GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TIR_2 - TIR domain
Pfam: PF13676 (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: CL0173
Length: 102
Sequences: 4007
Seq/Len: 39.28
HH_delta: 0.096 (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
61_Y67_C0.895462.735
53_V74_A0.742512.268
13_A56_L0.694532.121
4_S61_Y0.635021.940
48_E73_A0.596531.822
37_E42_E0.593211.812
17_A21_E0.574811.756
9_D60_N0.562361.718
64_S67_C0.553491.691
12_F56_L0.528581.614
16_L56_L0.523451.599
55_V61_Y0.512721.566
52_C80_P0.487481.489
3_I56_L0.481141.470
43_I66_W0.476081.454
59_P87_D0.470731.438
1_V25_I0.466661.425
45_R49_R0.462061.411
12_F86_L0.445121.360
19_R22_S0.428121.308
18_E22_S0.427931.307
9_D58_S0.42751.306
69_F72_G0.423441.293
17_A29_L0.422341.290
3_I17_A0.418061.277
66_W70_E0.415151.268
4_S70_E0.412891.261
28_F46_A0.396961.212
42_E45_R0.389141.189
7_S30_D0.388181.186
58_S64_S0.378851.157
53_V79_K0.378421.156
48_E77_R0.377551.153
72_G76_K0.372741.138
2_F64_S0.371321.134
38_D41_E0.365821.117
14_E31_R0.362511.107
19_R23_A0.358341.094
40_R44_E0.351811.075
28_F33_I0.35161.074
56_L86_L0.345871.056
14_E29_L0.337191.030
57_L85_R0.334231.021
37_E45_R0.333281.018
30_D70_E0.333211.018
57_L83_P0.331291.012
18_E21_E0.329961.008
8_E60_N0.329751.007
7_S39_W0.329371.006
33_I39_W0.326450.997
73_A76_K0.324180.990
64_S70_E0.324070.990
55_V74_A0.320470.979
26_R32_D0.317610.970
55_V83_P0.317390.969
30_D33_I0.314880.962
42_E46_A0.313360.957
3_I20_L0.312160.953
10_R31_R0.311730.952
33_I42_E0.31170.952
10_R14_E0.309270.945
17_A27_V0.308910.943
33_I36_G0.30610.935
86_L89_C0.305970.935
1_V54_I0.303560.927
6_S64_S0.301650.921
53_V81_I0.300140.917
28_F42_E0.297790.910
34_P37_E0.296320.905
15_R18_E0.29570.903
12_F15_R0.294170.898
33_I43_I0.291490.890
46_A50_S0.28870.882
4_S55_V0.288510.881
26_R51_D0.284510.869
57_L62_L0.282970.864
6_S60_N0.277730.848
58_S61_Y0.276120.843
40_R72_G0.275510.841
35_P82_I0.274670.839
40_R69_F0.272770.833
21_E26_R0.271890.830
1_V27_V0.269950.825
72_G75_W0.266220.813
5_Y30_D0.26610.813
28_F43_I0.26250.802
44_E73_A0.25790.788
33_I46_A0.256950.785
38_D44_E0.256330.783
34_P42_E0.255860.781
15_R19_R0.252310.771
10_R18_E0.25190.769
45_R48_E0.251790.769
11_E14_E0.251630.769
26_R29_L0.247950.757
44_E48_E0.247020.754
28_F32_D0.244860.748
39_W42_E0.243820.745
50_S54_I0.242990.742
21_E27_V0.241710.738
60_N63_K0.24140.737
5_Y28_F0.239580.732
17_A24_G0.237410.725
55_V67_C0.237210.725
55_V71_L0.235250.719
29_L32_D0.235130.718
10_R42_E0.232520.710
20_L25_I0.231910.708
69_F75_W0.229430.701
14_E18_E0.228840.699
21_E38_D0.228270.697
77_R80_P0.225260.688
39_W44_E0.224720.686
50_S82_I0.222860.681
30_D39_W0.22190.678
2_F43_I0.221370.676
43_I70_E0.220930.675
67_C70_E0.217350.664
52_C82_I0.215740.659
43_I47_I0.215370.658
3_I13_A0.214980.657
44_E69_F0.214120.654
13_A29_L0.213510.652
36_G83_P0.213050.651
57_L61_Y0.212550.649
32_D35_P0.21180.647
61_Y71_L0.210510.643
22_S40_R0.208360.636
53_V61_Y0.207580.634
3_I27_V0.206830.632
23_A75_W0.201950.617
7_S43_I0.201790.616
70_E74_A0.201580.616
3_I54_I0.20090.614
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
4eo7A199.60.096
3ub2A199.60.118
2js7A199.60.127
3h16A199.50.175
2j67A199.50.198
1fyxA199.50.198
3j0aA199.40.234
3jrnA199.40.242
3oziA199.40.243
1t3gA199.40.248

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