GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Yippee-Mis18 - Yippee zinc-bindingDNA-binding Mis18 centromere assembly
Pfam: PF03226 (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. )
Length: 96
Sequences: 2705
Seq/Len: 28.18
HH_delta: 0.358 (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
7_N65_T1.201893.155
8_C63_C1.104142.899
42_R59_F1.054962.769
10_T62_G1.011242.655
60_C63_C1.003992.636
58_L82_E0.984572.585
17_E31_F0.892012.342
45_M54_T0.890822.339
10_T61_S0.811752.131
31_F77_E0.744751.955
43_E54_T0.72721.909
5_C8_C0.703311.846
13_A80_Y0.676941.777
72_E78_Q0.668431.755
17_E32_N0.656291.723
5_C60_C0.611131.604
8_C60_C0.606491.592
41_D78_Q0.605951.591
6_K65_T0.6031.583
47_G53_H0.565371.484
5_C63_C0.551381.447
10_T38_V0.550981.446
40_V59_F0.54841.440
59_F64_N0.547581.437
47_G54_T0.544781.430
40_V64_N0.544691.430
4_Q9_K0.52741.384
2_V11_I0.505431.327
46_T53_H0.480671.262
11_I34_V0.449181.179
58_L67_L0.434351.140
48_E53_H0.427551.122
9_K88_E0.423591.112
44_L47_G0.407551.070
15_S18_L0.405941.066
40_V61_S0.398011.045
73_S76_E0.392831.031
38_V61_S0.392091.029
3_F15_S0.380440.999
4_Q88_E0.368240.967
35_S38_V0.364480.957
82_E87_L0.357110.937
4_Q14_D0.355890.934
32_N35_S0.353240.927
7_N63_C0.353110.927
45_M48_E0.350510.920
84_K89_K0.334610.878
63_C68_G0.332110.872
39_P44_L0.323430.849
6_K88_E0.311190.817
4_Q11_I0.308460.810
55_V69_W0.307960.808
3_F84_K0.306950.806
12_L67_L0.30670.805
82_E86_I0.29960.786
60_C68_G0.29670.779
2_V34_V0.293920.772
44_L48_E0.293850.771
58_L70_K0.291140.764
38_V43_E0.286820.753
26_G30_L0.284150.746
57_D66_I0.282740.742
33_N70_K0.281330.739
2_V87_L0.278550.731
56_R72_E0.276880.727
38_V62_G0.273010.717
48_E54_T0.270770.711
20_S23_G0.269190.707
45_M53_H0.268550.705
18_L28_A0.266170.699
43_E48_E0.263060.691
18_L27_K0.262930.690
41_D54_T0.262690.690
13_A18_L0.262620.689
41_D56_R0.260210.683
42_R45_M0.25910.680
55_V66_I0.2570.675
8_C62_G0.254990.669
46_T54_T0.251520.660
14_D34_V0.250220.657
44_L54_T0.249980.656
22_H27_K0.248620.653
23_G88_E0.245560.645
57_D71_Y0.244850.643
19_V76_E0.243620.640
28_A69_W0.238490.626
27_K69_W0.238220.625
43_E46_T0.237260.623
2_V14_D0.234030.614
19_V71_Y0.232370.610
80_Y83_G0.229040.601
8_C38_V0.228560.600
43_E53_H0.228240.599
15_S27_K0.226640.595
5_C10_T0.224510.589
33_N58_L0.223970.588
27_K71_Y0.22380.588
27_K57_D0.222730.585
40_V43_E0.222720.585
83_G86_I0.222180.583
37_G43_E0.222140.583
67_L82_E0.219450.576
34_V76_E0.219370.576
33_N80_Y0.217390.571
66_I71_Y0.216930.569
59_F84_K0.216610.569
36_N62_G0.216170.567
57_D69_W0.214840.564
20_S29_Y0.214580.563
71_Y81_K0.214070.562
10_T34_V0.212790.559
37_G40_V0.212470.558
83_G89_K0.209150.549
27_K66_I0.208830.548
19_V29_Y0.207320.544
69_W81_K0.205420.539
84_K87_L0.203590.534
19_V66_I0.202380.531
36_N40_V0.202170.531
32_N61_S0.201930.530
14_D32_N0.201730.530
7_N60_C0.200470.526
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
3hcgA0.937599.40.358
3e0mA0.937599.40.36
3e0oA0.927199.40.371
3hcjA0.937599.30.377
2k8dA0.937599.30.378
3cxkA0.937599.30.378
2l1uA0.937599.30.393
2kaoA0.927199.20.414
3maoA0.927199.20.414
2kv1A0.927199.20.42

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