.476
127_Y196_G0.103210.476
43_S133_A0.103030.475
161_K164_G0.102830.474
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
3qnkA0.95491000.105
3jq1A0.90231000.133
3ihvA0.94741000.153
3otnA0.87591000.177
3i4gA0.93611000.178
3jq0A0.80081000.182
3jysA0.88721000.188
3nqpA0.87221000.203
3iv0A0.80831000.22
3lewA0.84211000.226

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