GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
STN - Secretin and TonB N terminus short domain
Pfam: PF07660 (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. )
Length: 52
Sequences: 2263
Seq/Len: 43.52
HH_delta: 0.096 (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
23_M28_A0.7552.641
30_D40_Y0.604842.116
26_E42_I0.575632.014
38_L49_I0.534951.871
31_Q34_K0.482291.687
26_E30_D0.481611.685
24_S27_E0.45951.607
23_M27_E0.454991.592
33_L36_T0.422051.476
11_N37_G0.40341.411
27_E30_D0.401761.405
18_L28_A0.390181.365
43_S46_T0.389581.363
42_I47_I0.379281.327
6_D9_D0.375771.315
33_L38_L0.368181.288
23_M31_Q0.351191.229
5_Y10_V0.345811.210
27_E31_Q0.329741.153
3_F47_I0.314831.101
21_K34_K0.305661.069
28_A33_L0.304471.065
13_K37_G0.304351.065
32_L36_T0.303171.061
33_L40_Y0.301761.056
12_G38_L0.29731.040
2_S7_D0.276870.969
2_S5_Y0.273220.956
40_Y47_I0.271730.951
44_G47_I0.259660.908
24_S28_A0.257830.902
31_Q35_G0.257110.899
18_L23_M0.255160.893
4_V7_D0.254940.892
30_D34_K0.246540.862
45_N48_V0.245790.860
3_F25_L0.242920.850
45_N49_I0.239390.837
8_D12_G0.239350.837
25_L29_L0.238750.835
9_D43_S0.234180.819
25_L28_A0.233740.818
2_S46_T0.225780.790
10_V13_K0.218970.766
2_S9_D0.216450.757
17_S22_N0.212910.745
2_S6_D0.203580.712
8_D36_T0.203260.711
3_F26_E0.202730.709
2_S10_V0.200440.701
29_L40_Y0.199970.700
14_K42_I0.198920.696
7_D12_G0.197360.690
7_D49_I0.195160.683
42_I46_T0.193970.679
19_D22_N0.193180.676
42_I48_V0.193130.676
12_G21_K0.1920.672
29_L33_L0.191510.670
19_D48_V0.191190.669
3_F28_A0.191080.668
10_V14_K0.186460.652
14_K35_G0.183290.641
9_D12_G0.182630.639
35_G39_T0.181810.636
21_K35_G0.181450.635
3_F16_V0.180710.632
21_K36_T0.179740.629
15_K36_T0.17880.625
15_K26_E0.177650.621
19_D39_T0.17750.621
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
4ar0A0.9423560.096
4av2A0.942338.20.182
2y3mA0.9423130.339
3gr5A0.942312.30.343
4g08A0.961511.20.357
2y9kA0.9615100.368
3cslA0.98087.30.404
3ossD0.942340.468
4e9jA0.94232.90.504
2w16A0.98082.80.507

Page generated in 0.0145 seconds.