GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PhoU - PhoU domain
Pfam: PF01895 (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: CL0297
Length: 88
Sequences: 4803
Seq/Len: 54.58
HH_delta: -0.001 (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_D33_L1.177742.531
17_E21_E1.144862.461
38_D79_D1.078442.318
37_I78_G1.032142.219
34_E75_E0.993882.136
34_E38_D0.975382.097
14_D29_E0.932392.004
15_A81_A0.887641.908
38_D75_E0.872491.875
75_E79_D0.787961.694
34_E79_D0.745581.603
33_L36_E0.727611.564
17_E26_L0.718071.543
10_E14_D0.703721.513
7_L36_E0.703411.512
8_V37_I0.692451.488
83_N86_E0.688781.480
14_D26_L0.676531.454
11_M33_L0.674951.451
30_I85_A0.652261.402
39_E43_E0.643661.384
8_V74_L0.633971.363
8_V81_A0.632651.360
44_I71_A0.597981.285
29_E33_L0.588151.264
9_E13_D0.583761.255
41_Y71_A0.575771.238
45_R69_R0.566481.218
65_V68_L0.559881.203
10_E33_L0.548311.179
76_R80_H0.539311.159
23_D26_L0.538441.157
18_A30_I0.517361.112
18_A27_A0.515491.108
48_I64_L0.511091.099
50_K54_N0.510891.098
36_E39_E0.504881.085
51_I64_L0.480831.034
31_I85_A0.479611.031
11_M78_G0.478511.029
21_E26_L0.474281.019
12_L81_A0.470481.011
48_I68_L0.46871.007
7_L37_I0.464530.998
3_E40_L0.461490.992
75_E78_G0.457380.983
6_E9_E0.452850.973
43_E47_Q0.452480.973
25_E28_Q0.449450.966
26_L29_E0.447110.961
11_M37_I0.44420.955
41_Y69_R0.440490.947
66_G69_R0.440430.947
28_Q32_Q0.435260.936
41_Y72_R0.434770.935
4_M41_Y0.428930.922
69_R72_R0.427870.920
7_L40_L0.420310.903
48_I71_A0.420240.903
51_I55_Q0.419510.902
6_E10_E0.414880.892
31_I82_V0.410970.883
24_S28_Q0.409240.880
17_E20_E0.406140.873
52_L61_L0.40440.869
1_I70_I0.389460.837
67_L70_I0.389130.836
34_E82_V0.388310.835
80_H83_N0.388060.834
49_L65_V0.384660.827
8_V77_I0.382720.823
41_Y73_D0.3820.821
2_S9_E0.378090.813
62_R66_G0.373350.802
15_A84_I0.372010.800
31_I86_E0.370480.796
30_I33_L0.368720.793
4_M37_I0.367240.789
5_G8_V0.362770.780
45_R49_L0.361110.776
52_L56_N0.360590.775
35_E82_V0.359340.772
23_D27_A0.357980.769
16_I20_E0.355620.764
41_Y45_R0.354150.761
3_E7_L0.35030.753
4_M40_L0.347340.747
35_E38_D0.346210.744
5_G74_L0.344750.741
3_E36_E0.344070.740
50_K53_K0.343960.739
45_R65_V0.343370.738
3_E6_E0.339910.731
82_V86_E0.339170.729
18_A22_R0.338870.728
72_R80_H0.337030.724
27_A85_A0.336540.723
11_M81_A0.334460.719
48_I67_L0.329890.709
76_R83_N0.329570.708
14_D30_I0.326490.702
14_D17_E0.322930.694
5_G9_E0.320630.689
7_L10_E0.317490.682
50_K55_Q0.31740.682
57_P61_L0.307540.661
42_R46_R0.30540.656
15_A30_I0.299130.643
1_I67_L0.29690.638
13_D17_E0.29230.628
40_L43_E0.291290.626
53_K62_R0.287840.619
53_K61_L0.28750.618
12_L16_I0.286180.615
73_D76_R0.284880.612
16_I81_A0.284310.611
52_L57_P0.28350.609
64_L67_L0.281510.605
57_P60_E0.281490.605
83_N87_I0.281160.604
47_Q50_K0.279990.602
7_L33_L0.278440.598
61_L64_L0.278070.598
18_A23_D0.276680.595
35_E39_E0.276390.594
51_I57_P0.275710.593
10_E13_D0.274090.589
46_R50_K0.273910.589
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
1t72A199.1-0.001
1xwmA0.977399.10.003
1sumB0.977399.10.003
2i0mA0.977399.10.004
1xwmA1990.015
1t72A0.9773990.022
1sumB1990.046
2i0mA198.90.062
2oltA0.954597.50.406
2oltA0.931894.20.586

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