GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
NOG1 - Nucleolar GTP-binding protein 1 (NOG1)
Pfam: PF06858 (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: CL0023
Length: 58
Sequences: 13487
Seq/Len: 232.53
HH_delta: 0.08 (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
18_L53_V1.78082.538
20_I55_N1.733332.470
23_P54_L1.688062.406
7_I40_E1.320271.882
38_F42_K1.266951.806
23_P57_I1.265671.804
21_I52_V1.237051.763
21_I54_L1.227581.749
36_S40_E1.156631.648
19_F34_Q0.96921.381
41_I50_V0.963191.373
25_E30_S0.953331.359
31_I34_Q0.924621.318
42_K50_V0.862441.229
36_S39_K0.853241.216
16_A49_P0.828141.180
16_A51_I0.79751.137
38_F50_V0.78191.114
39_K42_K0.758881.082
40_E44_L0.739931.054
8_T12_H0.738011.052
22_D25_E0.725421.034
54_L57_I0.699610.997
29_Y33_E0.691440.985
10_L14_A0.690160.984
28_G32_E0.673430.960
22_D56_K0.660550.941
40_E43_P0.658390.938
9_A12_H0.651960.929
19_F38_F0.612740.873
44_L47_N0.610570.870
10_L40_E0.599380.854
34_Q37_L0.587640.837
8_T15_D0.581010.828
30_S34_Q0.580110.827
8_T11_A0.579690.826
29_Y34_Q0.579630.826
17_I41_I0.578840.825
39_K43_P0.576190.821
11_A44_L0.574480.819
28_G31_I0.571250.814
19_F37_L0.552620.788
17_I48_K0.547280.780
15_D49_P0.544220.776
33_E37_L0.541480.772
19_F32_E0.537780.766
22_D55_N0.53610.764
32_E36_S0.531710.758
25_E28_G0.52670.751
7_I43_P0.509610.726
33_E36_S0.487150.694
33_E38_F0.481950.687
44_L48_K0.480790.685
7_I10_L0.471760.672
10_L48_K0.467170.666
9_A16_A0.461410.658
18_L51_I0.449380.640
7_I44_L0.448780.640
19_F41_I0.441170.629
17_I49_P0.435870.621
19_F50_V0.430310.613
29_Y32_E0.426920.608
14_A17_I0.413250.589
37_L41_I0.403740.575
30_S33_E0.396170.565
19_F25_E0.395930.564
29_Y40_E0.39410.562
8_T31_I0.389160.555
40_E58_D0.38490.549
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
3q3jB0.9483980.08
1u0lA0.93197.90.117
2j0vA0.948397.90.117
3gj0A0.948397.90.119
1gwnA0.948397.90.119
2hupA0.948397.90.122
2xtzA0.982897.90.123
2atxA0.948397.90.124
4gzlA0.948397.90.124
3regA0.948397.90.126

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