GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Y_Y_Y - Y_Y_Y domain
Pfam: PF07495 (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: CL0159
Length: 66
Sequences: 1872
Seq/Len: 28.36
HH_delta: -0.115 (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
11_R46_R2.177446.334
13_R44_E1.501694.368
15_E44_E1.304853.796
40_K62_T0.918252.671
40_K64_T0.907862.641
8_I47_A0.700732.038
48_K54_W0.693022.016
42_T62_T0.651831.896
18_D33_Y0.619471.802
9_R48_K0.554011.612
11_R23_T0.546311.589
31_I43_L0.545411.587
15_E42_T0.543611.581
44_E60_S0.517381.505
14_L33_Y0.487251.417
49_D53_K0.479231.394
33_Y43_L0.467441.360
42_T60_S0.448621.305
27_Y30_S0.409171.190
21_W46_R0.407061.184
12_Y24_L0.404961.178
24_L31_I0.399081.161
14_L43_L0.395781.151
14_L17_F0.382621.113
17_F35_N0.381051.108
38_P65_I0.379771.105
12_Y31_I0.368341.071
17_F37_P0.367541.069
22_I25_G0.351931.024
43_L59_K0.344331.002
11_R54_W0.339760.988
13_R21_W0.332390.967
53_K56_S0.325160.946
49_D52_G0.32480.945
4_N7_N0.293390.853
9_R23_T0.290840.846
13_R20_E0.289420.842
23_T27_Y0.28460.828
17_F34_T0.283770.825
23_T57_D0.280450.816
10_Y47_A0.268080.780
34_T37_P0.267960.779
14_L41_Y0.263770.767
18_D22_I0.255130.742
59_K62_T0.243940.710
13_R18_D0.243160.707
45_V59_K0.239140.696
27_Y32_S0.238220.693
30_S57_D0.23130.673
53_K57_D0.230840.671
5_P8_I0.230760.671
17_F32_S0.22590.657
8_I48_K0.22450.653
50_N53_K0.223120.649
14_L18_D0.222070.646
5_P47_A0.220820.642
9_R26_S0.220570.642
10_Y28_S0.218520.636
15_E19_D0.216080.629
52_G56_S0.213820.622
8_I50_N0.210330.612
12_Y22_I0.209620.610
35_N65_I0.196630.572
8_I49_D0.19460.566
51_N55_S0.194150.565
14_L53_K0.192610.560
24_L27_Y0.192530.560
38_P66_L0.186370.542
16_G41_Y0.184730.537
3_S50_N0.184570.537
38_P41_Y0.184130.536
12_Y45_V0.183080.533
22_I63_I0.182050.530
3_S59_K0.181670.528
9_R25_G0.178470.519
59_K63_I0.178050.518
3_S30_S0.17750.516
45_V61_L0.177390.516
3_S19_D0.176720.514
54_W57_D0.175050.509
9_R34_T0.174770.508
48_K55_S0.173620.505
46_R59_K0.173270.504
31_I34_T0.17260.502
52_G55_S0.172210.501
23_T60_S0.172080.501
37_P62_T0.171960.500
3_S6_E0.169080.492
47_A55_S0.168330.490
39_G63_I0.167260.487
5_P64_T0.164560.479
43_L61_L0.162640.473
30_S59_K0.162490.473
21_W43_L0.158290.460
28_S61_L0.156850.456
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
4a2lA0.984899.5-0.115
3v9fA0.984899.5-0.111
3ottA0.984899.5-0.107
2e7mA0.924294.60.629
3v6oA0.984891.90.663
1axiB0.984891.50.666
2yrlA0.939491.10.67
3pddA0.924290.80.672
2dtgE0.939490.80.672
2d9qB0.969790.70.673

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