GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Complex1_LYR_1 - Complex1_LYR-like
Pfam: PF13232 (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: CL0491
Length: 61
Sequences: 1487
Seq/Len: 24.38
HH_delta: 0.8 (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
35_R38_K0.817862.827
40_V49_L0.814352.815
40_V45_K0.659442.279
10_L30_I0.54681.890
31_R35_R0.535071.850
6_L53_G0.534331.847
7_Y31_R0.495051.711
9_Q54_R0.441691.527
33_R36_R0.441031.524
43_P47_A0.417521.443
10_L34_F0.393331.360
29_R33_R0.389441.346
8_R12_R0.375111.297
32_D36_R0.37261.288
49_L53_G0.351761.216
13_E57_L0.345861.195
28_R32_D0.34431.190
11_L27_R0.343521.187
37_N40_V0.334431.156
5_S9_Q0.328871.137
33_R52_E0.320681.108
27_R31_R0.311931.078
14_A26_F0.311841.078
48_K51_K0.311591.077
52_E56_E0.307771.064
51_K55_K0.307561.063
18_P21_N0.304111.051
2_Q54_R0.299711.036
4_L12_R0.297091.027
42_D46_I0.29681.026
12_R15_S0.296691.026
45_K48_K0.28880.998
3_V50_L0.284260.983
4_L47_A0.283680.981
17_F26_F0.281440.973
26_F29_R0.281430.973
11_L30_I0.278070.961
14_A27_R0.273810.946
44_E48_K0.264770.915
24_S28_R0.263020.909
25_Y29_R0.261230.903
47_A51_K0.256630.887
29_R32_D0.254220.879
24_S32_D0.24660.852
37_N49_L0.246490.852
49_L52_E0.245880.850
40_V46_I0.244170.844
41_T46_I0.242220.837
13_E16_K0.239330.827
34_F53_G0.236710.818
48_K52_E0.23630.817
3_V34_F0.226480.783
13_E18_P0.225740.780
54_R58_E0.225660.780
22_F26_F0.225360.779
8_R58_E0.224630.776
45_K49_L0.222710.770
6_L34_F0.222560.769
7_Y11_L0.219290.758
14_A30_I0.217370.751
36_R55_K0.216020.747
53_G57_L0.215160.744
6_L10_L0.214680.742
3_V49_L0.209610.725
20_Y23_R0.209330.724
34_F50_L0.2010.695
55_K58_E0.1980.684
49_L56_E0.19770.683
25_Y28_R0.197250.682
42_D45_K0.19610.678
53_G56_E0.194720.673
33_R56_E0.194410.672
24_S51_K0.192420.665
18_P55_K0.190950.660
5_S58_E0.190920.660
44_E47_A0.187410.648
20_Y24_S0.1870.646
2_Q50_L0.185920.643
17_F21_N0.185030.640
23_R28_R0.183250.633
32_D35_R0.179660.621
11_L15_S0.17920.619
9_Q15_S0.177730.614
50_L54_R0.177510.614
8_R31_R0.176660.611
52_E58_E0.17540.606
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
2ld7A0.950820.90.8
2ke4A116.80.808
2ymbA0.967215.40.811
3fflA0.983611.60.82
4a5xA0.885211.30.821
2bidA0.573810.30.824
1ddbA0.57389.50.827
1s94A0.868990.829
2w2uA0.78698.80.829
4kk2A0.6237.30.835
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