GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF3553 - Protein of unknown function (DUF3553)
Pfam: PF12073 (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. )
Length: 52
Sequences: 1811
Seq/Len: 34.83
HH_delta: 0.126 (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
5_M49_K1.407923.497
8_R48_E1.165942.896
29_T39_V0.98642.450
8_R17_I0.899542.234
6_L17_I0.836732.078
27_R39_V0.785791.952
22_S29_T0.768651.909
31_N37_K0.768021.908
28_V42_G0.720921.791
7_V47_L0.675681.678
19_Q31_N0.672091.669
24_I27_R0.59831.486
6_L19_Q0.568751.413
21_Q37_K0.528091.312
23_N28_V0.521341.295
8_R50_V0.511121.270
3_P23_N0.502831.249
2_E5_M0.486471.208
26_G42_G0.47331.176
29_T37_K0.465241.156
21_Q31_N0.462051.148
15_W38_K0.45861.139
17_I33_E0.456341.134
41_D44_R0.443281.101
6_L33_E0.383040.951
3_P22_S0.358690.891
24_I39_V0.351050.872
40_I45_V0.340490.846
27_R41_D0.337380.838
23_N42_G0.337360.838
28_V40_I0.325170.808
7_V20_V0.32040.796
15_W46_A0.298960.743
3_P21_Q0.298450.741
10_P48_E0.297730.740
20_V23_N0.289470.719
38_K44_R0.281640.700
15_W40_I0.276380.687
2_E17_I0.274540.682
8_R34_H0.270110.671
3_P6_L0.270010.671
10_P17_I0.267380.664
11_D36_G0.266570.662
9_H15_W0.260340.647
15_W45_V0.255640.635
11_D43_S0.245720.610
8_R11_D0.245440.610
6_L24_I0.242460.602
10_P35_A0.238830.593
17_I50_V0.238330.592
10_P46_A0.233790.581
5_M22_S0.230770.573
25_G41_D0.229750.571
34_H48_E0.22870.568
38_K43_S0.227670.566
25_G43_S0.223840.556
24_I41_D0.221850.551
4_G20_V0.220880.549
24_I43_S0.210220.522
11_D25_G0.208930.519
2_E6_L0.208210.517
15_W27_R0.205830.511
2_E19_Q0.20470.508
2_E31_N0.203540.506
19_Q33_E0.20190.502
7_V30_V0.200670.498
9_H16_G0.198530.493
21_Q38_K0.192960.479
34_H37_K0.190280.473
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
1pjrA0.903898.70.126
3dmqA195.50.55
3mlqE0.9038910.626
2lqkA0.865490.40.631
2eyqA0.903889.90.635
3qiiA0.884658.60.724
3p8dA0.8846520.734
1vbvA0.923151.10.735
1qp2A150.80.736
2do3A0.980845.60.743

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