GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HMG_box_5 - HMG (high mobility group) box 5
Pfam: PF14887 (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: CL0114
Length: 85
Sequences: 2341
Seq/Len: 27.54
HH_delta: 0.114 (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
62_R66_E1.308173.139
50_L54_K1.067572.561
59_D62_R1.00562.413
18_V40_Q0.980452.352
18_V21_D0.859942.063
45_E48_E0.84112.018
44_M48_E0.759281.822
17_S52_W0.743531.784
61_K65_R0.713991.713
8_K59_D0.699941.679
14_W44_M0.6651.596
15_Q37_M0.619791.487
8_K12_E0.619521.486
13_I55_K0.614511.474
12_E15_Q0.603261.447
68_R72_S0.603011.447
36_A39_A0.599231.438
39_A43_Q0.594941.427
60_Q64_E0.573921.377
51_K55_K0.550461.321
55_K59_D0.540761.297
55_K58_E0.538031.291
18_V37_M0.517981.243
13_I59_D0.512451.230
58_E61_K0.506991.216
57_A61_K0.506791.216
21_D25_K0.506671.216
69_E72_S0.506671.216
62_R65_R0.502621.206
54_K57_A0.494721.187
36_A40_Q0.489021.173
63_Y67_L0.483731.161
54_K58_E0.476061.142
30_R33_A0.471981.132
46_K53_I0.470611.129
8_K16_Q0.460291.104
29_D33_A0.459871.103
67_L71_R0.45111.082
20_G23_L0.445291.068
3_L70_M0.440361.057
46_K50_L0.439281.054
20_G24_A0.433681.041
53_I57_A0.401890.964
10_A53_I0.386280.927
17_S55_K0.38480.923
50_L53_I0.382970.919
15_Q34_L0.382280.917
14_W52_W0.379140.910
7_P13_I0.370360.889
15_Q19_I0.370.888
34_L38_E0.365760.878
61_K64_E0.364940.876
40_Q43_Q0.362210.869
31_K34_L0.359130.862
63_Y68_R0.351630.844
11_Q38_E0.335130.804
22_Y37_M0.326640.784
56_A60_Q0.323040.775
59_D66_E0.314250.754
11_Q41_W0.30850.740
22_Y26_F0.308460.740
19_I38_E0.304450.730
48_E51_K0.304240.730
10_A56_A0.301990.725
4_P63_Y0.29970.719
40_Q44_M0.298010.715
65_R69_E0.297480.714
26_F29_D0.28260.678
44_M52_W0.278110.667
44_M51_K0.274050.658
13_I52_W0.27320.655
9_T12_E0.273090.655
38_E42_S0.273040.655
16_Q19_I0.27180.652
6_T71_R0.26950.647
22_Y40_Q0.266860.640
14_W37_M0.266190.639
14_W18_V0.266090.638
6_T11_Q0.266060.638
41_W49_K0.265910.638
30_R34_L0.261420.627
5_E19_I0.254970.612
4_P67_L0.252260.605
47_K50_L0.250550.601
45_E51_K0.249280.598
23_L26_F0.247920.595
52_W56_A0.247720.594
12_E31_K0.245880.590
20_G32_K0.245230.588
64_E68_R0.244830.587
39_A42_S0.243330.584
67_L70_M0.242950.583
4_P70_M0.241820.580
22_Y25_K0.240420.577
31_K37_M0.238540.572
12_E16_Q0.237870.571
8_K13_I0.236950.569
12_E38_E0.232140.557
25_K33_A0.23170.556
16_Q20_G0.230270.552
29_D36_A0.22540.541
11_Q15_Q0.219980.528
42_S53_I0.218890.525
11_Q35_K0.217490.522
9_T15_Q0.21730.521
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
1l8yA199.50.114
1aabA0.894199.50.132
2eqzA0.835399.50.143
2cs1A199.50.146
2co9A199.50.147
3nm9A0.847199.50.149
1k99A199.50.15
2lhjA0.882499.50.153
3tmmA0.964799.50.157
2yrqA0.870699.50.16

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