GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TGS - TGS domain
Pfam: PF02824 (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: CL0072
Length: 60
Sequences: 7322
Seq/Len: 122.03
HH_delta: 0.015 (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_K57_E2.0072.883
19_V37_A1.962512.819
40_N54_D1.720862.472
44_V48_H1.454532.089
39_V54_D1.388631.995
20_L24_Y1.26711.820
24_Y32_K1.239571.781
51_E54_D1.201081.725
39_V48_H1.192231.713
38_K43_L1.121841.611
18_T21_D1.001371.438
17_S21_D0.927821.333
22_V50_L0.920581.322
13_L17_S0.902831.297
11_K25_S0.884341.270
36_A43_L0.884321.270
39_V56_V0.872291.253
24_Y31_A0.863981.241
11_K26_I0.85791.232
38_K59_I0.840741.208
33_R60_T0.834361.199
21_D24_Y0.832451.196
20_L46_L0.826771.188
36_A59_I0.814921.171
13_L25_S0.754031.083
39_V44_V0.748571.075
41_G55_V0.748211.075
19_V44_V0.746251.072
40_N52_D0.742251.066
16_G49_P0.729441.048
14_P17_S0.718361.032
34_A46_L0.705321.013
22_V56_V0.703441.010
43_L59_I0.693540.996
37_A58_I0.680330.977
13_L16_G0.666050.957
29_S32_K0.618330.888
34_A58_I0.586460.842
34_A38_K0.5850.840
45_D48_H0.570650.820
57_E60_T0.566390.814
23_A58_I0.543570.781
14_P25_S0.517890.744
13_L22_V0.516290.742
24_Y28_S0.513470.738
36_A45_D0.512690.736
18_T49_P0.512170.736
23_A27_H0.504250.724
48_H51_E0.503610.723
29_S33_R0.502520.722
30_L60_T0.494150.710
48_H54_D0.4910.705
17_S25_S0.480440.690
19_V39_V0.475170.683
21_D25_S0.463780.666
39_V51_E0.457190.657
20_L31_A0.453170.651
22_V26_I0.433460.623
27_H30_L0.432880.622
23_A30_L0.425170.611
23_A46_L0.425130.611
23_A37_A0.421790.606
30_L34_A0.420120.603
35_V59_I0.418670.601
19_V46_L0.405210.582
30_L58_I0.395070.567
38_K41_G0.374240.538
19_V50_L0.372440.535
35_V43_L0.362470.521
20_L47_D0.361420.519
19_V48_H0.360730.518
39_V42_Q0.360710.518
34_A45_D0.343390.493
31_A34_A0.335460.482
28_S33_R0.335080.481
46_L58_I0.334460.480
20_L23_A0.330.474
36_A46_L0.329230.473
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
3hvzA198.50.015
2kmmA198.50.033
1tkeA198.50.048
1nyrA198.40.055
1qf6A198.40.073
1wwtA198.40.073
1tygB0.9598.20.133
2k5pA0.9598.10.156
1f0zA0.9598.10.16
2kl0A0.9333980.171

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