GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CUT - CUT domain
Pfam: PF02376 (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: 87
Sequences: 5519
Seq/Len: 63.44
HH_delta: 0.275 (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
22_L48_L2.432173.960
21_W25_N1.392492.267
30_R41_Q1.355742.208
35_K64_P1.26322.057
43_T47_L1.227361.999
32_F44_L1.178931.920
30_R34_K1.14281.861
21_W24_R1.081251.761
42_G45_S1.034471.684
31_V35_K1.02111.663
20_E24_R1.019831.661
45_S49_R0.992161.616
29_Q45_S0.981611.598
17_R71_W0.956631.558
41_Q45_S0.933811.521
46_D50_K0.912751.486
36_V64_P0.800621.304
14_I18_I0.800581.304
28_S31_V0.794921.294
57_L60_K0.767841.250
47_L57_L0.756031.231
19_K23_K0.749581.221
43_T46_D0.74491.213
32_F65_Y0.729781.188
25_N66_I0.717911.169
27_I32_F0.702381.144
27_I35_K0.700711.141
31_V34_K0.69071.125
68_M71_W0.689751.123
40_S43_T0.683351.113
46_D51_P0.670461.092
19_K48_L0.639441.041
21_W67_R0.630661.027
29_Q41_Q0.626891.021
67_R71_W0.592640.965
36_V39_R0.557870.908
15_A48_L0.553810.902
70_N74_L0.548480.893
54_W57_L0.544250.886
17_R20_E0.539490.878
39_R44_L0.539170.878
59_P63_E0.529030.861
47_L54_W0.527650.859
47_L53_P0.520940.848
36_V57_L0.520720.848
52_K56_K0.516860.842
60_K64_P0.504450.821
33_A44_L0.502320.818
67_R72_L0.50210.818
69_Y73_S0.498010.811
18_I65_Y0.497810.811
55_N73_S0.487070.793
17_R21_W0.484020.788
33_A41_Q0.475210.774
59_P69_Y0.472940.770
59_P70_N0.469750.765
25_N65_Y0.468630.763
39_R57_L0.464310.756
22_L29_Q0.462930.754
71_W74_L0.459830.749
27_I31_V0.455520.742
36_V61_G0.453920.739
21_W65_Y0.453250.738
33_A36_V0.450020.733
38_N60_K0.448630.731
39_R43_T0.441870.720
15_A19_K0.434560.708
42_G46_D0.434390.707
27_I64_P0.432310.704
53_P57_L0.429590.700
21_W71_W0.42660.695
62_R69_Y0.423220.689
20_E23_K0.423170.689
62_R67_R0.419170.683
17_R75_P0.417730.680
29_Q44_L0.416250.678
58_K62_R0.412630.672
13_E17_R0.409290.666
62_R72_L0.397530.647
43_T51_P0.393740.641
44_L47_L0.392020.638
12_K16_R0.390010.635
22_L27_I0.387570.631
39_R47_L0.380820.620
71_W77_E0.377260.614
29_Q48_L0.3750.611
19_K29_Q0.371290.605
40_S46_D0.361630.589
53_P58_K0.360780.587
22_L32_F0.358350.584
16_R20_E0.356380.580
17_R72_L0.356260.580
12_K59_P0.351020.572
61_G65_Y0.349330.569
29_Q33_A0.348830.568
39_R60_K0.346970.565
32_F61_G0.342910.558
21_W32_F0.34170.556
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
3mlfA0.965598.90.275
3ivpA0.95498.90.286
3omtA0.827698.90.288
3qq6A0.873698.90.29
3op9A0.942598.90.29
4ichA0.988598.90.29
2bnmA0.95498.80.295
1adrA0.862198.80.303
2kpjA0.942598.80.305
2r1jL0.770198.80.311

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