GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TOBE_3 - TOBE-like domain
Pfam: PF12857 (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: 58
Sequences: 3109
Seq/Len: 53.6
HH_delta: 0.15 (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
9_A25_L1.548883.081
12_R26_K1.47172.927
8_P52_R1.236592.460
48_Q51_D1.107572.203
25_L55_L1.049392.087
10_R52_R0.996561.982
21_V40_R0.977311.944
24_E33_P0.941971.874
6_G54_Y0.907691.805
12_R33_P0.899331.789
8_P54_Y0.865631.722
10_R26_K0.847261.685
16_P43_R0.825781.643
13_R24_E0.69061.374
16_P40_R0.67341.339
40_R43_R0.664731.322
22_R35_E0.643861.281
11_V23_L0.625951.245
26_K31_G0.59451.183
20_E37_E0.548381.091
22_R37_E0.535541.065
9_A27_R0.51871.032
47_L53_V0.50931.013
6_G56_R0.507171.009
9_A53_V0.505221.005
11_V53_V0.504341.003
13_R49_P0.493540.982
39_P42_R0.491670.978
25_L53_V0.488610.972
15_R22_R0.479740.954
28_L52_R0.474380.944
26_K33_P0.450260.896
41_E44_Q0.448170.891
14_V21_V0.437190.870
11_V47_L0.427940.851
42_R45_L0.427150.850
7_L57_P0.413060.822
14_V49_P0.411660.819
27_R31_G0.408140.812
7_L27_R0.405040.806
9_A34_I0.38950.775
12_R24_E0.386140.768
17_V21_V0.384330.764
27_R32_E0.367180.730
16_P21_V0.36140.719
14_V23_L0.359940.716
22_R41_E0.359230.715
46_G51_D0.359180.714
39_P56_R0.353540.703
5_G57_P0.349380.695
23_L38_L0.347420.691
27_R34_I0.347150.691
17_V20_E0.342750.682
36_V57_P0.339670.676
26_K32_E0.327730.652
19_P37_E0.326430.649
24_E35_E0.305940.609
19_P22_R0.305830.608
43_R46_G0.301040.599
38_L45_L0.290310.577
9_A55_L0.288960.575
18_G32_E0.287740.572
28_L31_G0.282660.562
19_P40_R0.281480.560
4_E39_P0.279040.555
28_L32_E0.278050.553
4_E42_R0.27770.552
39_P47_L0.276110.549
39_P45_L0.270830.539
17_V37_E0.270440.538
15_R24_E0.270110.537
10_R28_L0.267340.532
38_L42_R0.266680.530
8_P28_L0.261810.521
5_G47_L0.256160.510
44_Q48_Q0.250210.498
42_R55_L0.24980.497
18_G22_R0.24070.479
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
1h9mA0.982896.90.15
1gutA0.982896.90.156
1fr3A0.965596.60.189
1b9mA0.965596.40.211
1oxxK0.913893.60.347
3rlfA0.93193.40.35
1g2910.9138930.359
1v43A0.913892.90.361
3gd7A0.948392.40.371
3fvqA0.913892.30.373

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