GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HTH_29 - Winged helix-turn helix
Pfam: PF13551 (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: CL0123
Length: 112
Sequences: 7623
Seq/Len: 68.06
HH_delta: 0.164 (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
15_I30_Y1.230642.411
15_I33_L1.119822.194
19_A29_V1.046032.049
63_R107_I1.008171.975
12_V21_R0.942391.846
12_V17_E0.935271.832
7_L21_R0.924811.812
65_Q69_L0.921551.805
26_R30_Y0.910141.783
87_A104_I0.904531.772
16_A26_R0.891751.747
8_L18_I0.887091.738
7_L12_V0.883731.731
102_S106_R0.857811.680
83_L105_R0.850451.666
8_L33_L0.845891.657
102_S105_R0.843961.653
59_S62_Q0.838711.643
58_L62_Q0.820131.607
39_G43_G0.819311.605
100_S103_T0.803261.573
27_R30_Y0.796691.561
18_I22_L0.792761.553
16_A20_R0.770051.508
63_R110_R0.766981.502
18_I29_V0.732711.435
105_R109_K0.715171.401
7_L22_L0.712481.396
82_T85_E0.698621.369
69_L89_W0.663271.299
28_T31_R0.648941.271
15_I26_R0.631991.238
33_L37_R0.629691.233
13_S17_E0.627351.229
101_P105_R0.622271.219
103_T106_R0.616921.208
81_W85_E0.612221.199
64_A68_E0.611751.198
40_G43_G0.605111.185
6_L9_A0.603421.182
7_L18_I0.586921.150
84_E101_P0.578591.133
81_W89_W0.578321.133
65_Q68_E0.577451.131
103_T107_I0.573611.124
27_R31_R0.572161.121
48_K51_G0.570421.117
24_I29_V0.556291.090
25_S28_T0.554531.086
32_W35_R0.539941.058
25_S31_R0.534951.048
6_L10_E0.533141.044
84_E88_E0.528791.036
66_L104_I0.527641.034
17_E20_R0.525151.029
13_S16_A0.524311.027
60_E64_A0.523951.026
67_I71_R0.518411.016
83_L101_P0.515511.010
87_A101_P0.502850.985
28_T32_W0.49770.975
99_V103_T0.492850.965
61_E64_A0.479130.939
69_L73_N0.478520.937
63_R67_I0.474540.930
66_L86_L0.470690.922
17_E21_R0.46280.907
83_L108_L0.46280.907
5_L36_Y0.457470.896
70_L108_L0.453170.888
68_E72_E0.437290.857
51_G55_R0.434080.850
103_T110_R0.432540.847
19_A26_R0.428510.839
86_L108_L0.428080.839
35_R39_G0.423810.830
30_Y34_K0.419970.823
74_P81_W0.418260.819
85_E89_W0.406550.796
22_L29_V0.402870.789
53_R56_K0.400290.784
46_P49_P0.399490.783
51_G54_P0.393110.770
18_I33_L0.391970.768
8_L15_I0.375160.735
58_L107_I0.37130.727
9_A36_Y0.362620.710
70_L86_L0.36260.710
82_T86_L0.362220.710
62_Q65_Q0.360240.706
66_L107_I0.35920.704
36_Y44_L0.345410.677
67_I107_I0.3450.676
31_R34_K0.340170.666
5_L9_A0.335020.656
107_I110_R0.329980.646
34_K37_R0.329780.646
73_N81_W0.329430.645
34_K38_E0.324360.635
7_L10_E0.322710.632
66_L70_L0.320150.627
16_A30_Y0.315440.618
24_I28_T0.31410.615
46_P51_G0.313590.614
84_E87_A0.312070.611
85_E88_E0.310620.608
69_L72_E0.310170.608
70_L73_N0.30960.606
62_Q107_I0.307550.602
87_A97_I0.307270.602
58_L63_R0.306950.601
52_G55_R0.301160.590
73_N80_R0.300350.588
64_A67_I0.299190.586
83_L104_I0.29890.586
83_L86_L0.296560.581
19_A24_I0.296480.581
100_S106_R0.293650.575
69_L86_L0.293570.575
8_L12_V0.291250.571
38_E45_L0.288940.566
56_K59_S0.287510.563
15_I19_A0.286260.561
87_A98_D0.28320.555
29_V33_L0.280820.550
40_G44_L0.279180.547
50_R53_R0.277940.544
25_S30_Y0.27540.539
30_Y33_L0.274510.538
9_A13_S0.274170.537
72_E89_W0.273670.536
36_Y43_G0.270710.530
45_L48_K0.269840.529
104_I107_I0.265220.520
96_G99_V0.264640.518
62_Q99_V0.259480.508
11_G18_I0.259440.508
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
1pdnC0.892999.20.164
1k78A0.901899.20.173
2k27A0.901899.10.175
1u78A0.8304990.217
3hotA0.8304990.227
2lvsA0.8393990.234
4fcyA0.946498.20.421
1hlvA0.964398.20.433
1tc3C0.366197.30.555
2elhA0.535797.10.573

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