GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HTH_28 - Helix-turn-helix domain
Pfam: PF13518 (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: 52
Sequences: 26748
Seq/Len: 514.38
HH_delta: 0.083 (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
8_L21_E2.245862.210
14_S17_E2.245442.210
15_V30_Y1.919941.889
28_T31_R1.864211.834
19_A29_V1.861861.832
4_Q8_L1.724961.697
5_I29_V1.66851.642
27_S30_Y1.653721.627
25_S28_T1.348371.327
26_R30_Y1.321221.300
15_V33_I1.314011.293
19_A26_R1.291061.270
30_Y34_K1.285831.265
31_R35_R1.228031.208
17_E21_E1.211651.192
24_I29_V1.210421.191
9_Y18_I1.192281.173
8_L18_I1.151731.133
9_Y33_I1.142321.124
35_R39_G1.13761.119
28_T32_W1.136631.118
16_R26_R1.106611.089
5_I22_F1.098281.081
27_S31_R1.037951.021
3_L7_E1.030451.014
34_K38_E1.028561.012
8_L22_F1.017791.002
34_K37_R1.006120.990
24_I28_T0.985420.970
36_Y42_E0.947250.932
17_E20_R0.936990.922
16_R20_R0.930830.916
18_I29_V0.841180.828
33_I37_R0.826630.813
4_Q7_E0.817680.805
36_Y40_G0.809270.796
15_V32_W0.806910.794
15_V26_R0.79220.780
35_R38_E0.762050.750
5_I18_I0.735090.723
7_E10_L0.710510.699
39_G42_E0.707590.696
4_Q22_F0.705650.694
32_W36_Y0.68330.672
8_L13_E0.680360.669
13_E21_E0.680320.669
15_V19_A0.670010.659
22_F29_V0.639970.630
18_I33_I0.622660.613
8_L11_E0.605130.595
6_V41_I0.600920.591
29_V33_I0.600590.591
31_R34_K0.597030.587
14_S26_R0.58930.580
3_L41_I0.588890.579
13_E17_E0.533330.525
3_L39_G0.529550.521
6_V10_L0.522150.514
32_W42_E0.521350.513
28_T34_K0.51420.506
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
1k78A197.90.083
2k27A197.90.089
1pdnC197.80.097
1u78A0.942397.60.148
2lvsA197.40.183
2jn6A197.40.183
2elhA197.30.202
3hotA0.980897.30.21
2jrtA197.20.22
1tc3C0.807797.20.223

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