GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DJ-1_PfpI - DJ-1PfpI family
Pfam: PF01965 (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: CL0014
Length: 147
Sequences: 7469
Seq/Len: 50.81
HH_delta: -0.007 (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
121_V145_A1.484873.019
93_K123_G1.44792.944
141_A144_E1.445662.939
94_K111_N1.216332.473
93_K122_D1.104962.247
12_E25_T1.016272.066
90_L95_V0.99872.031
121_V141_A0.941761.915
94_K113_V0.929491.890
93_K126_L0.924591.880
67_F72_K0.859411.747
31_D59_D0.836641.701
29_T32_E0.818591.664
91_K110_A0.818521.664
68_Y74_I0.805351.638
68_Y125_N0.79271.612
66_E70_A0.792021.610
6_S9_D0.784551.595
40_A73_P0.775561.577
127_I145_A0.773161.572
104_D107_N0.766871.559
62_E65_K0.761411.548
61_L65_K0.758161.542
76_A84_L0.756421.538
93_K125_N0.746621.518
121_V127_I0.74281.510
62_E66_E0.741571.508
76_A128_T0.741421.508
73_P145_A0.734381.493
12_E23_K0.727321.479
94_K122_D0.720771.466
118_P137_E0.711631.447
14_T23_K0.684421.392
129_G134_S0.665171.353
68_Y126_L0.663041.348
59_D62_E0.660851.344
28_K32_E0.660351.343
71_G125_N0.651871.325
141_A145_A0.647831.317
58_K62_E0.642961.307
94_K120_V0.640951.303
75_A138_F0.637261.296
39_D72_K0.624151.269
81_P97_S0.618461.258
38_Y67_F0.617431.255
63_L67_F0.616581.254
86_A108_A0.615781.252
75_A142_I0.612521.245
65_K69_E0.607631.236
71_G74_I0.603131.226
127_I138_F0.597271.214
61_L87_A0.582221.184
68_Y89_L0.579491.178
96_T120_V0.579141.178
113_V117_D0.566081.151
79_H101_D0.556991.133
105_L110_A0.551451.121
23_K27_D0.550441.119
119_V141_A0.54731.113
43_L83_V0.541981.102
102_E106_E0.541691.101
42_I75_A0.539121.096
88_G91_K0.53021.078
66_E69_E0.519981.057
61_L86_A0.514831.047
121_V125_N0.509621.036
76_A81_P0.507581.032
40_A142_I0.504821.026
42_I138_F0.50391.025
12_E26_P0.499521.016
117_D137_E0.498061.013
94_K117_D0.496511.010
130_R134_S0.49161.000
68_Y71_G0.484290.985
94_K114_D0.48260.981
95_V111_N0.481440.979
104_D113_V0.479870.976
85_A111_N0.474560.965
73_P142_I0.474430.965
41_L67_F0.4720.960
98_Y131_G0.46620.948
73_P127_I0.464460.944
94_K112_Y0.461690.939
5_V33_I0.461020.937
136_I140_L0.459540.934
35_P66_E0.458930.933
99_P112_Y0.457110.929
38_Y41_L0.4470.909
43_L64_L0.445230.905
48_G52_D0.439930.895
7_P30_L0.436720.888
5_V28_K0.434110.883
76_A80_G0.431790.878
40_A75_A0.430620.876
127_I142_I0.429850.874
43_L60_L0.428620.872
64_L87_A0.422340.859
35_P67_F0.422120.858
108_A111_N0.421250.857
7_P59_D0.412190.838
73_P125_N0.410880.835
104_D108_A0.408720.831
135_A139_A0.4060.826
61_L64_L0.402390.818
137_E140_L0.398980.811
68_Y93_K0.397310.808
51_D54_R0.396190.806
54_R86_A0.395890.805
92_G110_A0.394030.801
95_V110_A0.392530.798
6_S26_P0.392080.797
43_L80_G0.390920.795
67_F70_A0.390090.793
77_I135_A0.385370.784
45_G132_P0.383570.780
28_K33_I0.382970.779
33_I38_Y0.381730.776
5_V63_L0.38130.775
129_G138_F0.370390.753
28_K34_D0.369470.751
105_L113_V0.369070.750
119_V127_I0.368520.749
77_I132_P0.365470.743
119_V138_F0.365050.742
91_K109_G0.364660.741
99_P131_G0.360810.734
109_G112_Y0.360750.734
63_L66_E0.35030.712
43_L76_A0.349720.711
98_Y132_P0.345260.702
86_A107_N0.34470.701
33_I63_L0.342030.695
82_A104_D0.341840.695
72_K125_N0.341790.695
125_N145_A0.341660.695
5_V38_Y0.337660.687
132_P135_A0.335190.682
65_K89_L0.33510.681
118_P121_V0.334560.680
77_I138_F0.333880.679
113_V118_P0.333690.678
84_L128_T0.333420.678
118_P130_R0.333010.677
139_A143_V0.331390.674
97_S112_Y0.323350.657
74_I125_N0.320450.652
44_P101_D0.320340.651
84_L87_A0.319190.649
75_A127_I0.318880.648
42_I129_G0.318170.647
41_L64_L0.318070.647
58_K65_K0.315730.642
118_P134_S0.313660.638
129_G139_A0.311680.634
122_D125_N0.31110.633
81_P98_Y0.309240.629
103_E106_E0.309210.629
4_V7_P0.307880.626
74_I126_L0.307240.625
85_A108_A0.305710.622
85_A90_L0.305010.620
123_G126_L0.304930.620
61_L83_V0.30450.619
127_I141_A0.303330.617
99_P130_R0.301720.613
64_L89_L0.300920.612
45_G77_I0.299790.610
14_T18_G0.295760.601
65_K87_A0.294520.599
85_A105_L0.293470.597
6_S13_V0.293050.596
60_L83_V0.292730.595
43_L87_A0.290830.591
58_K61_L0.290810.591
43_L84_L0.289680.589
35_P70_A0.2880.586
38_Y72_K0.287310.584
140_L144_E0.287280.584
98_Y101_D0.285560.581
64_L74_I0.283830.577
64_L83_V0.283710.577
34_D66_E0.283290.576
119_V137_E0.282940.575
137_E141_A0.281390.572
82_A101_D0.280720.571
30_L33_I0.279080.567
47_H100_N0.278940.567
130_R133_G0.277720.565
79_H132_P0.276210.562
33_I67_F0.276070.561
88_G95_V0.275770.561
9_D29_T0.275240.560
85_A107_N0.275140.559
119_V135_A0.274370.558
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
4hcjA0.9388100-0.007
3ewnA0.9321000.033
3fseA0.94561000.033
3noqA0.925299.90.042
3l18A0.938899.90.06
3er6A0.945699.90.06
3mgkA0.938899.90.068
2rk3A0.959299.90.075
4e08A0.952499.90.075
2vrnA0.945699.90.075

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