GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PUA - PUA domain
Pfam: PF01472 (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: CL0178
Length: 74
Sequences: 3191
Seq/Len: 43.12
HH_delta: 0.062 (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
2_R40_V1.18582.811
38_A46_V1.094312.594
7_D42_E0.964472.286
46_V49_V0.902842.140
41_D45_E0.802861.903
5_V39_I0.800851.898
4_V26_E0.78371.858
2_R38_A0.719621.706
32_R35_D0.718941.704
50_G60_K0.699951.659
10_V41_D0.696551.651
36_E51_R0.683991.621
4_V40_V0.680821.614
2_R28_D0.654011.550
31_F52_A0.641091.520
33_K54_M0.632561.499
38_A49_V0.631641.497
10_V47_I0.610861.448
54_M62_M0.609111.444
60_K63_K0.576761.367
10_V14_L0.561371.331
58_E61_K0.557691.322
5_V47_I0.553281.312
27_V31_F0.548751.301
6_D9_A0.539641.279
25_V42_E0.524971.244
6_D25_V0.518161.228
55_S58_E0.506851.201
39_I48_A0.492891.168
11_E15_N0.491541.165
9_A23_G0.470371.115
39_I50_G0.462811.097
4_V28_D0.455431.080
37_V50_G0.451031.069
27_V56_S0.408570.969
5_V19_L0.404970.960
19_L39_I0.402070.953
52_A59_I0.398660.945
57_E60_K0.389350.923
53_N66_K0.3860.915
12_A23_G0.376350.892
32_R55_S0.371050.880
37_V52_A0.370860.879
30_D60_K0.364850.865
7_D43_D0.364310.864
13_I19_L0.351770.834
31_F35_D0.350680.831
41_D47_I0.348560.826
3_V37_V0.346030.820
40_V46_V0.341840.810
5_V9_A0.34170.810
18_S66_K0.338480.802
31_F56_S0.335860.796
4_V42_E0.333880.791
8_G23_G0.332570.788
11_E14_L0.332410.788
17_A23_G0.329360.781
40_V44_G0.328990.780
12_A17_A0.328560.779
14_L45_E0.324760.770
12_A15_N0.323950.768
7_D11_E0.32380.768
53_N63_K0.31620.750
22_P66_K0.315480.748
9_A12_A0.312990.742
53_N58_E0.309430.734
21_A59_I0.300190.712
5_V10_V0.296980.704
15_N65_G0.281730.668
61_K65_G0.275390.653
22_P64_K0.272530.646
12_A19_L0.27150.644
7_D10_V0.268510.637
6_D22_P0.26650.632
33_K55_S0.260490.617
3_V27_V0.258270.612
22_P65_G0.255910.607
21_A54_M0.253210.600
10_V42_E0.251630.596
17_A22_P0.248960.590
21_A62_M0.24640.584
36_E49_V0.244770.580
36_E40_V0.240360.570
2_R44_G0.237660.563
12_A22_P0.235220.558
24_V39_I0.232420.551
22_P39_I0.231610.549
4_V46_V0.231490.549
21_A64_K0.230480.546
8_G12_A0.227790.540
7_D45_E0.227420.539
26_E60_K0.226620.537
10_V48_A0.225870.535
31_F59_I0.224770.533
33_K58_E0.223880.531
33_K59_I0.222840.528
7_D44_G0.220870.524
18_S48_A0.219420.520
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
3zv0C199.40.062
1iq8A199.30.071
1q7hA199.30.11
3d79A199.30.11
3r90A199.20.129
2cx0A199.20.13
2j5vA199.10.164
3vseA0.986598.90.253
2q07A0.905498.80.27
4dmgA0.959598.70.304

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