GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Sod_Fe_C - Ironmanganese superoxide dismutases C-terminal domain
Pfam: PF02777 (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: 106
Sequences: 2263
Seq/Len: 21.35
HH_delta: -0.052 (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
85_K88_D1.391513.071
20_N23_A1.189082.625
101_V104_K1.153492.546
101_V105_R1.138962.514
8_K12_E1.075172.373
7_L103_E1.065892.353
71_I90_V1.029842.273
43_D50_S1.029332.272
23_A27_A0.958492.116
29_A38_V0.927382.047
9_K12_E0.913412.016
29_A71_I0.887461.959
20_N24_E0.87381.929
10_A106_Y0.857161.892
14_D48_K0.847761.871
10_A13_E0.828881.830
41_V52_I0.828371.828
80_L83_G0.800221.766
32_V53_S0.78891.741
27_A31_S0.788661.741
88_D91_E0.763311.685
26_T91_E0.761981.682
69_L102_V0.72941.610
43_D46_D0.710821.569
71_I93_F0.680881.503
43_D65_L0.672361.484
26_T30_L0.647211.429
100_E103_E0.643731.421
39_W54_T0.642991.419
24_E27_A0.636531.405
29_A90_V0.631621.394
2_K19_D0.604181.334
21_F25_F0.600431.325
41_V50_S0.599291.323
30_L90_V0.588451.299
19_D22_K0.585321.292
9_K13_E0.57011.258
17_S20_N0.56631.250
30_L87_A0.557891.231
26_T90_V0.552541.220
93_F97_I0.548341.210
25_F71_I0.547121.208
10_A14_D0.535561.182
6_K9_K0.52671.163
73_V86_R0.525251.159
82_Y92_A0.518891.145
32_V38_V0.50791.121
26_T94_W0.499061.102
2_K12_E0.497681.099
78_Y86_R0.495561.094
50_S65_L0.490461.083
18_F21_F0.485131.071
42_Y106_Y0.483351.067
57_H70_C0.477011.053
98_N101_V0.471971.042
28_A51_I0.461381.018
69_L97_I0.458791.013
4_S103_E0.454321.003
41_V65_L0.452140.998
6_K103_E0.451860.997
22_K95_N0.448620.990
94_W97_I0.447920.989
21_F51_I0.447810.988
7_L11_I0.445170.983
38_V53_S0.444390.981
25_F93_F0.434550.959
97_I102_V0.430330.950
2_K8_K0.428990.947
28_A53_S0.425410.939
42_Y47_G0.419940.927
36_G73_V0.417180.921
3_P8_K0.415290.917
15_F24_E0.409740.904
5_G9_K0.409590.904
92_A95_N0.402090.888
79_Y84_N0.38840.857
23_A91_E0.387440.855
28_A38_V0.384310.848
100_E104_K0.378790.836
12_E17_S0.376280.831
52_I65_L0.37150.820
39_W70_C0.370510.818
32_V55_P0.364620.805
7_L102_V0.354590.783
7_L106_Y0.351780.776
22_K26_T0.347680.767
68_L102_V0.343960.759
19_D23_A0.337470.745
72_D75_E0.331660.732
61_I67_P0.323590.714
35_S56_N0.321570.710
99_W102_V0.317240.700
4_S100_E0.314990.695
70_C89_Y0.314730.695
72_D76_H0.311530.688
18_F22_K0.31080.686
2_K22_K0.309380.683
57_H81_D0.307260.678
14_D49_L0.305670.675
24_E51_I0.303050.669
11_I21_F0.301470.665
15_F49_L0.299450.661
10_A42_Y0.298490.659
62_I65_L0.297040.656
24_E28_A0.296780.655
3_P18_F0.295580.652
32_V51_I0.292040.645
42_Y68_L0.29040.641
4_S18_F0.289920.640
8_K18_F0.289050.638
81_D96_V0.285910.631
11_I18_F0.283770.626
55_P58_D0.282430.623
39_W57_H0.27470.606
14_D50_S0.270170.596
28_A32_V0.266840.589
74_W79_Y0.26550.586
1_G8_K0.263370.581
1_G103_E0.262680.580
90_V94_W0.261790.578
27_A30_L0.261420.577
42_Y66_I0.25620.566
25_F38_V0.255530.564
88_D92_A0.253340.559
43_D47_G0.253250.559
5_G18_F0.250260.552
32_V86_R0.24870.549
59_T62_I0.248620.549
4_S7_L0.246160.543
22_K94_W0.2450.541
18_F94_W0.242610.536
85_K91_E0.242140.534
29_A73_V0.241170.532
4_S8_K0.240380.531
6_K106_Y0.238290.526
38_V71_I0.236680.522
33_F60_P0.236570.522
91_E95_N0.23620.521
1_G95_N0.235890.521
5_G103_E0.234230.517
39_W60_P0.234070.517
57_H62_I0.23330.515
52_I63_W0.232030.512
78_Y99_W0.230940.510
52_I62_I0.230350.508
35_S79_Y0.228590.505
68_L101_V0.228490.504
54_T89_Y0.227970.503
58_D62_I0.225170.497
43_D48_K0.224730.496
72_D79_Y0.223770.494
76_H79_Y0.22180.490
32_V78_Y0.221350.489
17_S24_E0.220140.486
58_D63_W0.217690.480
41_V67_P0.217210.479
55_P70_C0.215850.476
34_G74_W0.21490.474
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
4ffkA1100-0.052
3js4A1100-0.047
3tqjA0.9906100-0.046
2cw3A1100-0.046
1ma1A1100-0.044
3ak2A1100-0.044
1b06A1100-0.043
1gv3A0.9906100-0.043
1bsmA1100-0.042
1idsA1100-0.041

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