GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ferritin_2 - Ferritin-like domain
Pfam: PF13668 (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: 137
Sequences: 5885
Seq/Len: 42.96
HH_delta: 0.271 (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
82_D85_S1.298223.269
84_A88_R0.910642.293
10_L62_L0.80312.022
51_E54_H0.789471.988
57_F119_S0.726021.828
40_V83_D0.719941.813
49_D52_Q0.676511.703
12_L100_A0.661541.666
99_S103_G0.652051.642
24_A48_A0.628231.582
88_R92_T0.627281.579
62_L65_G0.617761.555
105_A121_A0.616281.552
61_A116_L0.613291.544
13_E54_H0.606491.527
61_A113_L0.599831.510
124_E127_H0.596691.502
105_A118_A0.588951.483
20_Y94_E0.577941.455
91_Y128_A0.557631.404
17_A52_Q0.546631.376
98_V102_K0.546011.375
58_L120_I0.540171.360
89_L92_T0.533931.344
115_A119_S0.532331.340
5_I107_Q0.527131.327
96_V100_A0.525471.323
11_N15_L0.521251.312
91_Y95_D0.519741.309
9_A101_Y0.5191.307
92_T95_D0.515691.298
42_D46_E0.506321.275
109_E118_A0.503441.268
85_S88_R0.501441.262
56_D60_A0.500431.260
21_Q48_A0.49771.253
6_L58_L0.495521.248
81_T85_S0.493871.243
102_K121_A0.489311.232
52_Q56_D0.486771.226
5_I104_A0.482381.214
7_N65_G0.480661.210
103_G107_Q0.479221.207
109_E114_K0.478391.204
53_G57_F0.477111.201
17_A48_A0.476621.200
9_A100_A0.466521.175
103_G106_P0.465781.173
114_K118_A0.46511.171
24_A45_Q0.44611.123
10_L55_V0.444641.119
95_D128_A0.439551.107
110_D113_L0.439271.106
94_E127_H0.437041.100
96_V99_S0.432151.088
44_F90_A0.431831.087
21_Q52_Q0.43171.087
57_F116_L0.430851.085
6_L62_L0.427191.076
98_V128_A0.42711.075
51_E127_H0.426821.075
51_E124_E0.426531.074
54_H124_E0.419861.057
54_H127_H0.41831.053
115_A118_A0.417221.050
45_Q49_D0.411071.035
43_L130_W0.407881.027
14_Y55_V0.405221.020
9_A117_A0.404421.018
118_A122_G0.402921.014
17_A21_Q0.402131.012
13_E51_E0.39991.007
42_D45_Q0.393720.991
7_N62_L0.393080.990
91_Y131_I0.391480.986
102_K106_P0.382270.962
64_G67_P0.382260.962
119_S122_G0.381990.962
58_L116_L0.381610.961
8_F100_A0.378420.953
35_A83_D0.377220.950
105_A117_A0.376510.948
57_F61_A0.374450.943
123_V126_R0.374230.942
125_A129_A0.37340.940
101_Y124_E0.370160.932
9_A58_L0.369740.931
9_A104_A0.360690.908
21_Q45_Q0.358420.902
6_L61_A0.356240.897
122_G125_A0.356190.897
8_F103_G0.348840.878
23_A89_L0.344470.867
16_E19_F0.341890.861
115_A122_G0.341040.859
10_L14_Y0.340970.858
106_P109_E0.340090.856
13_E124_E0.339870.856
98_V121_A0.338830.853
56_D59_Q0.335860.846
22_Q25_E0.333720.840
43_L47_I0.331030.833
41_R45_Q0.330430.832
48_A52_Q0.330040.831
47_I130_W0.328580.827
78_D92_T0.32690.823
18_D22_Q0.325950.821
116_L120_I0.324170.816
25_E45_Q0.323480.814
23_A90_A0.318060.801
43_L46_E0.316030.796
111_P114_K0.315890.795
12_L16_E0.315350.794
98_V125_A0.312770.787
25_E59_Q0.312170.786
38_P41_R0.311160.783
44_F86_F0.311130.783
85_S89_L0.310530.782
50_Q123_V0.308290.776
15_L19_F0.307760.775
54_H94_E0.307390.774
95_D99_S0.305740.770
104_A117_A0.30280.762
90_A131_I0.302720.762
14_Y18_D0.300720.757
58_L117_A0.299750.755
95_D98_V0.299440.754
60_A63_E0.294320.741
111_P115_A0.293120.738
38_P42_D0.292780.737
87_L131_I0.285620.719
21_Q49_D0.283570.714
47_I90_A0.283560.714
83_D86_F0.282780.712
50_Q53_G0.281960.710
20_Y127_H0.27890.702
93_L101_Y0.277220.698
50_Q54_H0.268920.677
12_L93_L0.268050.675
7_N11_N0.267280.673
16_E51_E0.260710.656
18_D21_Q0.260610.656
118_A121_A0.257390.648
21_Q24_A0.257140.647
23_A86_F0.256730.646
92_T96_V0.255430.643
24_A41_R0.255210.643
106_P111_P0.254450.641
121_A125_A0.254060.640
122_G126_R0.253250.638
97_G124_E0.253050.637
101_Y104_A0.251330.633
120_I123_V0.251240.633
97_G123_V0.250410.630
46_E53_G0.250290.630
5_I103_G0.249340.628
13_E94_E0.246550.621
69_P73_Y0.24610.620
25_E56_D0.244990.617
97_G101_Y0.244580.616
37_D40_V0.24420.615
108_I113_L0.244050.614
59_Q63_E0.242950.612
100_A103_G0.242930.612
57_F123_V0.241760.609
100_A104_A0.241430.608
23_A80_F0.239750.604
47_I131_I0.239580.603
12_L96_V0.238350.600
21_Q25_E0.235870.594
13_E16_E0.235110.592
5_I8_F0.234890.591
93_L96_V0.234460.590
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
2oh3A0.963599.50.271
2fzfA0.941699.50.29
1vjxA0.934399.40.318
4am5A0.948999.40.338
3unoA0.956299.40.341
1eumA0.956299.30.347
1krqA0.956299.30.35
1s3qA0.956299.30.354
1lkoA0.948999.30.357
1nfvA0.948999.30.362

Page generated in 0.0172 seconds.