GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CarD_CdnL_TRCF - CarD-likeTRCF domain
Pfam: PF02559 (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: 98
Sequences: 1753
Seq/Len: 17.89
HH_delta: 0.25 (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
19_E37_E0.806354.073
22_E35_V0.716783.621
16_G36_L0.680363.437
31_Q49_D0.592512.993
23_E30_K0.565432.856
25_E30_K0.547532.766
37_E41_D0.514022.597
35_V43_T0.507942.566
68_D78_R0.419572.119
16_G38_Y0.383591.938
7_Y17_R0.372641.882
62_E65_P0.368421.861
25_E28_G0.354371.790
23_E32_E0.334481.690
78_R82_L0.334161.688
40_D69_K0.292781.479
12_N53_K0.284171.435
11_P55_G0.277251.401
82_L86_D0.26671.347
76_K80_R0.266241.345
24_I45_Y0.264141.334
91_A95_K0.262441.326
92_E95_K0.262321.325
66_L91_A0.258721.307
68_D74_E0.25781.302
35_V45_Y0.243281.229
56_R91_A0.241.212
60_S63_E0.220251.113
22_E45_Y0.219461.109
3_K6_D0.217571.099
87_I95_K0.214961.086
84_S87_I0.21221.072
80_R84_S0.210821.065
93_L97_L0.209131.056
92_E96_L0.202771.024
6_D56_R0.201331.017
36_L92_E0.198811.004
61_R64_A0.198451.002
35_V41_D0.197010.995
76_K95_K0.196920.995
17_R37_E0.193750.979
24_I27_G0.1910.965
34_Y51_A0.189270.956
67_L71_G0.184440.932
90_A98_A0.183670.928
4_I18_I0.183570.927
19_E43_T0.180910.914
33_Y47_P0.179950.909
19_E35_V0.179870.909
74_E82_L0.179790.908
59_G82_L0.179730.908
1_M56_R0.179570.907
72_S75_W0.17860.902
89_E92_E0.177470.896
45_Y59_G0.176320.891
14_G47_P0.175360.886
50_N53_K0.173520.877
81_K93_L0.17280.873
31_Q94_I0.170110.859
46_V54_I0.168920.853
7_Y64_A0.167760.847
55_G85_G0.16720.845
71_G98_A0.166960.843
88_E91_A0.166470.841
57_Y67_L0.164160.829
50_N78_R0.163270.825
12_N50_N0.162060.819
82_L97_L0.161840.818
26_F83_K0.16160.816
2_F47_P0.161180.814
46_V50_N0.16070.812
52_D61_R0.160440.810
87_I97_L0.160230.809
2_F8_V0.159490.806
47_P58_V0.159470.806
38_Y90_A0.156910.793
13_H44_I0.156690.792
80_R83_K0.155070.783
8_V70_L0.15290.772
5_G17_R0.15240.770
73_I84_S0.152080.768
83_K95_K0.148610.751
20_G43_T0.147930.747
21_I33_Y0.14770.746
23_E31_Q0.147380.744
15_V57_Y0.147380.744
81_K92_E0.146480.740
38_Y93_L0.146440.740
1_M86_D0.146310.739
49_D65_P0.145760.736
10_H97_L0.145530.735
64_A95_K0.145230.734
60_S95_K0.142780.721
24_I33_Y0.140620.710
13_H45_Y0.13880.701
69_K72_S0.137270.693
2_F43_T0.137120.693
19_E94_I0.137070.692
62_E70_L0.136750.691
17_R52_D0.136750.691
10_H18_I0.134580.680
60_S67_L0.134580.680
12_N79_K0.134370.679
9_V75_W0.134140.678
84_S88_E0.134070.677
40_D53_K0.133710.675
26_F29_E0.133340.674
5_G19_E0.132970.672
38_Y71_G0.132470.669
85_G95_K0.132030.667
15_V42_D0.131540.664
73_I77_K0.13140.664
34_Y54_I0.130760.661
1_M77_K0.130730.660
38_Y57_Y0.129950.656
26_F64_A0.129870.656
82_L96_L0.129810.656
19_E22_E0.129520.654
86_D89_E0.129040.652
6_D32_E0.128780.651
50_N55_G0.128760.650
56_R87_I0.128750.650
69_K81_K0.128740.650
32_E48_V0.128710.650
75_W82_L0.128530.649
54_I57_Y0.128260.648
12_N46_V0.127740.645
88_E94_I0.127630.645
46_V75_W0.127440.644
1_M63_E0.127240.643
15_V28_G0.127150.642
41_D64_A0.126780.640
11_P86_D0.1260.636
77_K92_E0.125670.635
6_D39_A0.12530.633
33_Y74_E0.124790.630
30_K61_R0.124530.629
1_M88_E0.124440.629
80_R85_G0.12420.627
25_E66_L0.124160.627
32_E71_G0.124110.627
6_D95_K0.124020.626
52_D60_S0.123950.626
77_K80_R0.123420.623
65_P71_G0.123160.622
78_R85_G0.123110.622
4_I63_E0.123010.621
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
2eyqA199.80.25
3mlqE0.714399.70.297
2lqkA0.642999.70.346
3dmqA0.908295.70.794
2ocaA0.653194.10.813
1pjrA0.510292.70.823
1g31A0.438862.20.872
1vbvA0.826543.70.885
4hw9A0.806138.40.889
2vv5A0.806133.20.892

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