GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
FKBP_C - FKBP-type peptidyl-prolyl cis-trans isomerase
Pfam: PF00254 (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: 94
Sequences: 6352
Seq/Len: 67.57
HH_delta: -0.055 (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
55_M61_R2.494793.534
56_K59_E1.91382.711
16_T24_V1.807642.560
60_K92_E1.777142.517
17_G25_F1.703812.413
12_T36_E1.6372.319
51_A63_F1.457522.065
55_M93_L1.392741.973
64_Y86_T1.382261.958
18_R24_V1.238311.754
60_K90_E1.233391.747
47_G65_V1.218461.726
7_E53_I1.21381.719
62_E88_V1.1971.696
6_K9_D1.169281.656
38_R43_Q1.143841.620
10_T38_R1.130171.601
19_L85_S1.128511.598
40_G49_E1.108731.570
62_E90_E1.089671.543
5_P11_V1.079031.528
5_P54_G1.076911.525
64_Y88_V1.066781.511
66_P69_L1.034721.466
50_E69_L1.031521.461
67_P86_T1.010331.431
16_T27_S1.004581.423
14_H28_S0.995951.411
5_P39_L0.989851.402
10_T36_E0.977581.385
19_L23_K0.95991.360
5_P93_L0.948471.343
16_T90_E0.902611.279
54_G61_R0.861841.221
24_V27_S0.860841.219
18_R90_E0.849151.203
55_M59_E0.842151.193
42_G49_E0.817951.159
13_I52_L0.799241.132
46_P50_E0.795821.127
75_G85_S0.761211.078
12_T34_P0.758441.074
39_L53_I0.715521.014
66_P86_T0.672540.953
13_I37_F0.654940.928
65_V70_A0.650850.922
20_E86_T0.641990.909
20_E64_Y0.62740.889
14_H32_G0.624560.885
20_E88_V0.615110.871
44_V48_L0.611910.867
16_T31_E0.581250.823
50_E53_I0.573430.812
11_V52_L0.568690.806
19_L25_F0.562770.797
27_S32_G0.56240.797
45_I71_Y0.562030.796
14_H34_P0.55670.789
56_K61_R0.54920.778
14_H92_E0.549020.778
17_G89_F0.537740.762
18_R88_V0.537060.761
51_A61_R0.534960.758
14_H27_S0.534060.756
13_I48_L0.532390.754
15_Y26_D0.525740.745
68_E73_E0.511780.725
39_L49_E0.502390.712
28_S31_E0.502270.711
64_Y67_P0.497780.705
52_L55_M0.492770.698
65_V69_L0.491970.697
48_L63_F0.477810.677
14_H31_E0.46990.666
73_E76_L0.465710.660
47_G51_A0.45290.642
5_P55_M0.449410.637
46_P49_E0.448540.635
9_D39_L0.443650.628
45_I65_V0.442140.626
37_F44_V0.435260.617
18_R62_E0.434960.616
27_S31_E0.429380.608
8_G49_E0.423130.599
70_A87_L0.420130.595
8_G40_G0.420060.595
71_Y89_F0.418760.593
67_P70_A0.41860.593
19_L87_L0.41440.587
39_L51_A0.410630.582
63_F91_I0.409210.580
5_P9_D0.402890.571
46_P69_L0.399980.567
15_Y35_F0.396360.561
38_R41_S0.394580.559
61_R93_L0.379030.537
50_E54_G0.376070.533
45_I89_F0.366590.519
13_I91_I0.360990.511
48_L71_Y0.360230.510
5_P52_L0.353760.501
51_A65_V0.350020.496
5_P57_V0.346330.491
43_Q49_E0.346310.491
20_E62_E0.342560.485
51_A91_I0.341860.484
54_G63_F0.339730.481
18_R22_G0.339440.481
8_G41_S0.335870.476
7_E40_G0.333370.472
7_E38_R0.332970.472
8_G38_R0.331610.470
17_G26_D0.330440.468
11_V39_L0.324890.460
47_G69_L0.324690.460
55_M63_F0.32250.457
48_L89_F0.318970.452
15_Y28_S0.315730.447
26_D31_E0.315650.447
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
4drjA0.989499.7-0.055
4driA0.989499.7-0.049
3jxvA0.989499.7-0.048
3o5eA0.989499.7-0.042
1kt0A0.989499.7-0.035
3uf8A0.978799.7-0.03
3o5qA0.989499.7-0.027
3kz7A199.7-0.023
1fd9A0.957499.7-0.011
2lgoA0.989499.7-0.011

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