GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Rotamase - PPIC-type PPIASE domain
Pfam: PF00639 (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: CL0487
Length: 95
Sequences: 4695
Seq/Len: 49.42
HH_delta: -0.016 (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
24_Y28_K2.244613.567
17_K21_E1.763062.801
26_Q31_E1.750612.782
60_G67_E1.552162.466
57_I62_L1.547872.459
74_K77_E1.409542.240
73_L79_S1.370442.178
22_E26_Q1.292532.054
64_P68_K1.224991.946
59_R71_F1.144991.819
19_K41_Y1.130521.796
24_Y80_K1.107981.761
25_E29_K1.072351.704
84_T87_G1.059451.683
24_Y90_I1.059431.683
23_I41_Y1.037291.648
73_L93_V1.007051.600
32_D35_A1.003091.594
83_E88_Y0.921741.465
58_S61_Q0.916971.457
32_D37_L0.873141.387
32_D36_E0.848371.348
36_E40_E0.842711.339
26_Q41_Y0.834461.326
23_I37_L0.813611.293
27_L37_L0.797331.267
67_E71_F0.793971.262
69_A82_I0.788281.253
25_E28_K0.770761.225
21_E25_E0.764181.214
84_T89_H0.757621.204
53_D94_E0.748641.190
53_D56_W0.74791.188
19_K22_E0.718321.141
35_A51_G0.71571.137
82_I91_I0.71241.132
73_L77_E0.712051.131
4_V23_I0.708231.125
63_P86_N0.704821.120
24_Y81_P0.702251.116
17_K88_Y0.702221.116
20_A24_Y0.69571.105
31_E37_L0.681611.083
68_K72_A0.681471.083
18_K22_E0.673291.070
81_P88_Y0.640081.017
37_L41_Y0.632151.004
27_L78_V0.616850.980
59_R67_E0.608430.967
22_E25_E0.597160.949
18_K21_E0.590810.939
78_V92_K0.586610.932
66_F89_H0.561080.892
36_E39_R0.534830.850
57_I70_L0.534650.850
19_K23_I0.521140.828
86_N89_H0.520370.827
69_A73_L0.50990.810
68_K71_F0.50250.798
28_K78_V0.494260.785
66_F91_I0.482040.766
62_L67_E0.472110.750
38_A52_G0.460180.731
4_V20_A0.45780.727
65_E84_T0.456940.726
74_K93_V0.452660.719
17_K83_E0.445830.708
23_I26_Q0.434610.691
22_E41_Y0.43410.690
70_L91_I0.424930.675
21_E80_K0.424810.675
20_A88_Y0.422540.671
20_A90_I0.421180.669
42_S47_S0.419470.667
62_L66_F0.416430.662
5_K44_D0.410260.652
26_Q29_K0.408630.649
34_F52_G0.405980.645
35_A39_R0.401650.638
78_V81_P0.400230.636
50_N53_D0.399710.635
24_Y78_V0.397480.632
65_E85_D0.397280.631
76_G94_E0.395770.629
42_S52_G0.395390.628
45_S48_A0.393110.625
35_A38_A0.391740.622
65_E68_K0.390560.621
57_I61_Q0.383480.609
21_E24_Y0.378870.602
34_F38_A0.377050.599
69_A72_A0.372950.593
76_G92_K0.36870.586
69_A80_K0.365210.580
30_G92_K0.364990.580
28_K80_K0.361310.574
26_Q37_L0.359080.571
38_A42_S0.355940.566
38_A51_G0.353770.562
73_L80_K0.352770.561
2_I23_I0.348420.554
24_Y79_S0.345550.549
38_A48_A0.345460.549
63_P85_D0.341540.543
39_R51_G0.339650.540
24_Y27_L0.338650.538
75_P93_V0.335340.533
54_L66_F0.334790.532
65_E86_N0.332150.528
17_K20_A0.330630.525
46_P49_E0.320660.510
69_A79_S0.317770.505
64_P67_E0.316330.503
79_S82_I0.307340.488
2_I34_F0.302290.480
42_S48_A0.301550.479
20_A81_P0.301180.479
79_S93_V0.300960.478
70_L79_S0.300310.477
38_A47_S0.297820.473
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
2lj4A0.989599.7-0.016
3gpkA0.957999.7-0.015
4g2pA0.989599.7-0.001
3tc5A0.989599.70.002
3i6cA0.989599.70.007
2pv1A0.978999.70.018
1j6yA0.989599.70.021
1yw5A0.989599.70.033
3nrkA0.989599.70.039
2jzvA0.989599.70.043

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