GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
KaiB - KaiB domain
Pfam: PF07689 (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: CL0172
Length: 82
Sequences: 21401
Seq/Len: 260.99
HH_delta: -0.046 (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
8_T11_S2.030452.664
20_R72_D1.901342.495
14_A55_L1.7882.346
24_E76_V1.697372.227
15_I34_V1.684682.210
56_I65_R1.656152.173
62_P65_R1.603442.104
37_V44_A1.498861.967
71_S74_Q1.453321.907
4_V34_V1.422821.867
47_D58_E1.306481.714
37_V52_T1.291071.694
72_D76_V1.24521.634
6_G36_D1.24141.629
17_N72_D1.18881.560
15_I19_R1.165241.529
56_I62_P1.145991.504
58_E62_P1.143571.500
13_R69_D1.138211.493
5_A52_T1.135891.490
49_I54_T1.131781.485
10_S13_R1.114691.463
25_Y76_V1.087841.427
17_N20_R1.032671.355
19_R23_E1.003641.317
66_L70_L0.9631.263
24_E72_D0.954311.252
59_S63_R0.947111.243
3_Y47_D0.918931.206
21_L25_Y0.880531.155
3_Y56_I0.872111.144
70_L74_Q0.869791.141
20_R23_E0.795041.043
42_E46_E0.794651.043
47_D56_I0.783041.027
10_S69_D0.779041.022
3_Y49_I0.773811.015
20_R24_E0.755220.991
66_L69_D0.750720.985
54_T65_R0.746040.979
9_P13_R0.73270.961
21_L72_D0.730790.959
42_E45_E0.724030.950
16_E19_R0.685350.899
43_L46_E0.685120.899
18_L32_L0.679710.892
36_D39_E0.675910.887
25_Y29_R0.663910.871
4_V15_I0.658960.865
9_P12_E0.658780.864
69_D74_Q0.641480.842
43_L47_D0.614080.806
14_A69_D0.61150.802
3_Y37_V0.607850.798
16_E20_R0.603480.792
19_R34_V0.597770.784
10_S52_T0.596070.782
41_P45_E0.591370.776
40_Q43_L0.590080.774
7_R12_E0.585030.768
35_I43_L0.584440.767
17_N69_D0.573840.753
4_V36_D0.573420.752
21_L75_L0.572550.751
25_Y28_G0.568940.746
18_L22_C0.564330.740
50_V67_I0.560470.735
12_E15_I0.55970.734
7_R38_L0.55710.731
14_A70_L0.547730.719
3_Y43_L0.543270.713
22_C32_L0.52690.691
14_A17_N0.522180.685
17_N21_L0.522160.685
10_S51_A0.520360.683
21_L76_V0.517550.679
73_T76_V0.517230.679
13_R17_N0.516040.677
31_E34_V0.514970.676
5_A10_S0.50720.665
64_R67_I0.501540.658
18_L55_L0.499440.655
8_T16_E0.496170.651
5_A38_L0.493340.647
22_C25_Y0.492330.646
72_D75_L0.47590.624
70_L75_L0.473890.622
6_G38_L0.473570.621
21_L24_E0.463950.609
18_L33_E0.459220.603
7_R52_T0.451240.592
14_A34_V0.45030.591
5_A37_V0.449270.589
55_L75_L0.447390.587
17_N71_S0.447260.587
55_L58_E0.441420.579
3_Y35_I0.432690.568
14_A18_L0.431740.566
12_E16_E0.430530.565
22_C31_E0.42680.560
66_L74_Q0.425190.558
8_T52_T0.423490.556
7_R10_S0.418410.549
16_E23_E0.418140.549
33_E58_E0.40860.536
24_E29_R0.407570.535
69_D75_L0.406730.534
35_I40_Q0.404070.530
28_G31_E0.399310.524
22_C27_G0.393740.517
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
2av4A0.987899.4-0.046
3qouA0.987899.4-0.018
3vfiA0.987899.4-0.013
2b5eA199.4-0.009
3f8uA0.987899.4-0.004
2qsiA0.987899.30.003
3apoA0.987899.30.007
2qgvA0.987899.30.008
3dxbA0.987899.30.01
4ekzA199.30.015

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