GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PLDc_2 - PLD-like domain
Pfam: PF13091 (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: CL0479
Length: 126
Sequences: 10151
Seq/Len: 80.56
HH_delta: 0.079 (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
31_A34_R1.885523.368
13_W39_R1.801423.218
39_R70_E1.619252.893
87_A118_L1.554912.778
6_K27_A1.495092.671
6_K30_D1.356982.424
37_K70_E1.331262.378
2_I27_A1.290242.305
87_A115_V1.23092.199
4_L88_I1.173622.097
4_L108_I1.158352.069
4_L82_I1.132752.024
78_K93_N1.102441.970
88_I106_G1.100041.965
13_W119_I1.068911.910
84_D119_I1.032441.844
12_I82_I0.972811.738
92_A106_G0.929831.661
5_I27_A0.921781.647
15_A75_L0.910141.626
27_A30_D0.901611.611
11_S84_D0.894191.597
3_D7_S0.887171.585
13_W123_D0.883591.579
119_I123_D0.867791.550
86_V108_I0.86061.537
13_W122_F0.84121.503
29_L67_A0.832921.488
76_H93_N0.811951.451
90_G106_G0.784081.401
29_L33_K0.778551.391
91_S104_E0.769481.375
4_L86_V0.76411.365
32_A69_I0.760191.358
15_A79_F0.727071.299
13_W37_K0.718711.284
5_I12_I0.711211.271
11_S37_K0.704131.258
8_A82_I0.688261.230
95_T98_S0.688161.229
81_I87_A0.666421.191
19_I40_I0.657191.174
11_S119_I0.647691.157
86_V110_D0.643361.149
30_D34_R0.624721.116
85_K110_D0.623561.114
11_S39_R0.621881.111
2_I6_K0.618651.105
88_I108_I0.618151.104
25_I29_L0.602111.076
81_I115_V0.594811.063
95_T102_N0.591171.056
80_Y94_L0.587251.049
98_S104_E0.586481.048
11_S83_D0.578561.034
4_L7_S0.571391.021
27_A31_A0.56931.017
8_A12_I0.565261.010
14_I94_L0.554250.990
89_I118_L0.553490.989
17_P43_D0.553450.989
39_R72_R0.552710.987
97_S101_R0.550110.983
92_A99_F0.548940.981
43_D74_R0.530770.948
109_I114_L0.527850.943
79_F118_L0.52680.941
116_K120_R0.514890.920
10_K85_K0.509960.911
117_E120_R0.506830.905
32_A67_A0.505220.903
89_I107_V0.50290.898
14_I80_Y0.502720.898
31_A36_V0.501650.896
55_A59_E0.493230.881
2_I23_D0.487970.872
112_P116_K0.484390.865
10_K83_D0.48190.861
22_P26_K0.477370.853
121_E124_Q0.476510.851
60_L63_L0.469810.839
59_E63_L0.468210.836
19_I25_I0.467020.834
98_S102_N0.465150.831
39_R123_D0.463130.827
14_I40_I0.462990.827
18_Y97_S0.459040.820
57_L60_L0.452080.808
56_S63_L0.448160.801
120_R123_D0.441420.789
10_K84_D0.440630.787
76_H91_S0.439040.784
54_L57_L0.438640.784
81_I119_I0.436880.780
76_H104_E0.436230.779
97_S102_N0.433640.775
19_I94_L0.431510.771
61_R65_K0.426080.761
12_I31_A0.425690.760
79_F121_E0.425310.760
81_I122_F0.422580.755
91_S98_S0.417920.747
15_A41_I0.415020.741
16_S94_L0.414030.740
29_L63_L0.41290.738
17_P95_T0.409930.732
9_Q83_D0.409070.731
13_W81_I0.403830.721
3_D6_K0.401540.717
12_I38_V0.399840.714
79_F122_F0.399210.713
57_L61_R0.393980.704
96_S100_R0.389630.696
28_L38_V0.374980.670
7_S86_V0.37480.670
38_V69_I0.374030.668
87_A109_I0.370620.662
120_R124_Q0.367990.657
113_E116_K0.364290.651
111_D114_L0.362720.648
83_D115_V0.359330.642
31_A38_V0.357490.639
12_I28_L0.357040.638
30_D33_K0.356210.636
15_A77_A0.355950.636
3_D86_V0.354220.633
56_S59_E0.353720.632
10_K37_K0.350680.626
59_E62_E0.350410.626
9_Q85_K0.349860.625
20_T95_T0.348590.623
9_Q34_R0.347550.621
31_A35_G0.344320.615
43_D46_Q0.343060.613
113_E117_E0.342880.613
29_L32_A0.338840.605
62_E65_K0.336390.601
19_I42_V0.335570.599
117_E121_E0.333040.595
62_E66_N0.32970.589
58_K61_R0.32940.588
65_K71_V0.329130.588
41_I72_R0.325970.582
93_N98_S0.324940.581
32_A38_V0.324120.579
82_I86_V0.322490.576
56_S60_L0.319950.572
57_L63_L0.318790.570
79_F87_A0.316670.566
5_I14_I0.316050.565
87_A114_L0.314860.562
47_D74_R0.312650.559
63_L67_A0.311930.557
3_D30_D0.308810.552
115_V119_I0.304320.544
5_I28_L0.303690.543
18_Y78_K0.302520.540
26_K30_D0.30210.540
40_I71_V0.301660.539
43_D75_L0.300180.536
76_H90_G0.299580.535
55_A58_K0.298880.534
32_A68_G0.297120.531
2_I30_D0.295730.528
84_D116_K0.295120.527
25_I63_L0.293980.525
29_L62_E0.293790.525
116_K119_I0.293540.524
8_A36_V0.29330.524
46_Q74_R0.288210.515
17_P74_R0.287810.514
26_K29_L0.287570.514
39_R122_F0.286970.513
74_R103_Y0.285340.510
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
4ggjA0.944499.80.079
1byrA0.960399.70.138
4gelA0.944499.70.145
3hsiA199.70.153
1v0wA0.968399.60.219
1xdpA0.968399.60.23
1xdpA0.944499.40.331
2o8rA0.952499.40.337
1v0wA0.992199.40.339
2o8rA0.968399.30.347

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