GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Sod_Fe_N - Ironmanganese superoxide dismutases alpha-hairpin domain
Pfam: PF00081 (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: 82
Sequences: 2212
Seq/Len: 26.98
HH_delta: -0.036 (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
32_Q36_N2.35485.452
37_N40_K1.258242.913
20_E24_E1.019922.361
18_I77_F1.001752.319
11_Y28_D0.889712.060
40_K43_E0.881232.040
36_N40_K0.875952.028
35_V71_H0.850421.969
38_L68_A0.849391.966
31_H78_W0.828221.917
5_P75_S0.772811.789
51_S54_E0.763721.768
23_M77_F0.743221.721
71_H75_S0.737861.708
3_E6_P0.713311.651
24_E28_D0.680641.576
10_A13_A0.6721.556
21_E24_E0.660731.530
12_D20_E0.657541.522
2_F42_L0.652461.510
11_Y24_E0.645491.494
8_P79_E0.640311.482
37_N67_N0.637061.475
21_E25_L0.614731.423
19_S22_T0.589781.365
38_L64_L0.580791.345
11_Y20_E0.574391.330
4_L27_H0.560751.298
44_K48_E0.555471.286
2_F38_L0.517971.199
11_Y27_H0.517871.199
62_A65_R0.503221.165
72_Y76_F0.502241.163
43_E48_E0.484661.122
59_A62_A0.47491.099
35_V39_N0.467831.083
52_L72_Y0.466921.081
50_K58_N0.464891.076
69_G73_N0.45991.065
33_G37_N0.437961.014
75_S79_E0.435791.009
47_L50_K0.407540.943
50_K54_E0.402750.932
32_Q35_V0.390610.904
65_R70_G0.388590.900
40_K44_K0.386180.894
34_Y70_G0.382410.885
54_E58_N0.382240.885
52_L56_I0.378790.877
25_L29_K0.378050.875
76_F79_E0.375930.870
26_H74_H0.375260.869
47_L51_S0.37330.864
42_L45_T0.362910.840
46_E50_K0.362410.839
76_F80_N0.360970.836
28_D32_Q0.351470.814
9_Y81_L0.348310.806
18_I81_L0.347460.804
65_R69_G0.333770.773
33_G36_N0.330350.765
18_I23_M0.330220.764
17_Y82_S0.321810.745
4_L31_H0.319520.740
12_D15_E0.317550.735
15_E20_E0.313350.725
30_H34_Y0.311730.722
41_A64_L0.308640.715
42_L55_I0.308570.714
26_H30_H0.307130.711
54_E57_S0.305870.708
41_A63_A0.305780.708
71_H78_W0.303480.703
2_F55_I0.301490.698
45_T48_E0.299670.694
53_E56_I0.298190.690
31_H75_S0.291090.674
45_T60_L0.288960.669
29_K32_Q0.286440.663
31_H71_H0.286150.662
7_L27_H0.285440.661
31_H34_Y0.284830.659
2_F49_G0.282280.653
29_K34_Y0.281280.651
71_H77_F0.277130.642
29_K69_G0.274670.636
5_P31_H0.271980.630
25_L28_D0.27160.629
52_L55_I0.271560.629
9_Y23_M0.270510.626
63_A68_A0.268920.623
19_S25_L0.267650.620
11_Y23_M0.267470.619
27_H32_Q0.262990.609
23_M73_N0.259620.601
38_L42_L0.259130.600
37_N63_A0.257830.597
4_L32_Q0.252850.585
19_S23_M0.251470.582
60_L80_N0.251250.582
26_H34_Y0.250950.581
22_T77_F0.245290.568
53_E57_S0.244980.567
9_Y14_L0.240250.556
69_G76_F0.240070.556
47_L61_R0.239460.554
2_F72_Y0.237880.551
49_G54_E0.237850.551
6_P10_A0.234770.544
18_I22_T0.234070.542
52_L66_N0.232680.539
57_S61_R0.231690.536
2_F52_L0.228280.528
23_M27_H0.228230.528
49_G57_S0.227950.528
41_A67_N0.226250.524
65_R68_A0.225450.522
45_T57_S0.225060.521
26_H78_W0.221190.512
42_L46_E0.22030.510
51_S58_N0.21690.502
44_K47_L0.216550.501
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
3kkyA199.9-0.036
1ix9A199.9-0.026
3lioA0.987899.9-0.025
4f6eA199.9-0.024
3tjtA199.9-0.021
4k2wA0.987899.9-0.02
3ceiA0.987899.9-0.018
3h1sA0.987899.9-0.017
3tqjA0.987899.9-0.017
4h3eA0.987899.9-0.016

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