GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
S4_2 - S4 domain
Pfam: PF13275 (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: CL0492
Length: 65
Sequences: 12028
Seq/Len: 185.05
HH_delta: 0.085 (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_N53_D2.300712.649
36_K56_E2.214142.549
42_E47_K2.086422.402
20_V26_A1.771852.040
34_E58_D1.547751.782
13_L17_A1.443871.662
13_L49_L1.437031.655
20_V29_L1.424021.640
33_G41_V1.419291.634
28_A32_E1.377911.586
36_K41_V1.319891.520
25_E28_A1.283041.477
29_L57_I1.28141.475
50_R53_D1.251361.441
37_V55_V1.202991.385
37_V47_K1.161491.337
33_G43_T1.153861.328
11_G27_K1.147211.321
31_Q45_R1.140841.313
15_K23_G1.103471.270
14_L26_A1.096331.262
25_E29_L1.048481.207
29_L34_E1.04831.207
8_I16_L1.03821.195
9_T46_G0.98971.139
8_I48_K0.982771.132
37_V42_E0.982431.131
12_Q23_G0.920291.060
39_G56_E0.867990.999
10_L42_E0.813710.937
49_L55_V0.810270.933
24_G27_K0.807260.929
8_I12_Q0.804820.927
9_T12_Q0.802630.924
44_R47_K0.777260.895
35_V57_I0.771410.888
14_L35_V0.760640.876
37_V53_D0.735730.847
11_G46_G0.726960.837
30_I45_R0.718360.827
8_I13_L0.715490.824
39_G54_V0.710770.818
10_L30_I0.684410.788
36_K39_G0.677320.780
27_K46_G0.632140.728
30_I35_V0.629730.725
40_E47_K0.609670.702
11_G45_R0.608130.700
38_N54_V0.60210.693
27_K31_Q0.591710.681
12_Q16_L0.580890.669
47_K50_R0.568730.655
26_A57_I0.547210.630
20_V25_E0.542360.624
36_K58_D0.53380.615
12_Q15_K0.525070.605
10_L37_V0.516920.595
27_K45_R0.509850.587
29_L32_E0.499940.576
10_L35_V0.476560.549
10_L55_V0.476130.548
28_A31_Q0.475070.547
19_L26_A0.471030.542
26_A30_I0.467240.538
24_G28_A0.464780.535
22_S27_K0.46330.533
12_Q27_K0.461510.531
22_S30_I0.46120.531
14_L57_I0.460230.530
38_N55_V0.440070.507
11_G23_G0.43670.503
15_K22_S0.433320.499
30_I33_G0.43310.499
19_L57_I0.4330.499
28_A34_E0.429780.495
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
1p9kA198.90.085
3r8nD198.60.169
2vqeD198.50.189
1v9fA198.50.202
1c05A198.50.202
3bbnD198.50.207
3hp7A0.984698.50.207
3dh3A0.953898.50.21
1dm9A0.984698.30.248
3j20D198.30.254

Page generated in 0.0249 seconds.