GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PTR2 - POT family
Pfam: PF00854 (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: CL0015
Length: 372
Sequences: 16589
Seq/Len: 44.59
HH_delta: 0.329 (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
34_G38_I1.165044.033
22_A35_L0.985233.411
19_T106_G0.834892.890
10_V46_G0.806172.791
12_L112_M0.793382.746
33_L37_Y0.79152.740
17_L39_G0.770122.666
353_A361_M0.735182.545
14_G39_G0.729632.526
7_G49_G0.709192.455
17_L20_L0.684082.368
32_Q35_L0.646542.238
14_G46_G0.60562.096
65_D69_R0.603062.088
71_D276_Y0.585652.027
9_I116_L0.582182.015
62_Y73_F0.579722.007
299_I303_F0.56771.965
21_S39_G0.562521.947
21_S35_L0.553961.918
354_P357_A0.543941.883
325_W329_P0.52671.823
63_D69_R0.526421.822
14_G42_L0.507891.758
273_R277_P0.499871.730
274_V278_L0.497981.724
301_A330_M0.487971.689
267_F336_I0.482441.670
14_G43_I0.482231.669
12_L116_L0.480681.664
263_F332_I0.477951.655
252_P255_W0.475491.646
18_L39_G0.473691.640
297_F337_P0.473461.639
16_V109_A0.472771.637
301_A337_P0.466921.616
10_V14_G0.464251.607
117_I121_S0.46181.599
12_L113_L0.452361.566
22_A32_Q0.44881.554
329_P333_F0.44841.552
22_A102_F0.441091.527
203_R207_L0.438141.517
2_K6_L0.436621.511
293_I297_F0.435211.507
5_L120_L0.430621.491
296_V300_L0.427371.479
255_W259_F0.421041.458
16_V20_L0.420341.455
135_S138_T0.418041.447
304_V330_M0.416311.441
274_V290_K0.407291.410
13_L17_L0.407191.410
69_R72_S0.403071.395
288_P292_G0.40221.392
134_G138_T0.401871.391
12_L109_A0.400571.387
292_G296_V0.397911.377
131_P134_G0.394981.367
38_I42_L0.392111.357
80_G84_G0.383521.328
91_L94_Y0.382411.324
204_V207_L0.379771.315
86_L262_I0.378961.312
35_L38_I0.374811.298
5_L116_L0.374011.295
103_L106_G0.373761.294
79_W265_I0.372861.291
131_P136_P0.372661.290
58_G77_F0.372371.289
100_G103_L0.372181.288
125_R128_K0.372091.288
289_Q292_G0.37121.285
203_R206_E0.371141.285
266_I269_P0.370261.282
136_P139_N0.370061.281
19_T102_F0.36831.275
194_F197_L0.366281.268
262_I266_I0.362691.256
303_F307_I0.361831.253
64_E70_R0.361261.251
269_P273_R0.358851.242
19_T109_A0.357811.239
330_M333_F0.356011.232
323_S326_W0.351031.215
241_M252_P0.350921.215
202_Q205_E0.350891.215
270_I273_R0.350311.213
126_Y129_V0.347471.203
103_L110_I0.345261.195
95_I103_L0.344091.191
132_P136_P0.343721.190
124_K128_K0.34211.184
194_F198_F0.341851.183
289_Q293_I0.340381.178
213_F368_L0.34011.177
195_W198_F0.338221.171
210_L214_L0.335451.161
202_Q206_E0.335221.160
6_L10_V0.33511.160
303_F306_A0.333591.155
294_G340_F0.330041.143
348_A352_F0.328941.139
232_T235_L0.328341.137
59_A74_F0.32631.130
72_S76_W0.326271.129
90_T94_Y0.324971.125
106_G110_I0.324931.125
133_G137_L0.324131.122
92_V104_G0.323281.119
2_K5_L0.322521.116
4_I54_I0.322421.116
134_G137_L0.320181.108
85_S261_P0.320051.108
103_L107_I0.319641.107
40_L44_A0.319051.104
135_S139_N0.318011.101
233_F238_V0.316891.097
134_G139_N0.315951.094
60_D358_P0.314061.087
95_I107_I0.312871.083
238_V241_M0.312471.082
132_P135_S0.311921.080
110_I114_L0.311831.079
93_P255_W0.311521.078
90_T258_S0.310481.075
35_L39_G0.308461.068
5_L9_I0.308171.067
343_G347_S0.306581.061
272_D276_Y0.305761.058
113_L117_I0.305531.058
12_L16_V0.304761.055
99_Y103_L0.30431.053
