GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Myb_DNA-bind_6 - Myb-like DNA-binding domain
Pfam: PF13921 (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: 60
Sequences: 5542
Seq/Len: 92.37
HH_delta: -0.082 (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
6_D38_R2.28694.138
12_L27_L1.227282.221
3_K7_E1.172362.122
13_V18_N1.097181.985
12_L26_H0.989361.790
7_E11_E0.926461.677
22_K25_E0.900731.630
16_Y22_K0.882311.597
34_Q37_N0.870331.575
6_D9_L0.759061.374
1_W9_L0.755851.368
5_E30_R0.753911.364
33_K41_N0.74091.341
7_E10_L0.737551.335
37_N41_N0.736611.333
19_D22_K0.724711.311
8_L11_E0.721161.305
20_W23_I0.68351.237
33_K36_R0.671371.215
27_L35_C0.664871.203
11_E15_K0.652241.180
9_L35_C0.640891.160
15_K26_H0.633561.147
33_K37_N0.621261.124
12_L23_I0.603631.092
36_R41_N0.599961.086
13_V17_G0.589191.066
10_L39_W0.577941.046
12_L15_K0.557531.009
23_I35_C0.542280.981
10_L14_K0.539980.977
22_K26_H0.531040.961
8_L27_L0.513140.929
31_T34_Q0.510370.924
21_K32_P0.507260.918
11_E14_K0.488210.883
5_E27_L0.449180.813
9_L38_R0.442450.801
23_I27_L0.442330.800
13_V39_W0.440760.798
40_R44_R0.440.796
12_L16_Y0.43910.795
9_L13_V0.42890.776
24_A35_C0.423840.767
36_R40_R0.42150.763
8_L29_N0.417010.755
31_T42_H0.416280.753
24_A31_T0.412150.746
1_W32_P0.408850.740
6_D43_L0.407070.737
1_W42_H0.396040.717
33_K42_H0.39590.716
8_L12_L0.381930.691
1_W34_Q0.38130.690
8_L26_H0.368950.668
30_R34_Q0.361230.654
1_W35_C0.352870.639
37_N40_R0.35260.638
4_E8_L0.35240.638
1_W33_K0.349070.632
44_R47_I0.345520.625
30_R37_N0.342910.621
19_D47_I0.341640.618
29_N51_P0.339750.615
20_W39_W0.337620.611
35_C39_W0.334470.605
19_D51_P0.332810.602
37_N42_H0.32840.594
1_W38_R0.324140.587
24_A27_L0.322310.583
21_K24_A0.313690.568
21_K31_T0.305560.553
26_H29_N0.302830.548
33_K40_R0.301790.546
32_P36_R0.299450.542
21_K25_E0.294190.532
42_H49_R0.290440.526
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
3osgA199.5-0.082
3zqcA199.5-0.067
2k9nA199.4-0.06
1gv2A199.4-0.05
1h89C199.4-0.045
1h8aC199.4-0.045
2dimA0.966799.4-0.042
1h89C199.4-0.019
1ignA0.983399.10.108
1ityA0.9990.142

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