GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
BrkDBD - Brinker DNA-binding domain
Pfam: PF09607 (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: 58
Sequences: 9823
Seq/Len: 169.36
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
17_Y34_K1.58952.032
32_A42_V1.480841.894
7_T10_F1.210031.547
14_V35_F1.200141.535
25_K43_R1.18031.509
23_N30_A1.173371.500
40_R44_K1.15971.483
29_R39_R1.144551.464
23_N34_K1.087811.391
40_R43_R1.083621.386
8_A12_L1.067321.365
17_Y21_D1.055031.349
13_K17_Y1.036891.326
12_L16_E1.00891.290
29_R33_R1.001871.281
18_A46_R0.984281.259
6_Y10_F0.97781.250
17_Y35_F0.95811.225
38_S41_Q0.949781.214
44_K48_Q0.946761.211
39_R43_R0.933391.194
43_R47_K0.923351.181
18_A31_A0.91741.173
25_K46_R0.913621.168
24_C29_R0.889111.137
24_C30_A0.872231.115
15_V19_E0.86941.112
16_E20_K0.831351.063
41_Q44_K0.81.023
13_K16_E0.778770.996
17_Y23_N0.759670.971
10_F13_K0.753940.964
11_K14_V0.748360.957
32_A39_R0.731590.935
30_A34_K0.723620.925
11_K45_W0.71890.919
45_W49_E0.70910.907
31_A42_V0.678190.867
19_E49_E0.665370.851
19_E46_R0.658510.842
11_K15_V0.65690.840
14_V42_V0.647290.828
10_F45_W0.64120.820
12_L49_E0.618670.791
6_Y45_W0.614090.785
29_R32_A0.610830.781
14_V18_A0.609030.779
17_Y31_A0.60520.774
31_A35_F0.585150.748
46_R50_E0.547780.700
7_T11_K0.54340.695
32_A38_S0.486770.622
18_A25_K0.485040.620
45_W48_Q0.483890.619
14_V31_A0.462150.591
30_A33_R0.457650.585
23_N31_A0.453340.580
37_V41_Q0.452520.579
19_E50_E0.451080.577
16_E19_E0.44480.569
13_K34_K0.441120.564
32_A37_V0.43560.557
38_S44_K0.43430.555
9_E13_K0.433190.554
42_V46_R0.422740.541
11_K50_E0.418780.535
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
2gloA0.931980.114
2jn6A0.948397.90.148
2elhA0.93197.70.174
2rn7A0.948397.70.179
1tc3C0.879397.70.186
4dyqA0.93197.60.198
2k27A0.93197.60.201
1u78A0.93197.50.226
1k78A0.93197.40.235
1jkoC0.896697.40.242

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