GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HemN_C - HemN C-terminal domain
Pfam: PF06969 (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: CL0123
Length: 66
Sequences: 2884
Seq/Len: 43.7
HH_delta: 0.053 (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
61_T64_G1.250563.169
2_S5_D0.947192.400
52_E59_R0.841672.133
23_L53_I0.79292.009
18_N65_R0.760081.926
9_E16_R0.724121.835
10_Y30_F0.672461.704
11_I21_I0.670241.698
22_D25_E0.592961.502
23_L57_R0.590381.496
20_G57_R0.585171.483
7_L26_F0.577171.462
20_G59_R0.569551.443
8_R12_M0.547191.386
24_S28_Q0.525851.332
54_D57_R0.508231.288
10_Y14_G0.501171.270
5_D8_R0.493771.251
9_E13_L0.489821.241
46_Q53_I0.475151.204
14_G18_N0.469841.190
10_Y29_R0.465611.180
39_Q43_E0.462871.173
54_D59_R0.455911.155
33_D36_E0.448731.137
43_E46_Q0.445311.128
48_D63_K0.43531.103
1_L6_R0.434141.100
13_L16_R0.426961.082
7_L37_E0.426351.080
43_E47_E0.417751.058
32_I37_E0.415331.052
32_I39_Q0.411541.043
16_R20_G0.409561.038
25_E29_R0.407951.034
1_L66_L0.404111.024
24_S56_G0.392130.994
44_E48_D0.391190.991
25_E28_Q0.383770.972
3_P6_R0.382460.969
23_L35_A0.376040.953
11_I26_F0.374480.949
27_E33_D0.373190.946
10_Y13_L0.361740.917
60_L65_R0.356430.903
4_E8_R0.352250.893
14_G21_I0.350510.888
15_L58_L0.349670.886
45_L50_L0.349360.885
52_E61_T0.347330.880
3_P7_L0.344960.874
12_M16_R0.338420.857
10_Y25_E0.329170.834
23_L58_L0.328810.833
1_L9_E0.326360.827
8_R13_L0.324880.823
9_E12_M0.322630.817
41_E44_E0.31830.806
10_Y26_F0.314680.797
35_A39_Q0.313260.794
50_L64_G0.30690.778
50_L63_K0.306360.776
14_G25_E0.305760.775
4_E37_E0.303390.769
12_M17_C0.302030.765
62_E66_L0.300180.761
19_E65_R0.29760.754
5_D15_L0.295750.749
33_D37_E0.292210.740
8_R11_I0.287170.728
42_L45_L0.287080.727
5_D17_C0.286640.726
22_D57_R0.285980.725
13_L17_C0.284040.720
9_E17_C0.282420.716
1_L5_D0.280140.710
6_R10_Y0.276230.700
14_G20_G0.27620.700
27_E34_F0.276150.700
44_E47_E0.275260.697
3_P30_F0.268360.680
9_E20_G0.267050.677
8_R17_C0.266850.676
42_L58_L0.264990.671
45_L51_L0.261550.663
27_E35_A0.260910.661
43_E53_I0.260280.659
16_R19_E0.24630.624
12_M60_L0.245540.622
12_M19_E0.237710.602
23_L34_F0.236050.598
12_M66_L0.232830.590
51_L58_L0.230820.585
48_D66_L0.229190.581
13_L60_L0.228940.580
41_E45_L0.227810.577
24_S43_E0.227430.576
46_Q51_L0.223280.566
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
1oltA1990.053
2o0mA0.969794.60.584
3hrsA0.969793.70.602
2p8tA0.924292.60.617
2h09A0.984891.80.625
2x4hA0.984891.50.629
1fx7A0.969790.80.634
1on2A0.984890.70.636
2fxaA0.939490.70.636
3nrvA0.939490.60.636

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