GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Surp - Surp module
Pfam: PF01805 (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: 55
Sequences: 666
Seq/Len: 12.11
HH_delta: -0.048 (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
8_T23_L0.527092.610
27_E30_N0.460592.281
20_E47_Y0.439092.174
9_A13_A0.344761.707
25_E28_R0.32761.622
6_D46_Y0.319321.581
4_I33_F0.286521.419
9_A51_L0.283311.403
2_R42_P0.277751.375
15_N19_F0.259181.283
33_F36_L0.2551.263
47_Y50_K0.249681.236
24_R37_F0.236541.171
2_R6_D0.234091.159
8_T41_S0.22791.129
6_D50_K0.223881.109
14_K19_F0.218171.080
12_V16_G0.2171.075
34_N41_S0.216411.072
26_R30_N0.209351.037
21_E28_R0.20671.024
8_T32_Q0.202731.004
11_F27_E0.202551.003
17_P48_R0.202421.002
34_N37_F0.200320.992
11_F33_F0.199150.986
4_I9_A0.197890.980
17_P38_P0.197860.980
13_A51_L0.195920.970
2_R25_E0.192830.955
23_L26_R0.190320.942
4_I11_F0.190180.942
24_R38_P0.189870.940
24_R39_S0.187930.931
12_V20_E0.184080.912
14_K41_S0.183610.909
41_S44_H0.183020.906
6_D20_E0.178890.886
12_V50_K0.178780.885
20_E46_Y0.177310.878
42_P48_R0.176830.876
50_K53_E0.176410.874
11_F19_F0.174450.864
46_Y49_W0.171580.850
24_R29_N0.170610.845
4_I7_K0.169310.838
28_R51_L0.169220.838
28_R52_A0.166010.822
15_N41_S0.165360.819
8_T15_N0.165340.819
19_F27_E0.165150.818
11_F15_N0.164260.813
2_R46_Y0.163170.808
9_A12_V0.161980.802
16_G30_N0.161650.800
38_P43_Y0.160460.795
47_Y51_L0.159890.792
17_P21_E0.159140.788
34_N39_S0.156760.776
21_E51_L0.155570.770
21_E24_R0.155260.769
2_R11_F0.155050.768
37_F46_Y0.154690.766
46_Y50_K0.154640.766
22_K26_R0.154120.763
38_P48_R0.154040.763
10_E26_R0.153690.761
22_K32_Q0.153690.761
39_S43_Y0.1510.748
18_E21_E0.150990.748
10_E13_A0.150560.746
45_A49_W0.150390.745
48_R52_A0.149940.742
23_L45_A0.149880.742
16_G19_F0.148330.735
5_I28_R0.147870.732
39_S45_A0.146930.728
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
1ug0A199.6-0.048
1x4oA199.6-0.031
2e60A0.981899.6-0.03
2dt6A0.981899.6-0.024
2dt7B0.981899.50.01
2e5zA0.945599.50.012
4dgwB0.945599.40.105
1x4pA0.963698.80.316
2gvsA0.818219.10.836
1k19A0.763618.50.837

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