GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF2427 - Domain of unknown function (DUF2427)
Pfam: PF10348 (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: CL0328
Length: 105
Sequences: 1147
Seq/Len: 10.92
HH_delta: 0.897 (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_M61_G0.459552.643
83_K87_I0.423722.437
86_W90_V0.394342.268
24_L57_L0.360592.074
81_H85_G0.347051.996
18_L22_I0.346071.990
63_F67_V0.34061.959
55_L93_I0.315571.815
62_L89_F0.271911.564
92_M99_G0.26751.538
36_G50_V0.266641.533
36_G51_Q0.266411.532
28_A54_F0.244551.406
33_Y51_Q0.244011.403
65_G68_Y0.242611.395
25_M89_F0.240591.384
23_V27_L0.238481.371
30_V34_P0.220391.267
29_W92_M0.220331.267
29_W58_M0.214281.232
47_H99_G0.212791.224
25_M38_V0.21231.221
56_V60_L0.193741.114
38_V97_I0.190291.094
26_T31_I0.189291.089
62_L66_S0.188721.085
39_L50_V0.188681.085
46_W51_Q0.18621.071
17_A67_V0.186041.070
20_A24_L0.185021.064
52_T87_I0.184171.059
33_Y54_F0.180071.036
72_T75_L0.178851.029
32_L54_F0.178691.028
79_N82_G0.174641.004
75_L86_W0.173580.998
27_L32_L0.170930.983
24_L60_L0.170410.980
59_I90_V0.17040.980
59_I93_I0.170280.979
74_D80_A0.170250.979
40_G46_W0.170220.979
69_N82_G0.169670.976
66_S86_W0.168840.971
33_Y92_M0.16720.962
59_I89_F0.1660.955
81_H99_G0.164830.948
18_L65_G0.164410.945
42_A46_W0.163920.943
47_H81_H0.163740.942
53_V56_V0.163220.939
34_P54_F0.161640.930
44_S57_L0.160780.925
91_L97_I0.160570.923
37_L48_L0.160480.923
38_V51_Q0.15980.919
31_I89_F0.159190.915
60_L91_L0.158570.912
51_Q65_G0.158460.911
24_L54_F0.157620.906
17_A31_I0.157350.905
28_A32_L0.156660.901
52_T93_I0.154570.889
95_Q99_G0.15390.885
33_Y58_M0.153270.881
30_V68_Y0.15160.872
19_Y23_V0.151230.870
25_M88_L0.149610.860
49_P53_V0.149280.858
70_G74_D0.149060.857
80_A84_M0.149030.857
17_A24_L0.148640.855
64_L68_Y0.147260.847
22_I68_Y0.146060.840
58_M89_F0.145930.839
61_G71_S0.145630.837
25_M62_L0.145530.837
50_V97_I0.143510.825
34_P65_G0.142640.820
47_H54_F0.141580.814
55_L96_V0.141420.813
48_L94_V0.140840.810
23_V64_L0.140580.808
79_N83_K0.140480.808
18_L68_Y0.139540.802
57_L87_I0.139460.802
63_F66_S0.139140.800
71_S87_I0.138390.796
26_T75_L0.13650.785
47_H95_Q0.135930.782
49_P87_I0.135880.781
39_L53_V0.135440.779
78_N83_K0.134910.776
80_A83_K0.133280.766
22_I79_N0.133050.765
35_I56_V0.1330.765
29_W46_W0.132040.759
42_A69_N0.131860.758
53_V98_L0.131320.755
43_R50_V0.130940.753
22_I65_G0.130190.749
29_W33_Y0.129890.747
98_L101_I0.129370.744
20_A37_L0.129260.743
16_S26_T0.128490.739
47_H50_V0.128490.739
97_I101_I0.12810.737
79_N86_W0.127780.735
37_L44_S0.127590.734
25_M85_G0.127340.732
69_N78_N0.127150.731
45_R56_V0.12710.731
22_I69_N0.125450.721
36_G40_G0.124780.718
60_L78_N0.124640.717
31_I39_L0.124420.716
32_L74_D0.124310.715
48_L99_G0.124230.714
28_A58_M0.124040.713
26_T50_V0.123960.713
23_V26_T0.12350.710
52_T79_N0.122930.707
20_A60_L0.122680.706
64_L67_V0.122290.703
80_A96_V0.122190.703
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
3u7dB0.161918.90.897
4gd3A0.752418.90.897
1fftA116.80.9
1kqfC0.676212.20.905
3mk7A0.96199.90.909
3ne5A0.90489.40.909
4dx5A0.94298.80.91
2v50A0.94298.60.911
2yevA0.9815.90.917
3w9iA0.94295.30.919
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