GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ferritin - Ferritin-like domain
Pfam: PF00210 (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: CL0044
Length: 142
Sequences: 7026
Seq/Len: 49.48
HH_delta: 0.099 (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
80_D83_E1.217652.890
107_E115_A0.912152.165
82_R86_E0.8772.081
50_E120_E0.796051.889
8_L55_I0.750111.780
54_R114_T0.721131.711
86_E90_E0.696431.653
107_E119_D0.683921.623
82_R136_L0.663051.574
42_E45_R0.659451.565
103_I119_D0.64761.537
3_A105_L0.647561.537
103_I122_L0.642361.524
97_E101_E0.632791.502
111_D114_T0.632281.501
15_S45_R0.630891.497
10_L98_E0.630351.496
33_L81_P0.624711.483
96_I100_R0.623261.479
25_F84_A0.620511.473
116_D120_E0.610571.449
18_Y92_E0.610561.449
100_R122_L0.598651.421
55_I60_G0.595321.413
130_W134_A0.594021.410
54_R117_F0.587461.394
21_M87_A0.585891.390
11_E47_H0.58031.377
89_L129_I0.577881.371
3_A102_L0.566141.344
18_Y44_E0.56181.333
116_D119_D0.559891.329
107_E112_P0.558911.326
89_L133_Q0.552041.310
89_L93_K0.543761.290
35_K39_D0.533991.267
125_E128_H0.531191.261
44_E47_H0.522881.241
101_E104_K0.521791.238
86_E136_L0.516891.227
90_E93_K0.513651.219
22_H41_A0.509641.209
93_K129_I0.503771.196
12_L48_A0.500561.188
87_A90_E0.50051.188
7_Q99_Y0.50021.187
31_P35_K0.497481.181
9_A13_Q0.489661.162
38_Q42_E0.486011.153
7_Q98_E0.484891.151
115_A119_D0.483241.147
22_H38_Q0.481671.143
44_E128_H0.475991.130
7_Q118_L0.47461.126
83_E86_E0.473271.123
4_L51_L0.471921.120
49_D53_E0.471561.119
67_V71_E0.466871.108
47_H128_H0.464151.102
96_I122_L0.460711.093
112_P115_A0.460421.093
51_L121_F0.459131.090
133_Q137_T0.458651.088
5_N60_G0.45581.082
96_I129_I0.452561.074
94_E98_E0.448261.064
6_E98_E0.443021.051
8_L48_A0.44251.050
5_N55_I0.436481.036
36_F39_D0.435711.034
85_L132_L0.434581.031
43_E47_H0.432361.026
17_Q91_D0.431541.024
19_L45_R0.431121.023
26_D38_Q0.430971.023
101_E105_L0.429491.019
100_R104_K0.428881.018
83_E87_A0.426321.012
50_E117_F0.422681.003
15_S41_A0.421261.000
46_E50_E0.416130.988
104_K110_G0.412350.979
23_W52_A0.409870.973
11_E125_E0.405940.963
19_L41_A0.404720.960
7_Q102_L0.403590.958
93_K97_E0.403260.957
11_E128_H0.403180.957
92_E128_H0.401780.953
11_E44_E0.3990.947
79_T83_E0.397630.944
26_D31_P0.395060.938
94_E97_E0.395010.937
92_E125_E0.393380.934
21_M84_A0.391270.929
7_Q51_L0.391160.928
102_L118_L0.390980.928
93_K133_Q0.388420.922
96_I126_E0.387780.920
40_Q131_M0.386320.917
43_E128_H0.386160.916
47_H92_E0.385390.915
54_R58_L0.384780.913
45_R49_D0.382140.907
124_E127_K0.381510.905
103_I118_L0.379980.902
106_A115_A0.379820.901
47_H125_E0.376570.894
37_F88_A0.376130.893
88_A132_L0.374820.890
36_F131_M0.371110.881
25_F81_P0.368380.874
37_F84_A0.367510.872
99_Y125_E0.367410.872
36_F40_Q0.361470.858
116_D123_E0.351810.835
41_A45_R0.351380.834
49_D52_A0.349970.831
11_E92_E0.343650.816
25_F37_F0.342360.812
129_I133_Q0.341070.809
44_E92_E0.338970.804
3_A6_E0.335880.797
42_E46_E0.335270.796
4_L55_I0.334940.795
51_L117_F0.333820.792
89_L132_L0.332540.789
126_E130_W0.331920.788
21_M88_A0.331610.787
19_L38_Q0.329820.783
12_L16_Q0.327620.778
22_H34_A0.327240.777
120_E123_E0.327230.777
112_P116_D0.326950.776
24_N28_P0.326240.774
28_P81_P0.325940.774
122_L126_E0.325910.773
35_K38_Q0.324060.769
47_H124_E0.323770.768
4_L114_T0.322080.764
6_E101_E0.320620.761
34_A38_Q0.319790.759
53_E56_L0.318920.757
50_E54_R0.317630.754
8_L12_L0.317310.753
110_G115_A0.316910.752
14_A44_E0.314820.747
119_D123_E0.31290.743
23_W49_D0.309250.734
39_D131_M0.309240.734
35_K46_E0.308830.733
55_I59_G0.308470.732
107_E110_G0.306110.726
11_E18_Y0.303950.721
40_Q92_E0.30390.721
15_S19_L0.303070.719
104_K112_P0.300290.713
50_E121_F0.299250.710
119_D122_L0.296470.704
85_L135_H0.295790.702
15_S48_A0.295190.701
54_R57_M0.294380.699
55_I58_L0.294190.698
47_H121_F0.292960.695
54_R111_D0.29280.695
70_P74_K0.292620.694
11_E99_Y0.291410.692
117_F121_F0.291330.691
36_F135_H0.29110.691
40_Q44_E0.290440.689
103_I115_A0.288220.684
106_A114_T0.286520.680
43_E46_E0.286320.679
51_L118_L0.28380.674
23_W38_Q0.282590.671
57_M113_E0.28190.669
17_Q87_A0.281070.667
38_Q41_A0.281060.667
134_A137_T0.280420.665
11_E14_A0.279990.664
26_D34_A0.278850.662
4_L54_R0.274910.652
81_P84_A0.272850.648
89_L136_L0.272750.647
99_Y118_L0.270860.643
59_G62_P0.267440.635
32_G35_K0.267430.635
3_A101_E0.26640.632
121_F125_E0.264720.628
18_Y125_E0.260980.619
58_L111_D0.260810.619
98_E101_E0.257970.612
68_E71_E0.257770.612
84_A88_A0.257660.611
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
4am5A0.964899.80.099
3uoiA0.964899.80.113
3unoA0.971899.80.117
1s3qA0.971899.70.126
3qz3A0.964899.70.128
2y3qA0.964899.70.129
3gvyA0.964899.70.129
1eumA0.971899.70.131
3a68A199.70.133
3r2kA0.957799.70.135

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