GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
STAS - STAS domain
Pfam: PF01740 (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: CL0502
Length: 117
Sequences: 6162
Seq/Len: 52.67
HH_delta: 0.067 (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
50_N84_V1.018452.504
55_M58_V0.927552.280
9_G49_K0.818072.011
73_I77_R0.79281.949
52_I86_V0.72631.785
50_N82_Q0.713161.753
93_R97_E0.707371.739
97_E102_I0.696261.712
66_I99_S0.690761.698
56_S87_G0.687721.691
76_L81_V0.680811.674
28_R71_D0.674521.658
24_A68_A0.672111.652
21_F62_D0.668481.643
16_D57_G0.667141.640
73_I105_I0.635071.561
32_R75_E0.626671.540
12_I52_I0.604591.486
88_L93_R0.594591.462
18_P59_S0.587341.444
10_V52_I0.586451.442
52_I84_V0.572311.407
31_I72_I0.562291.382
20_F23_N0.56121.380
19_L58_V0.551561.356
14_R57_G0.530681.305
54_D87_G0.522861.285
85_L88_L0.508831.251
53_L83_L0.507661.248
73_I83_L0.48291.187
50_N81_V0.482871.187
70_V74_K0.481091.183
61_I65_G0.47311.163
10_V50_N0.46891.153
30_R33_K0.467591.149
69_L105_I0.466861.148
19_L65_G0.464221.141
35_I76_L0.463911.140
33_K37_E0.459531.130
55_M88_L0.449471.105
14_R54_D0.444491.093
15_L27_F0.44131.085
28_R32_R0.438531.078
66_I101_L0.432491.063
21_F64_S0.412641.014
34_L38_D0.410771.010
10_V86_V0.408391.004
26_E30_R0.406741.000
25_E29_D0.406721.000
89_N92_V0.40530.996
67_Q70_V0.404040.993
62_D95_I0.399990.983
18_P21_F0.39460.970
26_E29_D0.394430.970
38_D81_V0.39150.962
90_P94_R0.390930.961
76_L83_L0.390710.960
30_R34_L0.388740.956
74_K77_R0.386440.950
49_K81_V0.383680.943
54_D86_V0.382980.941
93_R102_I0.375520.923
88_L96_L0.374750.921
35_I38_D0.370890.912
53_L72_I0.3690.907
15_L58_V0.368980.907
33_K36_D0.36740.903
28_R62_D0.360910.887
18_P60_F0.355220.873
63_S95_I0.350440.861
18_P58_V0.350060.861
11_L51_V0.347750.855
61_I92_V0.347350.854
13_I31_I0.34330.844
60_F65_G0.342120.841
35_I51_V0.341310.839
16_D58_V0.340650.837
70_V104_F0.339970.836
6_T11_L0.33850.832
29_D33_K0.3380.831
34_L37_E0.335660.825
95_I99_S0.335230.824
24_A64_S0.335220.824
53_L85_L0.335060.824
14_R56_S0.332070.816
20_F60_F0.329720.811
88_L92_V0.324730.798
17_G58_V0.323160.794
19_L27_F0.318120.782
59_S89_N0.3170.779
77_R82_Q0.31620.777
51_V81_V0.316060.777
60_F63_S0.309850.762
72_I76_L0.309750.761
64_S68_A0.308580.759
101_L105_I0.307550.756
63_S67_Q0.30550.751
32_R36_D0.300730.739
60_F95_I0.291480.717
67_Q71_D0.287130.706
6_T37_E0.285470.702
12_I86_V0.283670.697
35_I79_R0.28270.695
9_G50_N0.282190.694
75_E78_R0.281590.692
7_H12_I0.280230.689
6_T38_D0.280220.689
38_D82_Q0.275240.677
27_F31_I0.265140.652
17_G23_N0.264590.650
58_V65_G0.263940.649
70_V73_I0.261810.644
28_R67_Q0.260280.640
91_D94_R0.26010.639
62_D67_Q0.25980.639
53_L69_L0.257520.633
75_E79_R0.257490.633
21_F61_I0.257190.632
94_R98_R0.255320.628
6_T10_V0.254870.627
13_I27_F0.254610.626
51_V76_L0.252650.621
15_L55_M0.252510.621
24_A27_F0.252260.620
67_Q100_G0.252190.620
54_D57_G0.250510.616
28_R68_A0.250310.615
28_R101_L0.248640.611
20_F26_E0.248540.611
100_G103_D0.245460.603
61_I100_G0.244760.602
63_S104_F0.244310.601
31_I51_V0.243860.599
99_S102_I0.240690.592
85_L105_I0.236580.582
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
2klnA0.948799.60.067
3lloA0.957399.60.071
4dghA0.914599.60.086
4dgfA0.90699.60.104
3ny7A0.90699.60.105
3t6oA0.90699.60.13
2ka5A0.897499.60.132
4hylA0.888999.50.145
1sboA0.90699.50.15
1th8B0.90699.50.157

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