GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HIT - HIT domain
Pfam: PF01230 (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: CL0265
Length: 98
Sequences: 5562
Seq/Len: 56.76
HH_delta: -0.022 (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
14_H50_E1.791833.402
11_E34_K1.75213.327
12_D50_E1.470072.791
35_R47_E1.38242.625
7_R19_L1.247442.368
16_V34_K1.115522.118
75_I90_F1.061372.015
8_V16_V1.012451.922
18_F32_I0.960351.823
10_Y54_L0.959411.822
44_P47_E0.954081.811
15_F54_L0.923951.754
9_V29_L0.917961.743
72_N95_R0.913331.734
57_K61_A0.895951.701
49_A53_Q0.879681.670
69_D80_A0.849241.612
27_G94_P0.847481.609
39_S42_D0.831181.578
51_L90_F0.807091.532
36_H87_H0.805891.530
15_F50_E0.804471.527
55_V90_F0.794731.509
48_R52_M0.747051.418
56_Q60_K0.743611.412
45_P53_Q0.734451.394
43_L88_L0.693421.317
6_A16_V0.684921.300
8_V11_E0.677361.286
37_V44_P0.664961.262
19_L62_L0.654731.243
37_V88_L0.642111.219
17_A29_L0.639531.214
45_P56_Q0.635851.207
48_R56_Q0.631921.200
39_S77_N0.63141.199
31_V92_V0.615821.169
17_A58_V0.595281.130
38_E42_D0.590521.121
40_L52_M0.584291.109
37_V47_E0.569441.081
14_H47_E0.564371.072
29_L58_V0.563891.071
12_D54_L0.561581.066
47_E50_E0.55861.061
79_P86_P0.540561.026
45_P49_A0.531821.010
50_E54_L0.521230.990
58_V62_L0.519580.986
23_P28_H0.519230.986
14_H46_E0.500940.951
54_L57_K0.500370.950
53_Q56_Q0.497380.944
35_R44_P0.487670.926
37_V43_L0.479560.910
57_K60_K0.476710.905
63_K71_Y0.474730.901
14_H35_R0.470260.893
53_Q57_K0.468310.889
52_M90_F0.463310.880
61_A65_A0.43780.831
62_L92_V0.437390.830
37_V42_D0.434140.824
38_E78_G0.432610.821
59_A63_K0.431990.820
25_S93_I0.429080.815
17_A31_V0.422010.801
41_S71_Y0.420240.798
52_M55_V0.41280.784
41_S77_N0.408670.776
72_N76_N0.408270.775
55_V73_V0.408080.775
43_L48_R0.407750.774
24_I84_S0.403620.766
10_Y57_K0.403530.766
39_S78_G0.401520.762
64_E67_G0.399460.758
24_I93_I0.397140.754
60_K64_E0.395130.750
29_L94_P0.390610.742
19_L29_L0.385490.732
74_I93_I0.382690.727
55_V92_V0.381250.724
51_L88_L0.380880.723
78_G81_A0.377710.717
18_F30_L0.377550.717
70_G81_A0.375070.712
50_E53_Q0.374010.710
55_V59_A0.367890.698
59_A71_Y0.365560.694
64_E94_P0.364810.693
38_E86_P0.363530.690
47_E51_L0.35830.680
71_Y92_V0.349180.663
20_D23_P0.344610.654
39_S86_P0.337770.641
39_S75_I0.335770.637
83_Q86_P0.335510.637
9_V19_L0.333850.634
5_P21_I0.33360.633
41_S63_K0.330680.628
81_A84_S0.330220.627
12_D57_K0.329210.625
17_A54_L0.328550.624
25_S28_H0.327880.623
40_L73_V0.325390.618
75_I88_L0.322040.611
29_L92_V0.321770.611
16_V32_I0.319580.607
19_L27_G0.318140.604
43_L47_E0.317040.602
51_L73_V0.316050.600
61_A64_E0.315440.599
65_A68_P0.314460.597
15_F51_L0.313910.596
12_D15_F0.312120.593
30_L91_H0.310450.589
39_S63_K0.307050.583
14_H54_L0.30620.581
59_A73_V0.303390.576
41_S59_A0.301580.573
54_L58_V0.299730.569
20_D24_I0.29840.567
28_H33_P0.295190.560
85_V89_H0.293370.557
28_H91_H0.285340.542
74_I82_G0.285030.541
40_L48_R0.284930.541
6_A18_F0.284690.541
31_V55_V0.283710.539
73_V90_F0.282610.537
49_A56_Q0.281250.534
40_L56_Q0.279710.531
49_A57_K0.279090.530
21_I91_H0.278570.529
9_V17_A0.278080.528
30_L33_P0.2760.524
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
3ksvA199.9-0.022
3lb5A199.9-0.017
3l7xA199.9-0.017
3imiA199.9-0.013
3o0mA199.9-0.01
1y23A199.80.015
2eo4A199.80.016
1emsA199.80.022
3anoA199.80.028
3n1sA199.80.039

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