GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Kunitz_BPTI - KunitzBovine pancreatic trypsin inhibitor domain
Pfam: PF00014 (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: CL0454
Length: 53
Sequences: 2340
Seq/Len: 44.15
HH_delta: -0.144 (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_C35_C2.261475.303
21_N28_E1.342723.148
45_E49_Q1.297333.042
17_R41_N1.255262.943
24_T28_E1.093732.565
6_P19_Y0.855292.006
14_N31_W0.850621.995
44_T47_E0.744191.745
18_W45_E0.698111.637
17_R43_P0.629231.475
4_L42_F0.613121.438
16_P29_Q0.610861.432
49_Q53_G0.598141.403
48_C52_C0.547711.284
4_L39_E0.534651.254
46_E50_K0.532831.249
10_P33_G0.49411.159
43_P47_E0.487431.143
19_Y28_E0.444621.043
3_L22_P0.436411.023
16_P31_W0.431831.013
9_G32_Y0.416530.977
10_P36_G0.411210.964
7_D37_G0.409470.960
8_E33_G0.403270.946
32_Y37_G0.401910.942
25_G53_G0.399580.937
9_G37_G0.390630.916
20_Y25_G0.388150.910
34_G37_G0.387160.908
37_G41_N0.364870.856
9_G34_G0.35920.842
38_N41_N0.358970.842
3_L51_T0.35610.835
47_E51_T0.330430.775
15_E31_W0.321850.755
27_C48_C0.31930.749
8_E12_S0.311290.730
7_D38_N0.311060.729
11_C33_G0.308410.723
30_F41_N0.305730.717
50_K53_G0.303970.713
3_L50_K0.301210.706
30_F34_G0.295110.692
32_Y38_N0.293970.689
13_G16_P0.293920.689
9_G30_F0.290710.682
23_S51_T0.286950.673
46_E49_Q0.285590.670
8_E16_P0.279170.655
47_E50_K0.277320.650
27_C52_C0.275330.646
23_S29_Q0.251270.589
14_N33_G0.24510.575
33_G36_G0.244020.572
19_Y30_F0.243980.572
3_L7_D0.242880.570
26_R53_G0.24220.568
22_P53_G0.240230.563
18_W28_E0.239990.563
7_D10_P0.237270.556
32_Y41_N0.237020.556
18_W29_Q0.236330.554
43_P50_K0.236250.554
12_S29_Q0.235590.552
21_N24_T0.23470.550
23_S53_G0.234580.550
4_L8_E0.229890.539
3_L25_G0.229460.538
3_L45_E0.229230.538
5_P8_E0.227960.535
4_L49_Q0.227560.534
30_F38_N0.224380.526
26_R31_W0.222640.522
15_E47_E0.220490.517
14_N36_G0.219660.515
5_P23_S0.218110.511
7_D36_G0.215420.505
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
1co7I199.2-0.144
2ddiA199.2-0.142
1yc0I199.2-0.136
1adzA199.1-0.126
3augA199.1-0.123
3aubA199.1-0.122
1y62A199.1-0.121
1dtkA199.1-0.121
1bunB199.1-0.12
1jc6A199.1-0.119

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