GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SAM_1 - SAM domain (Sterile alpha motif)
Pfam: PF00536 (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: CL0003
Length: 64
Sequences: 3118
Seq/Len: 48.72
HH_delta: -0.103 (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
38_T41_D1.149363.315
20_Y52_H0.789282.276
30_D33_D0.699352.017
13_K21_A0.695462.006
47_I56_I0.647931.869
13_K18_E0.61591.776
7_D31_G0.583131.682
9_S21_A0.576711.663
11_W34_L0.567671.637
39_E53_R0.564121.627
9_S25_E0.558741.612
31_G34_L0.533531.539
39_E57_L0.513851.482
22_E26_K0.511931.476
41_D54_K0.511541.475
33_D36_S0.468331.351
43_E53_R0.461371.331
23_N26_K0.454731.312
49_K52_H0.453181.307
8_V31_G0.418331.207
5_V25_E0.417031.203
19_Q52_H0.392631.132
50_L54_K0.391281.129
40_E43_E0.377341.088
55_K58_R0.376671.086
14_S59_A0.374191.079
40_E44_E0.364571.051
31_G35_L0.36221.045
12_L24_F0.355321.025
12_L21_A0.355181.024
11_W59_A0.35361.020
51_G54_K0.349141.007
17_L20_Y0.347471.002
53_R57_L0.346060.998
15_L59_A0.332650.959
56_I60_I0.330050.952
5_V8_V0.327810.945
42_L53_R0.323250.932
10_E14_S0.313940.905
17_L52_H0.308340.889
57_L61_Q0.300560.867
35_L60_I0.300110.866
21_A25_E0.298520.861
51_G55_K0.29060.838
24_F29_I0.283880.819
34_L37_L0.279860.807
26_K29_I0.277610.801
57_L60_I0.273750.790
47_I52_H0.2730.787
59_A62_K0.272950.787
28_Y32_E0.267930.773
58_R61_Q0.266840.770
52_H59_A0.266790.769
12_L56_I0.262890.758
11_W17_L0.259230.748
7_D44_E0.250570.723
54_K58_R0.249930.721
6_E25_E0.248390.716
30_D55_K0.248090.716
8_V11_W0.245360.708
24_F37_L0.243210.701
7_D14_S0.24240.699
11_W63_L0.241850.698
27_N37_L0.239370.690
5_V9_S0.235860.680
47_I53_R0.23570.680
49_K53_R0.2350.678
58_R62_K0.233490.673
43_E48_T0.233050.672
49_K55_K0.232810.671
36_S39_E0.230910.666
30_D41_D0.230090.664
39_E43_E0.229120.661
32_E39_E0.228610.659
5_V24_F0.227080.655
7_D10_E0.222770.643
48_T57_L0.222470.642
24_F47_I0.22160.639
42_L47_I0.221010.637
10_E19_Q0.219760.634
8_V29_I0.219370.633
17_L55_K0.218310.630
18_E21_A0.217950.629
22_E40_E0.216790.625
32_E36_S0.215150.621
29_I34_L0.215090.620
30_D34_L0.213250.615
26_K36_S0.213240.615
31_G60_I0.212740.614
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
2f3nA198.9-0.103
3bq7A198.9-0.098
3bs5A198.9-0.095
3tadC198.9-0.089
2gleA198.9-0.089
2e8oA198.9-0.075
3bs5B198.8-0.073
3bs7A198.8-0.068
1v85A198.8-0.067
2eanA198.8-0.067

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