GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Torsin - Torsin
Pfam: PF06309 (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: CL0023
Length: 127
Sequences: 4006
Seq/Len: 31.54
HH_delta: 0.43 (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
26_N75_E0.710642.562
20_E24_Q0.696172.509
102_V111_S0.594172.142
25_R75_E0.524111.889
29_G34_V0.511211.843
115_G118_S0.497691.794
22_D25_R0.491141.770
41_I69_V0.481861.737
31_H35_E0.443161.597
116_N119_R0.406161.464
116_N124_L0.405861.463
114_R117_V0.401571.448
60_G66_K0.39931.439
72_L75_E0.381831.376
86_F90_F0.380061.370
112_W115_G0.368971.330
36_V39_N0.368321.328
38_V69_V0.365871.319
58_F70_S0.364241.313
117_V120_C0.35821.291
24_Q31_H0.356331.284
113_I117_V0.350081.262
89_Q116_N0.346231.248
101_N111_S0.338471.220
101_N104_E0.334911.207
26_N72_L0.334641.206
103_D107_E0.334591.206
87_V120_C0.331761.196
113_I118_S0.323971.168
90_F93_T0.322561.163
32_L35_E0.316691.142
38_V42_K0.316271.140
94_H97_P0.315831.138
86_F92_A0.314961.135
34_V37_V0.313181.129
115_G119_R0.311651.123
103_D106_K0.31041.119
27_L68_F0.309831.117
100_S103_D0.307911.110
114_R119_R0.307461.108
67_N88_H0.302741.091
71_R88_H0.302691.091
87_V116_N0.302081.089
24_Q34_V0.299451.079
27_L72_L0.299371.079
20_E35_E0.299271.079
72_L76_H0.298091.075
108_Q111_S0.297551.073
42_K76_H0.297441.072
34_V38_V0.295991.067
39_N43_G0.295371.065
40_A44_H0.294241.061
24_Q72_L0.280271.010
40_A54_L0.275340.993
38_V76_H0.275130.992
101_N105_Y0.27460.990
27_L69_V0.271740.980
54_L59_H0.270550.975
95_H98_H0.270250.974
26_N68_F0.265990.959
39_N42_K0.264490.953
44_H57_S0.262050.945
104_E107_E0.260260.938
116_N120_C0.259140.934
85_P121_P0.258510.932
22_D75_E0.255820.922
91_I94_H0.255510.921
22_D76_H0.255330.920
119_R124_L0.255190.920
112_W116_N0.254250.916
61_W64_T0.253710.915
20_E42_K0.249510.899
35_E38_V0.248480.896
44_H70_S0.247760.893
36_V42_K0.24570.886
68_F72_L0.245640.885
101_N109_L0.245430.885
29_G63_G0.245380.885
104_E108_Q0.245050.883
21_K25_R0.242520.874
32_L36_V0.240940.869
29_G72_L0.238630.860
33_A36_V0.236850.854
86_F99_N0.235170.848
44_H116_N0.234750.846
59_H110_K0.232760.839
98_H101_N0.230860.832
58_F67_N0.228920.825
44_H53_P0.228420.823
94_H98_H0.228030.822
29_G38_V0.226390.816
101_N108_Q0.225510.813
74_A123_S0.2250.811
114_R120_C0.224580.810
100_S108_Q0.2230.804
89_Q96_F0.22090.796
114_R122_R0.220760.796
30_Q33_A0.220450.795
37_V69_V0.218720.788
27_L34_V0.216490.780
44_H112_W0.215930.778
105_Y108_Q0.21560.777
71_R75_E0.214310.773
117_V123_S0.213220.769
113_I116_N0.211960.764
44_H119_R0.209760.756
24_Q35_E0.20960.756
40_A43_G0.208420.751
117_V121_P0.208340.751
103_D108_Q0.207230.747
87_V91_I0.205860.742
26_N30_Q0.205770.742
30_Q62_T0.205430.741
51_R57_S0.204060.736
88_H92_A0.203470.733
23_L75_E0.203420.733
30_Q35_E0.201860.728
70_S86_F0.201690.727
33_A58_F0.200820.724
41_I73_I0.199870.720
29_G41_I0.199290.718
54_L57_S0.198530.716
60_G65_G0.1980.714
104_E111_S0.197650.712
64_T68_F0.19650.708
63_G66_K0.193750.698
95_H99_N0.193560.698
27_L30_Q0.189580.683
51_R54_L0.189370.683
30_Q36_V0.187410.676
101_N107_E0.187320.675
67_N93_T0.18720.675
63_G67_N0.183450.661
55_V94_H0.183380.661
94_H100_S0.183140.660
21_K32_L0.18110.653
56_L69_V0.18110.653
112_W118_S0.180710.651
89_Q94_H0.180220.650
27_L38_V0.178040.642
41_I54_L0.176550.636
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
3pxiA0.921399.40.43
1qvrA0.984399.40.445
3hwsA0.881999.30.453
1r6bX0.960699.30.456
4fcwA0.921399.30.467
3cf2A0.929199.30.468
1um8A0.913499.30.48
3sylA0.944999.20.488
3t15A0.818999.20.493
3cf2A0.929199.20.496

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