GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PH - PH domain
Pfam: PF00169 (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: CL0266
Length: 104
Sequences: 8114
Seq/Len: 78.02
HH_delta: -0.082 (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
3_K94_R1.694813.623
7_L22_F1.296442.771
22_F31_Y1.280212.736
7_L86_A1.14582.449
72_F96_I1.104662.361
3_K98_A1.092982.336
86_A92_R0.988872.114
6_W21_Y0.915081.956
6_W19_K0.883381.888
31_Y45_G0.875951.872
88_S91_E0.846471.809
89_E93_K0.831171.777
8_L85_S0.814531.741
73_E83_L0.811771.735
22_F84_F0.758471.621
70_N89_E0.738071.578
71_C85_S0.730361.561
25_R30_L0.723691.547
23_V32_Y0.703631.504
94_R98_A0.700461.497
70_N85_S0.682621.459
56_P92_R0.676271.445
95_W99_I0.670571.433
19_K87_E0.664921.421
72_F86_A0.66061.412
9_K31_Y0.653991.398
17_W85_S0.636281.360
43_P46_S0.625771.338
8_L19_K0.615951.317
10_K17_W0.60381.291
76_T79_G0.602891.289
22_F29_L0.599451.281
87_E91_E0.598371.279
55_R73_E0.585661.252
92_R96_I0.58241.245
70_N92_R0.57471.228
20_R31_Y0.572881.224
24_L98_A0.56591.210
73_E81_S0.562861.203
4_E23_V0.532491.138
96_I100_Q0.527161.127
90_E94_R0.517461.106
32_Y43_P0.516571.104
49_L52_C0.508541.087
72_F92_R0.507251.084
3_K91_E0.483421.033
28_Y46_S0.461170.986
93_K97_Q0.458540.980
5_G91_E0.457780.978
4_E21_Y0.456260.975
57_D73_E0.4560.975
9_K20_R0.455550.974
56_P100_Q0.447490.956
89_E92_R0.445720.953
97_Q101_K0.444040.949
47_I82_Y0.436290.933
52_C76_T0.431480.922
30_L46_S0.427750.914
68_R85_S0.415850.889
48_P52_C0.41570.889
33_K44_K0.406960.870
11_S14_R0.388490.830
98_A102_A0.383070.819
54_V57_D0.377670.807
11_S18_K0.375090.802
75_T81_S0.369010.789
59_S69_K0.367040.785
6_W35_S0.36620.783
98_A101_K0.360270.770
40_D43_P0.359230.768
52_C84_F0.358780.767
4_E35_S0.357850.765
52_C74_I0.357040.763
55_R75_T0.355020.759
91_E95_W0.353570.756
48_P51_D0.346150.740
68_R71_C0.337130.721
86_A96_I0.336190.719
53_T75_T0.334540.715
23_V30_L0.324180.693
15_K18_K0.316430.676
9_K84_F0.315760.675
7_L84_F0.315530.674
21_Y35_S0.312390.668
51_D77_P0.311760.666
56_P59_S0.311620.666
17_W83_L0.311320.665
6_W87_E0.311260.665
72_F99_I0.311160.665
76_T81_S0.306630.655
91_E94_R0.306480.655
12_S15_K0.305770.654
30_L43_P0.304840.652
9_K82_Y0.302430.646
24_L29_L0.299570.640
10_K83_L0.298390.638
21_Y34_S0.295090.631
5_G95_W0.293390.627
6_W34_S0.292980.626
5_G9_K0.291850.624
56_P60_S0.289530.619
31_Y84_F0.287090.614
46_S56_P0.28430.608
29_L33_K0.283540.606
73_E78_N0.283460.606
28_Y48_P0.282660.604
57_D60_S0.282070.603
8_L87_E0.281480.602
34_S40_D0.27990.598
11_S16_K0.279510.597
20_R33_K0.27660.591
55_R58_P0.274490.587
12_S16_K0.273050.584
54_V96_I0.271340.580
46_S49_L0.270340.578
41_S44_K0.268110.573
74_I84_F0.266970.571
8_L13_S0.265930.568
94_R97_Q0.265070.567
56_P93_K0.264440.565
29_L99_I0.264180.565
27_S48_P0.26410.564
11_S26_D0.261740.559
56_P96_I0.261270.558
72_F84_F0.258330.552
79_G82_Y0.257150.550
22_F52_C0.256670.549
4_E34_S0.255890.547
8_L68_R0.254080.543
8_L17_W0.254070.543
97_Q100_Q0.252430.540
25_R28_Y0.251290.537
96_I99_I0.247330.529
26_D50_D0.244470.523
10_K14_R0.243650.521
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
1v88A0.903899.5-0.082
1x1fA0.923199.5-0.059
1btkA0.990499.5-0.047
4h8sA0.903899.5-0.047
2r09A0.913599.5-0.037
2i5fA0.971299.5-0.037
1x05A0.971299.5-0.036
3a8pA0.951999.5-0.035
1wi1A0.942399.5-0.034
2q13A0.903899.5-0.033

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