GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
S1_2 - S1 domain
Pfam: PF13509 (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: 61
Sequences: 11387
Seq/Len: 186.67
HH_delta: 0.072 (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
6_T45_E3.34574.553
6_T43_E2.223223.025
8_K43_E1.986542.703
10_V26_E1.734542.360
4_I45_E1.724372.347
4_I47_F1.715252.334
39_K42_D1.485182.021
7_L19_L1.480662.015
17_Y38_L1.421.932
15_F28_L1.232921.678
16_G28_L1.184451.612
10_V20_D1.070091.456
12_K17_Y1.059391.442
21_D27_V1.019671.388
33_E49_Y1.00481.367
34_V38_L0.961181.308
9_V38_L0.938461.277
19_L29_L0.902681.228
7_L46_V0.88241.201
20_D23_E0.84551.151
5_N46_V0.829861.129
11_D26_E0.805981.097
13_N18_F0.777851.059
29_L46_V0.752481.024
20_D26_E0.729470.993
34_V37_P0.728650.992
30_P33_E0.693960.944
31_K36_E0.682570.929
27_V48_V0.671040.913
8_K20_D0.670090.912
11_D40_V0.66420.904
12_K40_V0.644040.876
31_K37_P0.639290.870
50_L54_G0.613950.835
15_F30_P0.606710.826
15_F18_F0.585540.797
12_K38_L0.576560.785
20_D24_G0.576050.784
5_N22_G0.571570.778
25_K54_G0.558070.759
5_N48_V0.543110.739
7_L27_V0.531310.723
8_K41_G0.515490.701
38_L42_D0.502910.684
29_L34_V0.484130.659
5_N47_F0.473720.645
19_L44_V0.47310.644
13_N28_L0.471850.642
29_L44_V0.47030.640
31_K34_V0.467210.636
23_E26_E0.466860.635
25_K52_K0.463690.631
21_D25_K0.460760.627
18_F21_D0.460750.627
5_N21_D0.458770.624
16_G30_P0.453440.617
9_V19_L0.453110.617
10_V40_V0.450650.613
17_Y34_V0.44140.601
9_V44_V0.432940.589
14_E37_P0.428050.583
12_K31_K0.423330.576
51_D54_G0.41850.570
17_Y29_L0.401230.546
7_L44_V0.397350.541
38_L44_V0.395280.538
17_Y33_E0.394980.537
14_E39_K0.39370.536
21_D48_V0.387060.527
25_K50_L0.386640.526
7_L29_L0.385380.524
31_K35_P0.38270.521
2_G49_Y0.380560.518
5_N20_D0.376380.512
12_K41_G0.373460.508
50_L53_E0.373310.508
2_G51_D0.36370.495
20_D25_K0.363230.494
21_D43_E0.34640.471
29_L33_E0.346130.471
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
4aidA198.80.072
3cdiA198.70.079
1e3pA198.70.11
3go5A198.60.125
3go5A0.950898.60.132
3psfA198.50.147
3cw2C198.50.152
2eqsA198.50.158
3bzcA198.50.158
2k4kA198.50.165

Page generated in 0.0294 seconds.