GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Pro_isomerase - Cyclophilin type peptidyl-prolyl cis-trans isomeraseCLD
Pfam: PF00160 (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: CL0475
Length: 155
Sequences: 5986
Seq/Len: 38.62
HH_delta: 0.01 (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
86_R133_D1.845973.426
13_V127_E1.629643.025
87_G129_M1.554042.884
85_R124_R1.447812.687
38_D152_S1.432242.658
109_L136_E1.345262.497
5_E11_R1.315192.441
3_D11_R1.310942.433
6_T9_L1.241622.305
5_E151_S1.220792.266
90_S106_F1.186562.202
26_E30_R1.15162.137
40_T53_G1.119092.077
23_K74_P1.089522.022
12_I132_L1.051631.952
15_E124_R1.034381.920
84_H90_S1.021841.897
4_I12_I0.9871.832
15_E126_I0.924271.716
12_I125_V0.906941.683
30_R34_S0.877791.629
41_K147_D0.874421.623
73_I101_N0.870831.616
16_L25_V0.855021.587
88_L124_R0.854081.585
4_I153_C0.84141.562
88_L108_T0.836451.553
4_I14_I0.835461.551
139_P145_K0.819271.521
15_E18_G0.81671.516
9_L134_K0.816411.515
14_I89_V0.808581.501
138_G148_V0.791741.470
108_T112_A0.788211.463
17_F124_R0.773721.436
74_P99_N0.772751.434
47_P136_E0.76331.417
18_G25_V0.75291.397
3_D154_G0.751151.394
51_I109_L0.737061.368
32_C153_C0.726591.349
85_R88_L0.715761.329
29_L33_T0.705131.309
45_I135_I0.698351.296
51_I135_I0.675871.254
5_E154_G0.663751.232
46_I50_V0.651471.209
87_G133_D0.651151.209
17_F20_E0.644691.197
5_E152_S0.640351.189
24_T91_M0.638881.186
47_P137_A0.625311.161
3_D13_V0.6241.158
42_F53_G0.621721.154
125_V132_L0.620551.152
141_D145_K0.615961.143
47_P140_T0.603391.120
23_K26_E0.594511.103
77_F117_G0.594381.103
2_V14_I0.594371.103
150_I153_C0.588881.093
133_D136_E0.588481.092
41_K59_N0.587731.091
57_T61_G0.579731.076
2_V29_L0.579441.075
21_A25_V0.573751.065
40_T55_D0.566691.052
7_S146_Q0.563851.047
20_E82_L0.556471.033
48_N110_S0.556441.033
34_S70_G0.554481.029
24_T122_F0.551661.024
107_I132_L0.551041.023
88_L121_V0.550841.022
26_E29_L0.549631.020
85_R111_D0.542211.006
135_I148_V0.536970.997
13_V126_I0.534340.992
83_K116_D0.531570.987
4_I150_I0.52970.983
131_V134_K0.527450.979
93_R100_S0.52470.974
30_R70_G0.522220.969
129_M132_L0.520120.965
90_S116_D0.51560.957
44_R52_Q0.514950.956
84_H116_D0.511120.949
35_G38_D0.505430.938
83_K90_S0.50360.935
49_F52_Q0.501990.932
129_M133_D0.499270.927
36_F56_P0.498520.925
30_R33_T0.486320.903
11_R154_G0.473740.879
90_S121_V0.473220.878
14_I107_I0.470750.874
9_L138_G0.469950.872
86_R129_M0.463450.860
10_G131_V0.460950.856
89_V122_F0.457790.850
69_G102_G0.45640.847
83_K113_P0.450730.837
24_T120_T0.449180.834
75_D101_N0.448170.832
72_P102_G0.446660.829
84_H106_F0.44650.829
28_F122_F0.445510.827
43_H104_Q0.440460.818
75_D93_R0.439570.816
12_I107_I0.439470.816
56_P59_N0.438390.814
41_K149_T0.437870.813
21_A120_T0.433350.804
72_P94_S0.429890.798
94_S100_S0.427420.793
56_P60_G0.423670.786
109_L132_L0.423090.785
20_E81_L0.422120.783
75_D100_S0.420390.780
93_R101_N0.419430.779
68_T71_E0.416270.773
138_G146_Q0.414380.769
86_R109_L0.412390.765
125_V129_M0.410780.762
42_F46_I0.406410.754
52_Q92_A0.406350.754
13_V128_G0.40120.745
93_R119_Y0.397010.737
92_A104_Q0.392630.729
31_L34_S0.392030.728
6_T10_G0.387850.720
6_T138_G0.38750.719
86_R111_D0.387390.719
127_E130_D0.387190.719
52_Q104_Q0.382180.709
45_I51_I0.379170.704
14_I125_V0.378590.703
140_T144_P0.377840.701
50_V114_H0.374170.694
48_N136_E0.372910.692
9_L131_V0.371790.690
18_G26_E0.370630.688
53_G105_F0.36980.686
12_I129_M0.369780.686
23_K73_I0.368910.685
125_V128_G0.367010.681
75_D99_N0.364170.676
143_R147_D0.362290.672
50_V109_L0.358870.666
44_R92_A0.357580.664
38_D153_C0.354060.657
39_G149_T0.353660.656
25_V29_L0.353410.656
91_M101_N0.350720.651
75_D119_Y0.348390.647
134_K137_A0.347110.644
12_I135_I0.346630.643
86_R110_S0.341120.633
77_F80_S0.338630.629
81_L84_H0.337080.626
130_D133_D0.335410.623
49_F115_L0.33440.621
24_T73_I0.332660.617
31_L103_S0.332410.617
113_P116_D0.331550.615
44_R106_F0.328120.609
130_D134_K0.327170.607
139_P142_E0.325070.603
24_T27_N0.32380.601
20_E80_S0.323660.601
17_F88_L0.323260.600
27_N73_I0.322940.599
85_R116_D0.321190.596
2_V25_V0.317980.590
151_S154_G0.317520.589
126_I130_D0.312820.581
108_T111_D0.31110.577
43_H92_A0.310440.576
40_T57_T0.308640.573
138_G141_D0.307880.571
55_D60_G0.307660.571
18_G21_A0.30610.568
9_L146_Q0.302940.562
71_E102_G0.302920.562
84_H108_T0.302020.561
128_G131_V0.30180.560
80_S84_H0.299850.557
18_G29_L0.297070.551
7_S151_S0.296940.551
39_G151_S0.296530.550
16_L123_G0.295290.548
101_N120_T0.294660.547
40_T150_I0.294430.546
6_T131_V0.292690.543
46_I49_F0.292070.542
41_K143_R0.290870.540
31_L36_F0.290460.539
36_F40_T0.289390.537
45_I148_V0.285550.530
134_K138_G0.284010.527
52_Q55_D0.283670.527
83_K117_G0.282370.524
140_T145_K0.282260.524
7_S149_T0.282050.524
55_D103_S0.280980.522
91_M122_F0.280050.520
17_F82_L0.279470.519
53_G89_V0.277480.515
40_T59_N0.27720.515
3_D153_C0.274190.509
45_I109_L0.273250.507
77_F81_L0.272140.505
138_G145_K0.271860.505
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
3bo7A0.97421000.01
1zkcA0.96131000.013
2b71A0.96131000.016
2k7nA0.96131000.018
2poeA0.96771000.02
2x7kA0.96131000.023
2ok3A0.96771000.024
1w74A0.94191000.024
1lopA0.95481000.026
3s6mA0.95481000.027

Page generated in 0.0506 seconds.