GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
P5CR_dimer - Pyrroline-5-carboxylate reductase dimerisation
Pfam: PF14748 (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: 107
Sequences: 2050
Seq/Len: 19.16
HH_delta: 0.098 (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
20_F49_F1.08532.675
23_F93_I1.077282.655
24_I56_L1.070182.638
54_K58_E1.003742.474
61_R69_E0.993452.449
21_F52_A0.949612.341
37_P40_E0.868582.141
28_A42_R0.839612.069
83_V87_G0.829662.045
50_I54_K0.799311.970
87_G92_A0.790931.949
61_R65_E0.769721.897
19_Y80_G0.753931.858
16_G48_T0.727411.793
7_D104_A0.709471.749
103_R106_E0.707981.745
54_K57_E0.671551.655
23_F89_L0.662861.634
27_L97_L0.662471.633
71_T78_I0.652971.609
65_E69_E0.651961.607
101_V105_K0.650121.602
46_A57_E0.62651.544
47_Q50_I0.625761.542
33_A98_E0.604811.491
32_V38_R0.600691.481
89_L93_I0.591291.457
86_K95_E0.577941.424
29_D38_R0.577491.423
78_I82_E0.575981.420
25_E67_R0.575841.419
89_L92_A0.575671.419
2_D5_Q0.556981.373
34_Q98_E0.55391.365
20_F23_F0.548731.352
85_E90_R0.546661.347
15_S76_T0.541321.334
33_A94_M0.531791.311
87_G95_E0.528181.302
25_E64_A0.522031.287
65_E68_D0.487411.201
29_D90_R0.483811.192
62_S65_E0.483591.192
71_T81_L0.482761.190
98_E102_E0.47981.183
91_A95_E0.478441.179
24_I45_V0.47281.165
83_V86_K0.466031.149
67_R71_T0.448271.105
31_A36_L0.438491.081
24_I49_F0.437831.079
9_A13_S0.436281.075
82_E86_K0.417971.030
84_L93_I0.417721.030
7_D105_K0.409781.010
76_T104_A0.406351.002
21_F55_L0.405981.001
9_A44_L0.402620.992
64_A67_R0.398950.983
22_L85_E0.39450.972
79_A82_E0.392890.968
84_L96_A0.388810.958
80_G96_A0.387190.954
36_L44_L0.381460.940
82_E95_E0.381180.939
13_S44_L0.376490.928
22_L81_L0.376260.927
46_A53_A0.376210.927
88_G92_A0.376140.927
68_D78_I0.375880.926
88_G91_A0.36940.910
10_T16_G0.367220.905
12_L97_L0.363580.896
33_A82_E0.355720.877
39_E43_K0.35390.872
29_D32_V0.344140.848
62_S68_D0.343270.846
50_I57_E0.340.838
83_V95_E0.338140.833
34_Q101_V0.333380.822
21_F56_L0.333040.821
11_A97_L0.332430.819
50_I53_A0.331590.817
72_T76_T0.328770.810
22_L90_R0.32690.806
18_A77_T0.318270.784
97_L100_A0.317040.781
5_Q8_A0.316670.780
5_Q40_E0.314510.775
46_A56_L0.311570.768
6_F9_A0.310710.766
21_F66_L0.30870.761
80_G100_A0.305740.754
56_L63_P0.302050.744
80_G83_V0.300890.742
83_V99_A0.297830.734
18_A80_G0.296920.732
81_L85_E0.296680.731
99_A102_E0.294280.725
79_A103_R0.290460.716
15_S100_A0.288510.711
13_S48_T0.288150.710
17_P70_V0.285870.705
8_A36_L0.285850.705
11_A101_V0.282860.697
28_A32_V0.27810.685
87_G91_A0.275990.680
9_A15_S0.275810.680
14_G17_P0.27450.677
10_T104_A0.272350.671
40_E43_K0.269890.665
7_D16_G0.269870.665
76_T107_L0.269140.663
14_G76_T0.267680.660
79_A83_V0.2650.653
42_R46_A0.264930.653
102_E105_K0.264240.651
16_G100_A0.261350.644
64_A68_D0.260710.643
26_A90_R0.255740.630
29_D33_A0.254710.628
80_G84_L0.254120.626
33_A79_A0.25140.620
22_L25_E0.250780.618
95_E98_E0.245280.605
44_L48_T0.2390.589
34_Q97_L0.2380.587
15_S79_A0.233430.575
30_A94_M0.226990.559
30_A101_V0.225210.555
40_E44_L0.222960.550
102_E106_E0.220760.544
100_A104_A0.220740.544
42_R63_P0.220470.543
47_Q57_E0.220320.543
78_I81_L0.219840.542
8_A34_Q0.214550.529
2_D39_E0.214310.528
12_L31_A0.214080.528
59_S62_S0.21390.527
22_L93_I0.211640.522
21_F59_S0.211410.521
67_R90_R0.208290.513
38_R42_R0.208180.513
28_A63_P0.207910.512
30_A97_L0.207870.512
10_T15_S0.206990.510
49_F89_L0.206280.508
16_G20_F0.20590.507
26_A93_I0.203620.502
24_I53_A0.202750.500
99_A103_R0.202380.499
16_G97_L0.201550.497
45_V53_A0.200420.494
31_A41_A0.198220.489
29_D68_D0.197270.486
6_F104_A0.19410.478
70_V77_T0.191740.473
82_E94_M0.191390.472
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
3triA199.90.098
3gt0A0.822499.80.277
2izzA199.70.356
2ahrA199.70.363
1yqgA199.60.423
2rcyA199.60.429
2f1kA0.943999.30.519
3b1fA0.934698.90.6
2pv7A0.925298.90.604
4kqwA0.934698.80.605

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