GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
LIM - LIM domain
Pfam: PF00412 (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: 58
Sequences: 3747
Seq/Len: 64.6
HH_delta: -0.121 (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
1_C4_C1.421033.560
2_A20_K1.088032.726
50_C53_C1.018222.551
30_S47_K0.996982.498
27_F41_F0.684441.715
42_Y51_K0.655281.642
23_H26_C0.645021.616
28_K33_G0.609741.528
29_C32_C0.60841.524
9_Y12_E0.600791.505
17_A41_F0.565591.417
34_K52_D0.555161.391
3_R28_K0.547451.372
3_R22_W0.538721.350
23_H29_C0.537781.347
53_C56_K0.506241.268
51_K55_Q0.492831.235
3_R33_G0.490181.228
26_C32_C0.465571.166
26_C29_C0.463451.161
36_L50_C0.432271.083
49_Y53_C0.411311.030
10_G13_I0.409221.025
12_E21_F0.402881.009
31_K49_Y0.402271.008
4_C8_I0.40091.004
18_M48_P0.3930.985
28_K35_P0.392810.984
22_W48_P0.381670.956
7_P10_G0.378110.947
1_C8_I0.376810.944
17_A27_F0.37410.937
8_I13_I0.367390.920
3_R47_K0.362260.908
52_D55_Q0.360850.904
11_T14_V0.360680.904
42_Y55_Q0.355960.892
31_K53_C0.353430.885
23_H32_C0.349940.877
42_Y53_C0.343330.860
32_C36_L0.33970.851
8_I11_T0.330790.829
24_P35_P0.318590.798
13_I42_Y0.306350.767
22_W41_F0.300540.753
39_G52_D0.297150.744
25_E28_K0.296880.744
22_W40_D0.293930.736
17_A48_P0.293660.736
1_C23_H0.293330.735
25_E35_P0.287440.720
44_K54_Y0.28690.719
6_K47_K0.279770.701
49_Y54_Y0.279520.700
4_C23_H0.277970.696
32_C50_C0.276490.693
43_E46_G0.274140.687
10_G24_P0.273980.686
6_K25_E0.272380.682
20_K46_G0.270540.678
12_E17_A0.269810.676
36_L48_P0.267940.671
31_K55_Q0.267550.670
36_L39_G0.265990.666
21_F24_P0.264020.661
30_S48_P0.263270.660
14_V38_D0.263020.659
4_C26_C0.262380.657
7_P18_M0.259390.650
38_D42_Y0.257590.645
17_A21_F0.255370.640
39_G55_Q0.254380.637
8_I21_F0.253440.635
27_F48_P0.252070.632
39_G56_K0.251760.631
24_P39_G0.251490.630
44_K49_Y0.251240.629
39_G42_Y0.245130.614
34_K38_D0.244060.611
21_F39_G0.241760.606
37_N48_P0.240140.602
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
2l4zA0.982898.9-0.121
1g47A198.8-0.1
3f6qB198.8-0.097
1b8tA0.982898.8-0.092
1j2oA0.982898.8-0.091
1rutX0.982898.8-0.088
1x61A198.8-0.088
1x63A198.8-0.087
1m3vA0.982898.8-0.085
1x4kA198.8-0.085

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