GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Rhodanese - Rhodanese-like domain
Pfam: PF00581 (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: 113
Sequences: 14084
Seq/Len: 124.64
HH_delta: 0.134 (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
25_Y29_H2.657433.447
69_D101_Y2.094712.717
25_Y35_N1.612292.091
22_P26_E1.587172.059
4_E8_M1.496241.941
15_L68_K1.465181.900
69_D99_N1.463541.898
29_H73_Y1.457671.891
5_L71_V1.376191.785
73_Y107_F1.319641.712
2_P109_A1.314841.705
72_F92_L1.276791.656
24_E79_R1.247871.618
28_G111_K1.21761.579
8_M69_D1.214081.575
71_V103_L1.198351.554
22_P35_N1.175971.525
105_G109_A1.153351.496
15_L34_V1.149731.491
21_S39_P1.144041.484
5_L103_L1.100651.428
75_S108_E1.097871.424
86_A95_L1.077991.398
80_S102_I1.075821.395
65_D68_K1.07331.392
16_L73_Y1.064131.380
5_L16_L1.016841.319
15_L70_I0.988481.282
2_P103_L0.947251.229
66_K97_F0.901611.169
30_I73_Y0.885061.148
21_S24_E0.884611.147
4_E7_E0.881971.144
75_S78_W0.881211.143
14_V71_V0.88091.142
76_S79_R0.877641.138
74_C77_G0.872771.132
33_A73_Y0.865851.123
17_I72_F0.858821.114
30_I110_W0.858011.113
84_A100_V0.852421.106
24_E75_S0.851161.104
85_A94_K0.82961.076
19_V83_A0.823281.068
103_L109_A0.819541.063
74_C79_R0.815221.057
28_G107_F0.797951.035
37_P40_S0.794531.030
78_W82_S0.792971.028
77_G102_I0.765460.993
103_L110_W0.764710.992
76_S108_E0.747890.970
14_V69_D0.742130.963
3_E7_E0.739840.960
8_M14_V0.727430.943
5_L9_L0.721320.936
8_M11_N0.712590.924
38_F83_A0.712150.924
2_P6_K0.708150.918
107_F111_K0.702780.911
73_Y103_L0.701040.909
19_V72_F0.696730.904
15_L65_D0.696680.904
6_K10_E0.681210.884
92_L96_G0.675290.876
6_K9_L0.668740.867
29_H35_N0.666350.864
21_S79_R0.65730.852
8_M71_V0.657060.852
108_E112_A0.656720.852
20_R107_F0.6480.840
74_C80_S0.64760.840
81_G102_I0.647020.839
64_I70_I0.642110.833
5_L14_V0.64160.832
77_G80_S0.634210.823
84_A102_I0.63120.819
23_E27_R0.630260.817
7_E10_E0.628990.816
72_F100_V0.626490.813
16_L71_V0.616510.800
23_E26_E0.60460.784
38_F82_S0.593760.770
25_Y33_A0.592050.768
16_L33_A0.580050.752
57_L60_L0.57490.746
22_P37_P0.571960.742
8_M101_Y0.563350.731
31_P110_W0.560010.726
80_S83_A0.559310.725
81_G85_A0.556660.722
2_P105_G0.553690.718
29_H33_A0.545120.707
61_G65_D0.539290.699
82_S85_A0.536660.696
8_M12_E0.535710.695
60_L64_I0.53470.693
36_I60_L0.532830.691
93_K100_V0.52490.681
77_G81_G0.520840.676
78_W81_G0.514410.667
20_R28_G0.513820.666
9_L16_L0.509950.661
13_S68_K0.507640.658
27_R75_S0.50540.655
93_K98_K0.497010.645
109_A112_A0.49640.644
20_R24_E0.494920.642
64_I67_D0.493290.640
26_E35_N0.489140.634
108_E111_K0.486120.630
57_L61_G0.484030.628
17_I36_I0.479040.621
20_R79_R0.478450.621
92_L97_F0.476270.618
58_K61_G0.472390.613
16_L30_I0.468780.608
65_D70_I0.465390.604
61_G66_K0.458660.595
5_L110_W0.458210.594
5_L30_I0.45520.590
30_I33_A0.451670.586
61_G95_L0.449060.582
6_K110_W0.44860.582
72_F84_A0.443990.576
106_G109_A0.442130.573
82_S86_A0.437180.567
83_A86_A0.436230.566
25_Y73_Y0.427880.555
67_D96_G0.425250.552
11_N14_V0.42340.549
21_S37_P0.421220.546
84_A93_K0.420890.546
7_E11_N0.420020.545
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
4f67A0.867399.70.134
1e0cA0.938199.70.136
3d1pA0.929299.70.137
3hzuA0.938199.70.142
1urhA0.938199.70.144
3olhA0.938199.70.144
1t3kA0.893899.70.144
1urhA0.938199.70.146
1e0cA0.938199.70.146
4jgtA0.938199.70.148

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