271_L340_F0.301681.044
275_V344_T0.299751.038
347_S351_E0.298341.033
13_L16_V0.296971.028
204_V210_L0.296811.027
335_L338_E0.293961.018
326_W329_P0.293351.016
332_I335_L0.292931.014
5_L119_F0.291131.008
300_L304_V0.290511.006
234_F238_V0.287510.995
240_Q252_P0.286330.991
109_A113_L0.276710.958
3_T6_L0.276530.957
278_L290_K0.275020.952
266_I270_I0.274640.951
34_G37_Y0.274450.950
11_Y47_T0.273970.948
78_Y82_N0.27260.944
62_Y69_R0.272010.942
116_L120_L0.271040.938
355_S358_P0.267760.927
11_Y43_I0.266820.924
364_I367_A0.266780.924
260_N335_L0.26670.923
226_M230_L0.266250.922
270_I274_V0.266040.921
54_I57_F0.26580.920
20_L35_L0.265380.919
263_F267_F0.264180.915
207_L210_L0.263870.913
235_L253_P0.263510.912
325_W328_V0.26340.912
4_I119_F0.263220.911
193_F197_L0.26270.909
72_S276_Y0.262040.907
257_Q261_P0.2620.907
11_Y50_I0.261210.904
121_S124_K0.261210.904
328_V332_I0.260250.901
294_G337_P0.259770.899
131_P135_S0.259650.899
57_F61_Q0.258220.894
82_N265_I0.257750.892
261_P265_I0.257320.891
4_I57_F0.257060.890
17_L35_L0.256840.889
212_R215_P0.256460.888
192_I197_L0.253570.878
338_E341_L0.253390.877
14_G17_L0.253280.877
89_P258_S0.253130.876
275_V279_L0.252520.874
55_S74_F0.252190.873
9_I13_L0.251370.870
84_G88_S0.248140.859
296_V299_I0.247370.856
212_R365_W0.247080.855
359_S363_G0.246980.855
6_L9_I0.246490.853
267_F270_I0.246290.853
96_Q254_A0.246130.852
337_P340_F0.246010.852
77_F80_G0.245630.850
218_L222_F0.24550.850
342_S346_E0.245270.849
72_S75_N0.245090.848
203_R210_L0.244550.847
329_P332_I0.244470.846
338_E342_S0.243890.844
292_G295_M0.242670.840
234_F327_Q0.242490.839
110_I113_L0.242390.839
52_P56_P0.242330.839
333_F337_P0.242190.838
327_Q330_M0.241990.838
11_Y46_G0.241140.835
132_P137_L0.238280.825
58_G73_F0.23730.821
232_T236_L0.236950.820
216_I365_W0.235690.816
258_S262_I0.235230.814
196_A202_Q0.235050.814
330_M334_W0.234750.813
70_R350_Y0.234410.811
18_L36_F0.233880.810
15_H43_I0.233670.809
77_F81_I0.23260.805
15_H19_T0.232210.804
294_G341_L0.232030.803
88_S92_V0.232010.803
220_W224_W0.231030.800
37_Y41_A0.231010.800
79_W82_N0.230760.799
231_N234_F0.230250.797
291_F344_T0.230090.797
297_F301_A0.229670.795
133_G138_T0.22950.794
114_L117_I0.229420.794
344_T347_S0.22880.792
301_A334_W0.228170.790
123_R126_Y0.227560.788
271_L274_V0.227430.787
53_N359_S0.227340.787
75_N275_V0.227190.786
191_E194_F0.227070.786
212_R352_F0.226690.785
15_H109_A0.226670.785
18_L21_S0.225420.780
59_A70_R0.225230.780
81_I342_S0.225040.779
50_I54_I0.22440.777
363_G367_A0.223060.772
349_A365_W0.222910.772
4_I8_S0.222540.770
269_P272_D0.222160.769
5_L8_S0.221960.768
197_L356_R0.221770.768
118_V121_S0.220440.763
119_F123_R0.220230.762
275_V347_S0.219920.761
237_Q240_Q0.219710.761
274_V277_P0.219120.759
202_Q207_L0.219020.758
360_S364_I0.218960.758
8_S116_L0.218780.757
250_G253_P0.218630.757
4_I53_N0.218380.756
48_G52_P0.218260.756
276_Y279_L0.218170.755
217_F225_Q0.217890.754
288_P291_F0.217790.754
205_E209_A0.217620.753
308_V330_M0.217550.753
216_I369_S0.215680.747
342_S345_G0.21530.745
118_V122_G0.215070.745
271_L294_G0.214520.743
40_L43_I0.214290.742
235_L241_M0.2140.741
56_P60_D0.213290.738
213_F361_M0.213270.738
328_V334_W0.212860.737
39_G42_L0.212480.736
256_L259_F0.212190.735
