GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Plug - TonB-dependent Receptor Plug Domain
Pfam: PF07715 (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: CL0072
Length: 108
Sequences: 20954
Seq/Len: 194.02
HH_delta: -0.027 (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
14_S18_E2.107263.755
13_T16_D1.550532.763
24_N27_D1.521252.711
11_V90_E1.466782.614
32_V91_V1.437522.562
82_P85_M1.434612.557
62_Y67_P1.234712.200
63_I68_I1.220822.176
16_D19_K1.174472.093
60_N67_P1.142852.037
20_T31_L1.142382.036
10_T93_K1.111151.980
27_D30_Q1.093021.948
11_V88_S1.040121.854
15_E19_K1.030561.837
5_S9_V1.024161.825
100_Y108_V1.013371.806
51_I107_G1.004911.791
32_V35_V0.911221.624
35_V51_I0.906021.615
15_E18_E0.887611.582
22_A28_L0.873461.557
9_V90_E0.864131.540
14_S87_E0.849841.514
50_S55_G0.843081.502
14_S17_I0.82111.463
23_Q27_D0.814781.452
34_G93_K0.796431.419
67_P103_N0.791851.411
92_L100_Y0.781011.392
25_L28_L0.758411.352
12_I32_V0.748441.334
51_I91_V0.747051.331
62_Y100_Y0.739021.317
92_L96_S0.699851.247
50_S58_R0.699091.246
37_V49_I0.694391.237
17_I28_L0.690291.230
10_T32_V0.688761.227
61_V78_L0.679691.211
77_G80_Y0.668211.191
35_V49_I0.637691.136
50_S54_F0.626491.116
62_Y108_V0.622251.109
54_F58_R0.612891.092
22_A27_D0.60821.084
22_A31_L0.599381.068
16_D20_T0.594161.059
33_P93_K0.586121.044
60_N104_A0.565361.007
10_T33_P0.562271.002
54_F106_G0.548970.978
3_Q90_E0.546260.973
55_G58_R0.545510.972
92_L108_V0.525580.937
8_S93_K0.518910.925
42_G94_G0.506930.903
4_K90_E0.499040.889
51_I93_K0.49450.881
27_D47_S0.494030.880
92_L97_S0.493040.879
63_I86_I0.470360.838
52_R93_K0.469640.837
54_F57_N0.46570.830
83_P86_I0.461430.822
41_G44_G0.460820.821
68_I94_G0.457380.815
12_I16_D0.454310.810
29_L35_V0.45230.806
7_S99_L0.441770.787
59_N106_G0.440410.785
32_V93_K0.439660.783
46_S79_N0.43880.782
62_Y65_G0.438570.782
16_D31_L0.437910.780
48_N58_R0.436950.779
7_S11_V0.43370.773
18_E21_P0.424070.756
28_L83_P0.419830.748
13_T18_E0.417420.744
8_S52_R0.414620.739
96_S99_L0.412050.734
4_K9_V0.411060.733
49_I61_V0.406120.724
105_I108_V0.405920.723
102_S105_I0.400950.715
51_I59_N0.400790.714
60_N108_V0.397580.709
36_S39_S0.397230.708
58_R105_I0.397030.708
40_S48_N0.393070.700
92_L99_L0.391680.698
81_I86_I0.381740.680
7_S94_G0.376540.671
4_K11_V0.371520.662
69_N103_N0.362310.646
6_P9_V0.360450.642
40_S44_G0.359610.641
22_A26_A0.359580.641
9_V92_L0.359220.640
33_P36_S0.352890.629
3_Q7_S0.35270.629
6_P94_G0.352380.628
26_A47_S0.34730.619
43_G46_S0.34530.615
54_F59_N0.342810.611
61_V64_D0.340320.606
13_T17_I0.337680.602
45_G48_N0.334770.597
46_S77_G0.333760.595
40_S43_G0.333290.594
34_G52_R0.333020.593
68_I81_I0.33080.590
63_I81_I0.329650.587
22_A83_P0.328650.586
44_G94_G0.328640.586
40_S50_S0.328190.585
62_Y102_S0.326230.581
47_S80_Y0.326020.581
29_L83_P0.325080.579
97_S102_S0.324170.578
22_A29_L0.322470.575
87_E90_E0.321490.573
104_A108_V0.320230.571
76_P80_Y0.31820.567
28_L32_V0.317550.566
41_G45_G0.315780.563
76_P79_N0.31410.560
98_A102_S0.310680.554
36_S50_S0.306540.546
25_L61_V0.305970.545
54_F96_S0.30490.543
30_Q37_V0.304590.543
8_S94_G0.301880.538
60_N103_N0.301830.538
23_Q28_L0.300850.536
61_V79_N0.299710.534
42_G46_S0.298970.533
12_I17_I0.298310.532
25_L89_I0.296820.529
95_P100_Y0.295980.527
36_S56_S0.295050.526
94_G97_S0.292280.521
6_P99_L0.286690.511
96_S108_V0.285390.509
47_S50_S0.284260.507
22_A25_L0.28390.506
17_I20_T0.280910.501
68_I80_Y0.28080.500
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
4b7oA0.981599.7-0.027
2gufA199.7-0.012
2hdiA0.981599.70.017
3v8xA0.990799.70.026
3fhhA0.981599.60.034
3efmA0.96399.60.04
1qfgA0.972299.60.045
3qlbA0.953799.60.067
4epaA0.935299.60.072
1kmoA199.60.073

Page generated in 0.022 seconds.