GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cystatin - Cystatin domain
Pfam: PF00031 (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: CL0121
Length: 94
Sequences: 1083
Seq/Len: 11.52
HH_delta: 0.018 (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
38_K57_E0.436162.682
63_C73_C0.335172.061
13_V42_A0.31681.948
45_Q49_G0.316151.944
37_V59_G0.312971.925
23_K26_E0.29171.794
35_K61_T0.290991.790
44_T50_I0.284291.748
51_N88_T0.273881.684
56_F87_F0.26341.620
45_Q48_A0.244031.501
17_A54_I0.239231.471
47_V51_N0.239011.470
43_T53_Y0.238061.464
5_P41_S0.236811.456
59_G75_F0.233571.436
12_E16_A0.218981.347
24_F87_F0.218221.342
35_K75_F0.217391.337
21_L25_N0.205951.267
13_V16_A0.205371.263
61_T73_C0.2041.255
34_F58_V0.201811.241
60_E76_Q0.201741.241
62_N74_P0.201371.238
41_S55_E0.197281.213
16_A89_V0.188561.160
6_V13_V0.187831.155
48_A51_N0.187821.155
25_N33_K0.186981.150
37_V82_T0.18171.117
48_A90_W0.170661.050
15_E43_T0.168461.036
44_T52_Y0.168071.034
40_I84_F0.166361.023
85_C89_V0.165431.017
87_F90_W0.162090.997
24_F28_S0.161430.993
34_F42_A0.161280.992
61_T75_F0.160760.989
20_A87_F0.16070.988
36_L56_F0.160640.988
25_N34_F0.159450.981
46_V51_N0.158610.975
26_E33_K0.158450.974
8_P11_P0.157220.967
13_V56_F0.156790.964
83_K87_F0.156770.964
17_A56_F0.155890.959
21_L33_K0.15580.958
71_E74_P0.152960.941
55_E84_F0.152610.939
31_G37_V0.151640.933
49_G90_W0.151560.932
5_P43_T0.150760.927
11_P15_E0.149830.921
70_F73_C0.14860.914
40_I57_E0.145450.895
54_I87_F0.144360.888
21_L58_V0.144240.887
64_K69_D0.144020.886
24_F58_V0.142350.875
7_D38_K0.14180.872
6_V54_I0.141360.869
6_V44_T0.138520.852
46_V49_G0.138260.850
62_N67_S0.138250.850
16_A25_N0.137560.846
53_Y86_K0.137470.845
51_N90_W0.137340.845
38_K66_S0.137040.843
28_S34_F0.13640.839
55_E86_K0.136230.838
19_F23_K0.135880.836
31_G38_K0.135180.831
24_F56_F0.134730.829
56_F83_K0.134570.828
25_N60_E0.134440.827
37_V75_F0.133730.822
8_P54_I0.133540.821
72_N76_Q0.132040.812
72_N75_F0.131920.811
33_K61_T0.131490.809
80_P84_F0.131110.806
62_N68_K0.131060.806
32_Y76_Q0.130980.806
11_P17_A0.130290.801
53_Y68_K0.130150.800
20_A42_A0.129340.795
36_L53_Y0.128310.789
8_P17_A0.128240.789
32_Y63_C0.126790.780
18_E22_D0.126420.778
19_F34_F0.123960.762
63_C75_F0.123180.758
22_D70_F0.12180.749
21_L43_T0.120610.742
10_D69_D0.120290.740
44_T47_V0.119370.734
46_V90_W0.116950.719
6_V23_K0.116770.718
32_Y64_K0.11540.710
23_K40_I0.114940.707
38_K62_N0.114910.707
24_F31_G0.114890.707
17_A36_L0.114350.703
49_G52_Y0.114250.703
43_T51_N0.114080.702
9_N13_V0.11390.701
19_F22_D0.113890.700
67_S86_K0.113260.697
28_S61_T0.113150.696
57_E70_F0.112950.695
69_D73_C0.112050.689
61_T85_C0.111920.688
40_I52_Y0.111910.688
39_V50_I0.111910.688
23_K27_Q0.11170.687
81_W89_V0.111540.686
48_A53_Y0.111340.685
19_F71_E0.111230.684
43_T88_T0.111120.683
13_V17_A0.110960.682
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
3gaxA0.989499.80.018
1yvbI199.80.046
2ch9A0.989499.80.048
1roaA0.989499.80.054
3l0rA0.968199.80.062
3mwzA0.989499.70.138
4eycA0.946899.60.223
3ul5A0.797999.50.281
2l4vA0.787299.50.284
3imaB0.787299.50.295

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