GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RnfC_N - RnfC Barrel sandwich hybrid domain
Pfam: PF13375 (v26) Consensus Sequence
Clan: CL0105
Length: 101
Sequences: 782
Seq/Len: 7.74
HH_delta: 0.676 (11Mar13)
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
78_T97_E0.6642.990
51_R76_T0.609062.742
73_V98_N0.60072.705
32_I72_S0.580092.612
45_V57_L0.512822.309
50_D56_Q0.487892.197
76_T97_E0.404441.821
29_K97_E0.391051.761
28_K97_E0.384521.731
82_D92_P0.380561.713
57_L60_E0.373071.680
47_K50_D0.351671.583
48_V79_A0.349661.574
42_A59_A0.340231.532
54_K74_S0.339031.527
31_V93_A0.332551.497
29_K78_T0.331841.494
30_V73_V0.312741.408
32_I58_I0.30771.385
51_R99_D0.303771.368
32_I69_I0.299481.348
43_E60_E0.293711.322
81_E95_V0.291191.311
83_F93_A0.290851.310
57_L68_P0.281941.269
30_V72_S0.276071.243
38_I65_L0.26851.209
27_P30_V0.258791.165
74_S99_D0.258071.162
54_K73_V0.257141.158
59_A94_I0.250991.130
45_V60_E0.233141.050
61_A66_S0.229671.034
44_P59_A0.229651.034
83_F95_V0.225131.014
32_I96_I0.224281.010
77_V94_I0.22271.003
88_G91_V0.22130.996
91_V94_I0.218320.983
79_A95_V0.215660.971
40_A62_E0.215550.971
37_H41_P0.214110.964
30_V98_N0.211260.951
26_L98_N0.210860.949
42_A68_P0.208540.939
34_L59_A0.204370.920
30_V96_I0.200870.904
28_K100_G0.200590.903
77_V96_I0.200150.901
40_A66_S0.198890.896
63_G66_S0.194890.878
54_K71_A0.194570.876
33_P36_Q0.193170.870
74_S78_T0.192380.866
83_F89_S0.190540.858
44_P58_I0.187850.846
53_K76_T0.184320.830
60_E68_P0.182590.822
74_S100_G0.180960.815
79_A83_F0.179870.810
59_A67_A0.179530.808
81_E93_A0.179010.806
48_V51_R0.178540.804
58_I96_I0.178430.803
53_K56_Q0.178320.803
40_A63_G0.177630.800
44_P94_I0.174990.788
74_S98_N0.172760.778
34_L44_P0.172490.777
36_Q39_G0.169150.762
33_P93_A0.166630.750
62_E82_D0.163780.737
44_P67_A0.162710.733
35_R91_V0.162060.730
59_A80_I0.160170.721
53_K99_D0.160050.721
31_V83_F0.160020.721
31_V95_V0.157980.711
24_L27_P0.157970.711
58_I68_P0.157820.711
71_A96_I0.155880.702
46_V77_V0.154430.695
84_P90_G0.153770.692
42_A67_A0.153080.689
34_L42_A0.15230.686
41_P64_F0.149310.672
29_K83_F0.147960.666
42_A61_A0.147840.666
46_V71_A0.145560.655
43_E48_V0.144980.653
43_E62_E0.144090.649
73_V96_I0.143850.648
48_V80_I0.142210.640
22_E92_P0.141740.638
28_K48_V0.141370.637
36_Q41_P0.141130.635
61_A67_A0.140070.631
21_I34_L0.139890.630
57_L67_A0.139380.628
25_P28_K0.138930.626
58_I72_S0.13880.625
42_A58_I0.136910.616
64_F67_A0.136730.616
71_A90_G0.136330.614
79_A82_D0.135040.608
60_E63_G0.134160.604
51_R71_A0.133230.600
77_V91_V0.133180.600
31_V84_P0.13120.591
34_L94_I0.130960.590
30_V71_A0.130530.588
32_I59_A0.129740.584
32_I70_H0.129670.584
54_K100_G0.129540.583
29_K95_V0.129460.583
28_K78_T0.129450.583
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
3dvaI0.782298.30.676
3hblA0.970398.20.69
1zy8K0.772398.10.693
3u9tA0.970398.10.697
3va7A0.940698.10.7
1y8oB0.9406980.704
2dncA0.8119980.705
2dneA0.8119980.708
3crkC0.7921980.709
1ghjA0.762497.90.717
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