86_L261_P0.212070.734
362_M367_A0.212060.734
16_V106_G0.211310.732
235_L250_G0.210850.730
358_P362_M0.210730.729
86_L258_S0.210050.727
195_W202_Q0.209540.725
54_I77_F0.209520.725
216_I220_W0.208960.723
82_N264_I0.208630.722
126_Y131_P0.207250.717
304_V307_I0.207210.717
338_E343_G0.206820.716
290_K293_I0.206570.715
334_W338_E0.205820.712
128_K133_G0.205760.712
94_Y98_N0.204250.707
117_I120_L0.204150.707
51_K77_F0.203840.706
215_P218_L0.203380.704
17_L42_L0.203180.703
133_G136_P0.201810.699
197_L202_Q0.201780.699
128_K131_P0.200830.695
298_A301_A0.200810.695
343_G346_E0.200730.695
75_N272_D0.200420.694
224_W227_Y0.200330.693
102_F106_G0.19970.691
72_S273_R0.199670.691
193_F198_F0.199440.690
8_S50_I0.198940.689
17_L21_S0.198680.688
8_S112_M0.198450.687
138_T197_L0.198260.686
219_F342_S0.198120.686
231_N235_L0.19760.684
333_F336_I0.197470.684
89_P261_P0.19720.683
87_F90_T0.19710.682
235_L238_V0.1970.682
337_P341_L0.196630.681
95_I99_Y0.196620.681
224_W228_S0.196390.680
220_W223_Y0.196160.679
346_E349_A0.195880.678
222_F226_M0.195650.677
206_E209_A0.195630.677
78_Y264_I0.195360.676
197_L203_R0.194840.674
92_V254_A0.194780.674
228_S231_N0.194420.673
198_F203_R0.194090.672
15_H40_L0.193890.671
127_R134_G0.19340.670
100_G104_G0.193180.669
76_W79_W0.193120.669
115_A118_V0.192980.668
71_D272_D0.192930.668
4_I50_I0.192730.667
81_I85_S0.192720.667
335_L339_Y0.192590.667
292_G299_I0.192510.666
83_I265_I0.19250.666
56_P59_A0.192110.665
295_M341_L0.191920.664
13_L113_L0.191920.664
82_N268_I0.191820.664
331_Y335_L0.191650.663
45_V48_G0.191620.663
304_V308_V0.191440.663
213_F220_W0.191290.662
353_A357_A0.191260.662
331_Y334_W0.191240.662
15_H18_L0.190910.661
297_F336_I0.190630.660
219_F226_M0.190610.660
237_Q241_M0.190360.659
261_P264_I0.19010.658
233_F237_Q0.190080.658
133_G139_N0.18980.657
18_L43_I0.18950.656
71_D347_S0.189470.656
123_R128_K0.189370.656
69_R73_F0.189190.655
16_V110_I0.189160.655
59_A350_Y0.189150.655
230_L331_Y0.188740.653
78_Y343_G0.188730.653
230_L233_F0.188370.652
364_I369_S0.187990.651
293_I296_V0.187530.649
253_P257_Q0.187490.649
3_T7_G0.187250.648
228_S233_F0.187210.648
125_R129_V0.186560.646
219_F341_L0.186470.646
275_V278_L0.186130.644
256_L260_N0.185530.642
234_F237_Q0.185490.642
301_A333_F0.184960.640
291_F345_G0.184740.640
111_G114_L0.184660.639
11_Y15_H0.184570.639
204_V209_A0.18450.639
129_V132_P0.184450.639
271_L344_T0.183930.637
262_I265_I0.183640.636
350_Y362_M0.18340.635
268_I272_D0.182820.633
39_G43_I0.182020.630
51_K346_E0.181880.630
227_Y264_I0.181690.629
209_A213_F0.181350.628
264_I268_I0.181250.627
251_I255_W0.181040.627
56_P359_S0.180580.625
34_G41_A0.180530.625
48_G56_P0.180350.624
82_N85_S0.179520.621
93_P251_I0.179280.621
366_F369_S0.179180.620
191_E195_W0.179010.620
346_E366_F0.178940.619
331_Y343_G0.178930.619
264_I269_P0.178130.617
360_S363_G0.177850.616
257_Q260_N0.17730.614
209_A212_R0.177020.613
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
4j05A0.87999.90.329
1pw4A0.79399.90.337
4apsA0.927499.90.352
4gc0A0.822699.90.382
3o7qA0.733999.90.396
2gfpA0.733999.90.397
2xutA0.924799.90.433
4iu9B0.728599.90.441
4jr9A0.731299.90.445
2cfqA0.766199.80.522

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