GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
S1 - S1 RNA binding domain
Pfam: PF00575 (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: CL0021
Length: 74
Sequences: 10068
Seq/Len: 136.05
HH_delta: -0.063 (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
9_E56_R2.932544.090
9_E54_T1.953012.724
3_K6_D1.92332.683
10_G22_V1.785452.490
7_I58_K1.7022.374
7_I56_R1.701332.373
11_K54_T1.590512.218
30_G71_L1.568482.188
50_K53_Q1.520312.120
20_V49_Y1.320331.842
36_E60_I1.228721.714
13_T23_D1.19421.666
13_T29_E1.179251.645
61_K70_R1.164111.624
19_G31_F1.161291.620
55_V73_L1.145341.597
63_D66_K1.13181.579
60_I72_S1.108831.547
10_G57_V1.089151.519
2_L25_G1.083111.511
8_V57_V1.048671.463
58_K72_S1.032611.440
18_F31_F1.011061.410
44_D47_E0.989921.381
4_E61_K0.970051.353
37_L45_P0.944151.317
37_L49_Y0.934911.304
15_V51_I0.910931.271
59_V71_L0.906781.265
32_I73_L0.830081.158
22_V32_I0.82431.150
36_E39_D0.82041.144
24_L69_I0.814581.136
15_V20_V0.802361.119
33_P70_R0.774531.080
36_E72_S0.758591.058
12_V22_V0.735541.026
14_S51_I0.735161.025
12_V49_Y0.728551.016
32_I71_L0.723281.009
33_P36_E0.706370.985
2_L59_V0.70160.979
18_F21_F0.695520.970
23_D29_E0.693790.968
16_E21_F0.690430.963
11_K23_D0.682990.953
20_V37_L0.653950.912
24_L30_G0.631030.880
2_L8_V0.621590.867
57_V71_L0.609650.850
42_I48_V0.608760.849
22_V71_L0.607680.848
14_S21_F0.599670.836
17_D46_S0.585420.817
32_I57_V0.566460.790
38_S42_I0.557440.777
32_I37_L0.52410.731
10_G71_L0.50950.711
42_I45_P0.499920.697
31_F70_R0.489160.682
23_D26_N0.486160.678
4_E60_I0.485710.677
43_D47_E0.484320.676
20_V32_I0.47280.659
15_V49_Y0.471050.657
63_D68_R0.470180.656
62_V69_I0.467710.652
4_E62_V0.443680.619
42_I46_S0.439110.612
59_V69_I0.435690.608
34_I42_I0.433590.605
40_D43_D0.421440.588
49_Y73_L0.420180.586
15_V34_I0.412990.576
26_N29_E0.410360.572
16_E31_F0.406850.567
59_V62_V0.404270.564
37_L48_V0.401330.560
49_Y53_Q0.401050.559
37_L73_L0.39940.557
18_F33_P0.393150.548
42_I47_E0.392420.547
8_V24_L0.383690.535
8_V59_V0.383610.535
40_D48_V0.379510.529
22_V57_V0.378730.528
28_I65_E0.375570.524
23_D27_G0.371260.518
46_S51_I0.368740.514
14_S29_E0.363480.507
41_R44_D0.358970.501
22_V30_G0.356190.497
25_G54_T0.341690.477
36_E58_K0.339530.474
10_G55_V0.332280.463
34_I45_P0.327360.457
21_F31_F0.327310.457
41_R46_S0.326810.456
13_T21_F0.319490.446
2_L6_D0.31920.445
10_G32_I0.319190.445
18_F35_S0.3170.442
24_L59_V0.315540.440
38_S45_P0.314450.439
57_V73_L0.313080.437
10_G21_F0.31110.434
30_G57_V0.310350.433
60_I70_R0.310090.433
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
3psfA199.3-0.063
3psiA199.2-0.061
4aidA0.986599.2-0.049
3bzcA199.2-0.047
1kl9A199.2-0.033
3cdiA0.986599.2-0.03
1e3pA0.986599.2-0.026
1q8kA199.2-0.021
2a19A199.1-0.011
2k4kA199.1-0.009

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