GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CSD - Cold-shock DNA-binding domain
Pfam: PF00313 (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: CL0021
Length: 66
Sequences: 3968
Seq/Len: 60.12
HH_delta: -0.06 (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
52_E61_V2.062313.893
28_F63_V1.83363.461
50_E62_N1.63043.078
45_D65_K1.286492.428
2_T48_E1.121232.116
20_D46_R1.108452.092
19_S23_G1.086832.052
48_E64_R1.054571.991
54_G57_G1.052421.987
19_S49_F1.0161.918
6_K25_D0.987311.864
53_E58_P0.958711.810
4_T46_R0.952311.798
2_T46_R0.928631.753
19_S22_G0.913121.724
32_D61_V0.912111.722
10_D42_K0.780061.472
34_S62_N0.779691.472
10_D40_S0.772941.459
34_S64_R0.742911.402
60_A63_V0.728941.376
54_G59_Q0.718341.356
51_V58_P0.712581.345
2_T20_D0.682471.288
3_G17_I0.639771.208
26_I51_V0.623541.177
16_F27_F0.618481.167
10_D38_F0.61391.159
28_F41_L0.581691.098
42_K45_D0.567811.072
4_T18_T0.561481.060
30_I39_R0.554771.047
33_L39_R0.534031.008
35_G65_K0.52560.992
7_W25_D0.520950.983
3_G49_F0.506940.957
19_S26_I0.505070.953
17_I47_V0.486920.919
5_V47_V0.484530.915
6_K18_T0.470850.889
12_K16_F0.462640.873
18_T44_G0.45160.852
32_D52_E0.428770.809
14_Y27_F0.411140.776
26_I49_F0.394210.744
8_F30_I0.390930.738
4_T20_D0.378480.714
35_G38_F0.372450.703
17_I49_F0.367830.694
42_K65_K0.3670.693
33_L41_L0.36660.692
7_W43_E0.363420.686
30_I33_L0.353630.668
50_E61_V0.346070.653
5_V41_L0.341630.645
32_D62_N0.324880.613
50_E64_R0.323740.611
12_K27_F0.323580.611
7_W28_F0.312930.591
30_I59_Q0.310370.586
26_I32_D0.306080.578
30_I38_F0.3060.578
54_G58_P0.303960.574
28_F33_L0.301380.569
14_Y29_H0.296870.560
9_D14_Y0.292870.553
15_G28_F0.289810.547
53_E61_V0.288010.544
16_F25_D0.28610.540
57_G60_A0.283340.535
60_A64_R0.28150.531
5_V28_F0.280140.529
36_N39_R0.27750.524
33_L38_F0.277020.523
32_D59_Q0.274490.518
55_K58_P0.27120.512
55_K59_Q0.270080.510
53_E59_Q0.267590.505
19_S28_F0.266280.503
11_E42_K0.262130.495
33_L36_N0.261540.494
5_V8_F0.258270.488
31_S39_R0.256030.483
49_F60_A0.253940.479
17_I43_E0.24890.470
8_F33_L0.247350.467
16_F29_H0.244680.462
30_I34_S0.241890.457
41_L47_V0.239660.452
31_S34_S0.234690.443
18_T22_G0.232070.438
52_E58_P0.229980.434
8_F13_G0.229330.433
33_L47_V0.229130.433
11_E46_R0.22690.428
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
2kcmA0.984899.7-0.06
3camA199.7-0.049
1g6pA0.984899.7-0.045
3i2zB199.7-0.045
2lssA199.7-0.043
1c9oA0.984899.6-0.033
3a0jA0.984899.6-0.027
3uljA199.6-0.022
3ts2A199.6-0.018
3aqqA0.969799.6-0.018

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