GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
KorB - KorB domain
Pfam: PF08535 (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: CL0123
Length: 93
Sequences: 5218
Seq/Len: 56.11
HH_delta: 0.279 (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
6_Q21_S1.200732.792
19_W23_H1.053522.449
7_E17_R1.041112.421
7_E11_K0.919162.137
18_S21_S0.915552.129
16_S19_W0.864632.010
9_I20_V0.845491.966
75_T78_A0.802751.866
8_E12_R0.795761.850
8_E11_K0.786081.828
6_Q24_L0.723851.683
22_N27_L0.723791.683
23_H44_D0.698271.623
13_L42_I0.675071.570
74_L82_L0.671821.562
35_E39_S0.65581.525
21_S25_A0.652061.516
5_T8_E0.636121.479
4_W12_R0.628691.462
10_A20_V0.606561.410
12_R42_I0.602591.401
2_F44_D0.583011.356
15_K20_V0.55531.291
19_W22_N0.550871.281
36_L66_V0.546951.272
22_N28_D0.545091.267
17_R21_S0.544651.266
78_A81_A0.519381.208
81_A85_E0.519241.207
60_E64_A0.498871.160
74_L79_V0.48961.138
13_L43_S0.473741.101
9_I43_S0.464341.080
81_A84_R0.452981.053
80_K83_R0.447351.040
46_R49_Y0.443961.032
35_E38_R0.442481.029
20_V24_L0.4361.014
4_W9_I0.43121.003
15_K19_W0.417420.971
4_W42_I0.414420.964
79_V83_R0.40930.952
59_P63_E0.407290.947
58_N62_V0.407180.947
45_I49_Y0.396860.923
36_L39_S0.390980.909
49_Y53_K0.389920.907
6_Q17_R0.389240.905
62_V66_V0.385490.896
58_N61_E0.382480.889
16_S23_H0.379880.883
46_R76_R0.378220.879
34_K38_R0.377360.877
37_V43_S0.377140.877
61_E64_A0.375020.872
65_L79_V0.37270.867
28_D33_I0.372390.866
10_A17_R0.368090.856
32_E35_E0.36150.840
32_E36_L0.361060.839
82_L85_E0.358290.833
16_S22_N0.352980.821
31_E34_K0.351250.817
6_Q20_V0.34650.806
19_W31_E0.336390.782
74_L78_A0.332860.774
31_E35_E0.330930.769
49_Y52_R0.330680.769
14_G36_L0.330350.768
45_I50_E0.32760.762
33_I36_L0.32440.754
34_K47_A0.324210.754
30_P34_K0.324040.753
18_S22_N0.31590.734
4_W8_E0.315590.734
71_E74_L0.303860.706
47_A51_L0.303060.705
54_L57_K0.302330.703
17_R45_I0.301440.701
10_A15_K0.300060.698
65_L83_R0.298850.695
61_E65_L0.294790.685
71_E79_V0.294780.685
57_K60_E0.29350.682
50_E54_L0.293170.682
9_I24_L0.292470.680
60_E63_E0.291590.678
22_N25_A0.28880.671
13_L33_I0.283290.659
79_V82_L0.281060.653
4_W24_L0.280190.651
23_H28_D0.278490.647
15_K33_I0.276660.643
48_L53_K0.275130.640
37_V47_A0.275080.640
30_P63_E0.274630.639
64_A72_E0.273750.636
6_Q9_I0.273050.635
33_I37_V0.272510.634
59_P62_V0.271620.632
10_A13_L0.270880.630
77_A81_A0.270510.629
76_R80_K0.268110.623
76_R79_V0.266020.619
16_S37_V0.265580.617
50_E53_K0.263740.613
22_N29_L0.261940.609
9_I13_L0.260320.605
11_K17_R0.257850.600
30_P59_P0.255150.593
6_Q10_A0.254780.592
71_E85_E0.254240.591
45_I52_R0.2530.588
59_P79_V0.252590.587
31_E38_R0.251960.586
7_E10_A0.250810.583
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
3r1fA0.95798.80.279
3qwgA0.892598.70.318
3op9A0.95798.70.325
3ivpA0.95798.70.326
1b0nA0.967798.60.331
3lfpA0.881798.60.352
2ebyA0.903298.50.367
1zugA0.623798.40.385
3t76A0.580698.40.392
1lmb30.688298.30.398

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