GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
FumaraseC_C - Fumarase C C-terminus
Pfam: PF10415 (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: 55
Sequences: 1706
Seq/Len: 31.02
HH_delta: 0.087 (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
39_T42_E1.583582.997
20_E24_E1.563592.959
20_E35_E1.364892.583
26_R34_E1.219022.307
29_R44_D1.188512.249
13_K16_E1.079192.042
42_E45_E1.007451.907
9_I14_A0.96771.831
20_E31_V0.960531.818
26_R31_V0.958351.814
13_K37_L0.904691.712
48_D51_R0.902151.707
24_E31_V0.90131.706
8_Y46_L0.869771.646
29_R40_E0.832121.575
40_E44_D0.816681.546
33_L40_E0.80171.517
16_E35_E0.783131.482
43_L47_L0.762141.442
20_E34_E0.716031.355
9_I13_K0.67461.277
8_Y42_E0.647111.225
5_L9_I0.631211.195
19_K23_A0.628581.190
27_S30_E0.62821.189
17_I32_V0.615551.165
32_V38_L0.541531.025
17_I31_V0.536941.016
30_E34_E0.504370.955
4_A7_P0.48370.915
26_R30_E0.480790.910
50_E53_T0.480130.909
6_N19_K0.465380.881
2_A18_A0.462670.876
24_E34_E0.459470.870
31_V35_E0.445740.844
12_E19_K0.443810.840
38_L46_L0.441380.835
28_V43_L0.427730.810
31_V34_E0.413630.783
20_E26_R0.409180.774
8_Y45_E0.384770.728
12_E15_A0.381930.723
32_V37_L0.379690.719
2_A14_A0.374590.709
1_L28_V0.374060.708
22_L25_G0.36440.690
13_K35_E0.361660.684
16_E23_A0.358460.678
38_L42_E0.355510.673
33_L39_T0.350080.663
16_E37_L0.349440.661
33_L43_L0.344060.651
28_V47_L0.34360.650
12_E16_E0.342320.648
11_Y18_A0.33960.643
18_A22_L0.324110.613
29_R33_L0.317180.600
11_Y15_A0.315120.596
42_E46_L0.314570.595
4_A49_P0.313280.593
14_A18_A0.312980.592
5_L32_V0.312660.592
5_L43_L0.304230.576
1_L47_L0.302580.573
2_A5_L0.290020.549
18_A28_V0.283030.536
16_E20_E0.281060.532
41_E45_E0.279840.530
1_L12_E0.269180.509
4_A32_V0.268310.508
4_A11_Y0.265860.503
49_P52_M0.2640.500
5_L10_G0.262170.496
6_N38_L0.258050.488
33_L44_D0.252660.478
4_A18_A0.243570.461
18_A25_G0.240040.454
17_I35_E0.239360.453
12_E52_M0.238460.451
25_G55_P0.23450.444
33_L36_G0.232190.439
19_K22_L0.228750.433
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
4hgvA199.30.087
3e04A199.30.107
3gtdA0.981899.20.129
3r6qA199.10.18
3ocfA0.927399.10.182
4admA199.10.199
1yfmA1990.214
1furA198.80.275
1vdkA198.80.278
1jswA198.70.297

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