GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Prok-RING_4 - Prokaryotic RING finger family 4
Pfam: PF14447 (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: CL0229
Length: 55
Sequences: 15808
Seq/Len: 287.42
HH_delta: -0.036 (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
29_I34_F1.824072.659
10_C13_C1.60412.338
42_C45_C1.527672.227
17_G20_G1.512742.205
13_C33_C1.377092.007
30_C33_C1.188391.732
22_V28_L1.162061.694
31_D35_P1.111161.620
8_Q16_V1.104441.610
11_V44_F0.99531.451
25_C45_C0.943591.375
9_P14_G0.938751.368
22_V29_I0.888461.295
41_G46_G0.86481.261
11_V14_G0.83491.217
9_P16_V0.80931.180
12_F43_P0.807481.177
13_C30_C0.802011.169
17_G21_T0.800261.166
29_I43_P0.758381.105
18_T30_C0.748841.092
21_T31_D0.742771.083
36_G40_N0.699741.020
23_L49_F0.646750.943
29_I44_F0.646360.942
33_C42_C0.596660.870
20_G28_L0.592590.864
35_P39_Y0.592470.864
23_L29_I0.572510.834
38_R49_F0.569470.830
17_G28_L0.56890.829
8_Q11_V0.568620.829
27_H45_C0.566020.825
7_E16_V0.562310.820
24_P50_E0.532680.776
41_G48_P0.530090.773
36_G39_Y0.520850.759
28_L31_D0.506760.739
39_Y50_E0.506080.738
37_E41_G0.50580.737
19_K31_D0.502440.732
11_V29_I0.497290.725
10_C33_C0.490060.714
29_I37_E0.4890.713
20_G34_F0.475390.693
14_G46_G0.471010.687
24_P47_T0.469680.685
37_E40_N0.460470.671
14_G44_F0.45940.670
12_F37_E0.458710.669
12_F15_F0.455780.664
25_C42_C0.454370.662
7_E28_L0.445250.649
13_C25_C0.44030.642
12_F46_G0.439770.641
22_V26_G0.437770.638
32_N35_P0.437430.638
47_T50_E0.428030.624
8_Q17_G0.427180.623
23_L27_H0.425460.620
7_E11_V0.425250.620
12_F29_I0.416180.607
40_N50_E0.412890.602
15_F46_G0.412810.602
36_G41_G0.410120.598
35_P47_T0.406850.593
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
2y1nA198.5-0.036
3lrqA198.5-0.036
1jm7B198.5-0.034
3fl2A198.5-0.018
3hcsA198.5-0.014
2ecyA198.5-0.013
1jm7A198.5-0.012
1z6uA198.5-0.01
2djbA198.5-0.005
1rmdA198.4-0.003

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